@article {6585, title = {Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression.}, journal = {Mol Ther}, volume = {32}, year = {2024}, month = {2024 Mar 06}, pages = {663-677}, abstract = {

BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for β-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in\ vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in\ vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.

}, keywords = {Fetal Hemoglobin, gamma-Globins, Gene Editing, Hematopoietic Stem Cells, Humans, Repressor Proteins, Zinc Fingers}, issn = {1525-0024}, doi = {10.1016/j.ymthe.2024.01.023}, author = {Rajendiran, Vignesh and Devaraju, Nivedhitha and Haddad, Mahdi and Ravi, Nithin Sam and Panigrahi, Lokesh and Paul, Joshua and Gopalakrishnan, Chandrasekar and Wyman, Stacia and Ariudainambi, Keerthiga and Mahalingam, Gokulnath and Periyasami, Yogapriya and Prasad, Kirti and George, Anila and Sukumaran, Dhiyaneshwaran and Gopinathan, Sandhiya and Pai, Aswin Anand and Nakamura, Yukio and Balasubramanian, Poonkuzhali and Ramalingam, Rajasekaran and Thangavel, Saravanabhavan and Velayudhan, Shaji R and Corn, Jacon E and Mackay, Joel P and Marepally, Srujan and Srivastava, Alok and Crossley, Merlin and Mohankumar, Kumarasamypet M} } @article {6582, title = {Disruption of DNA methylation-mediated cranial neural crest proliferation and differentiation causes orofacial clefts in mice.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jan 16}, pages = {e2317668121}, abstract = {

Orofacial clefts of the lip and palate are widely recognized to result from complex gene-environment interactions, but inadequate understanding of environmental risk factors has stymied development of prevention strategies. We interrogated the role of DNA methylation, an environmentally malleable epigenetic mechanism, in orofacial development. Expression of the key DNA methyltransferase enzyme DNMT1 was detected throughout palate morphogenesis in the epithelium and underlying cranial neural crest cell (cNCC) mesenchyme, a highly proliferative multipotent stem cell population that forms orofacial connective tissue. Genetic and pharmacologic manipulations of DNMT activity were then applied to define the tissue- and timing-dependent requirement of DNA methylation in orofacial development. cNCC-specific inactivation targeting initial palate outgrowth resulted in OFCs, while later targeting during palatal shelf elevation and elongation did not. Conditional deletion reduced cNCC proliferation and subsequent differentiation trajectory, resulting in attenuated outgrowth of the palatal shelves and altered development of cNCC-derived skeletal elements. Finally, we found that the cellular mechanisms of cleft pathogenesis observed in vivo can be recapitulated by pharmacologically reducing DNA methylation in multipotent cNCCs cultured in vitro. These findings demonstrate that DNA methylation is a crucial epigenetic regulator of cNCC biology, define a critical period of development in which its disruption directly causes OFCs, and provide opportunities to identify environmental influences that contribute to OFC risk.

}, keywords = {Animals, Cell Proliferation, Cleft Lip, Cleft Palate, DNA Methylation, DNA Modification Methylases, Mice, Neural Crest}, issn = {1091-6490}, doi = {10.1073/pnas.2317668121}, author = {Ulschmid, Caden M and Sun, Miranda R and Jabbarpour, Christopher R and Steward, Austin C and Rivera-Gonz{\'a}lez, Kenneth S and Cao, Jocelyn and Martin, Alexander A and Barnes, Macy and Wicklund, Lorena and Madrid, Andy and Papale, Ligia A and Joseph, Diya B and Vezina, Chad M and Alisch, Reid S and Lipinski, Robert J} } @article {6586, title = {Effect of reconstituted, lyophilized cold aqueous extract of Aloe vera on human whole blood clotting time - A pilot study.}, journal = {J Ayurveda Integr Med}, volume = {15}, year = {2024}, month = {2024 Mar 12}, pages = {100887}, issn = {0975-9476}, doi = {10.1016/j.jaim.2024.100887}, author = {Melenshia, Deena Susie and Amirtham, Soosai Manickam and Rebekah, Grace and Vinod, Elizabeth and Kachroo, Upasana} } @article {6583, title = {Photostimulated Extended Nitric Oxide (NO) Release from Water-Soluble Block Copolymer to Enhance Antibacterial Activity.}, journal = {Biomacromolecules}, volume = {25}, year = {2024}, month = {2024 Jan 08}, pages = {77-88}, abstract = {

-Nitrosamines are well established motifs to release nitric oxide (NO) under photoirradiation. Herein, a series of amphiphilic -nitrosamine-based block copolymers () are developed to attain controlled NO release under photoirradiation (365 nm, 3.71 mW/cm). The water-soluble forms micellar architecture in aqueous medium and exhibits a sustained NO release of 92-160 μM within 11.5 h, which is 36.8-64.0\% of the calculated value. To understand the NO release mechanism, a small molecular NO donor () resembling the NO releasing functional motif of is synthesized, which displays a burst NO release in DMSO within 2.5 h. The radical nature of the released NO is confirmed by electron paramagnetic resonance (EPR) spectroscopy. The gradual NO release from micellar enhances antibacterial activity over and exhibits a superior bactericidal effect on Gram-positive . In relation to biomedical applications, this work offers a comprehensive insight into tuning light-triggered NO release to improve antibacterial activity.

}, keywords = {Anti-Bacterial Agents, Micelles, Nitric Oxide, Polymers, Staphylococcus aureus}, issn = {1526-4602}, doi = {10.1021/acs.biomac.3c00822}, author = {Paul, Soumya and Ashrit, Priya and Kumar, Manish and Mete, Sourav and Ghosh, Shilpendu and Vemula, Praveen Kumar and Mukherjee, Arindam and De, Priyadarsi} } @article {6587, title = {Sleep fragmentation induces heart failure in a hypertrophic cardiomyopathy mouse model by altering redox metabolism.}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Mar 15}, pages = {109075}, abstract = {

Sleep fragmentation (SF) disrupts normal biological rhythms and has major impacts on cardiovascular health; however, it has never been shown to be a risk factor involved in the transition from cardiac hypertrophy to heart failure (HF). We now demonstrate devastating effects of SF on hypertrophic cardiomyopathy (HCM). We generated a transgenic mouse model harboring a patient-specific myosin binding protein C3 (MYBPC3) variant displaying HCM, and measured the progression of pathophysiology in the presence and absence of SF. SF induces mitochondrial damage, sarcomere disarray, and apoptosis in HCM mice; these changes result in a transition of hypertrophy to an HF phenotype by chiefly targeting redox metabolic pathways. Our findings for the first time show that SF is a risk factor for HF transition and have important implications in clinical settings where HCM patients with sleep disorders have worse prognosis, and strategic intervention with regularized sleep patterns might help such patients.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2024.109075}, author = {Bose, Karthikeyan and Agrawal, Radhika and Sairam, Thiagarajan and Mil, Jessenya and Butler, Matthew P and Dhandapany, Perundurai S} } @article {6593, title = {SMART-lipid nanoparticles enabled mRNA vaccine elicits cross-reactive humoral responses against the omicron sub-variants.}, journal = {Mol Ther}, year = {2024}, month = {2024 Feb 27}, abstract = {

The continual emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has necessitated the development of broad cross-reactive vaccines. Recent findings suggest that enhanced antigen presentation could lead to cross-reactive humoral responses against the emerging variants. Toward enhancing the antigen presentation to dendritic cells (DCs), we developed a novel shikimoylated mannose receptor targeting lipid nanoparticle (SMART-LNP) system that could effectively deliver mRNAs into DCs. To improve the translation of mRNA, we developed spike domain-based trimeric S1 (TS1) mRNA with optimized codon sequence, base modification, and engineered 5{\textquoteright} and 3{\textquoteright} UTRs. In a mouse model, SMART-LNP-TS1 vaccine could elicit robust broad cross-reactive IgGs against Omicron sub-variants, and induced interferon-γ-producing T\ cells against SARS-CoV-2 virus compared with non-targeted LNP-TS1 vaccine. Further, T\ cells analysis revealed that SMART-LNP-TS1 vaccine induced long-lived memory T\ cell subsets, T helper 1 (Th1)-dominant and cytotoxic T\ cells immune responses against the SARS-CoV-2 virus. Importantly, SMART-LNP-TS1 vaccine produced strong Th1-predominant humoral and cellular immune responses. Overall, SMART-LNPs can be explored for precise antigenic mRNA delivery and robust immune responses. This platform technology can be explored further as a next-generation delivery system for mRNA-based immune therapies.

}, issn = {1525-0024}, doi = {10.1016/j.ymthe.2024.02.028}, author = {Mahalingam, Gokulnath and Rachamalla, Hari Krishnareddy and Arjunan, Porkizhi and Karuppusamy, Karthik V and Periyasami, Yogapriya and Mohan, Aruna and Subramaniyam, Kanimozhi and M, Salma and Rajendran, Vigneshwar and Moorthy, Mahesh and Varghese, George M and Mohankumar, Kumarasamypet M and Thangavel, Saravanabhavan and Srivastava, Alok and Marepally, Srujan} } @article {6584, title = {Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening.}, journal = {Heliyon}, volume = {10}, year = {2024}, month = {2024 Jan 15}, pages = {e23864}, abstract = {

Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), F{\"o}rster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target{\textquoteright}s role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.

}, issn = {2405-8440}, doi = {10.1016/j.heliyon.2023.e23864}, author = {Kumar, Vikrant and Chunchagatta Lakshman, Puneeth Kumar and Prasad, Thazhe Kootteri and Manjunath, Kavyashree and Bairy, Sneha and Vasu, Akshaya S and Ganavi, B and Jasti, Subbarao and Kamariah, Neelagandan} } @article {3727, title = {Diosgenin enhances liposome-enabled nucleic acid delivery and CRISPR/Cas9-mediated gene editing by modulating endocytic pathways}, journal = {Frontiers in Bioengineering and Biotechnology}, volume = {10}, year = {2023}, month = {01/2023}, doi = {10.3389/fbioe.2022.1031049}, url = {https://doi.org/10.3389\%2Ffbioe.2022.1031049}, author = {Brijesh Lohchania and Abisha Crystal Christopher and Porkizhi Arjunan and Gokulnath Mahalingam and Durga Kathirvelu and Aishwarya Prasannan and Vigneshwaran Venkatesan and Pankaj Taneja and Mohan Kumar KM and Saravanabhavan Thangavel and Srujan Marepally} } @article {3870, title = {High-affinity binding of celastrol to monomeric α-synuclein mitigates in~vitro aggregation.}, journal = {J Biomol Struct Dyn}, year = {2023}, month = {2023 Feb 06}, pages = {1-11}, abstract = {

α-Synuclein (αSyn) aggregation is associated with Parkinson{\textquoteright}s disease (PD). The region αSyn acts as the nucleation {\textquoteright}master controller{\textquoteright} and αSyn as a {\textquoteright}secondary nucleation site{\textquoteright}. They drive monomeric αSyn to aggregation. Small molecules targeting these motifs are promising for disease-modifying therapy. Using computational techniques, we screened thirty phytochemicals for αSyn binding. The top three compounds were experimentally validated for their binding affinity. Amongst them, celastrol showed high binding affinity. NMR analysis confirmed stable αSyn-celastrol interactions involving several residues in the N-terminus and NAC regions but not in the C-terminal tail. Importantly, celastrol interacted extensively with the key motifs that drive αSyn aggregation. Thioflavin-T assay indicated that celastrol reduced αSyn aggregation. Thus, celastrol holds promise as a potent drug candidate for PD.Communicated by Ramaswamy H. Sarma.

}, issn = {1538-0254}, doi = {10.1080/07391102.2023.2175379}, author = {R, Kavya and Aouti, Snehal and Jos, Sneha and Prasad, Thazhe Kootteri and K N, Kumuda and Unni, Sruthi and Padmanabhan, Balasundaram and Kamariah, Neelagandan and Padavattan, Sivaraman and Mythri, Rajeswara Babu} } @article {2885, title = {An Amphiphilic Double-Brush Polymer Hydrogel for Sustained Release of Small Molecules and Biologics: Insulin Delivering-Hydrogel to Control Hyperglycemia}, year = {2022}, doi = { https://doi.org/10.1002/cnma.202200184}, author = {Dhayani, Ashish and Bej, Sujoy and Mudnakudu-Nagaraju, Kiran K and Chakraborty, Saheli and Srinath, Preetham and Kumar, Ashok H and PS, Ann Maria and Kristi, Anand and Ramakrishnan, S and Vemula PK} } @article {2365, title = {Blood progenitor redox homeostasis through olfaction-derived systemic GABA in hematopoietic growth control in Drosophila.}, journal = {Development}, volume = {149}, year = {2022}, month = {2022 Apr 15}, abstract = {

The role of reactive oxygen species (ROS) in myeloid development is well established. However, its aberrant generation alters hematopoiesis. Thus, a comprehensive understanding of events controlling ROS homeostasis forms the central focus of this study. We show that, in homeostasis, myeloid-like blood progenitor cells of the Drosophila larvae, which reside in a specialized hematopoietic organ termed the lymph gland, use TCA to generate ROS. However, excessive ROS production leads to lymph gland growth retardation. Therefore, to moderate blood progenitor ROS, Drosophila larvae rely on olfaction and its downstream systemic GABA. GABA internalization and its breakdown into succinate by progenitor cells activates pyruvate dehydrogenase kinase (PDK), which controls inhibitory phosphorylation of pyruvate dehydrogenase (PDH). PDH is the rate-limiting enzyme that connects pyruvate to the TCA cycle and to oxidative phosphorylation. Thus, GABA metabolism via PDK activation maintains TCA activity and blood progenitor ROS homeostasis, and supports normal lymph gland growth. Consequently, animals that fail to smell also fail to sustain TCA activity and ROS homeostasis, which leads to lymph gland growth retardation. Overall, this study describes the requirement of animal odor-sensing and GABA in myeloid ROS regulation and hematopoietic growth control.

}, issn = {1477-9129}, doi = {10.1242/dev.199550}, author = {Goyal, Manisha and Tomar, Ajay and Madhwal, Sukanya and Mukherjee, Tina} } @article {2466, title = {The CCR5 Gene Edited CD34+CD90+ Hematopoietic Stem Cell Population Serves as an Optimal Graft Source for HIV Gene Therapy}, journal = {Front. Immunol}, year = {2022}, abstract = {

Transplantation of allogenic hematopoietic stem and progenitor cells (HSPCs) with C-C chemokine receptor type 5 (CCR5) Δ32 genotype generates HIV-1 resistant immune cells. CCR5 gene edited autologous HSPCs can be a potential alternative to hematopoietic stem cell transplantation (HSCT) from HLA-matched CCR5 null donor. However, the clinical application of gene edited autologous HSPCs is critically limited by the quality of the graft, as HIV also infects the HSPCs. In this study, by using mobilized HSPCs from healthy donors, we show that the CD34+CD90+ hematopoietic stem cells (HSCs) express 7-fold lower CD4/CCR5 HIV receptors, higher levels of SAMHD1 anti-viral restriction factor, and possess lower susceptibility to HIV infection than the CD34+CD90- hematopoietic progenitor cells. Further, the treatment with small molecule cocktail of Resveratrol, UM729 and SR1(RUS) improved the in vivo engraftment potential of CD34+CD90+ HSCs. To demonstrate that CD34+CD90+ HSC population as an ideal graft for HIV gene therapy, we sort purified CD34+CD90+ HSCs, treated with RUS and then gene edited the CCR5 with single sgRNA. On transplantation, 100,000 CD34+CD90+ HSCs were sufficient for long-term repopulation of the entire bone marrow of NBSGW mice. Importantly, the gene editing efficiency of ~90\% in the infused product was maintained in vivo, facilitating the generation of CCR5 null immune cells, resistant to HIV infection. Altogether, CCR5 gene editing of CD34+CD90+ HSCs provide an ideal gene manipulation strategy for autologous HSCT based gene therapy for HIV infection.

}, doi = {https://doi.org/10.3389/fimmu.2022.792684}, author = {Karthik V. Karuppusamy and John Paul Demosthenes and Vigneshwaran Venkatesan and Abisha Crystal Christopher and Prathibha Babu and Manojkumar K. Azhagiri and Annlin Jacob and Veena Vadhini Ramalingam and Sumathi Rangaraj and Mohankumar Kumarasamypet Murugesan and Srujan Marepally and George Varghese and Alok Srivastava and Rajesh Kannangai and Saravanabhavan Thangavel} } @article {2425, title = {Decoding the Kinetic Pathways toward a Lipid/DNA Complex of Alkyl Alcohol Cationic Lipids Formed in a Microfluidic Channel.}, journal = {J Phys Chem B}, volume = {126}, year = {2022}, month = {2022 Jan 27}, pages = {588-600}, abstract = {

Complexes of cationic liposomes with DNA have emerged as promising nonviral vectors for delivering genetic information into cells for gene therapy. Kinetics of the liposome/DNA complex (lipoplex) formation on a millisecond time scale are studied by monitoring time evolution of fluorescence of 8-anilino-1-naphthalene sulfonic acid (ANS) and ethidium bromide (EtBr) in a continuous flow microfluidic channel coupled to a fluorescence microscope. The formation of lipoplexes between calf thymus DNA and liposomes based on two novel cationic lipids (Lip1810 and Lip1814) are found to follow a two-step process with kinetic constants for the Lip1814/DNA complex ( = 1120-1383 s, = 0.227-1.45 s) being significantly different from those ( = 68.53-98.5 s, = 32.3-60.19 s) corresponding to formation of the Lip1810/DNA complex. The kinetic pathway leading to the formation of Lip1814/DNA complex is whereas the formation of Lip1810/DNA complex occurs by a . The observed difference in the kinetics of lipoplex formation likely originates from different structures of the lipid/DNA complexes.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.1c07263}, author = {Mukherjee, Dipanjan and Hasan, Md Nur and Ghosh, Ria and Ghosh, Gourab and Bera, Arpan and Prasad, Sujanthi Easwara and Hiwale, Ankita and Vemula, Praveen K and Das, Ranjan and Pal, Samir Kumar} } @article {2503, title = {Dual control of dopamine in Drosophila myeloid-like progenitor cell proliferation and regulation of lymph gland growth.}, journal = {EMBO Rep}, year = {2022}, month = {2022 Apr 27}, pages = {e52951}, abstract = {

In Drosophila, definitive haematopoiesis takes place in a specialized organ termed "lymph gland". It harbours multi-potent stem-like blood progenitor cells whose development controls overall growth of this haematopoietic tissue and formation of mature blood cells. With respect to its development, neurotransmitters have emerged as potent regulators of blood-progenitor cell development and function. In this study, we extend our understanding of neurotransmitters and show that progenitors are self-sufficient with regard to synthesizing dopamine, a well-established neurotransmitter. These cells also have modules for dopamine sensing through the receptor and transporter. We found that modulating expression of these components in progenitor cells affected lymph gland growth, which suggested growth-promoting function of dopamine in blood-progenitor cells. Cell-cycle analysis of developing lymph glands revealed an unexpected requirement for intracellular dopamine in moderating the progression of early progenitor cells from S to G2 phase of the cell cycle, while activation of dopamine receptor signalling later in development regulated their progression from G2 and entry into mitosis. The dual capacity in which dopamine operated, first intracellularly to coordinate S/G2 transition and later extracellularly in G2/M transition, was critical for the growth of the lymph gland. Overall, the data presented highlight a novel non-canonical use of dopamine in the myeloid system that reveals an uncharacterized function of intracellular dopamine in cell-cycle phasing with outcomes on haematopoietic growth and immunity as well.

}, issn = {1469-3178}, doi = {10.15252/embr.202152951}, author = {Kapoor, Ankita and Padmavathi, Achalla and Madhwal, Sukanya and Mukherjee, Tina} } @article {3715, title = {Efficient and error-free correction of sickle mutation in human erythroid cells using prime editor-2.}, journal = {Front Genome Ed}, volume = {4}, year = {2022}, month = {2022}, pages = {1085111}, abstract = {

Sickle cell anaemia (SCA) is one of the common autosomal recessive monogenic disorders, caused by a transverse point mutation (GAG \> GTG) at the sixth codon of the beta-globin gene, which results in haemolytic anaemia due to the fragile RBCs. Recent progress in genome editing has gained attention for the therapeutic cure for SCA. Direct correction of SCA mutation by homology-directed repair relies on a double-strand break (DSB) at the target site and carries the risk of generating beta-thalassaemic mutations if the editing is not error-free. On the other hand, base editors cannot correct the pathogenic SCA mutation resulting from A \> T base transversion. Prime editor (PE), the recently described CRISPR/Cas 9 based gene editing tool that enables precise gene manipulations without DSB and unintended nucleotide changes, is a viable approach for the treatment of SCA. However, the major limitation with the use of prime editing is the lower efficiency especially in human erythroid cell lines and primary cells. To overcome these limitations, we developed a modular lenti-viral based prime editor system and demonstrated its use for the precise modelling of SCA mutation and its subsequent correction in human erythroid cell lines. We achieved highly efficient installation of SCA mutation (up to 72\%) and its subsequent correction in human erythroid cells. For the first time, we demonstrated the functional restoration of adult haemoglobin without any unintended nucleotide changes or indel formations using the PE2 system. We also validated that the off-target effects mediated by the PE2 system is very minimal even with very efficient on-target conversion, making it a safe therapeutic option. Taken together, the modular lenti-viral prime editor system developed in this study not only expands the range of cell lines targetable by prime editor but also improves the efficiency considerably, enabling the use of prime editor for myriad molecular, genetic, and translational studies.

}, issn = {2673-3439}, doi = {10.3389/fgeed.2022.1085111}, author = {George, Anila and Ravi, Nithin Sam and Prasad, Kirti and Panigrahi, Lokesh and Koikkara, Sanya and Rajendiran, Vignesh and Devaraju, Nivedhitha and Paul, Joshua and Pai, Aswin Anand and Nakamura, Yukio and Kurita, Ryo and Balasubramanian, Poonkuzhali and Thangavel, Saravanabhavan and Marepally, Srujan and Velayudhan, Shaji R and Srivastava, Alok and Mohankumar, Kumarasamypet M} } @article {3341, title = {Erythroid lineage-specific lentiviral RNAi vectors suitable for molecular functional studies and therapeutic applications.}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 08 18}, pages = {14033}, abstract = {

Numerous genes exert multifaceted roles in hematopoiesis. Therefore, we generated novel\ lineage-specific RNA interference\ (RNAi) lentiviral\ vectors, H23B-Ery-Lin-shRNA\ and H234B-Ery-Lin-shRNA, to probe the functions of these genes in erythroid cells\ without affecting other hematopoietic lineages. The lineage specificity of these vectors was confirmed by\ transducing multiple hematopoietic cells to express a fluorescent protein. Unlike the previously reported erythroid lineage RNAi vector, our vectors were designed for cloning the short hairpin RNAs (shRNAs) for\ any gene, and they also provide superior knockdown of the target gene expression with a\ single shRNA integration per cell. High-level lineage-specific downregulation of BCL11A and ZBTB7A,\ two\ well-characterized transcriptional repressors of HBG in adult erythroid cells, was achieved with substantial induction of fetal hemoglobin with a single-copy lentiviral vector integration. Transduction of primary healthy donor CD34 cells with these vectors resulted in\ \>80\% reduction in the target\ protein levels and up to 40\% elevation in the γ-chain levels in the differentiated erythroid cells. Xenotransplantation of the human CD34 cells transduced with H23B-Ery-Lin-shBCL11A\ LV in immunocompromised mice showed ~ 60\% reduction in BCL11A protein expression with ~\ 40\% elevation of γ-chain levels in the erythroid cells derived from the transduced CD34 cells. Overall, the novel erythroid lineage-specific lentiviral RNAi vectors described in this study provide a\ high-level knockdown of target gene expression in the erythroid cells, making them suitable for their use in gene therapy for hemoglobinopathies. Additionally, the design of these vectors also makes them ideal for high-throughput RNAi screening for studying normal and pathological erythropoiesis.

}, keywords = {Animals, Cell Line, Tumor, Cell Lineage, DNA-Binding Proteins, Genetic Vectors, Humans, Lentivirus, Mice, RNA Interference, RNA, Small Interfering, Transcription Factors, Transduction, Genetic}, issn = {2045-2322}, doi = {10.1038/s41598-022-13783-0}, author = {Bagchi, Abhirup and Devaraju, Nivedhitha and Chambayil, Karthik and Rajendiran, Vignesh and Venkatesan, Vigneshwaran and Sayed, Nilofer and Pai, Aswin Anand and Nath, Aneesha and David, Ernest and Nakamura, Yukio and Balasubramanian, Poonkuzhali and Srivastava, Alok and Thangavel, Saravanabhavan and Mohankumar, Kumarasamypet M and Velayudhan, Shaji R} } @article {2472, title = {FMRP protects the lung from xenobiotic stress by facilitating the Integrated Stress Response.}, journal = {J Cell Sci}, year = {2022}, month = {2022 Mar 23}, abstract = {

Stress response pathways protect the lung from the damaging effects of environmental toxicants. Here we investigate the role of the Fragile X Mental Retardation Protein (FMRP), a multifunctional protein implicated in stress responses, in the lung. We report that FMRP is expressed in murine and human lungs, in the airways and more broadly. Analysis of airway stress responses in mice and in a murine cell line ex vivo, using the well-established Naphthalene (Nap) injury model, reveals that FMRP-deficient cells exhibit increased expression of markers of oxidative and genotoxic stress and increased cell death. Further inquiry shows that FMRP-deficient cells fail to actuate the Integrated Stress Response Pathway (ISR) and upregulate the transcription factor ATF4. Knockdown of ATF4 expression phenocopies the loss of FMRP. We extend our analysis of the role of FMRP to human bronchial BEAS-2B cells, using a 9, 10-Phenanthrenequinone air pollutant model, to find FMRP-deficient BEAS-2B also fail to actuate the ISR and exhibit greater susceptibility. Taken together, our data suggest that FMRP has a conserved role in protecting the airways by facilitating the ISR.

}, issn = {1477-9137}, doi = {10.1242/jcs.258652}, author = {Basu, Deblina Sain and Bhavsar, Rital and Gulami, Imtiyaz and Chavda, Saraswati and Lingamallu, Sai Manoz and Muddashetty, Ravi and Veeranna, Chandrakanth and Chattarji, Sumantra and Thimmulappa, Rajesh and Bhattacharya, Aditi and Guha, Arjun} } @article {3346, title = {Function of FMRP Domains in Regulating Distinct Roles of Neuronal Protein Synthesis.}, journal = {Mol Neurobiol}, volume = {59}, year = {2022}, month = {2022 Dec}, pages = {7370-7392}, abstract = {

The Fragile-X Mental Retardation Protein (FMRP) is an RNA binding protein that regulates translation of mRNAs essential for synaptic development and plasticity. FMRP interacts with a specific set of mRNAs, aids in their microtubule-dependent transport and regulates their translation through its association with ribosomes. However, the biochemical role of FMRP{\textquoteright}s domains in forming neuronal granules and associating with microtubules and ribosomes is currently undefined. We report that the C-terminus domain of FMRP is sufficient to bind to ribosomes akin to the full-length protein. Furthermore, the C-terminus domain alone is essential and responsible for FMRP-mediated neuronal translation repression. However, dendritic distribution of FMRP and its microtubule association is favored by the synergistic combination of FMRP domains rather than individual domains. Interestingly, we show that the phosphorylation of hFMRP at Serine-500 is important in modulating the dynamics of translation by controlling ribosome association. This is a fundamental mechanism governing the size and number of FMRP puncta that contain actively translating ribosomes. Finally through the use of pathogenic mutations, we emphasize the hierarchical contribution of FMRP{\textquoteright}s domains in translation regulation.

}, keywords = {Fragile X Mental Retardation Protein, Fragile X Syndrome, Humans, Microtubules, Neurons, Protein Biosynthesis, Ribosomes, RNA, Messenger}, issn = {1559-1182}, doi = {10.1007/s12035-022-03049-1}, author = {D{\textquoteright}Souza, Michelle Ninochka and Ramakrishna, Sarayu and Radhakrishna, Bindushree K and Jhaveri, Vishwaja and Ravindran, Sreenath and Yeramala, Lahari and Nair, Deepak and Palakodeti, Dasaradhi and Muddashetty, Ravi S} } @article {2545, title = {Genome Engineering of Hematopoietic Stem Cells Using CRISPR/Cas9 System.}, journal = {Methods Mol Biol}, volume = {2429}, year = {2022}, month = {2022}, pages = {307-331}, abstract = {

Ex vivo genetic manipulation of autologous hematopoietic stem and progenitor cells (HSPCs) is a viable strategy for the treatment of hematologic and primary immune disorders. Targeted genome editing of HSPCs using the CRISPR-Cas9 system provides an effective platform to edit the desired genomic locus for therapeutic purposes with minimal off-target effects. In this chapter, we describe the detailed methodology for the CRISPR-Cas9 mediated gene knockout, deletion, addition, and correction in human HSPCs by viral and nonviral approaches. We also present a comprehensive protocol for the analysis of genome modified HSPCs toward the erythroid and megakaryocyte lineage in vitro and the long-term multilineage reconstitution capacity in the recently developed NBSGW mouse model that supports human erythropoiesis.

}, keywords = {Animals, CRISPR-Cas Systems, Gene Editing, Hematopoietic Stem Cell Transplantation, Hematopoietic Stem Cells, Mice, Transplantation, Autologous}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1979-7_20}, author = {Devaraju, Nivedhitha and Rajendiran, Vignesh and Ravi, Nithin Sam and Mohankumar, Kumarasamypet M} } @article {2465, title = {Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin.}, journal = {Elife}, volume = {11}, year = {2022}, month = {2022 02 11}, abstract = {

Naturally occurring point mutations in the promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the -123 region. Base editing at -123 and -124 bp of promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of -123T \> C and -124T \> C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.

}, keywords = {Adenine, Anemia, Sickle Cell, beta-Globins, beta-Thalassemia, Cell Line, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, Cytosine, Fetal Hemoglobin, gamma-Globins, Gene Editing, Hematopoietic Stem Cells, Humans, Point Mutation, Promoter Regions, Genetic}, issn = {2050-084X}, doi = {10.7554/eLife.65421}, author = {Ravi, Nithin Sam and Wienert, Beeke and Wyman, Stacia K and Bell, Henry William and George, Anila and Mahalingam, Gokulnath and Vu, Jonathan T and Prasad, Kirti and Bandlamudi, Bhanu Prasad and Devaraju, Nivedhitha and Rajendiran, Vignesh and Syedbasha, Nazar and Pai, Aswin Anand and Nakamura, Yukio and Kurita, Ryo and Narayanasamy, Muthuraman and Balasubramanian, Poonkuzhali and Thangavel, Saravanabhavan and Marepally, Srujan and Velayudhan, Shaji R and Srivastava, Alok and DeWitt, Mark A and Crossley, Merlin and Corn, Jacob E and Mohankumar, Kumarasamypet M} } @article {2400, title = {Inflammation-specific targeted carriers for local drug delivery to inflammatory bowel disease.}, journal = {Biomaterials}, volume = {281}, year = {2022}, month = {2022 Jan 05}, pages = {121364}, abstract = {

Delivering drugs directly to the inflamed intestinal sites to treat inflammatory bowel disease (IBD), particularly Crohn{\textquoteright}s and ulcerative colitis, is highly challenging. Recent advances in colitis therapy medications are expanding opportunities for improving local on-site drug availability by minimising the associated systemic side-effects. Drug delivery with targeted carrier systems has shown the potential to increase site-specificity, stability, and therapeutic efficacy. Herein, we report the development of a strong anionic charged inflammation targeted nanocarriers (IT-NCs) loaded with an immunosuppressant model drug. This system showed preferential adhesion on a charge-modified surface in vitro, and in both dextran sulfate sodium (DSS) and TNBS colitis mice in vivo models. IT-NCs showed improved colitis phenotype therapeutic efficacy in both animal models compared to free drug. Furthermore, ex vivo study of colon tissue biopsies from patients with colitis revealed that IT-NCs adhered preferentially to inflamed biopsies compared to normal. Together, our results suggest that IT-NCs have promising therapeutic potential as delivery carriers{\textquoteright} in colitis management.

}, issn = {1878-5905}, doi = {10.1016/j.biomaterials.2022.121364}, author = {Kotla, Niranjan G and Singh, Rajbir and Baby, Becca V and Rasala, Swetha and Rasool, Jawad and Hynes, Sean O and Martin, Darrell and Egan, Laurence J and Vemula, Praveen K and Jala, Venkatakrishna R and Rochev, Yury and Pandit, Abhay} } @article {2502, title = {Influence of Hydrophobicity in the Hydrophilic Region of Cationic Lipids on Enhancing Nucleic Acid Delivery and Gene Editing.}, journal = {ACS Appl Bio Mater}, volume = {5}, year = {2022}, month = {2022 Apr 18}, pages = {1489-1500}, abstract = {

Intracellular delivery of biomolecules using non-viral vectors critically depends on the vectors{\textquoteright} ability to allow the escape and release of the contents from the endosomes. Prior findings demonstrated that aromatic/hydrophobic group-containing amino acids such as phenylalanine (F) and tryptophan (W) destabilize cellular membranes by forming pores in the lipid bilayer. Taking cues from these findings, we have developed four α-tocopherol-based cationic amphiphiles by varying the aromatic/hydrophobic amino acids such as glycine (G), proline (P), phenylalanine (F), and tryptophan (W) as head groups and triazole in the linker region to study their impact on endosomal escape for the enhanced transfection efficacy. The lipids tocopherol-triazole-phenylalanine (TTF) and tocopherol-triazole-tryptophan (TTW) exhibited similar potential to commercial transfecting reagents, Lipofectamine (LF) 3000 and Lipofectamine Messenger Max (LFMM), respectively, in transfecting plasmid DNA and messenger RNA in multiple cultured cell lines. The TTW liposome was also found to be effective in delivering Cas9 mRNA and demonstrated equal efficiency of gene editing AAVS1 locus compared to LFMM in CHO, Neuro-2a, and EA.HY926 cell lines. In this current investigation, it is shown that the synthesized cationic lipids with aromatic hydrophobic R group-containing amino acids are safe, economic, and actually more efficient in nucleic acid delivery and genome-editing applications. These findings can be further explored in the genome-editing approach for treating genetic disorders.

}, keywords = {alpha-Tocopherol, Amino Acids, Cations, Gene Editing, Gene Transfer Techniques, Hydrophobic and Hydrophilic Interactions, Lipids, Nucleic Acids, Phenylalanine, Triazoles, Tryptophan}, issn = {2576-6422}, doi = {10.1021/acsabm.1c01226}, author = {Rapaka, Hithavani and Manturthi, Shireesha and Arjunan, Porkizhi and Venkatesan, Vigneshwaran and Thangavel, Saravanabhavan and Marepally, Srujan and Patri, Srilakshmi V} } @article {3642, title = {Intermittent scavenging of storage lesion from stored red blood cells by electrospun nanofibrous sheets enhances their quality and shelf-life.}, journal = {Nat Commun}, volume = {13}, year = {2022}, month = {2022 Dec 01}, pages = {7394}, abstract = {

Transfusion of healthy red blood cells (RBCs) is a lifesaving process. However, upon storing RBCs, a wide range of damage-associate molecular patterns (DAMPs), such as cell-free DNA, nucleosomes, free-hemoglobin, and poly-unsaturated-fatty-acids are generated. DAMPs can further damage RBCs; thus, the quality of stored RBCs declines during the storage and limits their shelf-life. Since these DAMPs consist of either positive or negative charged species, we developed taurine and acridine containing electrospun-nanofibrous-sheets (Tau-AcrNFS), featuring anionic, cationic charges and an DNA intercalating group on their surfaces. We show that Tau-AcrNFS are efficient in scavenging DAMPs from stored human and mice RBCs ex vivo. We find that intermittent scavenging of DAMPs by Tau-AcrNFS during the storage reduces the loss of RBC membrane integrity and reduces discocytes-to-spheroechinocytes transformation in stored-old-RBCs. We perform RBC-transfusion studies in mice to reveal that intermittent removal of DAMPs enhances the quality of stored-old-RBCs equivalent to freshly collected RBCs, and increases their shelf-life by ~22\%. Such prophylactic technology may lead to the development of novel blood bags or medical device, and may therefore impact healthcare by reducing transfusion-related adverse effects.

}, keywords = {Acridines, Animals, Drug-Related Side Effects and Adverse Reactions, Erythrocytes, Humans, Mice, Nanofibers, Research Personnel}, issn = {2041-1723}, doi = {10.1038/s41467-022-35269-3}, author = {Pandey, Subhashini and Mahato, Manohar and Srinath, Preethem and Bhutani, Utkarsh and Goap, Tanu Jain and Ravipati, Priusha and Vemula, Praveen Kumar} } @article {2423, title = {Lysate-based pipeline to characterize microtubule-associated proteins uncovers unique microtubule behaviours.}, journal = {Nat Cell Biol}, volume = {24}, year = {2022}, month = {2022 Feb}, pages = {253-267}, abstract = {

The microtubule cytoskeleton forms complex macromolecular assemblies with a range of microtubule-associated proteins (MAPs) that have fundamental roles in cell architecture, division and motility. Determining how an individual MAP modulates microtubule behaviour is an important step in understanding the physiological roles of various microtubule assemblies. To characterize how MAPs control microtubule properties and functions, we developed an approach allowing for medium-throughput analyses of MAPs in cell-free conditions using lysates of mammalian cells. Our pipeline allows for quantitative as well as ultrastructural analyses of microtubule-MAP assemblies. Analysing 45 bona fide and potential mammalian MAPs, we uncovered previously unknown activities that lead to distinct and unique microtubule behaviours such as microtubule coiling or hook formation, or liquid-liquid phase separation along the microtubule lattice that initiates microtubule branching. We have thus established a powerful tool for a thorough characterization of a wide range of MAPs and MAP variants, thus opening avenues for the determination of mechanisms underlying their physiological roles and pathological implications.

}, issn = {1476-4679}, doi = {10.1038/s41556-021-00825-4}, author = {Jijumon, A S and Bodakuntla, Satish and Genova, Mariya and Bangera, Mamata and Sackett, Violet and Besse, Laetitia and Maksut, Fatlinda and Henriot, Veronique and Magiera, Maria M and Sirajuddin, Minhajuddin and Janke, Carsten} } @article {3342, title = {Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival.}, journal = {Life Sci Alliance}, volume = {5}, year = {2022}, month = {2022 Sep 09}, abstract = {

Cell death, survival, or growth decisions in T-cell subsets depend on interplay between cytokine-dependent and metabolic processes. The metabolic requirements of T-regulatory cells (Tregs) for their survival and how these are satisfied remain unclear. Herein, we identified a necessary requirement of methionine uptake and usage for Tregs survival upon IL-2 deprivation. Activated Tregs have high methionine uptake and usage to S-adenosyl methionine, and this uptake is essential for Tregs survival in conditions of IL-2 deprivation. We identify a solute carrier protein SLC43A2 transporter, regulated in a Notch1-dependent manner that is necessary for this methionine uptake and Tregs viability. Collectively, we uncover a specifically regulated mechanism of methionine import in Tregs that is required for cells to adapt to cytokine withdrawal. We highlight the need for methionine availability and metabolism in contextually regulating cell death in this immunosuppressive population of T cells.

}, keywords = {Interleukin-2, Methionine, Racemethionine, Solute Carrier Proteins, T-Lymphocytes, Regulatory}, issn = {2575-1077}, doi = {10.26508/lsa.202201663}, author = {Saini, Neetu and Naaz, Afsana and Metur, Shree Padma and Gahlot, Pinki and Walvekar, Adhish and Dutta, Anupam and Davathamizhan, Umamaheswari and Sarin, Apurva and Laxman, Sunil} } @article {3338, title = {Modulation of biliverdin dynamics and spectral properties by Sandercyanin.}, journal = {RSC Adv}, volume = {12}, year = {2022}, month = {2022 Jul 06}, pages = {20296-20304}, abstract = {

Biliverdin IX-alpha (BV), a tetrapyrrole, is found ubiquitously in most living organisms. It functions as a metabolite, pigment, and signaling compound. While BV is known to bind to diverse protein families such as heme-metabolizing enzymes and phytochromes, not many BV-bound lipocalins (ubiquitous, small lipid-binding proteins) have been studied. The molecular basis of binding and conformational selectivity of BV in lipocalins remains unexplained. Sandercyanin (SFP)-BV complex is a blue lipocalin protein present in the mucus of the Canadian walleye (). In this study, we present the structures and binding modes of BV to SFP. Using a combination of designed site-directed mutations, X-ray crystallography, UV/VIS, and resonance Raman spectroscopy, we have identified multiple conformations of BV that are stabilized in the binding pocket of SFP. In complex with the protein, these conformers generate varied spectroscopic signatures both in their absorption and fluorescence spectra. We show that despite no covalent anchor, structural heterogeneity of the chromophore is primarily driven by the D-ring pyrrole of BV. Our work shows how conformational promiscuity of BV is correlated to the rearrangement of amino acids in the protein matrix leading to modulation of spectral properties.

}, issn = {2046-2069}, doi = {10.1039/d2ra02880h}, author = {Ghosh, Swagatha and Mondal, Sayan and Yadav, Keerti and Aggarwal, Shantanu and Schaefer, Wayne F and Narayana, Chandrabhas and Subramanian, Ramaswamy} } @article {3640, title = {Nanobody derived using a peptide epitope from the spike protein receptor-binding motif inhibits entry of SARS-CoV-2 variants.}, journal = {J Biol Chem}, volume = {299}, year = {2022}, month = {2022 Nov 22}, pages = {102732}, abstract = {

The emergence of new escape mutants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has escalated its penetration among the human population and has reinstated its status as a global pandemic. Therefore, developing effective antiviral therapy against emerging SARS-CoV variants and other viruses in a short period becomes essential. Blocking SARS-CoV-2 entry into human host cells by disrupting the spike glycoprotein-angiotensin-converting enzyme 2 interaction has already been exploited for vaccine development and monoclonal antibody therapy. Unlike the previous reports, our study used a nine-amino acid peptide from the receptor-binding motif of the spike protein as an epitope. We report the identification of an efficacious nanobody N1.2 that blocks the entry of pseudovirus-containing SARS-CoV-2 spike as the surface glycoprotein. Moreover, using mCherry fluorescence-based reporter assay, we observe a more potent neutralizing effect against both the hCoV19 (Wuhan/WIV04/2019) and the Omicron (BA.1) pseudotyped spike virus with a bivalent version of the N1.2 nanobody. In summary, our study presents a rapid and efficient methodology to use peptide sequences from a protein-receptor interaction interface as epitopes for screening nanobodies against potential pathogenic targets. We propose that this approach can also be widely extended to target other viruses and pathogens in the future.

}, issn = {1083-351X}, doi = {10.1016/j.jbc.2022.102732}, author = {Mendon, Nivya and Ganie, Rayees A and Kesarwani, Shubham and Dileep, Drisya and Sasi, Sarika and Lama, Prakash and Chandra, Anchal and Sirajuddin, Minhajuddin} } @article {3339, title = {NMDAR mediated dynamic changes in mA inversely correlates with neuronal translation.}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 07 05}, pages = {11317}, abstract = {

Epitranscriptome modifications are crucial in translation regulation and essential for maintaining cellular homeostasis. N6 methyladenosine (mA) is one of the most abundant and well-conserved epitranscriptome modifications, which is known to play a pivotal role in diverse aspects of neuronal functions. However, the role of mA modifications with respect to activity-mediated translation regulation and synaptic plasticity has not been studied. Here, we investigated the role of mA modification in response to NMDAR stimulation. We have consistently observed that 5\ min NMDAR stimulation causes an increase in eEF2 phosphorylation. Correspondingly, NMDAR stimulation caused a significant increase in the mA signal at 5\ min time point, correlating with the global translation inhibition. The NMDAR induced increase in the mA signal is accompanied by the redistribution of the mA marked RNAs from translating to the non-translating pool of ribosomes. The increased mA levels are well correlated with the reduced FTO levels observed on NMDAR stimulation. Additionally, we show that inhibition of FTO prevents NMDAR mediated changes in mA levels. Overall, our results establish RNA-based molecular readout which corelates with the NMDAR-dependent translation regulation which helps in understanding changes in protein synthesis.

}, keywords = {Adenosine, Neurons, Phosphorylation, Receptors, N-Methyl-D-Aspartate, RNA}, issn = {2045-2322}, doi = {10.1038/s41598-022-14798-3}, author = {Gowda, Naveen Kumar Chandappa and Nawalpuri, Bharti and Ramakrishna, Sarayu and Jhaveri, Vishwaja and Muddashetty, Ravi S} } @article {3716, title = {Omicron infection increases IgG binding to spike protein of predecessor variants.}, journal = {J Med Virol}, year = {2022}, month = {2022 Dec 22}, abstract = {

BACKGROUND: SARS-CoV-2 transmission in India in 2020-2022 was driven predominantly by Wild (Wuhan-Hu-1and D614G), Delta, and Omicron variants. The aim of this study was to examine the effect of infections on the humoral immune response and cross-reactivity to spike proteins of Wuhan-Hu-1, Delta, C.1.2., and Omicron.

OBJECTIVES: Residual archival sera (N=81) received between January 2020 and March 2022 were included. Infection status was inferred by a positive SARS-CoV-2 RT-PCR and/or serology (anti-N and anti-S antibodies) and sequencing of contemporaneous samples (N=18) to infer lineage. We estimated the levels and cross-reactivity of infection-induced sera including Wild, Delta, Omicron as well as vaccine breakthrough infections (Delta and Omicron).

RESULTS: We found ~2-fold increase in spike-specific IgG antibody binding in post-Omicron infection compared to the pre-Omicron period, whilst the change in pre- and post-Delta infections were similar. Further investigation of Omicron-specific humoral responses revealed primary Omicron infection as an inducer of cross-reactive antibodies against predecessor variants, in spite of weaker degree of humoral response compared to Wuhan-Hu-1 and Delta infection. Intriguingly, Omicron vaccine-breakthrough infections when compared with primary infections, exhibited increased humoral responses against RBD (7.7-fold) and Trimeric S (Trimeric form of spike protein) (34.6-fold) in addition to increased binding of IgGs towards previously circulating variants (4.2 - 6.5-fold). Despite Delta breakthrough infections showing a higher level of humoral response against RBD (2.9-fold) and Trimeric S (5.7-fold) compared to primary Delta sera, a demonstrably reduced binding (36-49\%) was observed to Omicron spike protein.

CONCLUSIONS: Omicron vaccine breakthrough infection results in increased intensity of humoral response and wider breadth of IgG binding to spike proteins of antigenically-distinct, predecessor variants. This article is protected by copyright. All rights reserved.

}, issn = {1096-9071}, doi = {10.1002/jmv.28419}, author = {Mahalingam, Gokulnath and Periyasami, Yogapriya and Arjunan, Porkizhi and Subaschandrabose, Rajesh Kumar and Mathivanan, Tamil Venthan and Mathew, Roshlin Susan and Ramya Devi, Kt and Premkumar, Prasanna Samuel and Muliyil, Jayaprakash and Srivastava, Alok and Moorthy, Mahesh and Marepally, Srujan} } @article {2884, title = {Preferential Expansion of Human CD34CD133CD90 Hematopoietic Stem Cells Enhances Gene-Modified Cell Frequency for Gene Therapy.}, journal = {Hum Gene Ther}, volume = {33}, year = {2022}, month = {2022 02}, pages = {188-201}, abstract = {

CD34CD133CD90 hematopoietic stem cells (HSCs) are responsible for long-term multilineage hematopoiesis, and the high frequency of gene-modified HSCs is crucial for the success of hematopoietic stem and progenitor cell (HSPC) gene therapy. However, the culture and gene manipulation steps of HSPC graft preparation significantly reduce the frequency of HSCs, thus necessitating large doses of HSPCs and reagents for the manipulation. In this study, we identified a combination of small molecules, Resveratrol, UM729, and SR1 that preferentially expands CD34CD133CD90 HSCs over other subpopulations of adult HSPCs in culture. The preferential expansion enriches the HSCs in culture, enhances the adhesion, and results in a sixfold increase in the long-term engraftment in NSG mice. Further, the culture-enriched HSCs are more responsive to gene modification by lentiviral transduction and gene editing, increasing the frequency of gene-modified HSCs up to 10-fold . The yield of gene-modified HSCs obtained by the culture enrichment is similar to the sort-purification of HSCs and superior to Cyclosporin-H treatment. Our study addresses a critical challenge of low frequency of gene modified HSCs in HSPC graft by developing and demonstrating a facile HSPC culture condition that increases the frequency of gene-modified cells . This strategy will improve the outcome of HSPC gene therapy and also simplify the gene manipulation process.

}, keywords = {Animals, Antigens, CD34, Fetal Blood, Genetic Therapy, Hematopoietic Stem Cell Transplantation, Hematopoietic Stem Cells, Humans, Mice, Mice, Inbred NOD, Mice, SCID}, issn = {1557-7422}, doi = {10.1089/hum.2021.089}, author = {Christopher, Abisha Crystal and Venkatesan, Vigneshwaran and Karuppusamy, Karthik V and Srinivasan, Saranya and Babu, Prathibha and Azhagiri, Manoj Kumar K and Chambayil, Karthik and Bagchi, Abhirup and Rajendiran, Vignesh and Ravi, Nithin Sam and Kumar, Sanjay and Marepally, Srujan Kumar and Mohankumar, Kumarasamypet Murugesan and Srivastava, Alok and Velayudhan, Shaji R and Thangavel, Saravanabhavan} } @article {2474, title = {Skin-Permeable Nano-Lithocholic Lipidoid Efficiently Alleviates Psoriasis-like Chronic Skin Inflammations.}, journal = {ACS Appl Mater Interfaces}, year = {2022}, month = {2022 Mar 29}, abstract = {

Long-term application of topical therapeutics for psoriasis has a plethora of side effects. Additionally, skin-permeating agents used in their formulations for deeper dermal delivery damage the skin. To address these limitations, we developed novel lithocholic acid analogues that could form lipid nanoparticles (nano-LCs) spontaneously in the aqueous milieu, permeate through the skin, penetrate the deeper dermal layers, and exert anti-inflammatory effects against psoriasis-like chronic skin inflammations. Prior findings demonstrated that lithocholic acid acts as a vitamin D receptor agonist without affecting the Ca metabolism and also as an antagonist for ephrin type-A receptor 2 (EphA2). Taking cues from the previous findings, lithocholic acid derivatives with twin alkyl chains (LC6, LC8, LC10, and LC-12) were synthesized, nanoparticles (nano-LCs) were prepared, and they were evaluated for their skin permeability and anti-inflammatory properties. Among these nano-LCs, nano-LC10 demonstrated superior anti-inflammatory properties and inhibition of keratinocyte proliferation in various cell-based evaluations. Furthermore, the therapeutic efficiency of nano-LC10 was evaluated in an imiquimod-induced psoriasis-like mouse model and demonstrated comparable efficiency with the standard topical formulation, Sorvate, in reducing skin inflammations. Nano-LC10 also reduced systemic inflammation, organ toxicity, and also proinflammatory serum cytokine levels. Overall, nano-lithocholic lipidoid (nano-LC10) can be a potential novel class of therapeutics for topical application in treating psoriasis.

}, issn = {1944-8252}, doi = {10.1021/acsami.1c19180}, author = {Rachamalla, Hari Krishnareddy and Voshavar, Chandrashekhar and Arjunan, Porkizhi and Mahalingam, Gokulnath and Chowath, Rashmi Praksash and Banerjee, Rajkumar and Vemula, Praveen Kumar and Marepally, Srujan} } @article {3345, title = {Snail maintains the stem/progenitor state of skin epithelial cells and carcinomas through the autocrine effect of matricellular protein Mindin.}, journal = {Cell Rep}, volume = {40}, year = {2022}, month = {2022 09 20}, pages = {111390}, abstract = {

Preservation of a small population of cancer stem cells (CSCs) within a heterogeneous carcinoma serves as a paradigm to understand how select cells in a tissue maintain their undifferentiated status. In both embryogenesis and cancer, Snail has been correlated with stemness, but the molecular underpinning of this phenomenon remains largely ill-defined. In models of cutaneous squamous cell carcinoma (cSCC), we discovered a non-epithelial-mesenchymal transition function for the transcription factor Snail in maintaining the stemness of epidermal keratinocytes. Snail-expressing cells secrete the matricellular protein Mindin, which functions in an autocrine fashion to activate a Src-STAT3 pathway to reinforce their stem/progenitor phenotype. This pathway is activated by the engagement of Mindin with the leukocyte-specific integrin, CD11b (ITGAM), which is also unexpectedly expressed by epidermal keratinocytes. Interestingly, disruption of this signaling module in human cSCC attenuates tumorigenesis, suggesting that targeting Mindin would be a promising therapeutic approach to hinder cancer recurrence.

}, keywords = {Carcinoma, Squamous Cell, Cell Line, Tumor, Epithelial Cells, Extracellular Matrix Proteins, Humans, Integrins, Neoplasm Proteins, Neoplasm Recurrence, Local, Neoplastic Stem Cells, Skin Neoplasms, Snail Family Transcription Factors}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.111390}, author = {Badarinath, Krithika and Dam, Binita and Kataria, Sunny and Zirmire, Ravindra K and Dey, Rakesh and Kansagara, Gaurav and Ajnabi, Johan and Hegde, Akshay and Singh, Randhir and Masudi, Tafheem and Sambath, Janani and Sachithanandan, Sasikala P and Kumar, Prashant and Gulyani, Akash and He, You-Wen and Krishna, Sudhir and Jamora, Colin} } @article {2463, title = {Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy.}, journal = {NPJ Genom Med}, volume = {7}, year = {2022}, month = {2022 Mar 14}, pages = {18}, abstract = {

Cardiomyopathy (CMP) is a heritable disorder. Over 50\% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5\% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 {\texttimes} 10 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.

}, issn = {2056-7944}, doi = {10.1038/s41525-022-00288-y}, author = {Lesurf, Robert and Said, Abdelrahman and Akinrinade, Oyediran and Breckpot, Jeroen and Delfosse, Kathleen and Liu, Ting and Yao, Roderick and Persad, Gabrielle and McKenna, Fintan and Noche, Ramil R and Oliveros, Winona and Mattioli, Kaia and Shah, Shreya and Miron, Anastasia and Yang, Qian and Meng, Guoliang and Yue, Michelle Chan Seng and Sung, Wilson W L and Thiruvahindrapuram, Bhooma and Lougheed, Jane and Oechslin, Erwin and Mondal, Tapas and Bergin, Lynn and Smythe, John and Jayappa, Shashank and Rao, Vinay J and Shenthar, Jayaprakash and Dhandapany, Perundurai S and Semsarian, Christopher and Weintraub, Robert G and Bagnall, Richard D and Ingles, Jodie and Mel{\'e}, Marta and Maass, Philipp G and Ellis, James and Scherer, Stephen W and Mital, Seema} } @article {2211, title = {Adiponectin receptor 1 variants contribute to hypertrophic cardiomyopathy that can be reversed by rapamycin.}, journal = {Sci Adv}, volume = {7}, year = {2021}, month = {2021 Jan}, abstract = {

Hypertrophic cardiomyopathy (HCM) is a heterogeneous genetic heart muscle disease characterized by hypertrophy with preserved or increased ejection fraction in the absence of secondary causes. However, recent studies have demonstrated that a substantial proportion of individuals with HCM also have comorbid diabetes mellitus (~10\%). Whether genetic variants may contribute a combined phenotype of HCM and diabetes mellitus is not known. Here, using next-generation sequencing methods, we identified novel and ultrarare variants in adiponectin receptor 1 () as risk factors for HCM. Biochemical studies showed that variants dysregulate glucose and lipid metabolism and cause cardiac hypertrophy through the p38/mammalian target of rapamycin and/or extracellular signal-regulated kinase pathways. A transgenic mouse model expressing an variant displayed cardiomyopathy that recapitulated the cellular findings, and these features were rescued by rapamycin. Our results provide the first evidence that variants can cause HCM and provide new insights into regulation.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abb3991}, author = {Dhandapany, Perundurai S and Kang, Soojeong and Kashyap, Deepak K and Rajagopal, Raksha and Sundaresan, Nagalingam R and Singh, Rajvir and Thangaraj, Kumarasamy and Jayaprakash, Shilpa and Manjunath, Cholenahally N and Shenthar, Jayaprakash and Lebeche, Djamel} } @article {2364, title = {Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes.}, journal = {Sci Rep}, volume = {11}, year = {2021}, month = {2021 Oct 26}, pages = {21088}, abstract = {

Evolutionary trends may underlie some aspects of the risk for common, non-communicable disorders, including psychiatric disease. We analyzed whole exome sequencing data from 80 unique individuals from India coming from families with two or more individuals with severe mental illness. We used Population Branch Statistics (PBS) to identify variants and genes under positive selection and identified 74 genes as candidates for positive selection. Of these, 20 were previously associated with Schizophrenia, Alzheimer{\textquoteright}s disease and cognitive abilities in genome wide association studies. We then checked whether any of these 74 genes were involved in common biological pathways or related to specific cellular or molecular functions. We found that immune related pathways and functions related to innate immunity such as antigen binding were over-represented. We also evaluated for the presence of Neanderthal introgressed segments in these genes and found Neanderthal introgression in a single gene out of the 74 candidate genes. However, the introgression pattern indicates the region is unlikely to be the source for selection. Our findings hint at how selection pressures in individuals from families with a history of severe mental illness may diverge from the general population. Further, it also provides insights into the genetic architecture of severe mental illness, such as schizophrenia and its link to immune factors.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-00123-x}, author = {Mahadevan, Jayant and Pathak, Ajai Kumar and Vemula, Alekhya and Nadella, Ravi Kumar and Viswanath, Biju and Jain, Sanjeev and Purushottam, Meera and Mondal, Mayukh} } @article {2328, title = {APOE4 Affects Basal and NMDAR-Mediated Protein Synthesis in Neurons by Perturbing Calcium Homeostasis.}, journal = {J Neurosci}, volume = {41}, year = {2021}, month = {2021 Oct 20}, pages = {8686-8709}, abstract = {

Apolipoprotein E (APOE), one of the primary lipoproteins in the brain has three isoforms in humans, APOE2, APOE3, and APOE4. APOE4 is the most well-established risk factor increasing the predisposition for Alzheimer{\textquoteright}s disease (AD). The presence of the APOE4 allele alone is shown to cause synaptic defects in neurons and recent studies have identified multiple pathways directly influenced by APOE4. However, the mechanisms underlying APOE4-induced synaptic dysfunction remain elusive. Here, we report that the acute exposure of primary cortical neurons or synaptoneurosomes to APOE4 leads to a significant decrease in global protein synthesis. Primary cortical neurons were derived from male and female embryos of Sprague Dawley (SD) rats or C57BL/6J mice. Synaptoneurosomes were prepared from P30 male SD rats. APOE4 treatment also abrogates the NMDA-mediated translation response indicating an alteration of synaptic signaling. Importantly, we demonstrate that both APOE3 and APOE4 generate a distinct translation response which is closely linked to their respective calcium signature. Acute exposure of neurons to APOE3 causes a short burst of calcium through NMDA receptors (NMDARs) leading to an initial decrease in protein synthesis which quickly recovers. Contrarily, APOE4 leads to a sustained increase in calcium levels by activating both NMDARs and L-type voltage-gated calcium channels (L-VGCCs), thereby causing sustained translation inhibition through eukaryotic translation elongation factor 2 (eEF2) phosphorylation, which in turn disrupts the NMDAR response. Thus, we show that APOE4 affects basal and activity-mediated protein synthesis responses in neurons by affecting calcium homeostasis. Defective protein synthesis has been shown as an early defect in familial Alzheimer{\textquoteright}s disease (AD). However, this has not been studied in the context of sporadic AD, which constitutes the majority of cases. In our study, we show that Apolipoprotein E4 (APOE4), the predominant risk factor for AD, inhibits global protein synthesis in neurons. APOE4 also affects NMDA activity-mediated protein synthesis response, thus inhibiting synaptic translation. We also show that the defective protein synthesis mediated by APOE4 is closely linked to the perturbation of calcium homeostasis caused by APOE4 in neurons. Thus, we propose the dysregulation of protein synthesis as one of the possible molecular mechanisms to explain APOE4-mediated synaptic and cognitive defects. Hence, the study not only suggests an explanation for the APOE4-mediated predisposition to AD, it also bridges the gap in understanding APOE4-mediated pathology.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0435-21.2021}, author = {Ramakrishna, Sarayu and Jhaveri, Vishwaja and Konings, Sabine C and Nawalpuri, Bharti and Chakraborty, Sumita and Holst, Bj{\o}rn and Schmid, Benjamin and Gouras, Gunnar K and Freude, Kristine K and Muddashetty, Ravi S} } @article {2362, title = {Astrocytic reactivity triggered by defective autophagy and metabolic failure causes neurotoxicity in frontotemporal dementia type 3.}, journal = {Stem Cell Reports}, volume = {16}, year = {2021}, month = {2021 Nov 09}, pages = {2736-2751}, abstract = {

Frontotemporal dementia type 3 (FTD3), caused by a point mutation in the charged multivesicular body protein 2B (CHMP2B), affects mitochondrial ultrastructure and the endolysosomal pathway in neurons. To dissect the astrocyte-specific impact of mutant CHMP2B expression, we generated astrocytes from human induced pluripotent stem cells (hiPSCs) and confirmed our findings in CHMP2B mutant mice. Our data provide mechanistic insights into how defective autophagy causes perturbed mitochondrial dynamics with impaired glycolysis, increased reactive oxygen species, and elongated mitochondrial morphology, indicating increased mitochondrial fusion in FTD3 astrocytes. This shift in astrocyte homeostasis triggers a reactive astrocyte phenotype and increased release of toxic cytokines, which accumulate in nuclear factor kappa b (NF-κB) pathway activation with increased production of CHF, LCN2, and C3 causing neurodegeneration.

}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2021.09.013}, author = {Chandrasekaran, Abinaya and Dittlau, Katarina Stoklund and Corsi, Giulia I and Haukedal, Henriette and Doncheva, Nadezhda T and Ramakrishna, Sarayu and Ambardar, Sheetal and Salcedo, Claudia and Schmidt, Sissel I and Zhang, Yu and Cirera, Susanna and Pihl, Maria and Schmid, Benjamin and Nielsen, Troels Tolstrup and Nielsen, J{\o}rgen E and Kolko, Miriam and Kobol{\'a}k, Julianna and Dinny{\'e}s, Andr{\'a}s and Hyttel, Poul and Palakodeti, Dasaradhi and Gorodkin, Jan and Muddashetty, Ravi S and Meyer, Morten and Aldana, Blanca I and Freude, Kristine K} } @article {2375, title = {Biophysical properties of the isolated spike protein binding helix of human ACE2.}, journal = {Biophys J}, volume = {120}, year = {2021}, month = {2021 07 20}, pages = {2785-2792}, abstract = {

The entry of the severe acute respiratory syndrome coronavirus 2 virus in human cells is mediated by the binding of its surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor. A 23-residue long helical segment (SBP1) at the binding interface of human ACE2 interacts with viral spike protein and therefore has generated considerable interest as a recognition element for virus detection. Unfortunately, emerging reports indicate that the affinity of SBP1 to the receptor-binding domain of the spike protein is much lower than that of the ACE2 receptor itself. Here, we examine the biophysical properties of SBP1 to reveal factors leading to its low affinity for the spike protein. Whereas SBP1 shows good solubility (solubility \> 0.8\ mM), circular dichroism spectroscopy shows that it is mostly disordered with some antiparallel β-sheet content and no helicity. The helicity is substantial (\>20\%) only upon adding high concentrations (>=20\% v/v) of 2,2,2-trifluoroethanol, a helix promoter. Fluorescence correlation spectroscopy and single-molecule photobleaching studies show that the peptide oligomerizes at concentrations \>50\ nM. We hypothesized that mutating the hydrophobic residues (F28, F32, and F40) of SBP1, which do not directly interact with the spike protein, to alanine would reduce peptide oligomerization without affecting its spike binding affinity. Whereas the mutant peptide (SBP1) shows substantially reduced oligomerization propensity, it does not show improved helicity. Our study shows that the failure of efforts, so far, to produce a short SBP1 mimic with a high affinity for the spike protein is not only due to the lack of helicity but is also due to the heretofore unrecognized problem of oligomerization.

}, keywords = {Angiotensin-Converting Enzyme 2, COVID-19, Humans, Peptidyl-Dipeptidase A, Protein Binding, SARS-CoV-2, Spike Glycoprotein, Coronavirus}, issn = {1542-0086}, doi = {10.1016/j.bpj.2021.06.017}, author = {Das, Anirban and Vishvakarma, Vicky and Dey, Arpan and Dey, Simli and Gupta, Ankur and Das, Mitradip and Vishwakarma, Krishna Kant and Roy, Debsankar Saha and Yadav, Swati and Kesarwani, Shubham and Venkatramani, Ravindra and Maiti, Sudipta} } @article {2272, title = {Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders.}, journal = {Neurochem Int}, volume = {147}, year = {2021}, month = {2021 Jul}, pages = {105055}, abstract = {

The diverse number of neurons in the cerebral cortex are generated during development by neural stem cells lining the ventricle, and they continue maturing postnatally. Dynamic chromatin regulation in these neural stem cells is a fundamental determinant of the emerging property of the functional neural network, and the chromatin remodellers are critical determinants of this process. Chromatin remodellers participate in several steps of this process from proliferation, differentiation, migration leading to complex network formation which forms the basis of higher-order functions of cognition and behaviour. Here we review the role of these ATP-dependent chromatin remodellers in cortical development in health and disease and highlight several key mouse mutants of the subunits of the complexes which have revealed how the remodelling mechanisms control the cortical stem cell chromatin landscape for expression of stage-specific transcripts. Consistent with their role in cortical development, several putative risk variants in the subunits of the remodelling complexes have been identified as the underlying causes of several neurodevelopmental disorders. A basic understanding of the detailed molecular mechanism of their action is key to understating how mutations in the same networks lead to disease pathologies and perhaps pave the way for therapeutic development for these complex multifactorial disorders.

}, issn = {1872-9754}, doi = {10.1016/j.neuint.2021.105055}, author = {D{\textquoteright}Souza, Leora and Channakkar, Asha S and Muralidharan, Bhavana} } @article {2326, title = {Correction of amygdalar dysfunction in a rat model of fragile X syndrome.}, journal = {Cell Rep}, volume = {37}, year = {2021}, month = {2021 Oct 12}, pages = {109805}, abstract = {

Fragile X syndrome (FXS), a commonly inherited form of autism and intellectual disability, is associated with emotional symptoms that implicate dysfunction of the amygdala. However, current understanding of the pathogenesis of the disease is based primarily on studies in the hippocampus and neocortex, where FXS defects have been corrected by inhibiting group I metabotropic glutamate receptors (mGluRs). Here, we observe that activation, rather than inhibition, of mGluRs in the basolateral amygdala reverses impairments in a rat model of FXS. FXS rats exhibit deficient recall of auditory conditioned fear, which is accompanied by a range of in\ vitro and in\ vivo deficits in synaptic transmission and plasticity. We find presynaptic mGluR5 in the amygdala, activation of which reverses deficient synaptic transmission and plasticity, thereby restoring normal fear learning in FXS rats. This highlights the importance of modifying the prevailing mGluR-based framework for therapeutic strategies to include circuit-specific differences in FXS pathophysiology.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109805}, author = {Fernandes, Giselle and Mishra, Pradeep K and Nawaz, Mohammad Sarfaraz and Donlin-Asp, Paul G and Rahman, Mohammed Mostafizur and Hazra, Anupam and Kedia, Sonal and Kayenaat, Aiman and Songara, Dheeraj and Wyllie, David J A and Schuman, Erin M and Kind, Peter C and Chattarji, Sumantra} } @article {2292, title = {Cross-diagnostic evaluation of minor physical anomalies in psychiatric disorders.}, journal = {J Psychiatr Res}, volume = {142}, year = {2021}, month = {2021 Jul 20}, pages = {54-62}, abstract = {

BACKGROUND: Minor physical anomalies (MPA) are markers of impaired neurodevelopment during the prenatal stage. Assessing MPA across psychiatric disorders may help understand their shared nature. In addition, MPA in family members would indicate a shared liability and endophenotype potential. We examined familial aggregation of MPA and their role as transdiagnostic and disorder-specific markers of 5 major psychiatric/neuropsychiatric conditions (schizophrenia, bipolar disorder, substance dependence, obsessive-compulsive disorder, and Alzheimer{\textquoteright}s dementia).

METHODS: Modified Waldrop{\textquoteright}s MPA scale was applied on 1321 individuals from 439 transdiagnostic multiplex families and 125 healthy population controls (HC). Stage of fetal development (morphogenetic/phenogenetic)- and anatomical location (craniofacial/peripheral)-based sub-scores were calculated. Familiality and endophenotypic potential of MPA were analyzed with serial negative binomial mixed-effect regression. Cross-diagnostic differences and the effect of family history density (FHD) of each diagnosis on MPA were assessed. Mixed-effects Cox models estimated the influence of MPA on age-at-onset of illness (AAO).

RESULTS: MPA were found to be heritable in families with psychiatric disorders, with a familiality of 0.52. MPA were higher in psychotic disorders after controlling for effects of sex and intrafamilial correlation. Morphogenetic variant MPA was noted to be lower in dementia in comparison to HC. FHD of schizophrenia and bipolar disorder predicted higher, and that of dementia and substance dependence predicted lower MPA. MPA brought forward the AAO [HR:1.07 (1.03-1.11)], and this was more apparent in psychotic disorders.

CONCLUSION: MPA are transmissible in families, are specifically related to the risk of developing psychoses, and predict an earlier age at onset. Neurodevelopmentally informed classification of MPA has the potential to enhance the etiopathogenic and translational understanding of psychiatric disorders.

}, issn = {1879-1379}, doi = {10.1016/j.jpsychires.2021.07.028}, author = {Sreeraj, Vanteemar S and Puzhakkal, Joan C and Holla, Bharath and Nadella, Ravi Kumar and Sheth, Sweta and Balachander, Srinivas and Ithal, Dhruva and Ali, Furkhan and Viswanath, Biju and Muralidharan, Kesavan and Venkatasubramanian, Ganesan and John, John P and Benegal, Vivek and Murthy, Pratima and Varghese, Mathew and Reddy, Yc Janardhan and Jain, Sanjeev} } @article {2329, title = {Distinct temporal expression of the GW182 paralog TNRC6A in neurons regulates dendritic arborization.}, journal = {J Cell Sci}, volume = {134}, year = {2021}, month = {2021 Aug 15}, abstract = {

Precise development of the dendritic architecture is a critical determinant of mature neuronal circuitry. MicroRNA (miRNA)-mediated regulation of protein synthesis plays a crucial role in dendritic morphogenesis, but the role of miRNA-induced silencing complex (miRISC) protein components in this process is less studied. Here, we show an important role of a key miRISC protein, the GW182 paralog TNRC6A, in the regulation of dendritic growth. We identified a distinct brain region-specific spatiotemporal expression pattern of GW182 during rat postnatal development. We found that the window of peak GW182 expression coincides with the period of extensive dendritic growth, both in the hippocampus and cerebellum. Perturbation of GW182 function during a specific temporal window resulted in reduced dendritic growth of cultured hippocampal neurons. Mechanistically, we show that GW182 modulates dendritic growth by regulating global somatodendritic translation and actin cytoskeletal dynamics of developing neurons. Furthermore, we found that GW182 affects dendritic architecture by regulating the expression of actin modulator LIMK1. Taken together, our data reveal a previously undescribed neurodevelopmental expression pattern of GW182 and its role in dendritic morphogenesis, which involves both translational control and actin cytoskeletal rearrangement. This article has an associated First Person interview with the first author of the paper.

}, issn = {1477-9137}, doi = {10.1242/jcs.258465}, author = {Nawalpuri, Bharti and Sharma, Arpita and Chattarji, Sumantra and Muddashetty, Ravi S} } @article {2324, title = {Duox generated reactive oxygen species activate ATR/Chk1 to induce G2 arrest in tracheoblasts.}, journal = {Elife}, volume = {10}, year = {2021}, month = {2021 Oct 08}, abstract = {

Progenitors of the thoracic tracheal system of adult (tracheoblasts) arrest in G2 during larval life and rekindle a mitotic program subsequently. G2 arrest is dependent on ATR-dependent phosphorylation of Chk1 that is actuated in the absence of detectable DNA damage. We are interested in the mechanisms that activate ATR/Chk1 (Kizhedathu et al., 2018, 2020). Here we report that levels of reactive oxygen species (ROS) are high in arrested tracheoblasts and decrease upon mitotic re-entry. High ROS is dependent on expression of Duox, an HO generating-Dual Oxidase. ROS quenching by overexpression of Superoxide Dismutase 1, or by knockdown of Duox, abolishes Chk1 phosphorylation and results in precocious proliferation. Tracheae deficient in Duox, or deficient in both Duox and regulators of DNA damage-dependent ATR/Chk1 activation (ATRIP/TOPBP1/ Claspin), can induce phosphorylation of Chk1 in response to micromolar concentrations of HO in minutes. The findings presented reveal that HO activates ATR/Chk1 in tracheoblasts by a non-canonical, potentially direct, mechanism.

}, issn = {2050-084X}, doi = {10.7554/eLife.68636}, author = {Kizhedathu, Amrutha and Chhajed, Piyush and Yeramala, Lahari and Sain Basu, Deblina and Mukherjee, Tina and Vinothkumar, Kutti R and Guha, Arjun} } @article {2323, title = {Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.}, journal = {Science}, year = {2021}, month = {2021 Oct 14}, pages = {eabj9932}, abstract = {

Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and reached population seropositivity of over 50\% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant B.1.617.2 (Delta) replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates; {\texttimes}1.5-fold, 20\% reduction). Seropositivity of an employee and family cohort increased from 42\% to 87.5\% between March and July 2021, with 27\% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

}, issn = {1095-9203}, doi = {10.1126/science.abj9932}, author = {Dhar, Mahesh S and Marwal, Robin and Vs, Radhakrishnan and Ponnusamy, Kalaiarasan and Jolly, Bani and Bhoyar, Rahul C and Sardana, Viren and Naushin, Salwa and Rophina, Mercy and Mellan, Thomas A and Mishra, Swapnil and Whittaker, Charles and Fatihi, Saman and Datta, Meena and Singh, Priyanka and Sharma, Uma and Ujjainiya, Rajat and Bhatheja, Nitin and Divakar, Mohit Kumar and Singh, Manoj K and Imran, Mohamed and Senthivel, Vigneshwar and Maurya, Ranjeet and Jha, Neha and Mehta, Priyanka and A, Vivekanand and Sharma, Pooja and Vr, Arvinden and Chaudhary, Urmila and Soni, Namita and Thukral, Lipi and Flaxman, Seth and Bhatt, Samir and Pandey, Rajesh and Dash, Debasis and Faruq, Mohammed and Lall, Hemlata and Gogia, Hema and Madan, Preeti and Kulkarni, Sanket and Chauhan, Himanshu and Sengupta, Shantanu and Kabra, Sandhya and Gupta, Ravindra K and Singh, Sujeet K and Agrawal, Anurag and Rakshit, Partha and Nandicoori, Vinay and Tallapaka, Karthik Bharadwaj and Sowpati, Divya Tej and Thangaraj, K and Bashyam, Murali Dharan and Dalal, Ashwin and Sivasubbu, Sridhar and Scaria, Vinod and Parida, Ajay and Raghav, Sunil K and Prasad, Punit and Sarin, Apurva and Mayor, Satyajit and Ramakrishnan, Uma and Palakodeti, Dasaradhi and Seshasayee, Aswin Sai Narain and Bhat, Manoj and Shouche, Yogesh and Pillai, Ajay and Dikid, Tanzin and Das, Saumitra and Maitra, Arindam and Chinnaswamy, Sreedhar and Biswas, Nidhan Kumar and Desai, Anita Sudhir and Pattabiraman, Chitra and Manjunatha, M V and Mani, Reeta S and Arunachal Udupi, Gautam and Abraham, Priya and Atul, Potdar Varsha and Cherian, Sarah S} } @article {2244, title = {Oxylipin biosynthesis reinforces cellular senescence and allows detection of senolysis.}, journal = {Cell Metab}, year = {2021}, month = {2021 Mar 31}, abstract = {

Cellular senescence is a stress or damage response that causes a permanent proliferative arrest and secretion of numerous factors with potent biological activities. This senescence-associated secretory phenotype (SASP) has been characterized largely for secreted proteins that participate in embryogenesis, wound healing, inflammation, and many age-related pathologies. By contrast, lipid components of the SASP are understudied. We show that senescent cells activate the biosynthesis of several oxylipins that promote segments of the SASP and reinforce the proliferative arrest. Notably, senescent cells synthesize and accumulate an unstudied intracellular prostaglandin, 1a,1b-dihomo-15-deoxy-delta-12,14-prostaglandin J2. Released 15-deoxy-delta-12,14-prostaglandin J2 is a biomarker of senolysis in culture and in\ vivo. This and other prostaglandin D2-related lipids promote the senescence arrest and SASP by activating RAS signaling. These data identify an important aspect of cellular senescence and a method to detect senolysis.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2021.03.008}, author = {Wiley, Christopher D and Sharma, Rishi and Davis, Sonnet S and Lopez-Dominguez, Jose Alberto and Mitchell, Kylie P and Wiley, Samantha and Alimirah, Fatouma and Kim, Dong Eun and Payne, Therese and Rosko, Andrew and Aimontche, Eliezer and Deshpande, Sharvari M and Neri, Francesco and Kuehnemann, Chisaka and Demaria, Marco and Ramanathan, Arvind and Campisi, Judith} } @article {2401, title = {Pharmacological intervention in young adolescents rescues synaptic physiology and behavioural deficits in Syngap1 mice.}, journal = {Exp Brain Res}, year = {2021}, month = {2021 Nov 05}, abstract = {

Haploinsufficiency in SYNGAP1 is implicated in intellectual disability (ID) and autism spectrum disorder (ASD) and affects the maturation of dendritic spines. The abnormal spine development has been suggested to cause a disbalance of excitatory and inhibitory (E/I) neurotransmission at distinct developmental periods. In addition, E/I imbalances in Syngap1 mice might be due to abnormalities in K-Cl co-transporter function (NKCC1, KCC2), in a maner similar to the murine models of Fragile-X and Rett syndromes. To study whether an altered intracellular chloride ion concentration represents an underlying mechanism of modified function of GABAergic synapses in Dentate Gyrus Granule Cells of Syngap1 recordings were performed at different developmental stages of the mice. We observed depolarised neurons at P14-15 as illustrated by decreased Cl reversal potential in Syngap1 mice. The KCC2 expression was decreased compared to Wild-type (WT) mice at P14-15. The GSK-3β inhibitor, 6-bromoindirubin-3{\textquoteright}-oxime (6BIO) that crosses the blood-brain barrier, was tested to restore the function of GABAergic synapses. We discovered that the intraperitoneal administration of 6BIO during the critical period or young adolescents [P30 to P80 (4-week to 10-week)] normalised an altered E/I balance, the deficits of synaptic plasticity, and behavioural performance like social novelty, anxiety, and memory of the Syngap1 mice. In summary, altered GABAergic function in Syngap1 mice is due to reduced KCC2 expression leading to an increase in the intracellular chloride concentration that can be counteracted by the 6BIO, which restored cognitive, emotional, and social symptoms by pharmacological intervention, particularly in adulthood.

}, issn = {1432-1106}, doi = {10.1007/s00221-021-06254-x}, author = {Verma, Vijaya and Kumar, M J Vijay and Sharma, Kavita and Rajaram, Sridhar and Muddashetty, Ravi and Manjithaya, Ravi and Behnisch, Thomas and Clement, James P} } @article {2376, title = {Proteome plasticity in response to persistent environmental change.}, journal = {Mol Cell}, volume = {81}, year = {2021}, month = {2021 08 19}, pages = {3294-3309.e12}, abstract = {

Temperature is a variable component of the environment, and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses, resulting in refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to reduction of temperature-sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find that many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and, importantly, cellular functions. We postulate that, in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.

}, keywords = {Acclimatization, Adaptation, Physiological, Animals, Environmental Exposure, Gene Expression Regulation, Fungal, Hot Temperature, Proteome, Saccharomycetales, Stress, Physiological, Transcriptome}, issn = {1097-4164}, doi = {10.1016/j.molcel.2021.06.028}, author = {Domnauer, Matthew and Zheng, Fan and Li, Liying and Zhang, Yanxiao and Chang, Catherine E and Unruh, Jay R and Conkright-Fincham, Juliana and McCroskey, Scott and Florens, Laurence and Zhang, Ying and Seidel, Christopher and Fong, Benjamin and Schilling, Birgit and Sharma, Rishi and Ramanathan, Arvind and Si, Kausik and Zhou, Chuankai} } @article {2202, title = {Psychiatric symptoms and syndromes transcending diagnostic boundaries in Indian multiplex families: The cohort of ADBS study.}, journal = {Psychiatry Res}, volume = {296}, year = {2021}, month = {2021 Feb}, pages = {113647}, abstract = {

Syndromes of schizophrenia, bipolar disorder, obsessive-compulsive disorder, substance use disorders and Alzheimer{\textquoteright}s dementia are highly heritable. About 10-20\% of subjects have another affected first degree relative (FDR), and thus represent a {\textquoteright}greater{\textquoteright} genetic susceptibility. We screened 3583 families to identify 481 families with multiple affected members, assessed 1406 individuals in person, and collected information systematically about other relatives. Within the selected families, a third of all FDRs were affected with serious mental illness. Although similar diagnoses aggregated within families, 62\% of the families also had members with other syndromes. Moreover, 15\% of affected individuals met criteria for co-occurrence of two or more syndromes, across their lifetime. Using dimensional assessments, we detected a range of symptom clusters in both affected and unaffected individuals, and across diagnostic categories. Our findings suggest that in multiplex families, there is considerable heterogeneity of clinical syndromes, as well as sub-threshold symptoms. These families would help provide an opportunity for further research using both genetic analyses and biomarkers.

}, issn = {1872-7123}, doi = {10.1016/j.psychres.2020.113647}, author = {Sreeraj, Vanteemar S and Holla, Bharath and Ithal, Dhruva and Nadella, Ravi Kumar and Mahadevan, Jayant and Balachander, Srinivas and Ali, Furkhan and Sheth, Sweta and Narayanaswamy, Janardhanan C and Venkatasubramanian, Ganesan and John, John P and Varghese, Mathew and Benegal, Vivek and Jain, Sanjeev and Reddy, Yc Janardhan and Viswanath, Biju} } @article {2373, title = {A regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes.}, journal = {Proc Natl Acad Sci U S A}, volume = {118}, year = {2021}, month = {2021 11 16}, abstract = {

The commitment of hematopoietic multipotent progenitors (MPPs) toward a particular lineage involves activation of cell type-specific genes and silencing of genes that promote alternate cell fates. Although the gene expression programs of early-B and early-T lymphocyte development are mutually exclusive, we show that these cell types exhibit significantly correlated microRNA (miRNA) profiles. However, their corresponding miRNA targetomes are distinct and predominated by transcripts associated with natural killer, dendritic cell, and myeloid lineages, suggesting that miRNAs function in a cell-autonomous manner. The combinatorial expression of miRNAs miR-186-5p, miR-128-3p, and miR-330-5p in MPPs significantly attenuates their myeloid differentiation potential due to repression of myeloid-associated transcripts. Depletion of these miRNAs caused a pronounced de-repression of myeloid lineage targets in differentiating early-B and early-T cells, resulting in a mixed-lineage gene expression pattern. De novo motif analysis combined with an assay of promoter activities indicates that B as well as T lineage determinants drive the expression of these miRNAs in lymphoid lineages. Collectively, we present a paradigm that miRNAs are conserved between developing B and T lymphocytes, yet they target distinct sets of promiscuously expressed lineage-inappropriate genes to suppress the alternate cell-fate options. Thus, our studies provide a comprehensive compendium of miRNAs with functional implications for B and T lymphocyte development.

}, keywords = {Animals, B-Lymphocytes, Cell Differentiation, Cell Lineage, Gene Expression, Gene Expression Profiling, Gene Regulatory Networks, Hematopoietic Stem Cells, Mice, MicroRNAs, Myeloid Cells, T-Lymphocytes}, issn = {1091-6490}, doi = {10.1073/pnas.2104297118}, author = {Nikhat, Sameena and Yadavalli, Anurupa D and Prusty, Arpita and Narayan, Priyanka K and Palakodeti, Dasaradhi and Murre, Cornelis and Pongubala, Jagan M R} } @article {2372, title = {Ribosomal protein S6 kinase beta-1 gene variants cause hypertrophic cardiomyopathy.}, journal = {J Med Genet}, year = {2021}, month = {2021 Dec 16}, abstract = {

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a genetic heart muscle disease with preserved or increased ejection fraction in the absence of secondary causes. Mutations in the sarcomeric protein-encoding genes predominantly cause HCM. However, relatively little is known about the genetic impact of signalling proteins on HCM.

METHODS AND RESULTS: Here, using exome and targeted sequencing methods, we analysed two independent cohorts comprising 401 Indian patients with HCM and 3521 Indian controls. We identified novel variants in ribosomal protein S6 kinase beta-1 () gene in two unrelated Indian families as a potential candidate gene for HCM. The two unrelated HCM families had the same heterozygous missense S6K1 variant (p.G47W). In a replication association study, we identified two S6K1 heterozygotes variants (p.Q49K and p.Y62H) in the UK Biobank cardiomyopathy cohort (n=190) compared with matched controls (n=16 479). These variants are neither detected in region-specific controls nor in the human population genome data. Additionally, we observed an S6K1 variant (p.P445S) in an Arab patient with HCM. Functional consequences were evaluated using representative S6K1 mutated proteins compared with wild type in cellular models. The mutated proteins activated the S6K1 and hyperphosphorylated the rpS6 and ERK1/2 signalling cascades, suggesting a gain-of-function effect.

CONCLUSIONS: Our study demonstrates for the first time that the variants in the gene are associated with HCM, and early detection of the variant carriers can help to identify family members at risk and subsequent preventive measures. Further screening in patients with HCM with different ethnic populations will establish the specificity and frequency of gene variants.

}, issn = {1468-6244}, doi = {10.1136/jmedgenet-2021-107866}, author = {Jain, Pratul Kumar and Jayappa, Shashank and Sairam, Thiagarajan and Mittal, Anupam and Paul, Sayan and Rao, Vinay J and Chittora, Harshil and Kashyap, Deepak K and Palakodeti, Dasaradhi and Thangaraj, Kumarasamy and Shenthar, Jayaprakash and Koranchery, Rakesh and Rajendran, Ranjith and Alireza, Haghighi and Mohanan, Kurukkanparampil Sreedharan and Rathinavel, Andiappan and Dhandapany, Perundurai S} } @article {2363, title = {SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 11}, pages = {114-119}, abstract = {

The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha). In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.

}, keywords = {Antibodies, Neutralizing, Cell Fusion, Cell Line, COVID-19 Vaccines, Female, Health Personnel, Humans, Immune Evasion, India, Kinetics, Male, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vaccination, Virus Replication}, issn = {1476-4687}, doi = {10.1038/s41586-021-03944-y}, author = {Mlcochova, Petra and Kemp, Steven A and Dhar, Mahesh Shanker and Papa, Guido and Meng, Bo and Ferreira, Isabella A T M and Datir, Rawlings and Collier, Dami A and Albecka, Anna and Singh, Sujeet and Pandey, Rajesh and Brown, Jonathan and Zhou, Jie and Goonawardane, Niluka and Mishra, Swapnil and Whittaker, Charles and Mellan, Thomas and Marwal, Robin and Datta, Meena and Sengupta, Shantanu and Ponnusamy, Kalaiarasan and Radhakrishnan, Venkatraman Srinivasan and Abdullahi, Adam and Charles, Oscar and Chattopadhyay, Partha and Devi, Priti and Caputo, Daniela and Peacock, Tom and Wattal, Chand and Goel, Neeraj and Satwik, Ambrish and Vaishya, Raju and Agarwal, Meenakshi and Mavousian, Antranik and Lee, Joo Hyeon and Bassi, Jessica and Silacci-Fegni, Chiara and Saliba, Christian and Pinto, Dora and Irie, Takashi and Yoshida, Isao and Hamilton, William L and Sato, Kei and Bhatt, Samir and Flaxman, Seth and James, Leo C and Corti, Davide and Piccoli, Luca and Barclay, Wendy S and Rakshit, Partha and Agrawal, Anurag and Gupta, Ravindra K} } @article {2290, title = {Strategies to target SARS-CoV-2 entry and infection using dual mechanisms of inhibition by acidification inhibitors.}, journal = {PLoS Pathog}, volume = {17}, year = {2021}, month = {2021 07}, pages = {e1009706}, abstract = {

Many viruses utilize the host endo-lysosomal network for infection. Tracing the endocytic itinerary of SARS-CoV-2 can provide insights into viral trafficking and aid in designing new therapeutic strategies. Here, we demonstrate that the receptor binding domain (RBD) of SARS-CoV-2 spike protein is internalized via the pH-dependent CLIC/GEEC (CG) endocytic pathway in human gastric-adenocarcinoma (AGS) cells expressing undetectable levels of ACE2. Ectopic expression of ACE2 (AGS-ACE2) results in RBD traffic via both CG and clathrin-mediated endocytosis. Endosomal acidification inhibitors like BafilomycinA1 and NH4Cl, which inhibit the CG pathway, reduce the uptake of RBD and impede Spike-pseudoviral infection in both AGS and AGS-ACE2 cells. The inhibition by BafilomycinA1 was found to be distinct from Chloroquine which neither affects RBD uptake nor alters endosomal pH, yet attenuates Spike-pseudovirus entry. By screening a subset of FDA-approved inhibitors for functionality similar to BafilomycinA1, we identified Niclosamide as a SARS-CoV-2 entry inhibitor. Further validation using a clinical isolate of SARS-CoV-2 in AGS-ACE2 and Vero cells confirmed its antiviral effect. We propose that Niclosamide, and other drugs which neutralize endosomal pH as well as inhibit the endocytic uptake, could provide broader applicability in subverting infection of viruses entering host cells via a pH-dependent endocytic pathway.

}, keywords = {Ammonium Chloride, Angiotensin-Converting Enzyme 2, Animals, Antiviral Agents, Cell Line, Chlorocebus aethiops, Chloroquine, Clathrin, COVID-19, Drug Synergism, Endocytosis, Endosomes, Humans, Hydrogen-Ion Concentration, Hydroxychloroquine, Macrolides, Niclosamide, Protein Binding, Protein Domains, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vero Cells, Virus Internalization}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1009706}, author = {Prabhakara, Chaitra and Godbole, Rashmi and Sil, Parijat and Jahnavi, Sowmya and Gulzar, Shah-E-Jahan and van Zanten, Thomas S and Sheth, Dhruv and Subhash, Neeraja and Chandra, Anchal and Shivaraj, Akshatha and Panikulam, Patricia and U, Ibrahim and Nuthakki, Vijay Kumar and Puthiyapurayil, Theja Parassini and Ahmed, Riyaz and Najar, Ashaq Hussain and Lingamallu, Sai Manoz and Das, Snigdhadev and Mahajan, Bhagyashri and Vemula, Praveen and Bharate, Sandip B and Singh, Parvinder Pal and Vishwakarma, Ram and Guha, Arjun and Sundaramurthy, Varadharajan and Mayor, Satyajit} } @article {2289, title = {Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library.}, journal = {Cell Chem Biol}, year = {2021}, month = {2021 Jun 01}, abstract = {

Genetic screening technologies to identify and validate macromolecular interactions (MMIs) essential for complex pathways remain an important unmet need for systems biology and therapeutics development. Here, we use a library of peptides from diverse prokaryal genomes to screen MMIs promoting the nuclear relocalization of Forkhead Box O3 (FOXO3a), a tumor suppressor more frequently inactivated by post-translational modification than mutation. A hit peptide engages the 14-3-3 family of signal regulators through a phosphorylation-dependent interaction, modulates FOXO3a-mediated transcription, and suppresses cancer cell growth. In a crystal structure, the hit peptide occupies the phosphopeptide-binding groove of 14-3-3ε in a conformation distinct from its natural peptide substrates. A biophysical screen identifies drug-like small molecules that displace the hit peptide from 14-3-3ε, providing starting points for structure-guided development. Our findings exemplify "protein interference," an approach using evolutionarily diverse, natural peptides to rapidly identify, validate, and develop chemical probes against MMIs essential for complex cellular phenotypes.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2021.05.009}, author = {Emery, Amy and Hardwick, Bryn S and Crooks, Alex T and Milech, Nadia and Watt, Paul M and Mithra, Chandan and Kumar, Vikrant and Giridharan, Saranya and Sadasivam, Gayathri and Mathivanan, Subashini and Sudhakar, Sneha and Bairy, Sneha and Bharatham, Kavitha and Hurakadli, Manjunath A and Prasad, Thazhe K and Kamariah, Neelagandan and Muellner, Markus and Coelho, Miguel and Torrance, Christopher J and McKenzie, Grahame J and Venkitaraman, Ashok R} } @article {2156, title = {Adverse childhood experiences in families with multiple members diagnosed to have psychiatric illnesses.}, journal = {Aust N Z J Psychiatry}, volume = {54}, year = {2020}, month = {2020 Nov}, pages = {1086-1094}, abstract = {

OBJECTIVE: Adverse childhood experiences are linked to the development of a number of psychiatric illnesses in adulthood. Our study examined the pattern of adverse childhood experiences and their relation to the age of onset of major psychiatric conditions in individuals from families that had ⩾2 first-degree relatives with major psychiatric conditions (multiplex families), identified as part of an ongoing longitudinal study.

METHODS: Our sample consisted of 509 individuals from 215 families. Of these, 268 were affected, i.e., diagnosed with bipolar disorder ( = 61), obsessive-compulsive disorder ( = 58), schizophrenia ( = 52), substance dependence ( = 59) or co-occurring diagnoses ( = 38), while 241 were at-risk first-degree relatives who were either unaffected ( = 210) or had other depressive or anxiety disorders ( = 31). All individuals were evaluated using the Adverse Childhood Experiences - International Questionnaire and total adverse childhood experiences exposure and severity scores were calculated.

RESULTS: It was seen that affected males, as a group, had the greatest adverse childhood experiences exposure and severity scores in our sample. A Cox mixed effects model fit by gender revealed that a higher total adverse childhood experiences severity score was associated with significantly increased risk for an earlier age of onset of psychiatric diagnoses in males. A similar model that evaluated the interaction of diagnosis revealed an earlier age of onset in obsessive-compulsive disorder and substance dependence, but not in schizophrenia and bipolar disorder.

CONCLUSION: Our study indicates that adverse childhood experiences were associated with an earlier onset of major psychiatric conditions in men and individuals diagnosed with obsessive-compulsive disorder and substance dependence. Ongoing longitudinal assessments in first-degree relatives from these families are expected to identify mechanisms underlying this relationship.

}, issn = {1440-1614}, doi = {10.1177/0004867420931157}, author = {Someshwar, Amala and Holla, Bharath and Pansari Agarwal, Preeti and Thomas, Anza and Jose, Anand and Joseph, Boban and Raju, Birudu and Karle, Hariprasad and Muthukumaran, M and Kodancha, Prabhath G and Kumar, Pramod and Reddy, Preethi V and Kumar Nadella, Ravi and Naik, Sanjay T and Mitra, Sayantanava and Mallappagiri, Sreenivasulu and Sreeraj, Vanteemar S and Balachander, Srinivas and Ganesh, Suhas and Murthy, Pratima and Benegal, Vivek and Reddy, Janardhan Yc and Jain, Sanjeev and Mahadevan, Jayant and Viswanath, Biju} } @article {2248, title = {Allosteric inhibition of MTHFR prevents futile SAM cycling and maintains nucleotide pools in one-carbon metabolism.}, journal = {J Biol Chem}, volume = {295}, year = {2020}, month = {2020 11 20}, pages = {16037-16057}, abstract = {

Methylenetetrahydrofolate reductase (MTHFR) links the folate cycle to the methionine cycle in one-carbon metabolism. The enzyme is known to be allosterically inhibited by SAM for decades, but the importance of this regulatory control to one-carbon metabolism has never been adequately understood. To shed light on this issue, we exchanged selected amino acid residues in a highly conserved stretch within the regulatory region of yeast MTHFR to create a series of feedback-insensitive, deregulated mutants. These were exploited to investigate the impact of defective allosteric regulation on one-carbon metabolism. We observed a strong growth defect in the presence of methionine. Biochemical and metabolite analysis revealed that both the folate and methionine cycles were affected in these mutants, as was the transsulfuration pathway, leading also to a disruption in redox homeostasis. The major consequences, however, appeared to be in the depletion of nucleotides. C isotope labeling and metabolic studies revealed that the deregulated MTHFR cells undergo continuous transmethylation of homocysteine by methyltetrahydrofolate (CHTHF) to form methionine. This reaction also drives SAM formation and further depletes ATP reserves. SAM was then cycled back to methionine, leading to futile cycles of SAM synthesis and recycling and explaining the necessity for MTHFR to be regulated by SAM. The study has yielded valuable new insights into the regulation of one-carbon metabolism, and the mutants appear as powerful new tools to further dissect out the intersection of one-carbon metabolism with various pathways both in yeasts and in humans.

}, keywords = {Adenosine Triphosphate, Allosteric Regulation, Humans, Methylation, Methylenetetrahydrofolate Reductase (NADPH2), S-Adenosylmethionine, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1083-351X}, doi = {10.1074/jbc.RA120.015129}, author = {Bhatia, Muskan and Thakur, Jyotika and Suyal, Shradha and Oniel, Ruchika and Chakraborty, Rahul and Pradhan, Shalini and Sharma, Monika and Sengupta, Shantanu and Laxman, Sunil and Masakapalli, Shyam Kumar and Bachhawat, Anand Kumar} } @article {1985, title = {Anabolic SIRT4 Exerts Retrograde Control over TORC1 Signaling by Glutamine Sparing in the Mitochondria.}, journal = {Mol Cell Biol}, volume = {40}, year = {2020}, month = {2020 Jan 03}, abstract = {

Anabolic and catabolic signaling mediated via mTOR and AMPK (AMP-activated kinase) have to be intrinsically coupled to mitochondrial functions for maintaining homeostasis and mitigate cellular/organismal stress. Although glutamine is known to activate mTOR, whether and how differential mitochondrial utilization of glutamine impinges on mTOR signaling has been less explored. Mitochondrial SIRT4, which unlike other sirtuins is induced in a fed state, is known to inhibit catabolic signaling/pathways through the AMPK-PGC1α/SIRT1-peroxisome proliferator-activated receptor α (PPARα) axis and negatively regulate glutamine metabolism via the tricarboxylic acid cycle. However, physiological significance of SIRT4 functions during a fed state is still unknown. Here, we establish SIRT4 as key anabolic factor that activates TORC1 signaling and regulates lipogenesis, autophagy, and cell proliferation. Mechanistically, we demonstrate that the ability of SIRT4 to inhibit anaplerotic conversion of glutamine to α-ketoglutarate potentiates TORC1. Interestingly, we also show that mitochondrial glutamine sparing or utilization is critical for differentially regulating TORC1 under fed and fasted conditions. Moreover, we conclusively show that differential expression of SIRT4 during fed and fasted states is vital for coupling mitochondrial energetics and glutamine utilization with anabolic pathways. These significant findings also illustrate that SIRT4 integrates nutrient inputs with mitochondrial retrograde signals to maintain a balance between anabolic and catabolic pathways.

}, issn = {1098-5549}, doi = {10.1128/MCB.00212-19}, author = {Shaw, Eisha and Talwadekar, Manasi and Rashida, Zeenat and Mohan, Nitya and Acharya, Aishwarya and Khatri, Subhash and Laxman, Sunil and Kolthur-Seetharam, Ullas} } @article {2112, title = {Corticosterone after acute stress prevents the delayed effects on the amygdala.}, journal = {Neuropsychopharmacology}, year = {2020}, month = {2020 Jul 06}, abstract = {

Even a single 2-hour episode of immobilization stress is known to trigger anxiety-like behavior and increase spine-density in the basolateral amygdala (BLA) of rats 10 days later. This delayed build-up of morphological and behavioral effects offers a stress-free time window of intervention after acute stress, which we used to test a protective role for glucocorticoids against stress. We observed that post-stress corticosterone, given 1 day after acute stress in drinking water, reversed enhanced anxiety-like behavior 10 days later. Quantification of spine-density on Golgi-stained BLA principal neurons showed that the same intervention also prevented the increase in spine numbers in the amygdala, at the same delayed time-point. Further, stress elevated serum corticosterone levels in rats that received vehicle in the drinking water. However, when stress was followed 24 h later by corticosterone in the drinking water, the surge in corticosterone was prevented. Together, these observations suggest that corticosterone, delivered through drinking water even 24 h after acute stress, is capable of reversing the delayed enhancing effects on BLA synaptic connectivity and anxiety-like behavior. Strikingly, although the immobilization-induced surge in corticosterone by itself has delayed detrimental effects on amygdalar structure and function, there exists a window of opportunity even after stress to mitigate its impact with a second surge of exogenously administered corticosterone. This provides a framework in the amygdala for analyzing how the initial physiological and endocrine processes triggered by traumatic stress eventually give rise to debilitating emotional symptoms, as well as the protective effects of glucocorticoids against their development.

}, issn = {1740-634X}, doi = {10.1038/s41386-020-0758-0}, author = {Chakraborty, Prabahan and Datta, Siddhartha and McEwen, Bruce S and Chattarji, Sumantra} } @article {2146, title = {Differential flexibility leading to crucial microelastic properties of asymmetric lipid vesicles for cellular transfection: A combined spectroscopic and atomic force microscopy studies.}, journal = {Colloids Surf B Biointerfaces}, volume = {196}, year = {2020}, month = {2020 Sep 21}, pages = {111363}, abstract = {

The role of microscopic elasticity of nano-carriers in cellular uptake is an important aspect in biomedical research. Herein we have used AFM nano-indentation force spectroscopy and F{\"o}rster resonance energy transfer (FRET) measurements to probe microelastic properties of three novel cationic liposomes based on di-alkyl dihydroxy ethyl ammonium chloride based lipids having asymmetry in their hydrophobic chains (Lip1818, Lip1814 and Lip1810). AFM data reveals that symmetry in hydrophobic chains of a cationic lipid (Lip1818) imparts higher rigidity to the resulting liposomes than those based on asymmetric lipids (Lip1814 and Lip1810). The stiffness of the cationic liposomes is found to decrease with increasing asymmetry in the hydrophobic lipid chains in the order of Lip1818 \> Lip1814 \> lip1810. FRET measurements between Coumarin 500 (Donor) and Merocyanine 540 (Acceptor) have revealed that full width at half-maxima (hw) of the probability distribution (P(r)) of donor-acceptor distance (r), increases in an order Lip1818 \< Lip1814 \< Lip1810 with increasing asymmetry of the hydrophobic lipid chains. This increase in width (hw) of the donor-acceptor distance distributions is reflective of increasing flexibility of the liposomes with increasing asymmetry of their constituent lipids. Thus, the results from AFM and FRET studies are complementary to each other and indicates that an increase in asymmetry of the hydrophobic lipid chains increases elasticity and or flexibility of the corresponding liposomes. Cell biology experiments confirm that liposomal flexibility or rigidity directly influences their cellular transfection efficiency, where Lip1814 is found to be superior than the other two liposomes manifesting that a critical balance between flexibility and rigidity of the cationic liposomes is key to efficient cellular uptake. Taken together, our studies reveal how asymmetry in the molecular architecture of the hydrophobic lipid chains influences the microelastic properties of the liposomes, and hence, their cellular uptake efficiency.

}, issn = {1873-4367}, doi = {10.1016/j.colsurfb.2020.111363}, author = {Mukherjee, Dipanjan and Rakshit, Tatini and Singh, Priya and Mondal, Suman and Paul, Debashish and Ahir, Manisha and Adhikari, Arghya and Puthiyapurayil, Theja P and Vemula, Praveen Kumar and Senapati, Dulal and Das, Ranjan and Pal, Samir Kumar} } @article {2067, title = {Distinct regulation of bioenergetics and translation by group I mGluR and NMDAR.}, journal = {EMBO Rep}, year = {2020}, month = {2020 Apr 29}, pages = {e48037}, abstract = {

Neuronal activity is responsible for the high energy consumption in the brain. However, the cellular mechanisms draining ATP upon the arrival of a stimulus are yet to be explored systematically at the post-synapse. Here, we provide evidence that a significant fraction of ATP is consumed upon glutamate stimulation to energize mGluR-induced protein synthesis. We find that both mGluR and NMDAR alter protein synthesis and ATP consumption with distinct kinetics at the synaptic-dendritic compartments. While mGluR activation leads to a rapid and sustained reduction in neuronal ATP levels, NMDAR activation has no immediate impact on the same. ATP consumption correlates inversely with the kinetics of protein synthesis for both receptors. We observe a persistent elevation in protein synthesis within 5\ minutes of mGluR activation and a robust inhibition of the same within 2\ minutes of NMDAR activation, assessed by the phosphorylation status of eEF2 and metabolic labeling. However, a delayed protein synthesis-dependent ATP expenditure ensues after 15\ minutes of NMDAR stimulation. We identify a central role for AMPK in the correlation between protein synthesis and ATP consumption. AMPK is dephosphorylated and inhibited upon mGluR activation, while it is phosphorylated upon NMDAR activation. Perturbing AMPK activity disrupts receptor-specific modulations of eEF2 phosphorylation and protein synthesis. Our observations, therefore, demonstrate that the regulation of the AMPK-eEF2 signaling axis by glutamate receptors alters neuronal protein synthesis and bioenergetics.

}, issn = {1469-3178}, doi = {10.15252/embr.201948037}, author = {Ghosh Dastidar, Sudhriti and Das Sharma, Shreya and Chakraborty, Sumita and Chattarji, Sumantra and Bhattacharya, Aditi and Muddashetty, Ravi S} } @article {2115, title = {A field-based quantitative analysis of sublethal effects of air pollution on pollinators.}, journal = {Proc Natl Acad Sci U S A}, volume = {117}, year = {2020}, month = {2020 Aug 25}, pages = {20653-20661}, abstract = {

While the impact of air pollution on human health is well studied, mechanistic impacts of air pollution on wild systems, including those providing essential ecosystem services, are largely unknown, but directly impact our health and well-being. India is the world{\textquoteright}s largest fruit producer, second most populous country, and contains 9 of the world{\textquoteright}s 10 most polluted cities. Here, we sampled Giant Asian honey bees, , at locations with varying air pollution levels in Bangalore, India. We observed significant correlations between increased respirable suspended particulate matter (RSPM) deposition and changes in bee survival, flower visitation, heart rate, hemocyte levels, and expression of genes related to lipid metabolism, stress, and immunity. Lab-reared exposed to these same sites also exhibited similar molecular and physiological differences. Our study offers a quantitative analysis on the current impacts of air pollution on insects, and indicates the urgency for more nonhuman studies to accurately assess the effects of pollution on our natural world.

}, issn = {1091-6490}, doi = {10.1073/pnas.2009074117}, author = {Thimmegowda, Geetha G and Mullen, Susan and Sottilare, Katie and Sharma, Ankit and Mohanta, Saptashi Soham and Brockmann, Axel and Dhandapany, Perundurai S and Olsson, Shannon B} } @article {2154, title = {Immune Control of Animal Growth in Homeostasis and Nutritional Stress in .}, journal = {Front Immunol}, volume = {11}, year = {2020}, month = {2020}, pages = {1528}, abstract = {

A large body of research implicates the brain and fat body (liver equivalent) as central players in coordinating growth and nutritional homeostasis in multicellular animals. In this regard, an underlying connection between immune cells and growth is also evident, although mechanistic understanding of this cross-talk is scarce. Here, we explore the importance of innate immune cells in animal growth during homeostasis and in conditions of nutrient stress. We report that larvae lacking blood cells eclose as small adults and show signs of insulin insensitivity. Moreover, when exposed to dietary stress of a high-sucrose diet (HSD), these animals are further growth retarded than normally seen in regular animals raised on HSD. In contrast, larvae carrying increased number of activated macrophage-like plasmatocytes show no defects in adult growth when raised on HSD and grow to sizes almost comparable with that seen with regular diet. These observations imply a central role for immune cell activity in growth control. Mechanistically, our findings reveal a surprising influence of immune cells on balancing fat body inflammation and insulin signaling under conditions of homeostasis and nutrient overload as a means to coordinate systemic metabolism and adult growth. This work integrates both the cellular and humoral arm of the innate immune system in organismal growth homeostasis, the implications of which may be broadly conserved across mammalian systems as well.

}, issn = {1664-3224}, doi = {10.3389/fimmu.2020.01528}, author = {P, Preethi and Tomar, Ajay and Madhwal, Sukanya and Mukherjee, Tina} } @article {2078, title = {Improved detection of RNA foci in amyotrophic lateral sclerosis post-mortem tissue using BaseScope{\texttrademark} shows a lack of association with cognitive dysfunction.}, journal = {Brain Commun}, volume = {2}, year = {2020}, month = {2020 Jan 31}, pages = {fcaa009}, abstract = {

The hexanucleotide repeat expansion is the commonest known genetic mutation in amyotrophic lateral sclerosis. A neuropathological hallmark is the intracellular accumulation of RNA foci. The role that RNA foci play in the pathogenesis of amyotrophic lateral sclerosis is widely debated. Historically, RNA foci have been identified using hybridization. Here, we have implemented BaseScope{\texttrademark}, a high-resolution modified hybridization technique. We demonstrate that previous studies have underestimated the abundance of RNA foci in neurons and glia. This improved detection allowed us to investigate the abundance, regional distribution and cell type specificity of antisense RNA foci in post-mortem brain and spinal cord tissue of six deeply clinically phenotyped patients and six age- and sex-matched controls. We find a correlation between RNA foci and the accumulation of transactive response DNA-binding protein of 43 kDa in spinal motor neurons ( = 0.93; = 0.008), but not in glia or cortical motor neurons. We also demonstrate that there is no correlation between the presence of RNA foci and the accumulation of transactive response DNA binding protein of 43 kDa in extra-motor brain regions. Furthermore, there is no association between the presence of RNA foci and cognitive indices. These results highlight the utility of BaseScope{\texttrademark} in the clinicopathological assessment of the role of antisense RNA foci in .

}, issn = {2632-1297}, doi = {10.1093/braincomms/fcaa009}, author = {Mehta, Arpan R and Selvaraj, Bhuvaneish T and Barton, Samantha K and McDade, Karina and Abrahams, Sharon and Chandran, Siddharthan and Smith, Colin and Gregory, Jenna M} } @article {2208, title = {Metabolic control of cellular immune-competency by odors in .}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 12 29}, abstract = {

Studies in different animal model systems have revealed the impact of odors on immune cells; however, any understanding on why and how odors control cellular immunity remained unclear. We find that employ an olfactory-immune cross-talk to tune a specific cell type, the lamellocytes, from hematopoietic-progenitor cells. We show that neuronally released GABA derived upon olfactory stimulation is utilized by blood-progenitor cells as a metabolite and through its catabolism, these cells stabilize Sima/HIFα protein. Sima capacitates blood-progenitor cells with the ability to initiate lamellocyte differentiation. This systemic axis becomes relevant for larvae dwelling in wasp-infested environments where chances of infection are high. By co-opting the olfactory route, the preconditioned animals elevate their systemic GABA levels leading to the upregulation of blood-progenitor cell Sima expression. This elevates their immune-potential and primes them to respond rapidly when infected with parasitic wasps. The present work highlights the importance of the olfaction in immunity and shows how odor detection during animal development is utilized to establish a long-range axis in the control of blood-progenitor competency and immune-priming.

}, issn = {2050-084X}, doi = {10.7554/eLife.60376}, author = {Madhwal, Sukanya and Shin, Mingyu and Kapoor, Ankita and Goyal, Manisha and Joshi, Manish K and Ur Rehman, Pirzada Mujeeb and Gor, Kavan and Shim, Jiwon and Mukherjee, Tina} } @article {2253, title = {Rethinking Exosomes: From Cell-to-Cell Courier Services to Individualized Medicines}, journal = {AAPS News magazine}, year = {2020}, month = {06/2020}, author = {Ghate, V and Chaudhari, P and Maxwell, A and Lewis, S and Pahal, S and Vemula PK} } @article {2250, title = {Role of connexins in female reproductive system and endometriosis.}, journal = {J Gynecol Obstet Hum Reprod}, volume = {49}, year = {2020}, month = {2020 Jun}, pages = {101705}, abstract = {

Gap junction form channels between the cells and facilitate the function of cellular cross talk. Connexins, the gap junction proteins play an essential role in female reproductive health and its expression anomalies are correlated with female reproductive disorders like polycystic ovarian syndrome, recurrent miscarriage, pre-term birth and endometriosis. Endometriosis is a chronic gynecologic disorder caused by ectopic endometrial lesions growing outside the uterine cavity. Embryonic implantation is adversely affected in case of endometriosis leading to infertility. Endometriosis also interferes with ovulatory functions, reduces fertilization and impaires blastocyst implantation. There lies a lacunae in understanding of the role of gap junctions protein connexins in endometriosis. Therefore, this study discusses the role of connexins in improving female fertility by taming the processes of oogenesis, germ line development, uterine receptivity, placental growth, implantation, decidualization and concludes by focusing the role of connexins in endometriosis.

}, keywords = {Connexins, Decidua, Embryo Implantation, Endometriosis, Endometrium, Female, Gap Junctions, Genitalia, Female, Humans, Infertility, Female, Oogenesis, Ovulation, Pregnancy, Uterus}, issn = {2468-7847}, doi = {10.1016/j.jogoh.2020.101705}, author = {Kaushik, Tripti and Mishra, Rakesh and Singh, Rakesh K and Bajpai, Surabhi} } @article {2059, title = {The Role of Dynamic miRISC During Neuronal Development.}, journal = {Front Mol Biosci}, volume = {7}, year = {2020}, month = {2020}, pages = {8}, abstract = {

Activity-dependent protein synthesis plays an important role during neuronal development by fine-tuning the formation and function of neuronal circuits. Recent studies have shown that miRNAs are integral to this regulation because of their ability to control protein synthesis in a rapid, specific and potentially reversible manner. miRNA mediated regulation is a multistep process that involves inhibition of translation before degradation of targeted mRNA, which provides the possibility to store and reverse the inhibition at multiple stages. This flexibility is primarily thought to be derived from the composition of miRNA induced silencing complex (miRISC). AGO2 is likely the only obligatory component of miRISC, while multiple RBPs are shown to be associated with this core miRISC to form diverse miRISC complexes. The formation of these heterogeneous miRISC complexes is intricately regulated by various extracellular signals and cell-specific contexts. In this review, we discuss the composition of miRISC and its functions during neuronal development. Neurodevelopment is guided by both internal programs and external cues. Neuronal activity and external signals play an important role in the formation and refining of the neuronal network. miRISC composition and diversity have a critical role at distinct stages of neurodevelopment. Even though there is a good amount of literature available on the role of miRNAs mediated regulation of neuronal development, surprisingly the role of miRISC composition and its functional dynamics in neuronal development is not much discussed. In this article, we review the available literature on the heterogeneity of the neuronal miRISC composition and how this may influence translation regulation in the context of neuronal development.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2020.00008}, author = {Nawalpuri, Bharti and Ravindran, Sreenath and Muddashetty, Ravi S} } @article {2077, title = {A sex difference in the response of the rodent postsynaptic density to synGAP haploinsufficiency.}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Jan 15}, abstract = {

SynGAP is a postsynaptic density (PSD) protein that binds to PDZ domains of the scaffold protein PSD-95. We previously reported that heterozygous deletion of in mice is correlated with increased steady-state levels of other key PSD proteins that bind PSD-95, although the level of PSD-95 remains constant (Walkup et al., 2016). For example, the ratio to PSD-95 of Transmembrane AMPA-Receptor-associated Proteins (TARPs), which mediate binding of AMPA-type glutamate receptors to PSD-95, was increased in young mice. Here we show that only females and not males show a highly significant correlation between an increase in TARP and a decrease in synGAP in the PSDs of rodents. The data reveal a sex difference in the adaptation of the PSD scaffold to synGAP haploinsufficiency.

}, issn = {2050-084X}, doi = {10.7554/eLife.52656}, author = {Mastro, Tara L and Preza, Anthony and Basu, Shinjini and Chattarji, Sumantra and Till, Sally M and Kind, Peter C and Kennedy, Mary B} } @article {2111, title = {Stress-induced modulation of endocannabinoid signaling leads to delayed strengthening of synaptic connectivity in the amygdala.}, journal = {Proc Natl Acad Sci U S A}, volume = {117}, year = {2020}, month = {2020 01 07}, pages = {650-655}, abstract = {

Even a brief exposure to severe stress strengthens synaptic connectivity days later in the amygdala, a brain area implicated in the affective symptoms of stress-related psychiatric disorders. However, little is known about the synaptic signaling mechanisms during stress that eventually culminate in its delayed impact on the amygdala. Hence, we investigated early stress-induced changes in amygdalar synaptic signaling in order to prevent its delayed effects. Whole-cell recordings in basolateral amygdala (BLA) slices from rats revealed higher frequency of miniature excitatory postsynaptic currents (mEPSCs) immediately after 2-h immobilization stress. This was replicated by inhibition of cannabinoid receptors (CBR), suggesting a role for endocannabinoid (eCB) signaling. Stress also reduced -arachidonoylethanolamine (AEA), an endogenous ligand of CBR. Since stress-induced activation of fatty acid amide hydrolase (FAAH) reduces AEA, we confirmed that oral administration of an FAAH inhibitor during stress prevents the increase in synaptic excitation in the BLA soon after stress. Although stress also caused an immediate reduction in synaptic inhibition, this was not prevented by FAAH inhibition. Strikingly, FAAH inhibition during the traumatic stressor was also effective 10 d later on the delayed manifestation of synaptic strengthening in BLA neurons, preventing both enhanced mEPSC frequency and increased dendritic spine-density. Thus, oral administration of an FAAH inhibitor during a brief stress prevents the early synaptic changes that eventually build up to hyperexcitability in the amygdala. This framework is of therapeutic relevance because of growing interest in targeting eCB signaling to prevent the gradual development of emotional symptoms and underlying amygdalar dysfunction triggered by traumatic stress.

}, keywords = {Administration, Oral, Amidohydrolases, Animals, Basolateral Nuclear Complex, Cannabinoid Receptor Antagonists, Disease Models, Animal, Emotions, Endocannabinoids, Enzyme Inhibitors, Excitatory Postsynaptic Potentials, Humans, Male, Rats, Receptor, Cannabinoid, CB1, Signal Transduction, Stress, Psychological}, issn = {1091-6490}, doi = {10.1073/pnas.1910322116}, author = {Yasmin, Farhana and Colangeli, Roberto and Morena, Maria and Filipski, Sarah and van der Stelt, Mario and Pittman, Quentin J and Hillard, Cecilia J and Teskey, G Campbell and McEwen, Bruce S and Hill, Matthew N and Chattarji, Sumantra} } @article {2064, title = {Temporal specificity and heterogeneity of Drosophila immune cells.}, journal = {EMBO J}, year = {2020}, month = {2020 Mar 12}, pages = {e104486}, abstract = {

Immune cells provide defense against non-self and have recently been shown to also play key roles in diverse processes such as development, metabolism, and tumor progression. The heterogeneity of Drosophila immune cells (hemocytes) remains an open question. Using bulk RNA sequencing, we find that the hemocytes display distinct features in the embryo, a closed and rapidly developing system, compared to the larva, which is exposed to environmental and metabolic challenges. Through single-cell RNA sequencing, we identify fourteen hemocyte clusters present in unchallenged larvae and associated with distinct processes, e.g., proliferation, phagocytosis, metabolic homeostasis, and humoral response. Finally, we characterize the changes occurring in the hemocyte clusters upon wasp infestation, which triggers the differentiation of a novel hemocyte type, the lamellocyte. This first molecular atlas of hemocytes provides insights and paves the way to study the biology of the Drosophila immune cells in physiological and pathological conditions.

}, issn = {1460-2075}, doi = {10.15252/embj.2020104486}, author = {Cattenoz, Pierre B and Sakr, Rosy and Pavlidaki, Alexia and Delaporte, Claude and Riba, Andrea and Molina, Nacho and Hariharan, Nivedita and Mukherjee, Tina and Giangrande, Angela} } @article {2039, title = {Temporal specificity and heterogeneity of the fly immune cells{\textquoteright} transcriptional landscape}, journal = {The EMBO Journal (in press)}, year = {2020}, abstract = {

Immune cells provide defense against the non-self, however recent data suggest roles well beyond innate immunity, in processes as diverse as development, metabolism and tumor progression. Nevertheless, the heterogeneity of these cells remains an open question. Using bulk RNA sequencing we find that the Drosophila immune cells (hemocytes) display distinct features in the embryo, a closed and rapidly developing system, compared to the larva, which is exposed to environmental and metabolic challenges. Through single cell RNA sequencing we identify fourteen hemocyte clusters present in unchallenged larvae and associated with distinct cellular processes e.g. proliferation, phagocytosis, metabolic homeostasis and humoral response. Finally, we characterize the changes occurring in the hemocyte clusters upon wasp infestation that triggers the differentiation of a novel cell type, the lamellocyte. This first molecular atlas provides precious insights and paves the way to study the biology of the Drosophila immune cells in physiological and pathological conditions.

}, author = {Cattenoz, Pierre B. and Sakr, Rosy and Pavlidaki, Alexia and Delaporte, Claude and Riba, Andrea and Molina, Nacho and Hariharan, Nivedita and Mukherjee, Tina and Giangrande, Angela} } @article {2113, title = {Understanding brain development - Indian researchers{\textquoteright} past, present and growing contribution.}, journal = {Int J Dev Biol}, volume = {64}, year = {2020}, month = {2020}, pages = {123-132}, abstract = {

The brain is the seat of all higher-order functions in the body. Brain development and the vast array of neurons and glia it produces is a baffling mystery to be studied. Neuroscientists using a vast number of model systems have been able to crack many of the nitty-gritty details using various model systems. One way has been to size down the problem by utilizing the power of genetics using simple model systems such as Drosophila to create a fundamental framework in order to unravel the basic principles of brain development. Scientists have used simpler organisms to uncover the fundamental principles of brain development and also to study the evo-devo angle to brain development. Complex circuitry has been unraveled in complex model systems, such as the mouse, to reveal the intricacies and regional specialization of brain function. This is an ever-growing field, and with newer genetic and molecular tools, together with several new centers of excellence, India{\textquoteright}s contribution to this fascinating field of study is continually rising. Here, I review the pioneering work done by Indian developmental neurobiologists in the past and their mounting contribution in the present.

}, issn = {1696-3547}, doi = {10.1387/ijdb.190204bm}, author = {Muralidharan, Bhavana} } @article {1645, title = {Altered steady state and activity-dependent de novo protein expression in fragile X syndrome.}, journal = {Nat Commun}, volume = {10}, year = {2019}, month = {2019 Apr 12}, pages = {1710}, abstract = {

Whether fragile X mental retardation protein (FMRP) target mRNAs and neuronal activity contributing to elevated basal neuronal protein synthesis in fragile X syndrome (FXS) is unclear. Our proteomic experiments reveal that the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation, but the proteins expressed differ under these conditions. Several altered proteins, including Hexokinase\ 1 and Ras, also are expressed in the blood of\ FXS model mice and pharmacological treatments previously reported to ameliorate phenotypes modify their abundance in blood. In addition, plasma levels of Hexokinase\ 1 and Ras differ between FXS patients and healthy volunteers. Our data suggest that brain-based de novo proteomics in FXS model mice can be used to find altered expression of proteins in blood that could serve as disease-state biomarkers in individuals with FXS.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09553-8}, author = {Bowling, Heather and Bhattacharya, Aditi and Zhang, Guoan and Alam, Danyal and Lebowitz, Joseph Z and Bohm-Levine, Nathaniel and Lin, Derek and Singha, Priyangvada and Mamcarz, Maggie and Puckett, Rosemary and Zhou, Lili and Aryal, Sameer and Sharp, Kevin and Kirshenbaum, Kent and Berry-Kravis, Elizabeth and Neubert, Thomas A and Klann, Eric} } @article {1646, title = {BDNF Induced Translation of Limk1 in Developing Neurons Regulates Dendrite Growth by Fine-Tuning Cofilin1 Activity.}, journal = {Front Mol Neurosci}, volume = {12}, year = {2019}, month = {2019}, pages = {64}, abstract = {

Dendritic growth and branching are highly regulated processes and are essential for establishing proper neuronal connectivity. There is a critical phase of early dendrite development when these are heavily regulated by external cues such as trophic factors. Brain-derived neurotrophic factor (BDNF) is a major trophic factor known to enhance dendrite growth in cortical neurons, but the molecular underpinnings of this response are not completely understood. We have identified that BDNF induced translational regulation is an important mechanism governing dendrite development in cultured rat cortical neurons. We show that BDNF treatment for 1 h in young neurons leads to translational up-regulation of an important actin regulatory protein LIM domain kinase 1 (Limk1), increasing its level locally in the dendrites. Limk1 is a member of serine/threonine (Ser/Thr) family kinases downstream of the Rho-GTPase pathway. BDNF induced increase in Limk1 levels leads to increased phosphorylation of its target protein cofilin1. We observed that these changes are maintained for long durations of up to 48 h and are mediating increase in number of primary dendrites and total dendrite length. Thus, we show that BDNF induced protein synthesis leads to fine-tuning of the actin cytoskeletal reassembly and thereby mediate dendrite development.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2019.00064}, author = {Ravindran, Sreenath and Nalavadi, Vijayalaxmi C and Muddashetty, Ravi S} } @article {1935, title = {Biomaterials for topical and transdermal drug delivery in reconstructive transplantation.}, journal = {Nanomedicine (Lond)}, year = {2019}, month = {2019 Oct 23}, abstract = {

Lifelong systemic immunosuppression remains the biggest challenge in vascularized composite allotransplantation (VCA) due to the adverse effects it causes. Since VCA is a life-enhancing procedure as compared with solid organ transplant which is life-saving;\ one needs to weigh the benefits and risks carefully. Thus, there is a huge unmet clinical need to design biomaterial-based vehicles that can deliver drugs more efficiently, topically and locally to eliminate adverse effects of systemic immune suppression. This review discusses several biomaterial-based systems that have been carefully designed, conceived and attempted to make VCA a more patient compliant approach. Variety of promising preclinical studies has shown the feasibility of the approaches, and clinical trials are required to bridge the gap. Several challenges for the future and new approaches have been discussed.

}, issn = {1748-6963}, doi = {10.2217/nnm-2019-0137}, author = {Dhayani, Ashish and Kalita, Sanjeeb and Mahato, Manohar and Srinath, Preethem and Vemula, Praveen K} } @article {1604, title = {Derivation of iPSC lines from two patients with familial Alzheimer{\textquoteright}s disease from India.}, journal = {Stem Cell Res}, volume = {34}, year = {2019}, month = {2019 Jan}, pages = {101370}, abstract = {

The current prevalence of diagnosable dementia in India is 1\% of people over 60 years (~3.7 million people), but is estimated to increase significantly, as ~15\% world{\textquoteright}s aged population (\>65 years) would be resident here by 2020 (Shah et al., 2016). While several mutations that pose a familial risk have been identified, the ethnic background may influence disease susceptibility, clinical presentation and treatment response. In this study, we report a detailed characterization of two representative HiPSC lines from a well-characterized dementia cohort from India. Availability of these lines, and associated molecular and clinical information, would be useful in the detailed exploration of the genomic contribution(s) to AD.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.101370}, author = {Najar, Ashaq H and Sneha, K M and Ashok, Aparna and Babu, Swathy and Subramaniam, Anand G and Kannan, Ramkrishnan and Viswanath, Biju and Purushottam, Meera and Varghese, Mathew and Parvez, Suhel and Panicker, Mitradas M and Mukherjee, Odity and Jain, Sanjeev} } @article {1982, title = {Differential Regulation of Translation by FMRP Modulates eEF2 Mediated Response on NMDAR Activity.}, journal = {Front Mol Neurosci}, volume = {12}, year = {2019}, month = {2019}, pages = {97}, abstract = {

SYNGAP1, a Synaptic Ras-GTPase activating protein, regulates synapse maturation during a critical developmental window. Heterozygous mutation in () has been shown to cause Intellectual Disability (ID) in children. Recent studies have provided evidence for altered neuronal protein synthesis in a mouse model of . However, the molecular mechanism behind the same is unclear. Here, we report the reduced expression of a known translation regulator, FMRP, during a specific developmental period in mice. Our results demonstrate that FMRP interacts with and regulates the translation of mRNA. We further show reduced translation leads to decreased FMRP level during development in which results in an increase in translation. These developmental changes are reflected in the altered response of eEF2 phosphorylation downstream of NMDA Receptor (NMDAR)-mediated signaling. In this study, we propose a cross-talk between FMRP and SYNGAP1 mediated signaling which can also explain the compensatory effect of impaired signaling observed in mice.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2019.00097}, author = {Paul, Abhik and Nawalpuri, Bharti and Shah, Devanshi and Sateesh, Shruthi and Muddashetty, Ravi S and Clement, James P} } @article {1739, title = {Effect of early maternal separation stress on attention, spatial learning and social interaction behaviour.}, journal = {Exp Brain Res}, volume = {237}, year = {2019}, month = {2019 Aug}, pages = {1993-2010}, abstract = {

Early life stress is known to influence affective and cognitive functions in later life but comprehensive explanation for the impact of early life stress on attentional functions, behavioural control and social behaviour is inadequate. The early life stress was induced by exposing rat pups to 6\ h of maternal separation and isolation (MS) stress from postnatal days 4-14 i.e. during SHRP period. The long-term impact of MS in these rats was evaluated by assessing anxiety, sociability, social preference, spatial learning and memory along with a detailed evaluation of attentional functions during young adulthood period. Adult male MS rats showed increased anxiety-like behaviour, impaired flexibility in social interactions, and increased reward-seeking behaviour. MS rats also showed faster spatial learning in the partially baited radial arm maze and exhibited moderately enhanced sustained attention in the 5-choice serial reaction time task (5CSRTT). These results suggest that early MS has both positive and negative consequences in adulthood. Increased cognitive ability in MS rats, as evidenced by the improved sustained attention and spatial learning and memory, is usually advantageous and indicates positive influences of early stressors that might lead to the development of resilience and enhanced compensatory mechanisms later in adulthood. MS stress has compromised flexibility in social behaviour that promotes solitary lifestyle and social isolation. Heightened reward-seeking behaviour, as shown by the MS rats, could be a predisposing factor for substance abuse and addiction. Thus, our study highlights the crucial and differential impact of early life challenges on behaviour during adulthood and suggests that the positive aspects could be an asset that may be utilized to suppress the negative effects of early life stress in adulthood.

}, issn = {1432-1106}, doi = {10.1007/s00221-019-05567-2}, author = {Kambali, Maltesh Y and Anshu, Kumari and Kutty, Bindu M and Muddashetty, Ravi S and Laxmi, T Rao} } @article {1611, title = {Emerging Role of microRNAs in Dementia.}, journal = {J Mol Biol}, year = {2019}, month = {2019 Feb 07}, abstract = {

MicroRNAs are small non-coding RNAs regulating mRNA translation. They play a crucial role in regulating homeostasis in neurons, especially in regulating local and stimulation dependent protein synthesis. Since activity-mediated protein synthesis in neurons is critical for memory and cognition, microRNAs have become key players in modulating these processes. Dementia is a broad term used for symptoms involving decline of memory and cognition. Several studies have implicated the dysregulation of microRNAs in many brain diseases like neurodegenerative diseases, neurodevelopmental disorders, brain injuries and dementia. In this review, we give an overview of microRNA-mediated regulation of proteins and cellular processes affected in dementia pathology, hence illustrating the importance of microRNAs in normal functioning. We also focus on a relatively less explored area in dementia pathology-the importance of activity-mediated protein synthesis at the synapse and the role of microRNAs in modulating this. Overall, this review will be helpful in looking at the significance of microRNAs in dementia from the perspective of defective regulation of protein synthesis and synaptic dysfunction.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2019.01.046}, author = {Ramakrishna, Sarayu and Muddashetty, Ravi S} } @article {1607, title = {Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes.}, journal = {Psychiatry Clin Neurosci}, volume = {73}, year = {2019}, month = {2019 Jan}, pages = {11-19}, abstract = {

AIM: Severe mental illnesses (SMI), such as bipolar disorder and schizophrenia, are highly heritable, and have a complex pattern of inheritance. Genome-wide association studies detect a part of the heritability, which can be attributed to common genetic variation. Examination of rare variants with next-generation sequencing may add to the understanding of the genetic architecture of SMI.

METHODS: We analyzed 32 ill subjects from eight multiplex families and 33 healthy individuals using whole-exome sequencing. Prioritized variants were selected by a three-step filtering process, which included: deleteriousness by five in silico algorithms; sharing within families by affected individuals; rarity in South Asian sample estimated using the Exome Aggregation Consortium data; and complete absence of these variants in control individuals from the same gene pool.

RESULTS: We identified 42 rare, non-synonymous deleterious variants (~5 per pedigree) in this study. None of the variants were shared across families, indicating a {\textquoteright}private{\textquoteright} mutational profile. Twenty (47.6\%) of the variant harboring genes were previously reported to contribute to the risk of diverse neuropsychiatric syndromes, nine (21.4\%) of which were of Mendelian inheritance. These included genes carrying novel deleterious variants, such as the GRM1 gene implicated in spinocerebellar ataxia 44 and the NIPBL gene implicated in Cornelia de Lange syndrome.

CONCLUSION: Next-generation sequencing approaches in family-based studies are useful to identify novel and rare variants in genes for complex disorders like SMI. The findings of the study suggest a potential phenotypic burden of rare variants in Mendelian disease genes, indicating pleiotropic effects in the etiology of SMI.

}, keywords = {Bipolar Disorder, Exome, Female, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Male, Pedigree, Phenotype, Schizophrenia}, issn = {1440-1819}, doi = {10.1111/pcn.12788}, author = {Ganesh, Suhas and Ahmed P, Husayn and Nadella, Ravi K and More, Ravi P and Seshadri, Manasa and Viswanath, Biju and Rao, Mahendra and Jain, Sanjeev and Mukherjee, Odity} } @article {1841, title = {Generation of a FMR1 homozygous knockout human embryonic stem cell line (WAe009-A-16) by CRISPR/Cas9 editing.}, journal = {Stem Cell Res}, volume = {39}, year = {2019}, month = {2019 Aug}, pages = {101494}, abstract = {

Mutations in FMR1 gene is the cause of Fragile X Syndrome (FXS) leading inherited cause of intellectual disability and autism spectrum disorders. FMR1 gene encodes Fragile X Mental Retardation Protein (FMRP) which is a RNA binding protein and play important role in synaptic plasticity and translational regulation in neurons. We have generated a homozygous FMR1 knockout (FMR1-KO) hESC line using CRISPR/Cas9 based genome editing. It created a homozygous 280 nucleotide deletion at exon1, removing the start codon. This FMR1-KO cell line maintains stem cell like morphology, pluripotency, normal karyotype and ability to in-vitro differentiation.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2019.101494}, author = {Giri, Subhajit and Purushottam, Meera and Viswanath, Biju and Muddashetty, Ravi S} } @article {1602, title = {Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line.}, journal = {Stem Cell Res}, volume = {34}, year = {2019}, month = {2019 Jan}, pages = {101349}, abstract = {

Alzheimer{\textquoteright}s disease (AD) is the most frequent neurodegenerative disease amongst the elderly. The SNPs rs429358 and rs7412 in the APOE gene are the most common risk factor for sporadic AD, and there are three different alleles commonly referred to as APOE-ε2, APOE-ε3 and APOE-ε4. Induced pluripotent stem cells (iPSCs) hold great promise to model AD as such cells can be differentiated in vitro to the required cell type. Here we report the use of CRISPR/Cas9 technology employed on iPSCs from a healthy individual with an APOE-ε3/ε4 genotype to obtain isogenic APOE-ε2/ε2, APOE-ε3/ε3, APOE-ε4/ε4 lines as well as an APOE-knock-out line.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.11.010}, author = {Schmid, Benjamin and Prehn, Kennie R and Nimsanor, Natakarn and Garcia, Blanca Irene Aldana and Poulsen, Ulla and J{\o}rring, Ida and Rasmussen, Mikkel A and Clausen, Christian and Mau-Holzmann, Ulrike A and Ramakrishna, Sarayu and Muddashetty, Ravi and Steeg, Rachel and Bruce, Kevin and Mackintosh, Peter and Ebneth, Andreas and Holst, Bj{\o}rn and Cabrera-Socorro, Alfredo} } @article {1609, title = {Generation of two iPSC lines with either a heterozygous V717I or a heterozygous KM670/671NL mutation in the APP gene.}, journal = {Stem Cell Res}, volume = {34}, year = {2019}, month = {2019 Jan}, pages = {101368}, abstract = {

Alzheimer{\textquoteright}s disease (AD) is the most common form of dementia, affecting millions of people worldwide. Mutations in the genes PSEN1, PSEN2 or APP are known to cause familial forms of AD with an early age of onset. In this study, specific pathogenic mutations in the APP gene were introduced into an iPSC line from a healthy individual by the use of CRISPR-Cas9. The study resulted in the generation of two new cell lines, one carrying the V717I APP mutation and one with the KM670/671NL APP mutation.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.101368}, author = {Frederiksen, Henriette R and Holst, Bj{\o}rn and Ramakrishna, Sarayu and Muddashetty, Ravi and Schmid, Benjamin and Freude, Kristine} } @article {1613, title = {INDEX-db: The Indian Exome Reference Database (Phase I).}, journal = {J Comput Biol}, volume = {26}, year = {2019}, month = {2019 Mar}, pages = {225-234}, abstract = {

Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.

}, issn = {1557-8666}, doi = {10.1089/cmb.2018.0199}, author = {Ahmed P, Husayn and V, Vidhya and More, Ravi Prabhakar and Viswanath, Biju and Jain, Sanjeev and Rao, Mahendra S and Mukherjee, Odity} } @article {1576, title = {KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation.}, journal = {EMBO Rep}, year = {2019}, month = {2019 Mar 11}, abstract = {

Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non-histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non-histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2-marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.

}, issn = {1469-3178}, doi = {10.15252/embr.201643260}, author = {Rao, Radhika Arasala and Ketkar, Alhad Ashok and Kedia, Neelam and Krishnamoorthy, Vignesh K and Lakshmanan, Vairavan and Kumar, Pankaj and Mohanty, Abhishek and Kumar, Shilpa Dilip and Raja, Sufi O and Gulyani, Akash and Chaturvedi, Chandra Prakash and Brand, Marjorie and Palakodeti, Dasaradhi and Rampalli, Shravanti} } @article {1600, title = {Making NSC and Neurons from Patient-Derived Tissue Samples.}, journal = {Methods Mol Biol}, volume = {1919}, year = {2019}, month = {2019}, pages = {9-24}, abstract = {

The human brain and mechanisms underlying its functioning has been a field of intense research due to its complexity, inaccessibility, and the large numbers of debilitating disorders affecting this organ. Model organisms have provided great insight into the functioning of the mammalian brain; however, there exist many features unique to humans which need detailed understanding. In this context, human pluripotent stem cells (HPSCs) have emerged as a promising resource.In the developing brain, cortical diversification is achieved by neural stem cells/neural progenitor cells (NSCs/NPCs) by altering its potency (from multipotent to unipotent) and differentiation capacity (from neurogenesis to gliogenesis). Recent development in tissue reprogramming allows for derivation of NSCs/NPCs from either healthy control subjects manipulated to carry disease mutations or affected individuals carrying specific disease-causing mutations allowing for detailed evaluation of cellular phenotype, pharmacological manipulation, and/or toxicological screening.In this chapter, we will discuss HPSC differentiation into neural stem cells (NSCs) and neurons. We will review the mechanism underlying in vivo neural differentiation and methods which recapitulate this in vitro. We describe a method of deriving NSCs and differentiated mature neurons highlighting key steps of the core protocol. We also provide detailed information of the transcription factor and morphogen map of the developing brain which can be used as a guide to derive region- and lineage-specific NSCs and differentiated neurons.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-9007-8_2}, author = {Mukherjee, Odity and Acharya, Shubhra and Rao, Mahendra} } @article {1644, title = {Myocardin ablation in a cardiac-renal rat model.}, journal = {Sci Rep}, volume = {9}, year = {2019}, month = {2019 Apr 10}, pages = {5872}, abstract = {

Cardiorenal syndrome is defined by primary heart failure conditions influencing or leading to renal injury or dysfunction. Dilated cardiomyopathy (DCM) is a major co-existing form of heart failure (HF) with renal diseases. Myocardin (MYOCD), a cardiac-specific co-activator of serum response factor (SRF), is increased in DCM porcine and patient cardiac tissues and plays a crucial role in the pathophysiology of DCM. Inhibiting the increased MYOCD has shown to be partially rescuing the DCM phenotype in porcine model. However, expression levels of MYOCD in the cardiac tissues of the cardiorenal syndromic patients and the effect of inhibiting MYOCD in a cardiorenal syndrome model remains to be explored. Here, we analyzed the expression levels of MYOCD in the DCM patients with and without renal diseases. We also explored, whether cardiac specific silencing of MYOCD expression could ameliorate the cardiac remodeling and improve cardiac function in a renal artery ligated rat model (RAL). We observed an increase in MYOCD levels in the endomyocardial biopsies of DCM patients associated with renal failure compared to DCM alone. Silencing of MYOCD in RAL rats by a cardiac homing peptide conjugated MYOCD siRNA resulted in attenuation of cardiac hypertrophy, fibrosis and restoration of the left ventricular functions. Our data suggest hyper-activation of MYOCD in the pathogenesis of the cardiorenal failure cases. Also, MYOCD silencing showed beneficial effects by rescuing cardiac hypertrophy, fibrosis, size and function in a cardiorenal rat model.

}, issn = {2045-2322}, doi = {10.1038/s41598-019-42009-z}, author = {Mittal, Anupam and Rana, Santanu and Sharma, Rajni and Kumar, Akhilesh and Prasad, Rishikesh and Raut, Satish K and Sarkar, Sagartirtha and Saikia, Uma Nahar and Bahl, Ajay and Dhandapany, Perundurai S and Khullar, Madhu} } @article {1744, title = {NMDAR mediated translation at the synapse is regulated by MOV10 and FMRP.}, journal = {Mol Brain}, volume = {12}, year = {2019}, month = {2019 Jul 10}, pages = {65}, abstract = {

Protein synthesis is crucial for maintaining synaptic plasticity and synaptic signalling. Here we have attempted to understand the role of RNA binding proteins, Fragile X Mental Retardation Protein (FMRP) and Moloney Leukemia Virus 10 (MOV10) protein in N-Methyl-D-Aspartate Receptor (NMDAR) mediated translation regulation. We show that FMRP is required for translation downstream of NMDAR stimulation and MOV10 is the key specificity factor in this process. In rat cortical synaptoneurosomes, MOV10 in association with FMRP and Argonaute 2 (AGO2) forms the inhibitory complex on a subset of NMDAR responsive mRNAs. On NMDAR stimulation, MOV10 dissociates from AGO2 and promotes the translation of its target mRNAs. FMRP is required to form MOV10-AGO2 inhibitory complex and to promote translation of MOV10 associated mRNAs. Phosphorylation of FMRP appears to be the potential switch for NMDAR mediated translation and in the absence of FMRP, the distinct translation response to NMDAR\ stimulation is lost. Thus, FMRP and MOV10 have an important regulatory role in NMDAR mediated translation at the synapse.

}, issn = {1756-6606}, doi = {10.1186/s13041-019-0473-0}, author = {Kute, Preeti Madhav and Ramakrishna, Sarayu and Neelagandan, Nagammal and Chattarji, Sumantra and Muddashetty, Ravi S} } @article {1984, title = {Novel Series of Methyl 3-(Substituted Benzoyl)-7-Substituted-2-Phenylindolizine-1-Carboxylates as Promising Anti-Inflammatory Agents: Molecular Modeling Studies.}, journal = {Biomolecules}, volume = {9}, year = {2019}, month = {2019 Oct 28}, abstract = {

The cyclooxygenase-2 (COX-2) enzyme is considered to be an important target for developing novel anti-inflammatory agents. Selective COX-2 inhibitors offer the advantage of lower adverse effects that are commonly associated with non-selective COX inhibitors. In this work, a novel series of methyl 3-(substituted benzoyl)-7-substituted-2-phenylindolizine-1-carboxylates was synthesized and evaluated for COX-2 inhibitory activity. Compound was identified as the most active compound of the series with an IC of 6.71 M, which is comparable to the IC of indomethacin, a marketed non-steroidal anti-inflammatory drug (NSAID). Molecular modeling and crystallographic studies were conducted to further characterize the compounds and gain better understanding of the binding interactions between the compounds and the residues at the active site of the COX-2 enzyme. The pharmacokinetic properties and potential toxic effects were predicted for all the synthesized compounds, which indicated good drug-like properties. Thus, these synthesized compounds can be considered as potential lead compounds for developing effective anti-inflammatory therapeutic agents.

}, issn = {2218-273X}, doi = {10.3390/biom9110661}, author = {Venugopala, Katharigatta N and Al-Attraqchi, Omar H A and Tratrat, Christophe and Nayak, Susanta K and Morsy, Mohamed A and Aldhubiab, Bandar E and Attimarad, Mahesh and Nair, Anroop B and Sreeharsha, Nagaraja and Venugopala, Rashmi and Haroun, Michelyne and Girish, Meravanige B and Chandrashekharappa, Sandeep and Alwassil, Osama I and Odhav, Bharti} } @article {1990, title = {Relax, Don{\textquoteright}t RAN Translate It.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Dec 04}, pages = {827-829}, abstract = {

The (GGGGCC)n repeat expansion in C9orf72, which is the most common cause of frontotemporal dementia and amyotrophic lateral sclerosis, is translated through repeat-associated non-AUG (RAN) translation. In this issue of Neuron, Cheng et\ al. (2019) report that the helicase DDX3X, which unwinds (or relaxes) RNA, suppresses RAN translation and toxicity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.11.014}, author = {Wilson, Katherine M and Muralidharan, Bhavana and Isaacs, Adrian M} } @article {1742, title = {The resolution revolution reaches India.}, journal = {Biophys Rev}, year = {2019}, month = {2019 Jul 02}, issn = {1867-2450}, doi = {10.1007/s12551-019-00558-7}, author = {Subramanian, Ramaswamy and Mayor, Satyajit and Vinothkumar, Kutti R} } @article {1844, title = {Serotonin is essential for eye regeneration in planaria Schmidtea mediterranea.}, journal = {FEBS Lett}, year = {2019}, month = {2019 Sep 17}, abstract = {

Planaria is an ideal system to study factors involved in regeneration and tissue homeostasis. Little is known about the role of metabolites and small molecules in stem cell maintenance and lineage specification in planarians. Using liquid chromatography and mass spectrometry (LC-MS)-based quantitative metabolomics, we determined the relative levels of metabolites in stem cells, progenitors, and differentiated cells of the planarian Schmidtea mediterranea. Tryptophan and its metabolic product serotonin are significantly enriched in stem cells and progenitor population. Serotonin biosynthesis in these cells is brought about by a non-canonical enzyme, phenylalanine hydroxylase (PAH). Knockdown of Smed-pah leads to complete disappearance of eyes in regenerating planaria, while exogenous supply of serotonin and its precursor rescue the eyeless phenotype. Our results demonstrate a key role for serotonin in eye regeneration.

}, issn = {1873-3468}, doi = {10.1002/1873-3468.13607}, author = {Sarkar, Arunabha and Mukundan, Namita and Sowndarya, Sai and Dubey, Vinay Kumar and Babu, Rosana and Lakshmanan, Vairavan and Rangiah, Kannan and Panicker, Mitradas M and Palakodeti, Dasaradhi and Subramanian, Sabarinath Peruvemba and Ramaswamy, Subramanian} } @article {1981, title = {Stromal cells downregulate miR-23a-5p to activate protective autophagy in acute myeloid leukemia.}, journal = {Cell Death Dis}, volume = {10}, year = {2019}, month = {2019 Sep 30}, pages = {736}, abstract = {

Complex molecular cross talk between stromal cells and the leukemic cells in bone marrow is known to contribute significantly towards drug-resistance. Here, we have identified the molecular events that lead to stromal cells mediated therapy-resistance in acute myeloid leukemia (AML). Our work demonstrates that stromal cells downregulate miR-23a-5p levels in leukemic cells to protect them from the chemotherapy induced apoptosis. Downregulation of miR-23a-5p in leukemic cells leads to upregulation of protective autophagy by targeting TLR2 expression. Further, autophagy inhibitors when used as adjuvants along with conventional drugs can improve drug sensitivity in vitro as well in vivo in a mouse model of leukemia. Our work also demonstrates that this mechanism of bone marrow stromal cell mediated regulation of miR-23a-5p levels and subsequent molecular events are relevant predominantly in myeloid leukemia. Our results illustrate the critical and dynamic role of the bone marrow microenvironment in modulating miRNA expression in leukemic cells which could contribute significantly to drug resistance and subsequent relapse, possibly through persistence of minimal residual disease in this environment.

}, issn = {2041-4889}, doi = {10.1038/s41419-019-1964-8}, author = {Ganesan, Saravanan and Palani, Hamenth Kumar and Lakshmanan, Vairavan and Balasundaram, Nithya and Alex, Ansu Abu and David, Sachin and Venkatraman, Arvind and Korula, Anu and George, Biju and Balasubramanian, Poonkuzhali and Palakodeti, Dasaradhi and Vyas, Neha and Mathews, Vikram} } @article {1986, title = {Sustained Secretion of the Antimicrobial Peptide S100A7 Is Dependent on the Downregulation of Caspase-8.}, journal = {Cell Rep}, volume = {29}, year = {2019}, month = {2019 Nov 26}, pages = {2546-2555.e4}, abstract = {

Antimicrobial peptides (AMPs) are the body{\textquoteright}s natural innate immune defense against a spectrum of pathogens and can also modulate cell proliferation, chemotaxis, angiogenesis, wound healing, and immune cell activity. Harnessing these diverse functions for prophylactic use is contingent upon understanding the regulatory mechanisms governing their unconventional secretion from cells. Analysis of the secretion of S100A7 (Psoriasin), an abundant AMP stored in differentiated keratinocytes of the skin, has revealed an unexpected biphasic secretory response to bacterial exposure. The core components regulating S100A7 secretion are NFκB/p38MAPK, caspase-1, and interleukin (IL)-1α. The initial activation of this core machinery is mediated by Toll-like receptor signaling, whereas the chronic response is mediated by Caspase-8 downregulation. Interestingly, there is a concomitant downregulation of Caspase-8 in inflammatory skin diseases wherein S100A7 is constitutively released. These results highlight the potential of targeting these components to control the release of AMPs from the skin in both homeostatic and disease conditions.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.10.090}, author = {Bhatt, Tanay and Bhosale, Aishwarya and Bajantri, Bhavya and Mathapathi, Mruthyunjaya Swamy and Rizvi, Abrar and Scita, Giorgio and Majumdar, Amitabha and Jamora, Colin} } @article {1959, title = {Sustained Secretion of the Antimicrobial Peptide S100A7 Is Dependent on the Downregulation of Caspase-8.}, year = {2019}, month = {09/2019}, abstract = {

Antimicrobial peptides (AMPs) are the body{\textquoteright}s natural innate immune defense against a spectrum of pathogens and can also modulate cell proliferation, chemotaxis, angiogenesis, wound healing, and immune cell activity. Harnessing these diverse functions for prophylactic use is contingent upon understanding the regulatory mechanisms governing their unconventional secretion from cells. Analysis of the secretion of S100A7 (Psoriasin), an abundant AMP stored in differentiated keratinocytes of the skin, has revealed an unexpected biphasic secretory response to bacterial exposure. The core components regulating S100A7 secretion are NFκB/p38MAPK, caspase-1, and interleukin (IL)-1α. The initial activation of this core machinery is mediated by Toll-like receptor signaling, whereas the chronic response is mediated by Caspase-8 downregulation. Interestingly, there is a concomitant downregulation of Caspase-8 in inflammatory skin diseases wherein S100A7 is constitutively released. These results highlight the potential of targeting these components to control the release of AMPs from the skin in both homeostatic and disease conditions.

Copyright {\textcopyright} 2019 The Author(s). Published by Elsevier Inc. All rights reserved.

}, author = {Bhatt,T and Bhosale,A and Bajantri,B and Mathapathi,MS and Rizvi,A and Scita,G and Majumdar,A and Jamora,C} } @article {1582, title = {Urolithin A, a Novel Natural Compound to Target PI3K/AKT/mTOR Pathway in Pancreatic Cancer.}, journal = {Mol Cancer Ther}, volume = {18}, year = {2019}, month = {2019 Feb}, pages = {301-311}, abstract = {

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy and is highly resistant to standard treatment regimens. Targeted therapies against , a mutation present in an overwhelming majority of PDAC cases, have been largely ineffective. However, inhibition of downstream components in the KRAS signaling cascade provides promising therapeutic targets in the management of PDAC and warrants further exploration. Here, we investigated Urolithin A (Uro A), a novel natural compound derived from pomegranates, which targets numerous kinases downstream of KRAS, in particular the PI3K/AKT/mTOR signaling pathways. We showed that treatment of PDAC cells with Uro A blocked the phosphorylation of AKT and p70S6K successfully inhibited the growth of tumor xenografts, and increased overall survival of Ptf1a;LSL-Kras;Tgfbr2 (PKT) mice compared with vehicle or gemcitabine therapy alone. Histologic evaluation of these Uro A-treated tumor samples confirmed mechanistic actions of Uro A via decreased phosphorylation of AKT and p70S6K, reduced proliferation, and increased cellular apoptosis in both xenograft and PKT mouse models. In addition, Uro A treatment reprogrammed the tumor microenvironment, as evidenced by reduced levels of infiltrating immunosuppressive cell populations such as myeloid-derived suppressor cells, tumor-associated macrophages, and regulatory T cells. Overall, this work provides convincing preclinical evidence for the utility of Uro A as a therapeutic agent in PDAC through suppression of the PI3K/AKT/mTOR pathway.

}, issn = {1538-8514}, doi = {10.1158/1535-7163.MCT-18-0464}, author = {Totiger, Tulasigeri M and Srinivasan, Supriya and Jala, Venkatakrishna R and Lamichhane, Purushottam and Dosch, Austin R and Gaidarski, Alexander A and Joshi, Chandrashekhar and Rangappa, Shobith and Castellanos, Jason and Vemula, Praveen Kumar and Chen, Xi and Kwon, Deukwoo and Kashikar, Nilesh and VanSaun, Michael and Merchant, Nipun B and Nagathihalli, Nagaraj S} } @article {1192, title = {Automation aided optimization of cloning, expression and purification of enzymes of the bacterial sialic acid catabolic and sialylation pathways enzymes for structural studies.}, journal = {Microb Biotechnol}, volume = {11}, year = {2018}, month = {2018 Mar}, pages = {420-428}, abstract = {

The process of obtaining a well-expressing, soluble and correctly folded constructs can be made easier and quicker by automating the optimization of cloning, expression and purification. While there are many semiautomated pipelines available for cloning, expression and purification, there is hardly any pipeline that involves complete automation. Here, we achieve complete automation of all the steps involved in cloning and in\ vivo expression screening. This is demonstrated using 18 genes involved in sialic acid catabolism and the surface sialylation pathway. Our main objective was to clone these genes into a His-tagged Gateway vector, followed by their small-scale expression optimization in\ vivo. The constructs that showed best soluble expression were then selected for purification studies and scaled up for crystallization studies. Our technique allowed us to quickly find conditions for producing significant quantities of soluble proteins in Escherichia coli, their large-scale purification and successful crystallization of a number of these proteins. The method can be implemented in other cases where one needs to screen a large number of constructs, clones and expression vectors for successful recombinant production of functional proteins.

}, issn = {1751-7915}, doi = {10.1111/1751-7915.13041}, author = {Bairy, Sneha and Gopalan, Lakshmi Narayanan and Setty, Thanuja Gangi and Srinivasachari, Sathya and Manjunath, Lavanyaa and Kumar, Jay Prakash and Guntupalli, Sai R and Bose, Sucharita and Nayak, Vinod and Ghosh, Swagatha and Sathyanarayanan, Nitish and Caing-Carlsson, Rhawnie and Wahlgren, Weixiao Yuan and Friemann, Rosmarie and Ramaswamy, S and Neerathilingam, Muniasamy} } @article {1209, title = {Cell density overrides the effect of substrate stiffness on human mesenchymal stem cells{\textquoteright} morphology and proliferation.}, journal = {Biomater Sci}, volume = {6}, year = {2018}, month = {2018 May 01}, pages = {1109-1119}, abstract = {

The effect of substrate stiffness on the cellular morphology, proliferation, and differentiation of human mesenchymal stem cells (hMSCs) has been extensively researched and well established. However, the majority of these studies are done with a low seeding density where cell to cell interactions do not play a significant role. While these conditions permit an analysis of cell-substratum interactions at the single cell level, such a model system fails to capture a critical aspect of the cellular micro-environment in vivo, i.e. the cell-cell interaction via matrix deformation (i.e., strain). To address this question, we seeded hMSCs on soft poly-acrylamide (PAA) gels, at a seeding density that permits cells to be mechanically interacting via the underlying substrate. We found that as the intercellular distance decreases with the increasing seeding density, cellular sensitivity towards the substrate rigidity becomes significantly diminished. With the increasing seeding density, the cell spread area increased on a soft substrate (500 Pa) but reduced on an even slightly stiffer substrate (2 kPa) as well as on glass making them indistinguishable at a high seeding density. Not only in terms of cell spread area but also at a high seeding density, cells formed mature focal adhesions and prominent stress fibres on a soft substrate similar to that of the cells being cultured on a stiff substrate. The decreased intercellular distance also influenced the proliferation rate of the cells: higher seeding density on the soft substrate showed cell cycle progression similar to that of the cells on glass substrates. In summary, this paper demonstrates how the effect of substrate rigidity on the cell morphology and fate is a function of inter-cellular distance when seeded on a soft substrate. Our AFM data suggest that such changes happen due to local strain stiffening of the soft PAA gel, an effect that has been rarely reported in the literature so far.

}, issn = {2047-4849}, doi = {10.1039/c7bm00853h}, author = {Venugopal, Balu and Mogha, Pankaj and Dhawan, Jyotsna and Majumder, Abhijit} } @article {1184, title = {Decreased expression of cell adhesion genes in cancer stem-like cells isolated from primary oral squamous cell carcinomas.}, journal = {Tumour Biol}, volume = {40}, year = {2018}, month = {2018 May}, pages = {1010428318780859}, abstract = {

The goal of this study was to isolate cancer stem-like cells marked by high expression of CD44, a putative cancer stem cell marker, from primary oral squamous cell carcinomas and identify distinctive gene expression patterns in these cells. From 1 October 2013 to 4 September 2015, 76 stage III-IV primary oral squamous cell carcinoma of the gingivobuccal sulcus were resected. In all, 13 tumours were analysed by immunohistochemistry to visualise CD44-expressing cells. Expression of CD44 within The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma RNA-sequencing data was also assessed. Seventy resected tumours were dissociated into single cells and stained with antibodies to CD44 as well as CD45 and CD31 (together referred as Lineage/Lin). From 45 of these, CD44Lin and CD44Lin subpopulations were successfully isolated using fluorescence-activated cell sorting, and good-quality RNA was obtained from 14 such sorted pairs. Libraries from five pairs were sequenced and the results analysed using bioinformatics tools. Reverse transcription quantitative polymerase chain reaction was performed to experimentally validate the differential expression of selected candidate genes identified from the transcriptome sequencing in the same 5 and an additional 9 tumours. CD44 was expressed on the surface of poorly differentiated tumour cells, and within the The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma samples, its messenger RNA levels were higher in tumours compared to normal. Transcriptomics revealed that 102 genes were upregulated and 85 genes were downregulated in CD44Lin compared to CD44Lin cells in at least 3 of the 5 tumours sequenced. The upregulated genes included those involved in immune regulation, while the downregulated genes were enriched for genes involved in cell adhesion. Decreased expression of PCDH18, MGP, SPARCL1 and KRTDAP was confirmed by reverse transcription quantitative polymerase chain reaction. Lower expression of the cell-cell adhesion molecule PCDH18 correlated with poorer overall survival in the The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma data highlighting it as a potential negative prognostic factor in this cancer.

}, issn = {1423-0380}, doi = {10.1177/1010428318780859}, author = {Mishra, Amrendra and Sriram, Harshini and Chandarana, Pinal and Tanavde, Vivek and Kumar, Rekha V and Gopinath, Ashok and Govindarajan, Raman and Ramaswamy, S and Sadasivam, Subhashini} } @article {1579, title = {Developing two reference control samples for the Indian population.}, journal = {Stem Cell Res}, volume = {30}, year = {2018}, month = {2018 07}, pages = {38-42}, abstract = {

Human induced Pluripotent Stem Cells (HiPSCs) have immense potential in research and therapeutics. Under the aegis of Department of Biotechnology funded national program entitled, "The Accelerator program for Discovery in Brain Disorders using Stem Cells (ADBS)" we have established a HiPSC biorepository (https://www.ncbs.res.in/adbs/bio-repository) with an objective to study severe mental illness. The repository comprises of HiPSC lines derived from healthy control donors and individuals with life time diagnosis of severe mental illness from dense families. In the current report we submit information regarding two population control reference lines (male = 1; female = 1) from this biorepository.

}, keywords = {Cell Differentiation, Humans, India, Induced Pluripotent Stem Cells}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.05.001}, author = {Iyer, Shruti and Bhatia, Priyanka and Rao, Mahendra and Mukherjee, Odity} } @article {1149, title = {Discovery biology of neuropsychiatric syndromes (DBNS): a center for integrating clinical medicine and basic science.}, journal = {BMC Psychiatry}, volume = {18}, year = {2018}, month = {2018 Apr 18}, pages = {106}, abstract = {

BACKGROUND: There is emerging evidence that there are shared genetic, environmental and developmental risk factors in psychiatry, that cut across traditional diagnostic boundaries. With this background, the Discovery biology of neuropsychiatric syndromes (DBNS) proposes to recruit patients from five different syndromes (schizophrenia, bipolar disorder, obsessive compulsive disorder, Alzheimer{\textquoteright}s dementia and substance use disorders), identify those with multiple affected relatives, and invite these families to participate in this study. The families will be assessed: 1) To compare neuro-endophenotype measures between patients, first degree relatives (FDR) and healthy controls., 2) To identify cellular phenotypes which differentiate the groups., 3) To examine the longitudinal course of neuro-endophenotype measures., 4) To identify measures which correlate with outcome, and 5) To create a unified digital database and biorepository.

METHODS: The identification of the index participants will occur at well-established specialty clinics. The selected individuals will have a strong family history (with at least another affected FDR) of mental illness. We will also recruit healthy controls without family history of such illness. All recruited individuals (N = 4500) will undergo brief clinical assessments and a blood sample will be drawn for isolation of DNA and peripheral blood mononuclear cells (PBMCs). From among this set, a subset of 1500 individuals (300 families and 300 controls) will be assessed on several additional assessments [detailed clinical assessments, endophenotype measures (neuroimaging- structural and functional, neuropsychology, psychophysics-electroencephalography, functional near infrared spectroscopy, eye movement tracking)], with the intention of conducting repeated measurements every alternate year. PBMCs from this set will be used to generate lymphoblastoid cell lines, and a subset of these would be converted to induced pluripotent stem cell lines and also undergo whole exome sequencing.

DISCUSSION: We hope to identify unique and overlapping brain endophenotypes for major psychiatric syndromes. In a proportion of subjects, we expect these neuro-endophenotypes to progress over time and to predict treatment outcome. Similarly, cellular assays could differentiate cell lines derived from such groups. The repository of biomaterials as well as digital datasets of clinical parameters, will serve as a valuable resource for the broader scientific community who wish to address research questions in the area.

}, issn = {1471-244X}, doi = {10.1186/s12888-018-1674-2}, author = {Viswanath, Biju and Rao, Naren P and Narayanaswamy, Janardhanan C and Sivakumar, Palanimuthu T and Kandasamy, Arun and Kesavan, Muralidharan and Mehta, Urvakhsh Meherwan and Venkatasubramanian, Ganesan and John, John P and Mukherjee, Odity and Purushottam, Meera and Kannan, Ramakrishnan and Mehta, Bhupesh and Kandavel, Thennarasu and Binukumar, B and Saini, Jitender and Jayarajan, Deepak and Shyamsundar, A and Moirangthem, Sydney and Vijay Kumar, K G and Thirthalli, Jagadisha and Chandra, Prabha S and Gangadhar, Bangalore N and Murthy, Pratima and Panicker, Mitradas M and Bhalla, Upinder S and Chattarji, Sumantra and Benegal, Vivek and Varghese, Mathew and Reddy, Janardhan Y C and Raghu, Padinjat and Rao, Mahendra and Jain, Sanjeev} } @article {1212, title = {Distinguishing States of Arrest: Genome-Wide Descriptions of Cellular Quiescence Using ChIP-Seq and RNA-Seq Analysis.}, journal = {Methods Mol Biol}, volume = {1686}, year = {2018}, month = {2018}, pages = {215-239}, abstract = {

Regenerative potential in adult stem cells is closely associated with the establishment of-and exit from-a temporary state of quiescence. Emerging evidence not only provides a rationale for the link between lineage determination programs and cell cycle regulation but also highlights the understanding of quiescence as an actively maintained cellular program, encompassing networks and mechanisms beyond mitotic inactivity or metabolic restriction. Interrogating the quiescent genome and transcriptome using deep-sequencing technologies offers an unprecedented view of the global mechanisms governing this reversibly arrested cellular state and its importance for cell identity. While many efforts have identified and isolated pure target stem cell populations from a variety of adult tissues, there is a growing appreciation that their isolation from the stem cell niche in vivo leads to activation and loss of hallmarks of quiescence. Thus, in vitro models that recapitulate the dynamic reversibly arrested stem cell state in culture and lend themselves to comparison with the activated or differentiated state are useful templates for genome-wide analysis of the quiescence network.In this chapter, we describe the methods that can be adopted for whole genome epigenomic and transcriptomic analysis of cells derived from one such established culture model where mouse myoblasts are triggered to enter or exit quiescence as homogeneous populations. The ability to synchronize myoblasts in G permits insights into the genome in "deep quiescence." The culture methods for generating large populations of quiescent myoblasts in either 2D or 3D culture formats are described in detail in a previous chapter in this series (Arora et al. Methods Mol Biol 1556:283-302, 2017). Among the attractive features of this model are that genes isolated from quiescent myoblasts in culture mark satellite cells in vivo (Sachidanandan et al., J Cell Sci 115:2701-2712, 2002) providing a validation of its approximation of the molecular state of true stem cells. Here, we provide our working protocols for ChIP-seq and RNA-seq analysis, focusing on those experimental elements that require standardization for optimal analysis of chromatin and RNA from quiescent myoblasts, and permitting useful and revealing comparisons with proliferating myoblasts or differentiated myotubes.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-7371-2_16}, author = {Srivastava, Surabhi and Gala, Hardik P and Mishra, Rakesh K and Dhawan, Jyotsna} } @article {1585, title = {Experiential contributions to social dominance in a rat model of fragile-X syndrome.}, journal = {Proc Biol Sci}, volume = {285}, year = {2018}, month = {2018 Jun 13}, abstract = {

Social withdrawal is one phenotypic feature of the monogenic neurodevelopmental disorder fragile-X. Using a {\textquoteright}knockout{\textquoteright} rat model of fragile-X, we examined whether deletion of the gene that causes this condition would affect the ability to form and express a social hierarchy as measured in a tube test. Male fragile-X {\textquoteright}knockout{\textquoteright} rats living together could successfully form a social dominance hierarchy, but were significantly subordinate to wild-type animals in mixed group cages. Over 10 days of repeated testing, the fragile-X mutant rats gradually showed greater variance and instability of rank during their tube-test encounters. This affected the outcome of future encounters with stranger animals from other cages, with the initial phenotype of wild-type dominance lost to a more complex picture that reflected, regardless of genotype, the prior experience of winning or losing. Our findings offer a novel insight into the complex dynamics of social interactions between laboratory living groups of fragile-X and wild-type rats. Even though this is a monogenic condition, experience has an impact upon future interactions with other animals. Gene/environment interactions should therefore be considered in the development of therapeutics.

}, issn = {1471-2954}, doi = {10.1098/rspb.2018.0294}, author = {Saxena, K and Webster, J and Hallas-Potts, A and Mackenzie, R and Spooner, P A and Thomson, D and Kind, P and Chatterji, S and Morris, R G M} } @article {1188, title = {Exploring membrane permeability of Tomatidine to enhance lipid mediated nucleic acid transfections}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, year = {2018}, pages = {-}, abstract = {

Abstract Intracellular delivery of nucleic acids is one of the critical steps in the transfections. Prior findings demonstrated various strategies including membrane fusion, endosomal escape for the efficient cytoplasmic delivery. In our continuing efforts to improve the nucleic acids transfections, we harnessed cell permeable properties of Tomatidine (T), a steroidal alkaloid abundantly found in green tomatoes for maximizing intracellular delivery of lipoplexes. We doped Tomatidine into liposomes of cationic lipid with amide linker (A) from our lipid library. Six liposomal formulations (AT) of Lipid A (1 mM) with varying concentrations of Tomatidine (0{\textendash}1 mM) were prepared and evaluated for their transfection efficacies. Owing to its signature characteristic of cell membrane permeability, Tomatidine modulated endocytosis process, enhanced the intracellular delivery of the lipoplexes, and in turn increased the transfection efficacy of cationic liposomes. Our findings provide {\textquoteleft}proof of concept{\textquoteright} for enhancing transfections in gene delivery applications with Tomatidine in cationic liposomal formulations. These findings can be further applied in lipid mediated gene therapy and drug delivery applications.

}, keywords = {Endocytosis}, issn = {0005-2736}, doi = {https://doi.org/10.1016/j.bbamem.2018.06.006}, url = {https://www.sciencedirect.com/science/article/pii/S0005273618301780}, author = {Vignesh K. Rangasami and Brijesh Lohchania and Chandrashekhar Voshavar and Harikrishna R. Rachamalla and Rajkumar Banerjee and Ashish Dhayani and Saravanabhavan Thangavel and Praveen K. Vemula and Srujan Marepally} } @article {1598, title = {FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation.}, journal = {iScience}, volume = {9}, year = {2018}, month = {2018 Nov 30}, pages = {399-411}, abstract = {

FMRP is an RNA-binding protein that is known to localize in the cytoplasm and in the nucleus. Here, we have identified an interaction of FMRP with a specific set of C/D box snoRNAs in the nucleus. C/D box snoRNAs guide 2{\textquoteright}O methylations of ribosomal RNA (rRNA) on defined sites, and this modification regulates rRNA folding and assembly of ribosomes. 2{\textquoteright}O methylation of rRNA is partial on several sites in human embryonic stem cells, which results in ribosomes with differential methylation patterns. FMRP-snoRNA interaction affects rRNA methylation on several of these sites, and in the absence of FMRP, differential methylation pattern of rRNA is significantly altered. We found that FMRP recognizes ribosomes carrying specific methylation patterns on rRNA and the recognition of methylation pattern by FMRP may potentially determine the translation status of its target mRNAs. Thus, FMRP integrates its function in the nucleus and in the cytoplasm.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2018.11.007}, author = {D{\textquoteright}Souza, Michelle Ninochka and Gowda, Naveen Kumar Chandappa and Tiwari, Vishal and Babu, Rosana Ottakandathil and Anand, Praveen and Dastidar, Sudhriti Ghosh and Singh, Randhir and James, Owen G and Selvaraj, Bhuvaneish and Pal, Rakhi and Ramesh, Arati and Chattarji, Sumantra and Chandran, Siddharthan and Gulyani, Akash and Palakodeti, Dasaradhi and Muddashetty, Ravi S} } @article {1586, title = {Hippocampal and amygdalar cell-specific translation is similar soon after stress but diverge over time.}, journal = {Hippocampus}, volume = {28}, year = {2018}, month = {2018 06}, pages = {441-452}, abstract = {

Stress is known to cause contrasting patterns of morphological and physiological plasticity in the hippocampus and amygdala. An obligatory cellular process underlying such neural changes is de novo translation and alterations in protein expression. Yet the nature of the translational response to stress in neurons remains largely unexplored. Even less is known about how glia are affected. Using a click-chemistry-based method to label the de novo proteome in live brain slices, we monitored translation in neurons and astrocytes of the basolateral amygdala (BLA) and dorsal hippocampal area CA3 (dCA3) in rats at different time-points after a single 2-hr exposure to immobilization stress. We observed enhancements in neuronal translation in both brain regions 1 hour after stress. This initial increase persisted in the BLA up to 10\ days afterwards. In contrast, dCA3 neuronal translation gradually decreased to below control levels 10\ days later. Translation profiles of dCA3 astrocytes followed timelines similar to neurons, but in BLA astrocytes translation peaked 1\ day later and remained elevated 10\ days later. Together our results demonstrate that stress causes an immediate upregulation of protein synthesis in both amygdalar and hippocampal neurons and astrocytes. However, these two areas eventually exhibit opposite temporal profiles of protein expression well after the end of stress. These findings identify new metrics of stress-induced plasticity at the level of cell-type specific proteomic landscape that may provide important insights into the molecular basis of the divergent temporal effects of stress across brain regions and biological scales.

}, issn = {1098-1063}, doi = {10.1002/hipo.22845}, author = {Madan, Jesvin S and Gupta, Kanika and Chattarji, Sumantra and Bhattacharya, Aditi} } @article {1145, title = {Induction of quiescence (G0) in bone marrow stromal stem cells enhances their stem cell characteristics.}, journal = {Stem Cell Res}, volume = {30}, year = {2018}, month = {2018 May 17}, pages = {69-80}, abstract = {

Several studies have suggested that bone marrow stromal steam cells (BMSC) exist in a quiescent state (G0) within the in vivo niche; however, an explicit analysis of the biology of G0 state-BMSC has not been reported. We hypothesized that induction of G0 in BMSC might enhance their stem cell properties. Thus, we induced quiescence in BMSC in vitro by (a) suspension culture in a viscous medium or (b) culture on soft polyacrylamide substrate; and examined their molecular and functional phenotype. Induction of G0 was confirmed by bromo-deoxyuridine (BrdU) labelling and analysis of cell cycle gene expression. Upon reactivation and re-entry into cell cycle, G0 state-BMSC exhibited enhanced clonogenic self-renewal, preferential differentiation into osteoblastic rather than adipocytic cells and increased ectopic bone formation when implanted subcutaneously in vivo in immune-deficient mice, compared to asynchronous proliferating (pre-G0) BMSC. Global gene expression profiling revealed reprogramming of the transcriptome during G0 state including significant alterations in relevant pathways and expression of secreted factors, suggesting altered autocrine and paracrine signaling by G0 state-BMSC and a possible mechanism for enhanced bone formation. G0 state-BMSC might provide a clinically relevant model for understanding the in vivo biology of BMSC.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.05.010}, author = {Rumman, Mohammad and Majumder, Abhijit and Harkness, Linda and Venugopal, Balu and Vinay, M B and Pillai, Malini S and Kassem, Moustapha and Dhawan, Jyotsna} } @article {1155, title = {"Just a spoonful of sugar...": import of sialic acid across bacterial cell membranes.}, journal = {Biophys Rev}, volume = {10}, year = {2018}, month = {2018 Apr}, pages = {219-227}, abstract = {

Eukaryotic cell surfaces are decorated with a complex array of glycoconjugates that are usually capped with sialic acids, a large family of over 50 structurally distinct nine-carbon amino sugars, the most common member of which is N-acetylneuraminic acid. Once made available through the action of neuraminidases, bacterial pathogens and commensals utilise host-derived sialic acid by degrading it for energy or repurposing the sialic acid onto their own cell surface to camouflage the bacterium from the immune system. A functional sialic acid transporter has been shown to be essential for the uptake of sialic acid in a range of human bacterial pathogens and important for host colonisation and persistence. Here, we review the state-of-play in the field with respect to the molecular mechanisms by which these bio-nanomachines transport sialic acids across bacterial cell membranes.

}, issn = {1867-2450}, doi = {10.1007/s12551-017-0343-x}, author = {North, Rachel A and Horne, Christopher R and Davies, James S and Remus, Daniela M and Muscroft-Taylor, Andrew C and Goyal, Parveen and Wahlgren, Weixiao Yuan and Ramaswamy, S and Friemann, Rosmarie and Dobson, Renwick C J} } @article {1583, title = {Mutation burden profile in familial Alzheimer{\textquoteright}s disease cases from India.}, journal = {Neurobiol Aging}, volume = {64}, year = {2018}, month = {2018 04}, pages = {158.e7-158.e13}, abstract = {

This study attempts to identify coding risk variants in genes previously implicated in Alzheimer{\textquoteright}s disease (AD) pathways, through whole-exome sequencing of subjects (N\ = 17) with AD, with a positive family history of dementia (familial AD). We attempted to evaluate the mutation burden in genes encoding amyloid precursor protein metabolism and previously linked to risk of dementias. Novel variants were identified in genes involved in amyloid precursor protein metabolism such as PSEN1 (chr 14:73653575, W161C, tgg \> tgT), PLAT (chr 8:42039530,G272R), and SORL1 (chr11:121414373,G601D). The mutation burden assessment of dementia-related genes for all 17 cases revealed 45 variants, which were either shared across subjects, or were present in just the 1 patient. The study shows that the clinical characteristics, and genetic correlates, obtained in this sample are broadly comparable to the other studies that have investigated familial forms of AD. Our study identifies rare deleterious genetic variations, in the coding region of genes involved in amyloid signaling, and other dementia-associated pathways.

}, keywords = {Aged, Alzheimer Disease, Amyloid beta-Protein Precursor, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Variation, Humans, India, LDL-Receptor Related Proteins, Membrane Transport Proteins, Middle Aged, Mutation, Presenilin-1, Risk, Signal Transduction, Tissue Plasminogen Activator, Whole Exome Sequencing}, issn = {1558-1497}, doi = {10.1016/j.neurobiolaging.2017.12.002}, author = {Syama, Adhikarla and Sen, Somdatta and Kota, Lakshmi Narayanan and Viswanath, Biju and Purushottam, Meera and Varghese, Mathew and Jain, Sanjeev and Panicker, Mitradas M and Mukherjee, Odity} } @article {1186, title = {Networks that link cytoskeletal regulators and diaphragm proteins underpin filtration function in Drosophila nephrocytes.}, journal = {Exp Cell Res}, volume = {364}, year = {2018}, month = {2018 Mar 15}, pages = {234-242}, abstract = {

Insect nephrocytes provide a valuable model for kidney disease, as they are structurally and functionally homologous to mammalian kidney podocytes. They possess an exceptional macromolecular assembly, the nephrocyte diaphragm (ND), which serves as a filtration barrier and helps maintain tissue homeostasis by filtering out wastes and toxic products. However, the elements that maintain nephrocyte architecture and the ND are not understood. We show that Drosophila nephrocytes have a unique cytoplasmic cluster of F-actin, which is maintained by the microtubule cytoskeleton and Rho-GTPases. A balance of Rac1 and Cdc42 activity as well as proper microtubule organization and endoplasmic reticulum structure, are required to position the actin cluster. Further, ND proteins Sns and Duf also localize to this cluster and regulate organization of the actin and microtubule cytoskeleton. Perturbation of any of these inter-dependent components impairs nephrocyte ultrafiltration. Thus cytoskeletal components, Rho-GTPases and ND proteins work in concert to maintain the specialized nephrocyte architecture and function.

}, issn = {1090-2422}, doi = {10.1016/j.yexcr.2018.02.015}, author = {Muraleedharan, Simi and Sam, Aksah and Skaer, Helen and Inamdar, Maneesha S} } @article {1152, title = {PAI1 mediates fibroblast-mast cell interactions in skin fibrosis.}, journal = {J Clin Invest}, volume = {128}, year = {2018}, month = {2018 May 01}, pages = {1807-1819}, abstract = {

Fibrosis is a prevalent pathological condition arising from the chronic activation of fibroblasts. This activation results from the extensive intercellular crosstalk mediated by both soluble factors and direct cell-cell connections. Prominent among these are the interactions of fibroblasts with immune cells, in which the fibroblast-mast cell connection, although acknowledged, is relatively unexplored. We have used a Tg mouse model of skin fibrosis, based on expression of the transcription factor Snail in the epidermis, to probe the mechanisms regulating mast cell activity and the contribution of these cells to this pathology. We have discovered that Snail-expressing keratinocytes secrete plasminogen activator inhibitor type 1 (PAI1), which functions as a chemotactic factor to increase mast cell infiltration into the skin. Moreover, we have determined that PAI1 upregulates intercellular adhesion molecule type 1 (ICAM1) expression on dermal fibroblasts, rendering them competent to bind to mast cells. This heterotypic cell-cell adhesion, also observed in the skin fibrotic disorder scleroderma, culminates in the reciprocal activation of both mast cells and fibroblasts, leading to the cascade of events that promote fibrogenesis. Thus, we have identified roles for PAI1 in the multifactorial program of fibrogenesis that expand its functional repertoire beyond its canonical role in plasmin-dependent processes.

}, issn = {1558-8238}, doi = {10.1172/JCI99088}, author = {Pincha, Neha and Hajam, Edries Yousaf and Badarinath, Krithika and Batta, Surya Prakash Rao and Masudi, Tafheem and Dey, Rakesh and Andreasen, Peter and Kawakami, Toshiaki and Samuel, Rekha and George, Renu and Danda, Debashish and Jacob, Paul Mazhuvanchary and Jamora, Colin} } @inbook {1193, title = {Prevention of Metal Exposure: Chelating Agents and Barrier Creams}, booktitle = {Metal Allergy: From Dermatitis to Implant and Device Failure}, year = {2018}, pages = {227{\textendash}246}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {

Metals are a group of elements which are ubiquitous in modern life. They are used in the fields of cosmetics, water purification, medicine, paint, food products, pesticides, and almost innumerable others. As the use of metals has increased in recent decades, so has human exposure to these elements. Metals such as mercury, lead, arsenic, nickel, and others have been implicated in negatively affecting human homeostasis by causing chronic inflammatory diseases, among other serious conditions. Both acute and chronic metal toxicity in vital organs could arise from local or systemic exposure to numerous metals. Although some metals have health benefits, overaccumulation of metals in body tissues can result in deleterious, toxic effects. Most exposure to metals occurs via cutaneous, inhalation, or oral routes. At the highest risk of negative effects of exposure are pregnant women and children. To ameliorate or prevent the toxic effects of metals, chelating agents and barrier creams are used widely in medical practice today. In this chapter, we will discuss preventing metal toxicity from overexposure via chelation therapy and skin barrier creams.

}, isbn = {978-3-319-58503-1}, doi = {10.1007/978-3-319-58503-1_18}, url = {https://doi.org/10.1007/978-3-319-58503-1_18}, author = {Mahato, Manohar and Sherman, Nicholas E. and Kiran Kumar Mudnakudu, N. and Joshi, Nitin and Briand, Elisabeth and Karp, Jeffrey M. and Vemula, Praveen Kumar}, editor = {Chen, Jennifer K and Thyssen, Jacob P.} } @article {1595, title = {Prevention of pesticide-induced neuronal dysfunction and mortality with nucleophilic poly-Oxime topical gel.}, journal = {Sci Adv}, volume = {4}, year = {2018}, month = {2018 Oct}, pages = {eaau1780}, abstract = {

Organophosphate-based pesticides inhibit acetylcholinesterase (AChE), which plays a pivotal role in neuromuscular function. While spraying in the field, farmworkers get exposed to pesticides through the dermal route. Internalized pesticide inhibits AChE, which leads to neurotoxicity, cardiotoxicity, cognitive dysfunction, loss of endurance, and death in severe cases. Here, we present a nucleophilic pyridine-2-aldoxime-functionalized chitosan-based topical gel (-Oxime gel) that rapidly deactivates organophosphates, methyl parathion (MPT), on the skin of rats, which leads to reduced AChE inhibition in the blood and tissues. Testing the robustness of -Oxime gel, we report reduction in AChE inhibition following repeated dermal administration of MPT in the presence of -Oxime gel. Furthermore, -Oxime gel prevented MPT-induced neuromuscular dysfunction, loss of endurance, and locomotor coordination. We observe a 100\% survival in rats following topical MPT administration in the presence of -Oxime gel. This prophylactic gel may therefore help farmworkers by limiting pesticide-induced toxicity and mortality.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aau1780}, author = {Thorat, Ketan and Pandey, Subhashini and Chandrashekharappa, Sandeep and Vavilthota, Nikitha and Hiwale, Ankita A and Shah, Purna and Sreekumar, Sneha and Upadhyay, Shubhangi and Phuntsok, Tenzin and Mahato, Manohar and Mudnakudu-Nagaraju, Kiran K and Sunnapu, Omprakash and Vemula, Praveen K} } @article {1580, title = {Targeting Phosphopeptide Recognition by the Human BRCA1 Tandem BRCT Domain to Interrupt BRCA1-Dependent Signaling.}, journal = {Cell Chem Biol}, volume = {25}, year = {2018}, month = {2018 06 21}, pages = {677-690.e12}, abstract = {

Intracellular signals triggered by DNA breakage flow through proteins containing BRCT (BRCA1 C-terminal) domains. This family, comprising 23 conserved phosphopeptide-binding modules in man, is inaccessible to small-molecule chemical inhibitors. Here, we develop Bractoppin, a drug-like inhibitor of phosphopeptide recognition by the human BRCA1 tandem (t)BRCT domain, which selectively inhibits substrate binding with nanomolar potency in\ vitro. Structure-activity exploration suggests that Bractoppin engages BRCA1 tBRCT residues recognizing pSer in the consensus motif, pSer-Pro-Thr-Phe, plus an abutting hydrophobic pocket that is distinct in structurally related BRCT domains, conferring selectivity. In cells, Bractoppin inhibits substrate recognition detected by F{\"o}rster resonance energy transfer, and diminishes BRCA1 recruitment to DNA breaks, in turn suppressing damage-induced G2 arrest and assembly of the recombinase, RAD51. But damage-induced MDC1 recruitment, single-stranded DNA (ssDNA) generation, and TOPBP1 recruitment remain unaffected. Thus, an inhibitor of phosphopeptide recognition selectively interrupts BRCA1 tBRCT-dependent signals evoked by DNA damage.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2018.02.012}, author = {Periasamy, Jayaprakash and Kurdekar, Vadiraj and Jasti, Subbarao and Nijaguna, Mamatha B and Boggaram, Sanjana and Hurakadli, Manjunath A and Raina, Dhruv and Kurup, Lokavya Meenakshi and Chintha, Chetan and Manjunath, Kavyashree and Goyal, Aneesh and Sadasivam, Gayathri and Bharatham, Kavitha and Padigaru, Muralidhara and Potluri, Vijay and Venkitaraman, Ashok R} } @article {1146, title = {Towards an arthritis flare-responsive drug delivery system.}, journal = {Nat Commun}, volume = {9}, year = {2018}, month = {2018 Apr 03}, pages = {1275}, abstract = {

Local delivery of therapeutics for the treatment of inflammatory arthritis (IA) is limited by short intra-articular half-lives. Since IA severity often fluctuates over time, a local drug delivery method that titrates drug release to arthritis activity would represent an attractive paradigm in IA therapy. Here we report the development of a hydrogel platform that exhibits disassembly and drug release controlled by the concentration of enzymes expressed during arthritis flares. In vitro, hydrogel loaded with triamcinolone acetonide (TA) releases drug on-demand upon exposure to enzymes or synovial fluid from patients with rheumatoid arthritis. In arthritic mice, hydrogel loaded with a fluorescent dye demonstrates flare-dependent disassembly measured as loss of fluorescence. Moreover, a single dose of TA-loaded hydrogel but not the equivalent dose of locally injected free TA reduces arthritis activity in the injected paw. Together, our data suggest flare-responsive hydrogel as a promising next-generation drug delivery approach for the treatment of IA.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03691-1}, author = {Joshi, Nitin and Yan, Jing and Levy, Seth and Bhagchandani, Sachin and Slaughter, Kai V and Sherman, Nicholas E and Amirault, Julian and Wang, Yufeng and Riegel, Logan and He, Xueyin and Rui, Tan Shi and Valic, Michael and Vemula, Praveen K and Miranda, Oscar R and Levy, Oren and Gravallese, Ellen M and Aliprantis, Antonios O and Ermann, Joerg and Karp, Jeffrey M} } @article {1594, title = {A versatile LC-MS/MS approach for comprehensive, quantitative analysis of central metabolic pathways.}, journal = {Wellcome Open Res}, volume = {3}, year = {2018}, month = {2018}, pages = {122}, abstract = {

Liquid chromatography-mass spectrometry (LC-MS/MS) based approaches are widely used for the identification and quantitation of specific metabolites, and are a preferred approach towards analyzing cellular metabolism. Most methods developed come with specific requirements such as unique columns, ion-pairing reagents and pH conditions, and typically allow measurements in a specific pathway alone. Here, we present a single column-based set of methods for simultaneous coverage of multiple pathways, primarily focusing on central carbon, amino acid, and nucleotide metabolism. We further demonstrate the use of this method for quantitative, stable isotope-based metabolic flux experiments, expanding its use beyond steady-state level measurements of metabolites. The expected kinetics of label accumulation pertinent to the pathway under study are presented with some examples. The methods discussed here are broadly applicable, minimize the need for multiple chromatographic resolution methods, and highlight how simple labeling experiments can be valuable in facilitating a comprehensive understanding of the metabolic state of cells.

}, issn = {2398-502X}, doi = {10.12688/wellcomeopenres.14832.1}, author = {Walvekar, Adhish and Rashida, Zeenat and Maddali, Hemanth and Laxman, Sunil} } @article {1158, title = {Co-expression of Tbx6 and Sox2 identifies a novel transient neuromesoderm progenitor cell state.}, journal = {Development}, volume = {144}, year = {2017}, month = {2017 12 15}, pages = {4522-4529}, abstract = {

Elongation of the body axis is a key aspect of body plan development. Bipotential neuromesoderm progenitors (NMPs) ensure axial growth of embryos by contributing both to the spinal cord and mesoderm. The current model for the mechanism controlling NMP deployment invokes Tbx6, a T-box factor, to drive mesoderm differentiation of NMPs. Here, we identify a new population of Tbx6 cells in a subdomain of the NMP niche in mouse embryos. Based on co-expression of a progenitor marker, Sox2, we identify this population as representing a transient cell state in the mesoderm-fated NMP lineage. Genetic lineage tracing confirms the presence of the NMP cell state. Furthermore, we report a novel aspect of the documented mutant phenotype, namely an increase from two to four ectopic neural tubes, corresponding to the switch in NMP niche, thus highlighting the importance of function in NMP fate decision. This study emphasizes the function of Tbx6 as a bistable switch that turns mesoderm fate {\textquoteright}on{\textquoteright} and progenitor state {\textquoteright}off{\textquoteright}, and thus has implications for the molecular mechanism driving NMP fate choice.

}, keywords = {Animals, Body Patterning, Cell Differentiation, Cell Lineage, Embryonic Stem Cells, Gene Expression Regulation, Developmental, Mesoderm, Mice, Mice, Transgenic, Neural Tube, SOXB1 Transcription Factors, Spinal Cord, Transcription Factors}, issn = {1477-9129}, doi = {10.1242/dev.153262}, author = {Javali, Alok and Misra, Aritra and Leonavicius, Karolis and Acharyya, Debalina and Vyas, Bhakti and Sambasivan, Ramkumar} } @article {1210, title = {C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.}, journal = {BMC Bioinformatics}, volume = {18}, year = {2017}, month = {2017 Sep 13}, pages = {392}, abstract = {

BACKGROUND: Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge.

RESULTS: We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge.

CONCLUSIONS: C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.

}, keywords = {Algorithms, Embryonic Stem Cells, Epigenomics, Genes, Genomics, HeLa Cells, Humans, Internet, K562 Cells, Promoter Regions, Genetic, Software, Transcription, Genetic, Web Browser}, issn = {1471-2105}, doi = {10.1186/s12859-017-1786-6}, author = {Sowpati, Divya Tej and Srivastava, Surabhi and Dhawan, Jyotsna and Mishra, Rakesh K} } @article {1163, title = {Hierarchies in light sensing and dynamic interactions between ocular and extraocular sensory networks in a flatworm.}, journal = {Sci Adv}, volume = {3}, year = {2017}, month = {2017 Jul}, pages = {e1603025}, abstract = {

Light sensing has independently evolved multiple times under diverse selective pressures but has been examined only in a handful among the millions of light-responsive organisms. Unsurprisingly, mechanistic insights into how differential light processing can cause distinct behavioral outputs are limited. We show how an organism can achieve complex light processing with a simple "eye" while also having independent but mutually interacting light sensing networks. Although planarian flatworms lack wavelength-specific eye photoreceptors, a 25 nm change in light wavelength is sufficient to completely switch their phototactic behavior. Quantitative photoassays, eye-brain confocal imaging, and RNA interference/knockdown studies reveal that flatworms are able to compare small differences in the amounts of light absorbed at the eyes through a single eye opsin and convert them into binary behavioral outputs. Because planarians can fully regenerate, eye-brain injury-regeneration studies showed that this acute light intensity sensing and processing are layered on simple light detection. Unlike intact worms, partially regenerated animals with eyes can sense light but cannot sense finer gradients. Planarians also show a "reflex-like," eye-independent (extraocular/whole-body) response to low ultraviolet A light, apart from the "processive" eye-brain-mediated (ocular) response. Competition experiments between ocular and extraocular sensory systems reveal dynamic interchanging hierarchies. In intact worms, cerebral ocular response can override the reflex-like extraocular response. However, injury-regeneration again offers a time window wherein both responses coexist, but the dominance of the ocular response is reversed. Overall, we demonstrate acute light intensity-based behavioral switching and two evolutionarily distinct but interacting light sensing networks in a regenerating organism.

}, issn = {2375-2548}, doi = {10.1126/sciadv.1603025}, author = {Shettigar, Nishan and Joshi, Asawari and Dalmeida, Rimple and Gopalkrishna, Rohini and Chakravarthy, Anirudh and Patnaik, Siddharth and Mathew, Manoj and Palakodeti, Dasaradhi and Gulyani, Akash} } @article {1199, title = {The miR-124 family of microRNAs is crucial for regeneration of the brain and visual system in the planarian Schmidtea mediterranea}, journal = {Development}, volume = {144}, year = {2017}, pages = {3211{\textendash}3223}, abstract = {

Brain regeneration in planarians is mediated by precise spatiotemporal control of gene expression and is crucial for multiple aspects of neurogenesis. However, the mechanisms underpinning the gene regulation essential for brain regeneration are largely unknown. Here, we investigated the role of the miR-124 family of microRNAs in planarian brain regeneration. The miR-124 family (miR-124) is highly conserved in animals and regulates neurogenesis by facilitating neural differentiation, yet its role in neural wiring and brain organization is not known. We developed a novel method for delivering anti-miRs using liposomes for the functional knockdown of microRNAs. Smed-miR-124 knockdown revealed a key role for these microRNAs in neuronal organization during planarian brain regeneration. Our results also demonstrated an essential role for miR-124 in the generation of eye progenitors. Additionally, miR-124 regulates Smed-slit-1, which encodes an axon guidance protein, either by targeting slit-1 mRNA or, potentially, by modulating the canonical Notch pathway. Together, our results reveal a role for miR-124 in regulating the regeneration of a functional brain and visual system.

}, issn = {0950-1991}, doi = {10.1242/dev.144758}, url = {http://dev.biologists.org/content/144/18/3211}, author = {Sasidharan, Vidyanand and Marepally, Srujan and Elliott, Sarah A. and Baid, Srishti and Lakshmanan, Vairavan and Nayyar, Nishtha and Bansal, Dhiru and S{\'a}nchez Alvarado, Alejandro and Vemula, Praveen Kumar and Palakodeti, Dasaradhi} } @article {1159, title = {Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region.}, journal = {Proc Natl Acad Sci U S A}, volume = {114}, year = {2017}, month = {2017 10 17}, pages = {11115-11120}, abstract = {

Point mutations in genes encoding sarcomeric proteins are the leading cause of inherited primary cardiomyopathies. Among them are mutations in the gene that encodes cardiac troponin T (TnT). These mutations are clustered in the tropomyosin (Tm) binding region of TnT, TNT1 (residues 80-180). To understand the mechanistic changes caused by pathogenic mutations in the TNT1 region, six hypertrophic cardiomyopathy (HCM) and two dilated cardiomyopathy (DCM) mutants were studied by biochemical approaches. Binding assays in the absence and presence of actin revealed changes in the affinity of some, but not all, TnT mutants for Tm relative to WT TnT. HCM mutants were hypersensitive and DCM mutants were hyposensitive to Ca in regulated actomyosin ATPase activities. To gain better insight into the disease mechanism, we modeled the structure of TNT1 and its interactions with Tm. The stability predictions made by the model correlated well with the affinity changes observed in vitro of TnT mutants for Tm. The changes in Ca sensitivity showed a strong correlation with the changes in binding affinity. We suggest the primary reason by which these mutations between residues 92 and 144 cause cardiomyopathy is by changing the affinity of TnT for Tm within the TNT1 region.

}, issn = {1091-6490}, doi = {10.1073/pnas.1710354114}, author = {Gangadharan, Binnu and Sunitha, Margaret S and Mukherjee, Souhrid and Chowdhury, Ritu Roy and Haque, Farah and Sekar, Narendrakumar and Sowdhamini, Ramanathan and Spudich, James A and Mercer, John A} } @article {1165, title = {Morphology transition in helical tubules of a supramolecular gel driven by metal ions.}, journal = {Chem Commun (Camb)}, volume = {53}, year = {2017}, month = {2017 Jan 26}, pages = {1538-1541}, abstract = {

Our aim to access a particular chemical functionality on helical tubules has been achieved by the rational molecular design and synthesis of glucono-appended cardanol derivatives. For the first time, we report a chiral molecular packing with α-helical tubules, and chiral symmetry-breaking upon exposure to Cu that generated the final ordered structure via an in situ morphological transition without undergoing any phase change.

}, issn = {1364-548X}, doi = {10.1039/c6cc09120b}, author = {Lalitha, Krishnamoorthy and Sridharan, Vellaisamy and Maheswari, C Uma and Vemula, Praveen Kumar and Nagarajan, Subbiah} } @article {1201, title = {Scaling the effect of hydrophobic chain length on gene transfer properties of di-alkyl{,} di-hydroxy ethylammonium chloride based cationic amphiphiles}, journal = {RSC Adv.}, volume = {7}, year = {2017}, pages = {25398-25405}, abstract = {

The success of gene therapy critically depends on the availability of efficient transfection vectors. Cationic lipids are the most widely studied non-viral vectors. The molecular architecture of the cationic lipid determines its transfection efficiency. Variations in alkyl chain lengths of lipids influence self-assembly and liposomal fusion with the cell membrane. These factors determine the transfection ability of the lipid. Thus{,} to probe the effect of asymmetry in hydrophobic chains on transfection efficiency{,} we designed and synthesized a series of cationic lipids by systematically varying one of the two alkyl chains linked to the quaternary nitrogen centre from C18 to C10 and keeping the other alkyl C18 chain constant (Lip1818-Lip1810). Transfection studies in multiple cultured mammalian cells (CHO{,} B16F10 and HeLa) revealed that the lipids with C18:C14 and C18:C12 alkyl chains (Lip1814 \& Lip1812) showed 20-30\% higher transfection efficacies than their counterparts at 2 : 1 and 4 : 1 lipid to pDNA charge ratios. Cryo-transmission electron images showed unilamellar vesicle structures for the liposomes of lipids. Mechanistic studies involving Small Angle X-ray Scattering (SAXS) revealed that asymmetry in the hydrophobic region has a significant impact on liposomal fusion with the plasma membrane model. Collectively{,} these findings demonstrate that chain length asymmetry in the hydrophobic region of cationic lipids has an important role in their liposome-DNA interactions at optimal 2 : 1 and 4 : 1 lipid to pDNA charge ratios{,} which in turn modulates their gene transfer properties.

}, doi = {10.1039/C7RA02271A}, url = {http://dx.doi.org/10.1039/C7RA02271A}, author = {Hiwale, Ankita A. and Voshavar, Chandrashekhar and Dharmalingam, Priya and Dhayani, Ashish and Mukthavaram, Rajesh and Nadella, Rasajna and Sunnapu, Omprakash and Gandhi, Sivaraman and Naidu, V. G. M. and Chaudhuri, Arabinda and Marepally, Srujan and Vemula, Praveen Kumar} } @article {1156, title = {Stimulation of hair follicle stem cell proliferation through an IL-1 dependent activation of γδT-cells.}, journal = {Elife}, volume = {6}, year = {2017}, month = {2017 Dec 04}, abstract = {

The cutaneous wound-healing program is a product of a complex interplay among diverse cell types within the skin. One fundamental process that is mediated by these reciprocal interactions is the mobilization of local stem cell pools to promote tissue regeneration and repair. Using the ablation of epidermal caspase-8 as a model of wound healing in , we analyzed the signaling components responsible for epithelial stem cell proliferation. We found that IL-1α and IL-7 secreted from keratinocytes work in tandem to expand the activated population of resident epidermal γδT-cells. A downstream effect of activated γδT-cells is the preferential proliferation of hair follicle stem cells. By contrast, IL-1α-dependent stimulation of dermal fibroblasts optimally stimulates epidermal stem cell proliferation. These findings provide new mechanistic insights into the regulation and function of epidermal cell-immune cell interactions and into how components that are classically associated with inflammation can differentially influence distinct stem cell niches within a tissue.

}, issn = {2050-084X}, doi = {10.7554/eLife.28875}, author = {Lee, Pedro and Gund, Rupali and Dutta, Abhik and Pincha, Neha and Rana, Isha and Ghosh, Subhasri and Witherden, Deborah and Kandyba, Eve and MacLeod, Amanda and Kobielak, Krzysztof and Havran, Wendy L and Jamora, Colin} } @article {1200, title = {Targeted delivery of microbial metabolite, urolithin A protects from chemically (DSS or TNBS) induced colitis in pre-clinical models}, journal = {The Journal of Immunology}, volume = {198}, year = {2017}, pages = {65.6{\textendash}65.6}, abstract = {

Epidemiological data suggests that consumption of diets rich in phytochemicals are protective in inflammatory bowel diseases (IBDs). However, the beneficial effects are not uniform among individuals and attributed to variations in gut microbiota, and altered capacity to generate certain metabolites. Urolithin A (UroA) (3,8-dihydroxybenzo[c]chromen-6-one) is a microbial metabolite, derived from ellagic acid and ellagitannins, major poly phenolic components in berries and pomegranates. Here, we examined therapeutic applications of UroA and mechanisms of action in IBDs. Our studies suggested that UroA significantly reduced LPS induced inflammatory mediators (e.g., IL-6, TNF-alpha and IL-12) as well as ROS production in mouse bone marrow-derived macrophages (BMDMs), dendritic and THP1 cells. Most importantly, UroA also reduced LPS induced systemic inflammation in mouse models. Next, we examined therapeutic applications of UroA in dextran sodium sulphate (DSS)-induced, 2,4,6-Trinitrobenzenesulfonic acid (TNBS)-induced colitis models. Treatment with UroA significantly reduced both acute and chronic DSS-induced colitis as well as TNBS induced colitis in mouse models. Most importantly, delivery of UroA utilizing inflammation targeting oral nano-particles (single treatment regimen) effectively mitigated the colitis in both models. In summary, these results highlight even presence of single microbial metabolite at right location at right time will have significant beneficial effects to protect from adverse inflammatory activities.

}, issn = {0022-1767}, url = {http://www.jimmunol.org/content/198/1_Supplement/65.6}, author = {Singh, Rajbir and Hegde, Bindu and Von Baby, Becca and Sadeep, C and Kotla, Niranjan and Chandrasekar, Bhargavi and Marepally, Srujan and Bodduluri, Haribabu and Vemula, Praveen K and Jala, Venkatakrishna R} } @article {1169, title = {In Situ Synthesis of Metal Nanoparticle Embedded Hybrid Soft Nanomaterials.}, journal = {Acc Chem Res}, volume = {49}, year = {2016}, month = {2016 Sep 20}, pages = {1671-80}, abstract = {

The allure of integrating the tunable properties of soft nanomaterials with the unique optical and electronic properties of metal nanoparticles has led to the development of organic-inorganic hybrid nanomaterials. A promising method for the synthesis of such organic-inorganic hybrid nanomaterials is afforded by the in situ generation of metal nanoparticles within a host organic template. Due to their tunable surface morphology and porosity, soft organic materials such as gels, liquid crystals, and polymers that are derived from various synthetic or natural compounds can act as templates for the synthesis of metal nanoparticles of different shapes and sizes. This method provides stabilization to the metal nanoparticles by the organic soft material and advantageously precludes the use of external reducing or capping agents in many instances. In this Account, we exemplify the green chemistry approach for synthesizing these materials, both in the choice of gelators as soft material frameworks and in the reduction mechanisms that generate the metal nanoparticles. Established herein is the core design principle centered on conceiving multifaceted amphiphilic soft materials that possess the ability to self-assemble and reduce metal ions into nanoparticles. Furthermore, these soft materials stabilize the in situ generated metal nanoparticles and retain their self-assembly ability to generate metal nanoparticle embedded homogeneous organic-inorganic hybrid materials. We discuss a remarkable example of vegetable-based drying oils as host templates for metal ions, resulting in the synthesis of novel hybrid nanomaterials. The synthesis of metal nanoparticles via polymers and self-assembled materials fabricated via cardanol (a bioorganic monomer derived from cashew nut shell liquid) are also explored in this Account. The organic-inorganic hybrid structures were characterized by several techniques such as UV-visible spectroscopy, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Utilization of silver nanoparticle-based hybrid nanomaterials as an antimicrobial material is another illustration of the advantage of hybrid nanomaterials. We envision that the results summarized in this Account will help the scientific community to design and develop diverse organic-inorganic hybrid materials using environmentally benign methods and that these materials will yield advanced properties that have multifaceted applications in various research fields.

}, issn = {1520-4898}, doi = {10.1021/acs.accounts.6b00201}, author = {Divya, Kizhmuri P and Miroshnikov, Mikhail and Dutta, Debjit and Vemula, Praveen Kumar and Ajayan, Pulickel M and John, George} } @article {615, title = {Notch1 regulated autophagy controls survival and suppressor activity of activated murine T-regulatory cells.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Cell survival is one of several processes regulated by the Notch pathway in mammalian cells. Here we report functional outcomes of non-nuclear Notch signaling to activate autophagy, a conserved cellular response to nutrient stress, regulating survival in murine natural T-regulatory cells (Tregs), an immune subset controlling tolerance and inflammation. Induction of autophagy required ligand-dependent, Notch intracellular domain (NIC) activity, which controlled mitochondrial organization and survival of activated Tregs. Consistently, NIC immune-precipitated Beclin and Atg14, constituents of the autophagy initiation complex. Further, ectopic expression of an effector of autophagy (Atg3) or recombinant NIC tagged to a nuclear export signal (NIC-NES), restored autophagy and suppressor function in Notch1(-/-) Tregs. Furthermore, Notch1 deficiency in the Treg lineage resulted in immune hyperactivity, implicating Notch activity in Treg homeostasis. Notch1 integration with autophagy, revealed in these experiments, holds implications for Notch regulated cell-fate decisions governing differentiation.

}, issn = {2050-084X}, doi = {10.7554/eLife.14023}, author = {Marcel, Nimi and Sarin, Apurva} } @article {1168, title = {Sterile Inflammation Enhances ECM Degradation in Integrin β1 KO Embryonic Skin.}, journal = {Cell Rep}, volume = {16}, year = {2016}, month = {2016 09 20}, pages = {3334-3347}, abstract = {

Epidermal knockout of integrin β1 results in complete disorganization of the basement membrane (BM), resulting in neonatal lethality. Here, we report that this disorganization is exacerbated by an early\ embryonic inflammatory response involving the recruitment of tissue-resident and monocyte-derived macrophages to the dermal-epidermal junction, associated with increased matrix metalloproteinase activity. Remarkably, the skin barrier in the integrin β1 knockout animals is intact, suggesting that this inflammatory response is initiated in a sterile environment. We demonstrate that the molecular mechanism involves de novo expression of integrin αvβ6 in the basal epidermal cells, which activates a TGF-β1 driven inflammatory cascade resulting in upregulation of dermal NF-κB in a Tenascin C-dependent manner. Importantly, treatment of β1 KO embryos in utero with small molecule inhibitors of TGF-βR1 and NF-κB results in marked rescue of the BM defects and amelioration of immune response, revealing an unconventional immuno-protective role for integrin β1 during BM remodeling.

}, keywords = {Animals, Extracellular Matrix, Inflammation, Integrin beta1, Macrophages, Mice, Mice, Knockout, Signal Transduction, Skin}, issn = {2211-1247}, doi = {10.1016/j.celrep.2016.08.062}, author = {Kurbet, Ambika S and Hegde, Samarth and Bhattacharjee, Oindrila and Marepally, Srujan and Vemula, Praveen K and Raghavan, Srikala} } @article {399, title = {Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies.}, journal = {J Biol Chem}, volume = {290}, year = {2015}, month = {2015 Mar 13}, pages = {7003-15}, abstract = {

The most frequent known causes of primary cardiomyopathies are mutations in the genes encoding sarcomeric proteins. Among those are 30 single-residue mutations in TPM1, the gene encoding α-tropomyosin. We examined seven mutant tropomyosins, E62Q, D84N, I172T, L185R, S215L, D230N, and M281T, that were chosen based on their clinical severity and locations along the molecule. The goal of our study was to determine how the biochemical characteristics of each of these mutant proteins are altered, which in turn could provide a structural rationale for treatment of the cardiomyopathies they produce. Measurements of Ca(2+) sensitivity of human β-cardiac myosin ATPase activity are consistent with the hypothesis that hypertrophic cardiomyopathies are hypersensitive to Ca(2+) activation, and dilated cardiomyopathies are hyposensitive. We also report correlations between ATPase activity at maximum Ca(2+) concentrations and conformational changes in TnC measured using a fluorescent probe, which provide evidence that different substitutions perturb the structure of the regulatory complex in different ways. Moreover, we observed changes in protein stability and protein-protein interactions in these mutants. Our results suggest multiple mechanistic pathways to hypertrophic and dilated cardiomyopathies. Finally, we examined a computationally designed mutant, E181K, that is hypersensitive, confirming predictions derived from in silico structural analysis.

}, keywords = {Actins, Adenosine Triphosphatases, Calcium, Cardiomyopathies, Humans, Models, Molecular, Myosins, Point Mutation, Protein Stability, Tropomyosin}, issn = {1083-351X}, doi = {10.1074/jbc.M114.596676}, author = {Gupte, Tejas M and Haque, Farah and Gangadharan, Binnu and Sunitha, Margaret S and Mukherjee, Souhrid and Anandhan, Swetha and Rani, Deepa Selvi and Mukundan, Namita and Jambekar, Amruta and Thangaraj, Kumarasamy and Sowdhamini, Ramanathan and Sommese, Ruth F and Nag, Suman and Spudich, James A and Mercer, John A} }