Department of Biotechnology
inStem (Institute for Stem Cell Science and Regenerative Medicine)

Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression.

Publication Type

Journal Article

Date of Publication

March 6, 2024

Journal

Molecular therapy : the journal of the American Society of Gene Therapy

Volume/Issue

32/3

ISSN

1525-0024

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.

Alternate Journal

Mol Ther

PubMed ID

38273654

PubMed Central ID

PMC10928131

Authors

Vignesh Rajendiran
Nivedhitha Devaraju
Mahdi Haddad
Nithin Sam Ravi
Lokesh Panigrahi
Joshua Paul
Chandrasekar Gopalakrishnan
Stacia Wyman
Keerthiga Ariudainambi
Gokulnath Mahalingam
Yogapriya Periyasami
Kirti Prasad
Anila George
Dhiyaneshwaran Sukumaran
Sandhiya Gopinathan
Aswin Anand Pai
Yukio Nakamura
Poonkuzhali Balasubramanian
Rajasekaran Ramalingam
Saravanabhavan Thangavel
Shaji R Velayudhan
Jacon E Corn
Joel P Mackay
Srujan Marepally
Alok Srivastava
Merlin Crossley
Kumarasamypet M Mohankumar

Keywords

gamma-Globins
Repressor Proteins
Zinc Fingers
Hematopoietic Stem Cells
Humans
Fetal Hemoglobin
Gene Editing