Dynamic allele usage of X-linked genes ameliorates neurodevelopmental disease phenotypes in brain organoids

M M. Bertin (Sorbonne Université, CNSR, MONARIS, UMR8233 2 , F-75005 Paris,) H H. Todorov S S. Frank S S. Käseberg R R. Menon E E. Gabassi C C. Foerster N N. Bobon F F. Furlanetto A A. Soliman H H. M. B. Ibrahim V V. Engelhardt L L. Birschmann H H. Brennenstuhl B B. Lohrer A A. Mas-Sanchez E E. Cesare J J. Winter J J. Krummeich J J. Winkler B B. Winner E E. Weis S S. Diederich K K. Luck P P. Lunt S S. Gerber P P. Baumann N N. Elvassore B B. Berninger M MF Basilicata S S. Schweiger S S. Falk M M. Karow

Abstract

Abstract While random X-chromosome inactivation in female cells of placental mammals silences one allele of the majority of X-chromosomal genes, a considerable fraction is only incompletely and variably inactivated. Human model systems to study the dynamics of incomplete X-inactivation are limited mostly to postmortem tissue, thereby disregarding developmental trajectories. Here, we used clonal human female induced pluripotent stem cells to track allele-specific expression of X-chromosomal genes along neural differentiation. We discovered dynamic reactivation and late-silencing of gene expression from the inactive X-chromosome leading to differentiation-induced locus- and lineage-specific usage of the two X-chromosomal alleles. In brain organoids modeling Opitz BBB/G syndrome, an X-linked neurodevelopmental disorder, reactivation of alleles from the inactive X-chromosome rescued cellular phenotypes and led to intermediate manifestations in female tissue. Taken together, our data demonstrate that alleles on the inactive X-chromosome can serve as a critical reservoir dynamically used during differentiation, thereby enhancing resilience of female neural tissue.

Article Details

Volume / Issue Vol. 17, Issue 1
Published January 14, 2026
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio

ISSN: 2041-1723 Open Access Life Sciences

Authors (33)

M

M. Bertin

Sorbonne Université, CNSR, MONARIS, UMR8233 2 , F-75005 Paris,

H

H. Todorov

S

S. Frank

S

S. Käseberg

R

R. Menon

E

E. Gabassi

C

C. Foerster

N

N. Bobon

F

F. Furlanetto

A

A. Soliman

H

H. M. B. Ibrahim

V

V. Engelhardt

L

L. Birschmann

H

H. Brennenstuhl

B

B. Lohrer

A

A. Mas-Sanchez

E

E. Cesare

J

J. Winter

J

J. Krummeich

J

J. Winkler

B

B. Winner

E

E. Weis

S

S. Diederich

K

K. Luck

P

P. Lunt

S

S. Gerber

P

P. Baumann

N

N. Elvassore

B

B. Berninger

M

MF Basilicata

S

S. Schweiger

S

S. Falk

M

M. Karow