Lineage-specific X chromosome inactivation escape and skew underlie sex-biased immune gene dosage and deleterious variant exposure
- 1Garvan Institute of Medical Research, Sydney, Australia; School of Biotechnology and Biomedical Sciences, UNSW, Sydney, Australia
Abstract
The X chromosome carries an unusually high density of immune genes and is a major contributor to sex differences in immune function and autoimmune diseases. In females, X-chromosome inactivation (XCI) has two major functional consequences: it shapes X-linked gene dosage through XCI escape and determines the cellular exposure of heterozygous X-linked variants through XCI skew. Yet because XCI creates a mosaic of cells expressing different parental X chromosomes, these properties have remained largely inaccessible in individual women, becoming measurable only where XCI is non-random or after aggregation across large cohorts. Consequently, how X-linked variation contributes to sex-biased immunity and differs between individual women has remained unresolved. Here we present scDaisyChain, a graph-based framework that reconstructs chromosome-scale X haplotypes directly from heterozygous SNPs and single-cell long-read transcriptomes. scDaisyChain achieves near-ground-truth accuracy in highly polymorphic mouse hybrids and shows strong concordance with orthogonal long-read whole-genome phasing in human samples. Applied to peripheral blood immune cells from healthy women, it reveals a lineage-specific escape program in which lymphoid cells escape XCI more broadly than monocytes, with corresponding gains in the inactive X chromatin accessibility and female-biased expression. Lineage-specific skew further alters the proportion of cells expressing each heterozygous X-linked variant, a property we term variant exposure. Predicted deleterious variants are preferentially found in low-exposure states, exemplified by a splice-altering TLR8 variant expressed in few cytotoxic T cells. In rheumatoid arthritis (RA), the monocyte compartment - which has the lowest escape in health - shows reproducible inactive X dysregulation converging on a trained-immunity programme linked to disease flare and synovial macrophage activation, with elevated escape of IL13RA1 and HDAC8. These findings establish lineage-specific escape, skew and variant exposure as quantifiable, patient-resolved determinants of sex-biased immune gene dosage and X-linked variant penetrance in health and autoimmune disease, resolving a dimension of female biology that has been previously inaccessible in individual donors.
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BibTeX
@misc{kavanagh2026lineagespecific,
title = {{Lineage-specific X chromosome inactivation escape and skew underlie sex-biased immune gene dosage and deleterious variant exposure}},
author = {D. Kavanagh and A. Steel and H. E. King and H. G. S. Vieira and K. R. Kumar and E. Masle-Farquhar and C. King and K. Skvortsova and R. J. Weatheritt},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.26.739472},
url = {https://www.biorxiv.org/content/10.64898/2026.08.26.739472v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Lineage-specific X chromosome inactivation escape and skew underlie sex-biased immune gene dosage and deleterious variant exposure
AU - D. Kavanagh
AU - A. Steel
AU - H. E. King
AU - H. G. S. Vieira
AU - K. R. Kumar
AU - E. Masle-Farquhar
AU - C. King
AU - K. Skvortsova
AU - R. J. Weatheritt
PY - 2026
DA - 2026/08/26
PB - bioRxiv
DO - 10.64898/2026.08.26.739472
UR - https://www.biorxiv.org/content/10.64898/2026.08.26.739472v1
AB - The X chromosome carries an unusually high density of immune genes and is a major contributor to sex differences in immune function and autoimmune diseases. In females, X-chromosome inactivation (XCI) has two major functional consequences: it shapes X-linked gene dosage through XCI escape and determines the cellular exposure of heterozygous X-linked variants through XCI skew. Yet because XCI creates a mosaic of cells expressing different parental X chromosomes, these properties have remained largely inaccessible in individual women, becoming measurable only where XCI is non-random or after aggregation across large cohorts. Consequently, how X-linked variation contributes to sex-biased immunity and differs between individual women has remained unresolved. Here we present scDaisyChain, a graph-based framework that reconstructs chromosome-scale X haplotypes directly from heterozygous SNPs and single-cell long-read transcriptomes. scDaisyChain achieves near-ground-truth accuracy in highly polymorphic mouse hybrids and shows strong concordance with orthogonal long-read whole-genome phasing in human samples. Applied to peripheral blood immune cells from healthy women, it reveals a lineage-specific escape program in which lymphoid cells escape XCI more broadly than monocytes, with corresponding gains in the inactive X chromatin accessibility and female-biased expression. Lineage-specific skew further alters the proportion of cells expressing each heterozygous X-linked variant, a property we term variant exposure. Predicted deleterious variants are preferentially found in low-exposure states, exemplified by a splice-altering TLR8 variant expressed in few cytotoxic T cells. In rheumatoid arthritis (RA), the monocyte compartment - which has the lowest escape in health - shows reproducible inactive X dysregulation converging on a trained-immunity programme linked to disease flare and synovial macrophage activation, with elevated escape of IL13RA1 and HDAC8. These findings establish lineage-specific escape, skew and variant exposure as quantifiable, patient-resolved determinants of sex-biased immune gene dosage and X-linked variant penetrance in health and autoimmune disease, resolving a dimension of female biology that has been previously inaccessible in individual donors.
ER -