Poster Presentation 47th Lorne Genome Conference 2026

Investigating the mechanism and function of unstable X chromosome inactivation in female-biased autoimmune disorders (133745)

Alice Steel 1 , Daisy Kavanagh 1 2 , Christopher Jara 1 3 , Karina Pazaky 1 , Etienne Masle-Farquhar 1 3 , Ksenia Skvortsova 1 2
  1. The Garvan Institute of Medical Research, Waverly, NEW SOUTH WALES, Australia
  2. School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, Australia
  3. St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, Australia

Autoimmune diseases, including systemic lupus erythematosus (SLE), present a strong gender bias with 80% of patients being women. The second X chromosome in XX females is normally silenced by an epigenetic process, X chromosome inactivation (XCI). However, recent studies revealed that lncRNA XIST, a master-regulator of XCI, transiently dissociates from the epigenetically silenced X (Xi) during normal development of immune cells [1], implying the possibility of partial X-reactivation in females.

This suggests that increased X chromosome dosage could contribute to autoimmune disease susceptibility, however this phenomenon lacks mechanistic and functional evidence. We aim to determine if X-chromosome reactivation is enriched in autoreactive-B-cells and if it's required for normal female B-cell development.

To address this, we performed allele-specific long-read single-cell transcriptional profiling coupled with whole-genome sequencing and B-cell-receptor sequencing of B-lymphocytes isolated from bone marrow and peripheral blood of healthy controls and patients with SLE.

We found that the largest increase in reactivated Xi-genes during B-lymphocyte development occurred in pro and pre-B cells. This aligns with reported XIST dissociation at these developmental stages, which are characterised by VDJ-recombination, integral to antigen recognition. For example, CD99, involved in immune cell adhesion and migration, was expressed from the Xi in 99% of cells at the pro-B stage. In peripheral blood naïve and memory B-cells, we observed significantly increased Xi-reactivation in SLE patients versus healthy controls.

For the first time, allele-specific long-read profiling has quantitatively resolved Xi-reactivation at gene and developmental-stage by identifying expression directly from the Xi. Establishing Xi-reactivation as a regulated feature of immune cell development provides a framework to mechanistically explore X-dosage effects. We plan to further investigate the mechanism of Xi-reactivation using CRISPR screens in cell lines, and to determine the importance of reactivated genes in SLE using CRISPR activation in a mouse model.

  1. 1. Syrett, C.M., et al., Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells. PLoS genetics, 2017. 13(10): p. e1007050.