Targeting the inactive X for correcting dosage imbalances in lupus

Women have two X chromosomes, but men only carry one. In women’s cells, one of the X chromosomes typically switches off most of its genes. We hypothesize that many of these genes turn back on in lupus. Because a large number of genes that control the immune system are on the X chromosome, switching them back on could cause the immune system to function abnormally. To test our hypothesis, we will measure whether silenced genes on the X chromosome have turned back on in cells from patients with lupus. We will then measure the effect of this reactivation on the immune system in mice and determine whether we can reverse it in cells from women with lupus.

What this means for people with lupus:

“Women are much more likely to develop lupus than are men, and the difference may be partly due to their chromosomes. Most genes on one chromosome in women normally shut down. We will test the hypothesis that some of these genes switch back on in lupus, disrupting the immune system. The work could reveal new targets for lupus therapies.”

Systemic lupus erythematosus (SLE) is a severe autoimmune disease that affects people of every race, age, and socioeconomic status, with females having the highest risk of disease. The underlying mechanisms responsible for observed sex disparity in SLE are unknown, yet there is strong evidence suggesting that X-chromosomes are involved. The X-chromosome contains the greatest absolute number of immunity-related genes of any chromosome, and some are abnormally over-expressed in SLE patients.

Female mammals have two X-chromosomes, and silence one X in a process called X-Chromosome Inactivation (XCI). XCI is initiated by expression of the long noncoding RNA Xist during embryogenesis, and transcriptional silencing on the inactive X (Xi) is maintained into adulthood by enrichment of Xist RNA and heterochromatic modifications on this chromosome. Unlike other somatic cells, we found that female lymphocytes exhibit a novel form of XCI in which Xist RNA is dynamically localized to the Xi. Specifically, our published and unpublished work shows that naïve mature T cells lack Xist clouds on their Xi, resulting in euchromatic features and loss of heterochromatic marks. However, upon stimulation, Xist RNA returns to the Xi of mature T cells and heterochromatic marks are established. This lymphocyte-specific dynamic mechanism of XCI maintenance predisposes genes for reactivation from the Xi, because deletion of either Xist RNA recruitment proteins ex vivo or Xist in vivo prevents Xist RNA localization to the Xi, impairs heterochromatin enrichment on the Xi, and increases X-linked gene expression. This proposal will test the hypothesis that Xist RNA localization to Xi is required for transcriptional repression in activated T cells, and that partial X-reactivation is a feature of female-biased SLE, responsible for increased expression of X-linked immunity genes. We will also investigate whether aberrant XIST RNA localization in SLE patient T cells can be corrected to restore X-linked gene expression levels. We believe that our hypothesis can be tested within the three-year period of this study, and that subsequent work investigating the therapeutic feasibility using female-biased mouse models can be conducted after this time period. This proposal takes a novel approach to understand the female-bias of autoimmunity centered on XCI, and will reveal a new therapeutic target for SLE that corrects gene dosage imbalances.