Altered X-chromosome inactivation in T cells may promote sex-biased autoimmune diseases
Authors: Donavon Sandoval-Heglund
Camille M Syrett
Montserrat C Anguera
Jianle Wang
Michael Atchison
Sarmistha Banerjee
Bam Paneru
Edward M Behrens
Vishal Sindhava
Journal: JCI Insight (2019)
Discipline: CLINICAL MEDICINE
Keywords: Autoimmunity; Cell Biology; Epigenetics; Noncoding RNAs; T cell development.
Affiliations: Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA., Division of Rheumatology, Children's Hospital of Philadelphia (CHOP), Philadelphia Pennsylvania, USA.

Abstract:  Systemic lupus erythematosus (SLE) is an autoimmune disorder that predominantly affects women and is driven by autoreactive T cell-mediated inflammation. It is known that individuals with multiple X-chromosomes are at increased risk for developing SLE; however, the mechanisms underlying this genetic basis are unclear. Here, we use single cell imaging to determine the epigenetic features of the inactive X (Xi) in developing thymocytes, mature T cell subsets, and T cells from SLE patients and mice. We show that Xist RNA and heterochromatin modifications transiently reappear at the Xi and are missing in mature single positive T cells. Activation of mature T cells restores Xist RNA and heterochromatin marks simultaneously back to the Xi. Notably, X-chromosome inactivation (XCI) maintenance is altered in T cells of SLE patients and late-stage-disease NZB/W F1 female mice, and we show that X-linked genes are abnormally upregulated in SLE patient T cells. SLE T cells also have altered expression of XIST RNA interactome genes, accounting for perturbations of Xi epigenetic features. Thus, abnormal XCI maintenance is a feature of SLE disease, and we propose that Xist RNA localization at the Xi could be an important factor for maintaining dosage compensation of X-linked genes in T cells. 

Retracted: No

PubPeer comments:
 Dear authors, We have with great interest and excitement discussed your paper u201cAltered X-chromosome inactivation in T cells may promote sex-biased autoimmune diseasesu201d during our weekly literature meeting. We appreciate your development of the hypothesis explaining the genetic basis of the sex-biased differences in immunity. We hope that your results might help tailor therapies which would decrease the risk of developing autoimmune diseases in female patients. We look forward to receiving more news from your studies. However, after reading your paper, we were left wondering about a few things that we think would be interesting to see explored or commented on, either here, or in future publications: 1. Could the localization patterns of Xist RNA in lymphocytes during development relate to the nuclear rearrangements of developing lymphocytes? These cells must relatively quickly change gene expression patterns, which will affect the local state of chromatin. Is it possible that chromatin rearrangements would affect the detection threshold of FISH? 2. Have you tested the X chromosome inactivation with any other technique than FISH? For example, have you measured methylation or other epigenetic modifications responsible for X chromosome inactivation and correlated it with your Xist RNA localization patterns? 3. In our opinion, your hypothesis would gain a lot of support if you could show a correlation between the expression of genes from the leaking X chromosome and the changes in the Xist RNA localization patterns. For example, if the TLR7 (or other immune-related genes present on the X chromosome) mRNA expression fluctuates following the decrease in the Xist RNA signal (on different stages of thymocyte development or in nau00efve vs activated T cells), it would support the notion for autoimmune tendency in a female immune system. Especially, if similar mRNA expression fluctuations would not occur in male T cells. 4. Throughout the paper, it seems that the cell-to-cell variation is quite high. Do you think this could be explained by a technical or biological phenomena? Were the biological replicates from the same litter? Why do nau00efve T cells in fig. 2 lack any inactivation of X chromosome, while in fig. 3 and 4 the phenomenon is not that striking? Did you check the purity of T cells following T cell enrichment? 5. In fig. 6 you are comparing the T cells from healthy donors with the T cells from SLE patients. As SLE might promote an exhausted phenotype of the T cells, have you considered comparing your samples to the T cells of patients suffering from other chronic inflammatory conditions, which is not sex-biased? 6. In fig. 7 and 8 you are investigating gene transcripts in T cells from SLE patients. However, it would be equally interesting to see how these transcripts are changing during murine thymocyte development or between nau00efve and activated T cells. Also, have you considered comparing your transcript expression results from the X chromosome to that of other inactivated genes found on other chromosomes? We would greatly appreciate it if you could share your thoughts on our comments above, as this may aid us (and other readers) in better understanding your work and thus help us all contribute to a fruitful scientific discussion. ,