Antigen hotspots reveal novel autoantibodies against XIST ribonucleoproteins in sex-biased autoimmune disease

Summary: Abstract Body: Four out of five patients with autoimmune diseases are women. The XIST ribonucleoprotein complex, comprising the female-specific XIST long noncoding RNA and more than 100 XIST-associated proteins, plays a crucial role in several autoimmune diseases that disproportionately affect women, who have elevated levels of anti-XIST RNP antibodies (AXA). However, the structural and clinical significance of AXA subtypes, as well as potential impact on disease phenotype, have remained unexplored. Here, by analyzing a publicly available database of human autoantigens, we find that AXA targets are enriched among autoantigens associated with female-biased autoimmune conditions. In addition, by mapping AXA targets to known protein binding sites within the XIST sequence, we find that AXA targets are concentrated at discrete “hotspots” along the length of XIST, notably the A-repeat. Cell-specific protein expression data nominated neutrophils as a predominant source of XIST "hotspot"-associated proteins, and we confirmed the presence of both XIST and “hotspot”-associated proteins in neutrophil extracellular traps during NETosis, an immunogenic programmed cell death pathway triggered by neutrophil activation upon which neutrophils extrude their nuclear content. Furthermore, we found that levels of autoantibodies against SPEN, a key XIST-associated protein that binds to the A-repeat, correlate with severe digital ischemia in systemic sclerosis in two independent cohorts at two centers. Together, these data show a plausible mechanism for the origin of AXA, guided by RNA structure and RNA-protein interactions, and show that AXA holds promise for disease endotyping and prognostication in female-biased autoimmune conditions. Jinwoo Lee¹, Bingyu Yan¹, Suhas Srinivasan¹, Quanming Shi¹, Diana Dou¹, Srijana Davuluri², Swarna Nandyala¹, Adrianne Woods³, Gwendolyn Leatherman³, Yanding Zhao¹, Roman Reggiardo¹, Manasi Sawant⁴, Hawa Thiam⁴, Ami Shah³, David Fiorentino¹, Lorinda Chung², Howard Chang¹ 1. Dermatology, Stanford University, Stanford, CA, United States. 2. Medicine, Stanford University, Stanford, CA, United States. 3. Scleroderma Center, Johns Hopkins Medicine, Baltimore, MD, United States. 4. Bioengineering, Stanford University, Stanford, CA, United States. Adaptive and Auto-Immunity