"Lnc"ing XIST Ribonucleoprotein Particles to Female Sex-Attributed Biases in Autoimmunity

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Project Summary / Abstract Autoimmune diseases (AD) are the third most prevalent disease in America, disproportionately impacting females 4x more than males. Despite the high prevalence and cost to society, there are few effective treatments and no definitive cure because the genetic factors and environmental triggers for autoimmunity remain poorly defined. Existing studies implicating hormonal differences to explain the sex differences in autoimmunity and immune response fail to reconcile the increased susceptibility to autoimmune diseases in Kleinfelter males, who have two X chromosomes (XXY) like females (XX) and unlike most males (XY). In XX individuals, the long noncoding RNA (lncRNA), XIST (Xist in mice), is required for silencing one of the X’s to achieve gene dosage compensation. This project aims to elucidate the XX-linked preponderance for autoimmune disease development through studying the female-specific lncRNA, XIST, and the proteins associating with XIST in the XIST ribonucleoprotein complex (RNP) as a potential immune complex trigger for autoimmunity. In this proposal, Dr. Dou proposes to test the novel hypothesis that Xist RNPs increase autoimmune risk using three multi-level aims: (1) In vitro, through controlled stimulation of immune cells with Xist RNPs, (2) In vivo, through autoimmune disease modeling in a transgenic Xist mouse wherein male mice viably express Xist RNPs, (3) diagnostically, using autoimmune disease patient serum to test reactivity against XIST RNP proteins. Completion of the project will build a comprehensive model of the pathways, genes, and specific immune cell types involved using powerful and high-resolution single-cell sequencing (Aims 1 and 2), disease models in mice (Aim 2), rigorous and specific clustered regularly interspaced short palindromic repeats (CRISPR) gene perturbation experiments (Aim 1), and a sensitive protein antigen array (Aim 3). This work will be performed in a world-class environment at Stanford University under the supervision of Dr. Howard Y. Chang, a lncRNA authority who excels at developing and applying sequencing techniques to study diseases, with co-mentorship from Dr. PJ Utz, a clinically trained rheumatologist with particular expertise in autoantibodies and autoimmune disease mouse models. An advisory committee and consisting of experts in single sequencing in immune cells (Dr. Satpathy), high throughput CRISPR screens (Dr. Bassik), proteomics (Dr. Lundberg) and autoimmunity (Dr. Fiorentino) will provide additional mentorship to Dr. Dou and the resources necessary to achieve her project goals. Completing the project and associated training plan will allow Dr. Dou to meet key milestones in her transition to independent investigator. The 3 Aims are designed for parallel investigations. The first half of each aim will be completed during the mentored K99 phase to provide the platform for the R00 independent phase. This project will be the springboard for Dr. Dou to launch an independent career and achieve her long-term goal of resolving the genetic and epigenetic factors underlying autoimmune diseases.