Abstract: Provided herein are methods and compositions for diagnosis and treatment of multiple sclerosis. Compositions and methods are provided, relating to novel peptides involved in autoimmune disease. In the experiments described herein, an unbiased approach was used to screen pathogenic CD4+ T cells from patients with multiple sclerosis (MS), and to determine the antigenic specificity of the T cell receptors (TCR) expressed by these pathogenic cells.

Abstract: Compositions and methods are provided for isolating, manipulating and using for therapeutic and other purposes, mammalian, MHC Class I restricted, antigen-specific regulatory T cells. The regulatory T cells can be characterized as CD8+ cells that specifically suppress the responses of self-reactive and/or pathogenic CD4+ T cells by cytotoxic mechanisms including, without limitation, perform, other components of the perforin/granzyme apoptosis pathway, etc. The regulatory T cells are antigen-specific, but are not activated by the same antigen as the self-reactive and/or pathogenic CD4+ T cells. In humans the regulatory T cells express inhibitory KIR proteins, e.g. one or more of KIR2DL2, KIR2DL3, and KIR3DL1.

Abstract: Provided herein am compositions and methods for characterizing and treating neurodegenerative disease. In particular, provided herein are compositions and methods for measuring T cell markers associated with Alzheimer's disease.

Abstract: Provided are systems and methods that can combine T cell receptor sequencing (TCRseq) and Assay for Transposase Accessible Chromatin using sequencing (ATAC-seq), and/or respective aspects thereof. Further provided are systems and methods that can combine ATAC-seq and perturbation sequencing (Perturb-seq), and/or respective aspects thereof.