Single-cell RNA-seq analysis of the T-cell lymphoproliferative and inflammatory disorders triggered by defective LAT signalosome

LatY136F mice in which tyrosine 136 of the LAT adaptor is mutated accumulate CD4+ T cells that trigger a fast-onset autoimmune and inflammatory condition called LAT signaling pathology (LSP). Its histopathological manifestations resemble those of human IgG4-related disease (IgG4-RD), an inflammatory condition unifying a constellation of clinical entities leading to multi-organ damage. Using single-cell RNA sequencing, we analyzed 5,030 CD4+ T cells isolated from the spleen of LatY136F mice over the period that leads to LSP installation. It charted the trajectory leading to full-fledged LSP and demonstrated that LSP involved T follicular helper (Tfh) cells, CD4+ cytotoxic T cells, and IgG1+ plasma cells. These cell types were also identified in the massive infiltrates found in LatY136F lung. Therefore, the LatY136F LSP entails all the cell types postulated to trigger human IgG4-RD. It offers the unique possibility to disentangle their pathological cross-talk as illustrated here using B cell-deficient LatY136F mice. Overall design: 53448 T cells were isolated from 44 spleen from 44 C57BL/6Rj mice and processed using the Chromium Single Cell 3' kit from 10X genomics (California, USA) for the library preparation and the Illumina HiSeq4000 . FASTQ raw files were processed using Cell Ranger software (v3.0.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.