Gurish, M. F. | Search bioRxiv

bioRxiv2019

CUX1 and IκBζ mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts

The role of stromal fibroblasts in chronic inflammation is unfolding. In rheumatoid arthritis (RA), leukocyte-derived cytokines tumor necrosis factor (TNF) and IL-17A work together, activating fibroblasts to become a dominant source of the hallmark cytokine IL-6. However, IL-17A alone has minimal effect on fibroblasts. To identify key mediators of the synergistic response to TNF and IL-17A in human synovial fibroblasts, we performed time series, dose response, and gene silencing transcriptomics experiments. Here we show that in combination with TNF, IL-17A selectively induces a specific set of genes mediated by factors including CUX1 and I{kappa}B{zeta}. In the promoters of CXCL1, CXCL2, and CXCL3, we found a putative CUX1-NF-{kappa}B binding motif not found elsewhere in the genome. CUX1 and NF-{kappa}B p65 mediate transcription of these genes independent of LIFR, STAT3, STAT4, and ELF3. Transcription of NFKBIZ, encoding the atypical I{kappa}B factor I{kappa}B{zeta}, is IL-17A dose-dependent, and I{kappa}B{zeta} only mediates the transcriptional response to TNF and IL-17A, but not to TNF alone. In fibroblasts, IL-17A response depends on CUX1 and I{kappa}B{zeta} to engage the NF-{kappa}B complex to produce chemoattractants for neutrophil and monocyte recruitment.

immunology↗

bioRxiv2017

Reverse Association Of Single Cells To Rheumatoid Arthritis Accounting For Mixed Effects Identifies An Expanded CD27- HLA-DR+ Effector Memory CD4+ T Cell Population

AO_SCPLOWBSTRACTC_SCPLOWHigh dimensional single-cell analyses have dramatically improved the ability to resolve complex mixtures of cells from human disease samples; however, identifying disease-associated cell types or cell states in patient samples remains challenging due to technical and inter-individual variation. Here we present Mixed effects modeling of Associations of Single Cells (MASC), a novel reverse single cell association strategy for testing whether case-control status influences the membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation. Applying MASC to mass cytometry analyses of CD4+ T cells from blood of rheumatoid arthritis (RA) patients and controls revealed a significantly expanded population of CD4+ T cells, identified as CD27- HLA-DR+ effector memory cells, in RA patients (OR = 1.7; p = 1.1 x 10-3). The frequency of CD27- HLA-DR+ cells was similarly elevated in blood samples from a second RA patient cohort, and CD27- HLA-DR+ cell frequency decreased in RA patients who respond to immunosuppressive therapy. Compared to peripheral blood, synovial fluid and synovial tissue samples from RA patients contained [~]5-fold higher frequencies of CD27- HLA-DR+ cells, which comprised [~]10% of synovial CD4+ T cells. We find that CD27- HLA-DR+ cells are abundant producers of IFN-{gamma} and also express perforin and granzyme A at elevated levels. Thus MASC identified the expansion of a unique Th1 skewed effector T cell population with cytotoxic capacity in RA. We propose that MASC is a broadly applicable method to identify disease-associated cell populations in high-dimensional single cell data.\n\nOO_SCPLOWNEC_SCPLOW SO_SCPLOWENTENCEC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWMixed-effects regression of single cells identifies a cytotoxic Th1-like CD4+ T cell subset while accounting for inter-individual and technical variation.

bioinformatics↗