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Reciprocal regulation of Th2 and stroma cells remodels mesenteric adipose tissue in type 2 inflammation

ABSTRACT: Reciprocal regulation of Th2 and stroma cells remodels mesenteric adipose tissue in type 2 inflammation

PROVIDER: PRJNA772755 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16490738_1.fastq.gz	Fastqsanger.gz
	SRR16490738_2.fastq.gz	Fastqsanger.gz
	SRR16490739_1.fastq.gz	Fastqsanger.gz
	SRR16490739_2.fastq.gz	Fastqsanger.gz
	SRR16490740_1.fastq.gz	Fastqsanger.gz

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Reciprocal regulation of Th2 and stroma cells remodels mesenteric adipose tissue in type 2 inflammation

Project description:Adipose tissue (AT) contains mesenchymal stromal cells (MSC) in stages of commitment to becoming specialized tissue cells, including adipocytes and fibroblasts, and immune cells which support tissue homeostasis. How MSC and immune cells interact during infection is poorly understood. We show that during intestinal helminth infection MSC in mesenteric AT (mAT) become enriched in non-differentiated progenitor cells. This is accompanied by MSC-intrinsic metabolic reprogramming supporting increased secretion of extracellular matrix (ECM), IL-33, and TSLP. In parallel, Th2 resident memory (Th2RM) cells populate the mAT and persist after infection is resolved. These cells express Areg, TGFβ and IL-5, and are necessary to promote infection induced changes within mAT, including MSC reprogramming and tissue eosinophilia. In turn, IL-33 and TSLP from MSC facilitate Th2RM activation and maintenance. Our findings link Th2RM cells to mAT remodeling during intestinal infection, underscoring the reciprocal dependence of stroma and resident immune cells for lasting tissue immunity.

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Project description:Total RNAof pTh17 cells from wild type (WT) and RASA3 KO (RASA3KO) mouse (C57BL/6) was extracted and RNA-seq libraries were generated. Reads (32-45 Million reads per sample) were analyzed with Salmon software to align and quantify the transcript expression. R packages in Bioconductor, tximport and tximportData were used to aggregate transcript-level quantifications to the gene level, with the R package biomaRt for gene and transcripts mapping. The option "lengthScaledTPM" for countsFromAbundance in tximport was used to obtain the estimated counts at the gene level using abundance estimates scaled based on the average transcript length over samples and the library size. R function voom in limma package was used to transform the estimated count data into log2 scale and estimate the mean-variance relationship so that it can be used to compute appropriate observation level weights, followed by linear modelling. For gene-level differential expression analysis, a linear model was fitted to the log scaled expression data with the genotypes (knockout and wild-type) as one covariate using empirical Bayes moderated t-statistics. The false discovery rate (FDR) was controlled using the Benjamini and Hochberg algorithm. Probes with FDR < 0.05 and fold-change > 2 were judged to be differentially expressed. 317 and 35 genes were identified to be significantly up- and down-regulated respectively. The R function CAMERA was used to determine whether each gene set was differentially expressed in the comparisons as a set. The differential expression patterns and to calculate the enrichment scores of Th1/Th2 (KEGG mmu04658) and Th17 (KEGG mmu04659) related genes in the knockout vs. wild-type comparisons. Our analysis demonstrated that increase of Th2 program and decrease Th17 program in RASA3 KO pTh17 cells, with no change of Th1 related genes. This study indicated that RASA3 is vital for the balance of pTh17-Th2 reciprocal programs.

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