PSXIV-17 Gene co-expression network analysis identifies important modules and genes for cow’s response to Mycobacterium avium ssp. paratuberculosis infection in the small intestine.

摘要

Johne’s disease (JD), caused by ssp. ( ), is an important economic disease of dairy cows. However, little is known about the mechanisms underlying JD development. Here, we combined weighted gene coexpression network (WGCNA) and enrichment analyses to identify important genes, pathways and transcription factors (TF)s regulating MAP infection in cow’s small intestine. Total RNA from ileum, ileum lymph node, mid-jejunum and mid-jejunum lymph node tissues from five MAP-infected and five healthy cows was subjected to RNA-sequencing (Illumina HiSeq2500) followed by bioinformatics processing (standard softwares). Raw read count was normalized with Deseq2 and the co-expression patterns of 5000 most highly variable genes were identified using WGCNA. Enrichment analyses were accomplished with EnrichR. Nine co-expressed gene modules were identified. Two of them, CYAN and DARKRED, were correlated to JD status (p<0.05). CTSH and MERTK were the hub genes (have the highest level of inter-connectivity with other genes in the module) of CYAN (401 genes) and DARKRED (110 genes) modules, respectively. CTSH is important for degradation of lysosomal proteins and MERTK is involved in phagocytosis of apoptotic cells (efferocytosis), which are important processes during MAP infection. Neutrophil degranulation and lysosome pathways were the most enriched (p.FDR≤3.04e-26) biological process and KEGG pathway for CYAN genes suggesting involvement in the maintenance of host integrity by MAP infection. Phagocytosis and Staphylococcus aureus infection were the most enriched (p.FDR≤0.003) GO and KEGG pathway for DARKRED genes suggesting participation in phagocytosis process and disease related pathways. The most significantly enriched TFs for CYAN and DARKRED modules were SPI1 (involved in activation of gene expression during myeloid/B-lymphoid cell development) and EP300 (involved in transcriptional regulation of genes via chromatin remodeling), respectively. This study highlighted important genes and networks involved in the host response to MAP infection in the small intestine which furthers understanding of the biology of JD.