The biological processes that are most enriched with genes showing diet-by-strain interactions were mainly related to immune system processes, specifically antigen processing and presentation.
Microarray experiments have provided a systems-level view of the major effects of high fat (HF) diet within individual tissues, and have shown that HF diet often increases the expression of genes disproportionately associated with immune system processes, such as the processing and presentation of antigens [15], [21] [24].
RNA-seq identified many more differentially expressed transcripts enriched in immune system processes.
Due to the many immune system processes that these enzymes regulate, alteration in their function could be detrimental to the host.
Human monocytes play fundamental roles in human physiology, including immune system processes, blood coagulation and circulation, bone remodeling and resorption, muscle system processes and nervous system development (see details in Table S4).
Genes associated with immune system processes, such matrilin and the p53-like protein gene were identified.
Surprisingly, MSC-derived MV selected miRNAs were associated to targets involved in the immune system processes, including leukocyte activation and differentiation and hemopoiesis regulation (Table S4).
Gene Ontology analysis identified the genes involved in immune system processes as Psme2, Cd40, Ccl22, Il1b, Sqstm1, Tap1, Il6, Il12b, Ifit1, Ccr7, Irf8, Isg15, Nfkbia, Nfkb1, Stat5a and Cdkn1a.
We found that the selected predictive genes upregulated during DCs activation fell into distinct functional classes, with major involvement in immune system processes (47%) cell differentiation (44%), metabolic process (42%) and cell death (31%).
We found an enrichment of functional gene categories related to the immune system processes such as leukocyte activation and differentiation, and cell survival/apoptosis signaling among the CS/CPB regulated genes.
The inflammatory infiltrate might be responsible for the increased expression of the genes involved in immune system processes and cell killing/death in the smDicer KO mice (Figure 5B).
