Gene network landscape of murine splenocytes reveals integrin as the A151 ODN-responsive hub in immune transcriptome

PURPOSE: Homeostatic restoration of an inflammatory response requires quenching of the immune system after pathogen threats vanish. A continued assault orchestrated by host defense results in tissue destruction or autoimmunity. A151 is the epitome of synthetic oligodeoxynucleotides (ODNs) that curb immune response by a subset of white corpuscles through repetitive telomere derived TTAGGG sequences. Nevertheless, the genuine effect A151 has on immune cell transcriptome still remains unknown. METHODS: We leveraged an integrative approach in which weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis of our in-house microarray data sets aided our understanding of how A151 ODN suppresses immune response in mouse splenocytes. We fed raw gene expression data from two different (scrambled ODN and A151 ODN) treatment groups with a varying number of replicate arrays (29 and 16, respectively) into WGCNA, limma, and GSEA separetely to understand different dimensions of the A151 ODN-driven immune modulation at the transcriptome level. RESULTS: Together with experimental and in silico validations, we demonstrated that A151 ODN acts on components of integrin complexes, namely Itgam and Itga6, to interfere with immune cell adhesion, and thereby, suppress the immune response in mouse. Furthermore, we revealed that cell adhesion by integrin complexes serves as a focal point for cellular response to A151 ODN treatment in immune cells. CONCLUSION: A refined set of co-hub genes led by Itgam and Itga6 plays a pivotal role in A151 ODN-driven suppression of immune response. Also, A151 ODN treatment appears to interfere with immune cell adhesion to quench immune response in mouse splenocytes. The outcome of this study sheds light on the molecular basis of immune suppression by a clinically useful DNA-based therapeutic agent and may open new revenues for A151 ODN research. Two-condition experiment, control (scrambled ODN)- vs. case (A151 ODN)-treated mouse splenocytes. Biological replicates: 29 control and 16 A151 ODN. One replicate per array. Dual channel, non-commercial arrays with a common reference design covering murine splenocyte genome using a set of 16897 unique probes.