MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes

Abstract

MicroRNAs (miRNAs) regulate specific immune mechanisms but their genome-wide regulation of T-lymphocyte activation is largely unknown. We performed a multidimensional functional genomics analysis to integrate genome-wide differential mRNA, miRNA, and protein expression as a function of human T-lymphocyte activation and time. We surveyed expression of 420 human miRNAs in parallel with genome-wide mRNA expression. We identified a unique signature of 71 differentially expressed miRNAs, 57 of which were previously not known as regulators of immune activation. The majority of miRNAs are upregulated, mRNA expression of these target genes is downregulated and this is a function of binding multiple miRNAs (combinatorial targeting). Our data reveal that consideration of this complex signature, rather than single miRNAs, is necessary to construct a full picture of miRNA-mediated regulation. Molecular network mapping of miRNA targets revealed the regulation of activation-induced immune signaling. In contrast, pathways populated by genes that are not miRNA targets are enriched for metabolism and biosynthesis. Finally, we specifically validated miR-155 (known) and miR-221 (novel in T-lymphocytes) using locked nucleic acid inhibitors. Inhibition of these 2 highly upregulated miRNAs in CD4+ T cells were shown to increase proliferation by removing suppression of 4 target genes linked to proliferation and survival. Thus, multiple lines of evidence link top functional networks directly to T-lymphocyte immunity underlining the value of mapping global gene, protein and miRNA expression.

Sexual dimorphism in autoimmunity

“…Females with SLE are reported to overexpress 18 X-linked miRNAs, compared with males with SLE that do not overexpress any miRNAs (78). Although the functions of the majority of X-linked miRNAs remain unknown, some of these miRNAs are reported to play a role in the regulation of immune responses or are associated with autoimmunity (106)(107)(108)(109)(110)(111).…”

Allogeneic T cell responses are regulated by a specific miRNA-mRNA network

“…Although bioinformatic analyses have greatly improved the ability to predict bona fide miRNA binding sites, the computational algorithms used are imperfect and disparate. In addition, these algorithms may have a high false-positive rate of target prediction (4,9,10) because of the inability to definitively distinguish direct and indirect miRNA target interactions, even when the miRNAs are coimmunoprecipitated with AGO proteins (11,12). Recently, AGO-CLIP has been demonstrated to provide a robust platform for the exploration of the specificity and range of miR actions and the identification of precise sequences of clinically relevant miRNA-mRNA interactions (11,(13)(14)(15).…”

“…Expression patterns and levels of miRNAs are regulated in concert with protein-coding genes (mRNAs) during immune responses (2). The mRNA and/or miR expression profiles in different T cell subsets, such as naive, effector, and memory CD8 T cells (3), CD8 T cells after nonspecific CD3/CD28 (CD3/28) activation (4), and tolerant CD8 T cells (5), as well as T cell activation responses to nonphysiological nominal antigen and OVA (6), have been recently reported. However, all of these analyses were performed using mRNA and miRNA profiling microarrays.…”

Gamma-Retroviral Vector Design for the Co-Expression of Artificial microRNAs and Therapeutic Proteins

“…As backbones for the amiR sequences we chose micro-RNA previously shown to be abundantly expressed in human lymphocytes, specifically miR-142, miR-146b, miR-150, miR-155, miR-16, and miR-223 [27][28][29][30]. Using a representative siRNA sequence targeted to TIPE2, we constructed 11 individual vectors with the amiRs inserted into one of two restriction enzyme sites within the intron of the tCD34 vector (Fig.…”