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Transcriptome‐wide mapping of the miR‐122 targetome revealed its mechanistic role in the maintenance of liver homeostasis
Author(s) -
Barajas Juan Martin,
Luna Joseph,
Teng KunYu,
Darnell Robert,
Ghoshal Kalpana
Publication year - 2017
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.31.1_supplement.757.14
Subject(s) - transcriptome , biology , microrna , hepatocellular carcinoma , liver cancer , context (archaeology) , in silico , mir 122 , false positive paradox , phenotype , glucose homeostasis , cancer , malignancy , homeostasis , cancer research , bioinformatics , computational biology , genetics , gene , microbiology and biotechnology , endocrinology , gene expression , insulin resistance , diabetes mellitus , paleontology , machine learning , computer science
Liver cancer has the second highest mortality rate among all malignancies, which implies a lack of molecular understanding of disease development and progression necessary to combat this deadly disease. miR‐122 is a conserved liver‐specific miRNA, that maintains metabolic homeostasis, suppresses tumor development, and promotes HCV replication. Loss of miR‐122 is associated with loss of hepatic phenotype, gain of malignancy‐associated features, and poor patient prognosis in hepatocellular carcinoma (HCC) patients. Recent in vivo work in our miR‐122 knockout (KO) mice have established miR‐122 as a bona fide tumor suppressor. These data suggest it is critical to identify the miR‐122 targetome in the liver to better understand its function. Previously, in silico prediction was the go‐to‐method for identification of miRNA targets. However, these methods are dependent on known or evolutionarily conserved functionality of the miRNA‐Ago complex and without reference to cellular context, can result in a high number of false positives and false negatives. To overcome this, the laboratory of Dr. Robert Darnell introduced a novel unbiased high‐throughput method known as Ago‐dHiTS‐CLIP (Ago‐CLIP) which has been applied in wild‐type (WT) and miRNA KO platforms to systematically and biochemically identify transcriptome‐wide miRNA‐mediated Ago maps. To this end, in collaboration with Dr. Darnell's laboratory, we performed Ago‐CLIP analysis in livers of 6 week‐old WT and KO mice as well as in benign human liver expressing relatively high levels of miR‐122 and matching HCC tumor exhibiting down‐regulation of miR‐122. Ago‐CLIP identified ~800 miR‐122 targets in mice and ~1400 in humans with only 309 targets conserved in both. Surprisingly, a majority of miR‐122 sites are in coding exons (30%) and 3′‐UTRs (30%) along with sites in the 5′UTR, introns, etc. RNA‐seq analysis revealed specific upregulation of these 3′UTR and CDS targets in miR‐122 KO livers, suggesting these are functional miR‐122 targets. Furthermore, Liver and Hepatocellular Carcinoma (LIHC) data from The Cancer Genome Atlas (TCGA) revealed alterations in 26 conserved miR‐122 target genes are predictive of overall patient prognosis. BCL9 , an exclusive CDS target and a critical component of Wnt/β‐catenin signaling, was found to be significantly predictive of patient survival and may play a key role in liver tumor progression. In summary, our analysis identified key targets involved in liver homeostasis and revealed a miR‐122 target‐signature predictive in human HCC. Support or Funding Information This work was supported by NIH grants RO1CA193244 and R01CA19324406S1 (K. Ghoshal).