miR-210 loss leads to widespread phenotypic and gene expression changes in human 293T cells

Hypoxia responses are critical for myriad physiological and pathological processes, such as development, tissue repair, would healing, and tumorigenesis. microRNAs (miRNAs) are a class of small non-coding RNAs that exert their functions by inhibiting the expression of their target genes, and miR-210 is the miRNA universally and most conspicuously upregulated by hypoxia in mammalian systems. For its relationship to hypoxia, miR-210 has been studied extensively, yet no consensus exists on the roles and mechanisms of miR-210 in human physiological processes or diseases, and we know little about genuine miR-210 target genes in humans.

To better investigate the functions and mechanisms of human miR-210, therefore, we derived the human miR-210 gene knockout (KO) 293T cell lines using the CRISPR/Cas9 technology. We then examined the cellular phenotypes and gene expression profiles of 293T cells under normoxia and hypoxia conditions.

We found that the loss of miR-210 altered a variety of cellular phenotypes including proliferation and apoptosis. Subsequent global gene expression analyses identified plausible mechanisms underlying these phenotypic changes in 293T cells. In particular, we showed that miR-210 might target the expression of BNIP3L as a potential mechanism to suppress apoptosis. Surprisingly, the mRNA levels of most previously reported miR-210 target genes were not induced upon miR-210 KO, suggesting a need to reexamining and studying human miR-210 functions directly and comprehensively. Thus, our work established a human cellular system and opportunity to unravel the complexity of the regulatory networks by miR-210.