The tumor suppressor MIR139 is silenced by POLR2M to promote AML oncogenesis

Abstract

MIR139 is a tumor suppressor and is commonly silenced in acute myeloid leukemia (AML). However, the tumor-suppressing activities of miR-139 and molecular mechanisms of MIR139-silencing remain largely unknown. Here, we studied the poorly prognostic MLL-AF9 fusion protein-expressing AML. We show that MLL-AF9 expression in hematopoietic precursors caused epigenetic silencing of MIR139, whereas overexpression of MIR139 inhibited in vitro and in vivo AML outgrowth. We identified novel miR-139 targets that mediate the tumor-suppressing activities of miR-139 in MLL-AF9 AML. We revealed that two enhancer regions control MIR139 expression and found that the polycomb repressive complex 2 (PRC2) downstream of MLL-AF9 epigenetically silenced MIR139 in AML. Finally, a genome-wide CRISPR-Cas9 knockout screen revealed RNA Polymerase 2 Subunit M (POLR2M) as a novel MIR139-regulatory factor. Our findings elucidate the molecular control of tumor suppressor MIR139 and reveal a role for POLR2M in the MIR139-silencing mechanism, downstream of MLL-AF9 and PRC2 in AML. In addition, we confirmed these findings in human AML cell lines with different oncogenic aberrations, suggesting that this is a more common oncogenic mechanism in AML. Our results may pave the way for new targeted therapy in AML.

MicroRNA-139, an Emerging Gate-Keeper in Various Types of Cancer

“…Despite a significant correlation between the expression of PDE2A and MIR139 in lung cancer cell lines [40], we and other investigators have shown that miR-139-5p and/or miR-139-3p expression is not correlated to PDE2A expression levels in leukemia [38], gastric [41] and colorectal cancer cells [42]. We have recently shown that MIR139 expression is strongly silenced in MLL-AF9 AML, whereas the expression of Pde2a was not affected [38]. These data indicate that post-transcriptional mechanisms other than splicing and subsequent processing of pri-miR-139 by the microprocessor complex play a role in the stability and processing of miR-139-5p and miR-139-3p.…”

“…Clinical data show that acute myeloid leukemia (AML) patients with the lowest miR-139 levels have a poor prognosis [46]. In agreement, we found that Mir139 KO HSPCs gave rise to more and larger colonies when transformed with the MLL-AF9 oncogene in colony-forming unit assays, showing that miR-139-depleted leukemia cells have a growth advantage [38]. Whether MIR139 silencing is a critical early driver of leukemogenesis still needs further investigation.…”

“…Despite a significant correlation between the expression of PDE2A and MIR139 in lung cancer cell lines [ 40 ], we and other investigators have shown that miR-139-5p and/or miR-139-3p expression is not correlated to PDE2A expression levels in leukemia [ 38 ], gastric [ 41 ] and colorectal cancer cells [ 42 ]. We have recently shown that MIR139 expression is strongly silenced in MLL-AF9 AML, whereas the expression of Pde2a was not affected [ 38 ].…”

“…An overview of the different in vitro and in vivo models used to study MIR139 in cancer can be found in Table 1. Mouse MLL-AF9 leukemia and human AML cell lines MOLM-13, THP-1, MV4-11, HL-60, HEL and U937, Kasumi-1, SKNO-1 MLL-AF9 AML, AML [38,46] Human AML and CML, AML cell lines NB4, HP-1, KG-1a, OCI-AML3, U937, HL-60 Human T-ALL cell lines HPB-ALL, TALL-1, KOPTK1, Jurkat, CCRF-CEM, Molt16 Diverse types of leukemia [47][48][49][50][51] Colon cancer cell lines HT29, SW480, SW620, KM12, SW116, HCT116, HCT-8, HCT-116, LoVo, Caco2, DLD1, LS180, NCM460, HcoEpic and Human colon cancer in NOD/SCID mice Colon cancer [42,[52][53][54][55][56][57][58][59][60][61] Human lung cancer cells, H460, IC11LC13, NSCLC cell lines A549, H1299, H1975, HCC827, H1650, H460, SK-MES-1 and SPC-A-1, PM2.…”

“…Genomic deletion of Pde2a in mice (B6; 129P2-Pde2A< tm1Dgen>/H; EM: 02366) is embryonically lethal and mutant mice die in utero at embryonic day (E) 15.5 [ 37 ]. In addition, despite multiple attempts of our research team, mice with a genomic deletion of the putative Pde2a promoter could not be generated, indicating that Pde2a is essential for survival [ 38 ]. In agreement, other investigators have found that Pde2a KO embryos display lethal defects in fetal liver development and hematopoiesis [ 39 ].…”