Genome-Wide Screening and Functional Analysis Identifies Tumor Suppressor Long Noncoding RNAs Epigenetically Silenced in Hepatocellular Carcinoma

Abstract

Long noncoding RNAs (lncRNA) play critical roles in the development of cancer, including hepatocellular carcinoma (HCC). However, the mechanisms underlying their deregulation remain largely unexplored. In this study, we report that two lncRNAs frequently downregulated in HCC function as tumor suppressors and are epigenetically silenced by histone methyltransferase EZH2. lncRNAs TCAM1P-004 and RP11-598D14.1 were inhibited by EZH-mediated trimethylation of H3K27me3 at their promoters. Downregulation of TCAM1P-004 and RP11-598D14.1 was frequently observed in HCC tumors compared with adjacent normal tissues. Both lncRNAs inhibited cell growth, cell survival, and transformation in HCC cells in vitro as well as tumor formation in vivo. Using RNA pull-down and mass spectrometry, we demonstrated that TCAM1P-004 bound IGF2BP1 and HIST1H1C, whereas RP11-598D14.1 bound IGF2BP1 and STAU1. These lncRNA-protein interactions were critical in regulating p53, MAPK, and HIF1a pathways that promoted cell proliferation in HCC. Overexpression of EZH2 was critical in repressing TCAM1P-004 and RP11-598D14.1, and EZH2-TCAM1P-004/ RP11-598D14.1-regulated pathways were prevalent in human HCC. Aberrant suppression of TCAM1P-004 and RP11-598D14.1 led to loss of their tumor-suppressive effects by disrupting the interaction with IGF2BP1, HIST1H1C, and STAU1, which in turn promoted HCC development and progression. Collectively, these findings demonstrate the role of TCAMP1P-004 and RP11-598D14.1 in suppressing tumor growth and suggest that EZH2 may serve as a therapeutic target in HCC. Significance: EZH2-mediated loss of lncRNAs TCAM1P-004 and RP11-598D14.1 hinders the formation of tumor suppressor lncRNA-protein complexes and subsequently promotes HCC growth.

Functions of N6-methyladenosine and its role in cancer

“…Mechanistically, p62 enhances stability of FERMT2 and other pro-metastatic factors through interacting with IGF2BP1 [102]. In HCC, TCAM1P-004 interacts with IGF2BP1, thereby suppressing IGF2 translation and enhancing DDIT3 expression, resulting in inhibition of cell proliferation and promotion of cell apoptosis [103].…”

Potential roles of N6-methyladenosine (m6A) in immune cells

“…mRNA binding protein Insulin-like growth factor 2 mRNA binding protein 1-3 (IGF2BP1-3) is suggested to stabilize target mRNAs in an m6A-dependent manner [ 63 ]. IGF2BPs promote the stability of target mRNA by recruiting RNA stabilizers such as ELAVL1 and MATR3 under normal conditions, and promote the storage of target mRNA by shifting to stress particles under stress conditions, enhancing the expression of target mRNA [ 64 ]. In HCC, TCAM1P-004 interacts with IGF2BP1 to inhibit the cell proliferation by suppressing the translation of IGF2 and increasing the expression of DDIT3 [ 64 ].…”

Progress in non-coding RNA research

“…药物敏感性相关. 如肝癌中miR-199a/b-3p [151] , miR-124 [152] , miR-26 [226,227] , TCAM1P-004 [158] , RP11-598D14.1 [158] , ICR [145] , LncSox4 [147] , lnc-β-Catm [156] , lncRNA-LET [159] , UFC1 [157] , lncRNA-ATB [144] , cir-cMTO1 [164] , circMAT2B [162] , cSMARCA5 [165] 的表达和 肝 癌 患 者 的 预 后 相 关 ; 胆 囊 癌 中 PA G B C [ 1 6 6 ] , GCASPC [36,167] 的表达和预后相关; 食管鳞癌中miR- ENST00000547963.1 [228] 的表达和预后相关; 胃癌中7 个miRNAs: miR-10b, miR-21, miR-223, miR-338, let-7a, miR-30a-5p, miR-126的组合 [229] , HOXC-AS3 [174] , PVT1 [175] , GClnc1 [177] , GAPLINC [179] , GMAN [180] 的表达 和预后相关; 结直肠癌中miR-150 [182] , miR-17-5p [206] , lncRNA-APC1 [211] , FEZF1-AS1 [184] , CCAL [185] , OLA1P2 [230] 的表达和预后相关; 胰腺癌中GLS-AS的 表达和预后相关 [186] . 肺癌中miR-128-3p [187] , miR-582-3p [214] , P53RRA [161] , MetaLnc9 [189] , MIR22HG [190] 的表 达和预后相关.…”