m6A modification of VEGFA mRNA by RBM15/YTHDF2/IGF2BP3 contributes to angiogenesis of hepatocellular carcinoma
Xiaoxin Xu
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorShuxiang Wu
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorYi Zhang
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorWeijie Fan
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorXinjian Lin
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorCorresponding Author
Kunqi Chen
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Correspondence Xu Lin and Kunqi Chen, Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, 1 Xue Fu North Rd, Fuzhou, Fujian 350122, China.
Email: [email protected] and [email protected]
Search for more papers by this authorCorresponding Author
Xu Lin
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Department of Medical Microbiology, Fujian Key Laboratory of Tumor Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
Correspondence Xu Lin and Kunqi Chen, Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, 1 Xue Fu North Rd, Fuzhou, Fujian 350122, China.
Email: [email protected] and [email protected]
Search for more papers by this authorXiaoxin Xu
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorShuxiang Wu
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorYi Zhang
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorWeijie Fan
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorXinjian Lin
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Search for more papers by this authorCorresponding Author
Kunqi Chen
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Correspondence Xu Lin and Kunqi Chen, Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, 1 Xue Fu North Rd, Fuzhou, Fujian 350122, China.
Email: [email protected] and [email protected]
Search for more papers by this authorCorresponding Author
Xu Lin
Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
Department of Medical Microbiology, Fujian Key Laboratory of Tumor Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
Correspondence Xu Lin and Kunqi Chen, Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, 1 Xue Fu North Rd, Fuzhou, Fujian 350122, China.
Email: [email protected] and [email protected]
Search for more papers by this authorXiaoxin Xu and Shuxiang Wu contributed equally to this work.
Abstract
Vascular endothelial growth factor A (VEGFA) plays a critical role as a potent angiogenesis factor and is highly expressed in hepatocellular carcinoma (HCC). Although the expression of VEGFA has been strongly linked to the aggressive nature of HCC, the specific posttranscriptional modifications that might contribute to VEGFA expression and HCC angiogenesis are not yet well understood. In this study, we aimed to investigate the epitranscriptome regulation of VEGFA in HCC. A comprehensive analysis integrating MeRIP-seq, RNA-seq, and crosslinking-immunprecipitation-seq data revealed that VEGFA was hypermethylated in HCC and identified the potential m6A regulators of VEGFA including a m6A methyltransferase complex component RBM15 and the two readers, YTHDF2 and IGF2BP3. Through rigorous cell and molecular biology experiments, RBM15 was validated as a key component of methyltransferase complex responsible for m6A methylation of VEGFA, which was subsequently recognized and stabilized by IGF2BP3 and YTHDF2, leading to enhanced VEGFA expression and VEGFA-related functions such as human umbilical vascular endothelial cells (HUVEC) migration and tube formation. In the HCC xenograft model, knockdown of RBM15, IGF2BP3, or YTHDF2 resulted in reduced expression of VEGFA, accompanied by significant inhibition of tumor growth closely associated with VEGFA expression and angiogenesis. Furthermore, our analysis of HCC clinical samples identified positive correlations between the expression levels of VEGFA and the regulators RBM15, IGF2BP3, and YTHDF2. Collectively, these findings offer novel insights into the posttranscriptional modulation of VEGFA and provide potential avenues for alternative approaches to antiangiogenesis therapy targeting VEGFA.
CONFLICT OF INTEREST STATEMENT
The authors declare no conflicts of interest.
Open Research
DATA AVAILABILITY STATEMENT
The data that supports the findings of this study are available in the supplementary material of this article. The present study incorporates all data produced or analyzed throughout the research and is comprehensively presented in the published article and its supplementary information documents. Additional queries may be directed towards the corresponding author.
Supporting Information
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1Sung H, Ferlay J, Siegel RL, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021; 71(3): 209-249.
- 2Llovet JM, Kelley RK, Villanueva A, et al. Hepatocellular carcinoma. Nat Rev Dis Primers. 2021; 7(1): 6.
- 3Hou Y, Zou Q, Ge R, Shen F, Wang Y. The critical role of CD133(+)CD44(+/high) tumor cells in hematogenous metastasis of liver cancers. Cell Res. 2012; 22(1): 259-272.
- 4Singh AK, Singh SV, Kumar R, Kumar S, Senapati S, Pandey AK. Current therapeutic modalities and chemopreventive role of natural products in liver cancer: progress and promise. World J Hepatol. 2023; 15(1): 1-18.
- 5Chen HM, Li H, Lin MX, et al. Research progress for RNA modifications in physiological and pathological angiogenesis. Front Genet. 2022; 13:952667.
- 6Apte RS, Chen DS, Ferrara N. VEGF in signaling and disease: beyond discovery and development. Cell. 2019; 176(6): 1248-1264.
- 7Finn RS, Qin S, Ikeda M, et al. Atezolizumab plus bevacizumab in unresectable hepatocellular carcinoma. N Engl J Med. 2020; 382(20): 1894-1905.
- 8Hirota K, Semenza GL. Regulation of angiogenesis by hypoxia-inducible factor 1. Crit Rev Oncol Hematol. 2006; 59(1): 15-26.
- 9Claesson-Welsh L, Welsh M. VEGFA and tumour angiogenesis. J Intern Med. 2013; 273(2): 114-127.
- 10Binet F, Sapieha P. ER stress and angiogenesis. Cell Metab. 2015; 22(4): 560-575.
- 11Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012; 485(7397): 201-206.
- 12Boccaletto P, Stefaniak F, Ray A, et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2022; 50(D1): D231-D235.
- 13Liu J, Yue Y, Han D, et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 2014; 10(2): 93-95.
- 14Zhou H, Yin K, Zhang Y, Tian J, Wang S. The RNA m6A writer METTL14 in cancers: roles, structures, and applications. Biochim Biophys Acta Rev Cancer. 2021; 1876(2):188609.
- 15Jia G, Fu Y, Zhao X, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011; 7(12): 885-887.
- 16Xue H, Wei Z, Chen K, et al. Prediction of RNA methylation status from gene expression data using classification and regression methods. Evol Bioinforma. 2020; 16:117693432091570.
10.1177/1176934320915707 Google Scholar
- 17Huang H, Weng H, Sun W, et al. Recognition of RNA N(6)-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nature Cell Biol. 2018; 20(3): 285-295.
- 18Du H, Zhao Y, He J, et al. YTHDF2 destabilizes m(6)A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat Commun. 2016; 7:12626.
- 19Huang H, Weng H, Zhou K, et al. Histone H3 trimethylation at lysine 36 guides m(6)A RNA modification co-transcriptionally. Nature. 2019; 567(7748): 414-419.
- 20Liu J, Li K, Cai J, et al. Landscape and regulation of m(6)A and m(6)Am methylome across human and mouse tissues. Mol Cell. 2020; 77(2): 426-440.e6.
- 21Ma H, Wang X, Cai J, et al. N(6-)Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019; 15(1): 88-94.
- 22Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37(8): 907-915.
- 23Meng J, Cui X, Rao MK, Chen Y, Huang Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 2013; 29(12): 1565-1567.
- 24Weinstein JN, Collisson EA, Mills GB, et al. The cancer genome Atlas Pan-Cancer analysis project. Nat Genet. 2013; 45(10): 1113-1120.
- 25Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014; 42(Database issue): D92-D97.
- 26Tang Y, Chen K, Song B, et al. m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. Nucleic Acids Res. 2021; 49(D1): D134-D143.
- 27Zhou Y, Zeng P, Li YH, Zhang Z, Cui Q. SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. Nucleic Acids Res. 2016; 44(10):e91.
- 28Huang HS, Huang XY, Yu HZ, Xue Y, Zhu PL. Circular RNA circ-RELL1 regulates inflammatory response by miR-6873-3p/MyD88/NF-κB axis in endothelial cells. Biochem Biophys Res Commun. 2020; 525(2): 512-519.
- 29Shams F, Moravvej H, Hosseinzadeh S, et al. Overexpression of VEGF in dermal fibroblast cells accelerates the angiogenesis and wound healing function: in vitro and in vivo studies. Sci Rep. 2022; 12(1):18529.
- 30Wege AK, Schmidt M, Ueberham E, et al. Co-transplantation of human hematopoietic stem cells and human breast cancer cells in NSG mice: a novel approach to generate tumor cell specific human antibodies. Mabs. 2014; 6(4): 968-977.
- 31Wu SX, Ye SS, Hong YX, et al. Hepatitis B virus small envelope protein promotes hepatocellular carcinoma angiogenesis via endoplasmic reticulum stress signaling to upregulate the expression of vascular endothelial growth factor A. J Virol. 2022; 96(4):e0197521.
- 32Wang F, Yang JL, Yu K, et al. Activation of the NF-κB pathway as a mechanism of alcohol enhanced progression and metastasis of human hepatocellular carcinoma. Mol Cancer. 2015; 14(1): 10.
- 33Jiang R, Tan Z, Deng L, et al. Interleukin-22 promotes human hepatocellular carcinoma by activation of STAT3. Hepatology. 2011; 54(3): 900-909.
- 34Lee TK, Man K, Ho JW, et al. FTY720: a promising agent for treatment of metastatic hepatocellular carcinoma. Clin Cancer Res. 2005; 11(23): 8458-8466.
- 35Li T, Fan J, Wang B, et al. TIMER: a web server for comprehensive analysis of Tumor-Infiltrating immune cells. Cancer Res. 2017; 77(21): e108-e110.
- 36Hu Y, Li Y, Huang Y, et al. METTL3 regulates the malignancy of cervical cancer via post-transcriptional regulation of RAB2B. Eur J Pharmacol. 2020; 879:173134.
- 37Jian D, Wang Y, Jian L, et al. METTL14 aggravates endothelial inflammation and atherosclerosis by increasing FOXO1 N6-methyladeosine modifications. Theranostics. 2020; 10(20): 8939-8956.
- 38Wang X, Tian L, Li Y, et al. RBM15 facilitates laryngeal squamous cell carcinoma progression by regulating TMBIM6 stability through IGF2BP3 dependent. J Exp Clin Cancer Res. 2021; 40(1): 80.
- 39Zhou D, Tang W, Xu Y, et al. METTL3/YTHDF2 m6A axis accelerates colorectal carcinogenesis through epigenetically suppressing YPEL5. Mol Oncol. 2021; 15(8): 2172-2184.
- 40Hong L, Pu X, Gan H, Weng l, Zheng Q. YTHDF2 inhibit the tumorigenicity of endometrial cancer via downregulating the expression of IRS1 methylated with m(6)A. J Cancer. 2021; 12(13): 3809-3818.
- 41Chen M, Wei L, Law CT, et al. RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2. Hepatology. 2018; 67(6): 2254-2270.
- 42Bokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman FM. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA (New York, N.Y.). 1997; 3(11): 1233-1247.
- 43Hou J, Zhang H, Liu J, et al. YTHDF2 reduction fuels inflammation and vascular abnormalization in hepatocellular carcinoma. Mol Cancer. 2019; 18(1): 163.
- 44Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017; 45(W1): W98-W102.
- 45Yang Y, Yan Y, Yin J, et al. O-GlcNAcylation of YTHDF2 promotes HBV-related hepatocellular carcinoma progression in an N(6)-methyladenosine-dependent manner. Signal Transduct Target Ther. 2023; 8(1): 63.
- 46Wang X, Lu Z, Gomez A, et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014; 505(7481): 117-120.
- 47Boo SH, Ha H, Kim YK. m(1)A and m(6)A modifications function cooperatively to facilitate rapid mRNA degradation. Cell Rep. 2022; 40(10):111317.
- 48Dixit D, Prager BC, Gimple RC, et al. The RNA m6A reader YTHDF2 maintains oncogene expression and is a targetable dependency in glioblastoma stem cells. Cancer Discovery. 2021; 11(2): 480-499.
- 49Wen J, Xue L, Wei Y, et al. YTHDF2 is a therapeutic target for HCC by suppressing immune evasion and angiogenesis through ETV5/PD-L1/VEGFA axis. Adv Sci (Weinh). 2024; 11(13):e2307242.
- 50Yang Z, Wang T, Wu D, Min Z, Tan J, Yu B. RNA N6-methyladenosine reader IGF2BP3 regulates cell cycle and angiogenesis in colon cancer. J Exp Clin Cancer Res. 2020; 39(1): 203.
- 51Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023; 51: D638-D646.
- 52Bateman A, Martin MJ, Orchard S, et al. UniProt: the universal protein knowledgebase in 2023. Nucleic Acids Res. 2023; 51: D523-D531.
- 53Uhlén M, Fagerberg L, Hallström BM, et al. Proteomics. tissue-based map of the human proteome. Science (New York, N.Y.). 2015; 347(6220):1260419.
- 54Patil DP, Chen CK, Pickering BF, et al. m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature. 2016; 537(7620): 369-373.
- 55Wang S, Chim B, Su Y, et al. Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3. Genes Dev. 2019; 33(15-16): 1048-1068.