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RBM4 modulates the proliferation and expression of inflammatory factors via the alternative splicing of regulatory factors in HeLa cells

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Abstract

Regulatory factors function by modulating a variety of cascade mechanisms in cells. RBM4 is a multifunctional RNA-binding protein in post-transcriptional gene regulation. Cytoplasmic RBM4 interacts with Ago2 to regulate inflammatory responses by affecting mRNA decay and cap-dependent translation. However, it is unclear whether RBM4 functions in inflammation regulation by its splicing factor role. Here, the cell biology, gene expression profile and alternative splicing pattern of HeLa cells with RBM4 overexpression (RBM-OE) were compared with the control. The results showed that RBM4-OE inhibited proliferation. RBM4-OE extensively affects the transcriptional level of genes involved in cell surface receptor signalling pathway, inflammatory responses and the response to lipopolysaccharide. RBM4 broadly regulated the alternative splicing of hundreds of genes with functions of protein binding, helicase activity, DNA binding and transcription co-activator. RBM4-regulated splicing of these genes plays an important role in apoptotic process and gene transcription regulation. As an example, exon inclusion of TNIP1 mediated by RBM4 affects the expression of its targets in inflammatory pathways. These results indicated that RBM4 can mediate the inflammatory response via splicing regulation, which adds to the understanding of the critical role of RBM4 in cancer complicated by inflammation. In conclusion, this study indicated a mechanism in which the dysregulation of alternative splicing can influence cellular biology and lead to various immune-related diseases.

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Data availability

All data generated or analysed during this study have been included in this published article and its supplementary information files. The datasets supporting the results of this article are available in the NCBI Gene Expression Omnibus and are accessible through GEO series accession number GSE134402.

References

  • Bettin A, Reyes I, Reyes N (2016) Gene expression profiling of prostate cancer-associated genes identifies fibromodulin as potential novel biomarker for prostate cancer. Int J Biol Markers 31:e153–e162

    CAS  PubMed  Google Scholar 

  • Brooks YS, Wang G, Yang Z, Smith KK, Bieberich E, Ko L (2009) Functional pre-mRNA trans-splicing of coactivator CoAA and corepressor RBM4 during stem/progenitor cell differentiation. J Biol Chem 284:18033–18046

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brudecki L, Ferguson DA, McCall CE, El Gazzar M (2013a) MicroRNA-146a and RBM4 form a negative feed-forward loop that disrupts cytokine mRNA translation following TLR4 responses in human THP-1 monocytes. Immunol Cell Biol 91:532–540

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brudecki L, Ferguson DA, McCall CE, El Gazzar M (2013b) Mitogen-activated protein kinase phosphatase 1 disrupts proinflammatory protein synthesis in endotoxin-adapted monocytes. Clin Vaccine Immunol 20:1396–1404

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen JY, Liu LP, Xu JF (2017) Decrease of RBM4 indicates poor prognosis in patients with hepatocellular carcinoma after hepatectomy. Onco Targets Ther 10:339–345

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chi YL, Lin JC (2018) RBM4a modulates the impact of PRDM16 on development of brown adipocytes through an alternative splicing mechanism. Biochim Biophys Acta 1865:1515–1525

    CAS  Google Scholar 

  • Cui S, Yang X, Zhang L, Zhao Y, Yan W (2018) LncRNA MAFG-AS1 promotes the progression of colorectal cancer by sponging miR-147b and activation of NDUFA4. Biochem Biophys Res Commun 506:251–258

    CAS  PubMed  Google Scholar 

  • El Gazzar M, Church A, Liu T, McCall CE (2011) MicroRNA-146a regulates both transcription silencing and translation disruption of TNF-alpha during TLR4-induced gene reprogramming. J Leukoc Biol 90:509–519

    PubMed  PubMed Central  Google Scholar 

  • El Haddad H, Chaftari AM, Hachem R, Chaftari P, Raad II (2018) Biomarkers of sepsis and bloodstream infections: the role of procalcitonin and proadrenomedullin with emphasis in patients with cancer. Clin Infect Dis 67:971–977

    PubMed  Google Scholar 

  • Fox AC, Robertson CM, Belt B, Clark AT, Chang KC, Leathersich AM, Dominguez JA, Perrone EE, Dunne WM, Hotchkiss RS, Buchman TG, Linehan DC, Coopersmith CM (2010) Cancer causes increased mortality and is associated with altered apoptosis in murine sepsis. Crit Care Med 38:886–893

    PubMed  PubMed Central  Google Scholar 

  • Fu XD, Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15:689–701

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fu M, Blackshear PJ (2017) RNA-binding proteins in immune regulation: a focus on CCCH zinc finger proteins. Nat Rev Immunol 17:130–143

    CAS  PubMed  Google Scholar 

  • Gowen BG, Chim B, Marceau CD, Greene TT, Burr P, Gonzalez JR, Hesser CR, Dietzen PA, Russell T, Iannello A, Coscoy L, Sentman CL, Carette JE, Muljo SA, Raulet DH (2015) A forward genetic screen reveals novel independent regulators of ULBP1, an activating ligand for natural killer cells. Elife. https://doi.org/10.7554/eLife.08474

    Article  PubMed  PubMed Central  Google Scholar 

  • Grivennikov SI, Greten FR, Karin M (2010) Immunity, inflammation, and cancer. Cell 140:883–899

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hentze MW, Castello A, Schwarzl T, Preiss T (2018) A brave new world of RNA-binding proteins. Nat Rev Mol Cell Biol 19:327–341

    CAS  PubMed  Google Scholar 

  • Hock J, Weinmann L, Ender C, Rudel S, Kremmer E, Raabe M, Urlaub H, Meister G (2007) Proteomic and functional analysis of Argonaute-containing mRNA–protein complexes in human cells. EMBO Rep 8:1052–1060

    PubMed  PubMed Central  Google Scholar 

  • Huang GW, Zhang YL, Liao LD, Li EM, Xu LY (2017) Natural antisense transcript TPM1-AS regulates the alternative splicing of tropomyosin I through an interaction with RNA-binding motif protein 4. Int J Biochem Cell Biol 90:59–67

    CAS  PubMed  Google Scholar 

  • Hube F, Guo J, Chooniedass-Kothari S, Cooper C, Hamedani MK, Dibrov AA, Blanchard AA, Wang X, Deng G, Myal Y, Leygue E (2006) Alternative splicing of the first intron of the steroid receptor RNA activator (SRA) participates in the generation of coding and noncoding RNA isoforms in breast cancer cell lines. DNA Cell Biol 25:418–428

    CAS  PubMed  Google Scholar 

  • Jones SA, Jenkins BJ (2018) Recent insights into targeting the IL-6 cytokine family in inflammatory diseases and cancer. Nat Rev Immunol 18:773–789

    CAS  PubMed  Google Scholar 

  • Kar A, Havlioglu N, Tarn WY, Wu JY (2006) RBM4 interacts with an intronic element and stimulates tau exon 10 inclusion. J Biol Chem 281:24479–24488

    CAS  PubMed  Google Scholar 

  • Karin M, Lawrence T, Nizet V (2006) Innate immunity gone awry: linking microbial infections to chronic inflammation and cancer. Cell 124:823–835

    CAS  PubMed  Google Scholar 

  • Kemmerer K, Fischer S, Weigand JE (2018) Auto-and cross-regulation of the hnRNPs D and DL. RNA 24:324–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lai MC, Kuo HW, Chang WC, Tarn WY (2003) A novel splicing regulator shares a nuclear import pathway with SR proteins. EMBO J 22:1359–1369

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li J, Wang Y, Rao X, Wang Y, Feng W, Liang H, Liu Y (2017) Roles of alternative splicing in modulating transcriptional regulation. BMC Syst Biol. https://doi.org/10.1186/s12918-12017-10465-12916

    Article  PubMed  PubMed Central  Google Scholar 

  • Liang YC, Lin WC, Lin YJ, Lin JC (2015) The impact of RNA binding motif protein 4-regulated splicing cascade on the progression and metabolism of colorectal cancer cells. Oncotarget 6:38046–38060

    PubMed  PubMed Central  Google Scholar 

  • Lin JC (2015) RBM4-MEF2C network constitutes a feed-forward circuit that facilitates the differentiation of brown adipocytes. RNA Biol 12:208–220

    PubMed  PubMed Central  Google Scholar 

  • Lin JC, Tarn WY (2005) Exon selection in alpha-tropomyosin mRNA is regulated by the antagonistic action of RBM4 and PTB. Mol Cell Biol 25:10111–10121

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Tarn WY (2009) RNA-binding motif protein 4 translocates to cytoplasmic granules and suppresses translation via argonaute2 during muscle cell differentiation. J Biol Chem 284:34658–34665

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Tarn WY (2012) Multiple roles of RBM4 in muscle cell differentiation. Front Biosci 4:181–189

    Google Scholar 

  • Lin JC, Hsu M, Tarn WY (2007) Cell stress modulates the function of splicing regulatory protein RBM4 in translation control. Proc Natl Acad Sci USA 104:2235–2240

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Yan YT, Hsieh WK, Peng PJ, Su CH, Tarn WY (2013) RBM4 promotes pancreas cell differentiation and insulin expression. Mol Cell Biol 33:319–327

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Lin CY, Tarn WY, Li FY (2014) Elevated SRPK1 lessens apoptosis in breast cancer cells through RBM4-regulated splicing events. RNA 20:1621–1631

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Chi YL, Peng HY, Lu YH (2016a) RBM4-Nova1-SRSF6 splicing cascade modulates the development of brown adipocytes. Biochim Biophys Acta 1859:1368–1379

    CAS  PubMed  Google Scholar 

  • Lin JC, Lu YH, Liu YR, Lin YJ (2016b) RBM4a-regulated splicing cascade modulates the differentiation and metabolic activities of brown adipocytes. Sci Rep. https://doi.org/10.1038/srep20665

    Article  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Lee YC, Liang YC, Fann YC, Johnson KR, Lin YJ (2017) The impact of the RBM4-initiated splicing cascade on modulating the carcinogenic signature of colorectal cancer cells. Sci Rep. https://doi.org/10.1038/srep44204

    Article  PubMed  PubMed Central  Google Scholar 

  • Lin JC, Lee YC, Tan TH, Liang YC, Chuang HC, Fann YC, Johnson KR, Lin YJ (2018) RBM4-SRSF3-MAP4K4 splicing cascade modulates the metastatic signature of colorectal cancer cell. Biochim Biophys Acta 1865:259–272

    CAS  Google Scholar 

  • Liu T, Yang H, Fan W, Tu J, Li TWH, Wang J, Shen H, Yang J, Xiong T, Steggerda J, Liu Z, Noureddin M, Maldonado SS, Annamalai A, Seki E, Mato JM, Lu SC (2018a) Mechanisms of MAFG dysregulation in cholestatic liver injury and development of liver cancer. Gastroenterology 155:557–571.e514

    CAS  PubMed  Google Scholar 

  • Liu Z, Mahale P, Engels EA (2018b) Sepsis and risk of cancer among elderly adults in the United States. Clin Infect Dis. 5:717–724

    Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408

    CAS  PubMed  Google Scholar 

  • Luo P, Jing W, Zhu M, Li ND, Zhou H, Yu MX, Liang CZ, Tu JC (2017) Decreased expression of LncRNA SRA1 in hepatocellular carcinoma and its clinical significance. Cancer Biomark 18:285–290

    CAS  PubMed  Google Scholar 

  • Mantovani A, Allavena P, Sica A, Balkwill F (2008) Cancer-related inflammation. Nature 454:436–444

    CAS  PubMed  Google Scholar 

  • Markus MA, Morris BJ (2009) RBM4: a multifunctional RNA-binding protein. Int J Biochem Cell Biol 41:740–743

    CAS  PubMed  Google Scholar 

  • Markus MA, Heinrich B, Raitskin O, Adams DJ, Mangs H, Goy C, Ladomery M, Sperling R, Stamm S, Morris BJ (2006) WT1 interacts with the splicing protein RBM4 and regulates its ability to modulate alternative splicing in vivo. Exp Cell Res 312:3379–3388

    CAS  PubMed  Google Scholar 

  • Markus MA, Yang YH, Morris BJ (2016) Transcriptome-wide targets of alternative splicing by RBM4 and possible role in cancer. Genomics 107:138–144

    CAS  PubMed  Google Scholar 

  • McClure C, Brudecki L, Yao ZQ, McCall CE, El Gazzar M (2015) Processing body formation limits proinflammatory cytokine synthesis in endotoxin-tolerant monocytes and murine septic macrophages. J Innate Immun 7:572–583

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mokart D, Saillard C, Sannini A, Chow-Chine L, Brun J-P, Faucher M, Blache J-L, Blaise D, Leone M (2014) Neutropenic cancer patients with severe sepsis: need for antibiotics in the first hour. Intensive Care Med 40:1173–1174

    PubMed  Google Scholar 

  • Nana-Sinkam SP, Crouser ED (2010) Altered immune surveillance: a common link between cancer and sepsis? Crit Care Med 38:1000–1001

    PubMed  Google Scholar 

  • Peng H-Y, Liang Y-C, Tan T-H, Chuang H-C, Lin Y-J, Lin J-C (2018) RBM4a-SRSF3-MAP4K4 splicing cascade constitutes a molecular mechanism for regulating brown adipogenesis. Int J Mol Sci. https://doi.org/10.3390/ijms19092646

    Article  PubMed  PubMed Central  Google Scholar 

  • Pereira B, Billaud M, Almeida R (2017) RNA-Binding proteins in cancer: old players and new actors. Trends Cancer 3:506–528

    CAS  PubMed  Google Scholar 

  • Qi Y, Yu J, Han W, Fan X, Qian H, Wei H, Tsai YH, Zhao J, Zhang W, Liu Q, Meng S, Wang Y, Wang Z (2016) A splicing isoform of TEAD4 attenuates the Hippo-YAP signalling to inhibit tumour proliferation. Nat Commun. https://doi.org/10.1038/ncomms11840

    Article  PubMed  PubMed Central  Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    CAS  PubMed  Google Scholar 

  • Shamilov R, Aneskievich BJ (2018) TNIP1 in autoimmune diseases: regulation of toll-like receptor signaling. J Immunol Res. https://doi.org/10.1155/2018/3491269

    Article  PubMed  PubMed Central  Google Scholar 

  • Su CH, Hung KY, Hung SC, Tarn WY (2017) RBM4 regulates neuronal differentiation of mesenchymal stem cells by modulating alternative splicing of pyruvate kinase M. Mol Cell Biol. https://doi.org/10.1128/mcb.00466-00416

    Article  PubMed  PubMed Central  Google Scholar 

  • Tarn WY, Kuo HC, Yu HI, Liu SW, Tseng CT, Dhananjaya D, Hung KY, Tu CC, Chang SH, Huang GJ, Chiu IM (2016) RBM4 promotes neuronal differentiation and neurite outgrowth by modulating Numb isoform expression. Mol Biol Cell 27:1676–1683

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tiedje C, Diaz-Munoz MD, Trulley P, Ahlfors H, Laass K, Blackshear PJ, Turner M, Gaestel M (2016) The RNA-binding protein TTP is a global post-transcriptional regulator of feedback control in inflammation. Nucleic Acids Res 44:7418–7440

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tsuji E, Hiki N, Nomura S, Fukushima R, Kojima J, Ogawa T, Mafune K, Mimura Y, Kaminishi M (2003) Simultaneous onset of acute inflammatory response, sepsis-like symptoms and intestinal mucosal injury after cancer chemotherapy. Int J Cancer 107:303–308

    CAS  PubMed  Google Scholar 

  • Turner M, Díaz-Muñoz MD (2018) RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 19:120–129

    CAS  PubMed  Google Scholar 

  • Uniacke J, Holterman CE, Lachance G, Franovic A, Jacob MD, Fabian MR, Payette J, Holcik M, Pause A, Lee S (2012) An oxygen-regulated switch in the protein synthesis machinery. Nature 486:126–129

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Chen D, Qian H, Tsai YS, Shao S, Liu Q, Dominguez D, Wang Z (2014) The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. Cancer Cell 26:374–389

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang C-J, Zhu C-C, Xu J, Wang M, Zhao W-Y, Liu Q, Zhao G, Zhang Z-Z (2019) The lncRNA UCA1 promotes proliferation, migration, immune escape and inhibits apoptosis in gastric cancer by sponging anti-tumor miRNAs. Mol Cancer 18:115

    PubMed  PubMed Central  Google Scholar 

  • Ward ST, Weston CJ, Shepherd EL, Hejmadi R, Ismail T, Adams DH (2016) Evaluation of serum and tissue levels of VAP-1 in colorectal cancer. BMC Cancer. https://doi.org/10.1186/s12885-12016-12183-12887

    Article  PubMed  PubMed Central  Google Scholar 

  • Williams MD, Braun LA, Cooper LM, Johnston J, Weiss RV, Qualy RL, Linde-Zwirble W (2004) Hospitalized cancer patients with severe sepsis: analysis of incidence, mortality, and associated costs of care. Crit Care 8:R291–R298

    PubMed  PubMed Central  Google Scholar 

  • Xia H, Chen D, Wu Q, Wu G, Zhou Y, Zhang Y, Zhang L (2017) CELF1 preferentially binds to exon-intron boundary and regulates alternative splicing in HeLa cells. Biochim Biophys Acta 1860:911–921

    CAS  Google Scholar 

  • Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39:W316–W322

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yong H, Zhu H, Zhang S, Zhao W, Wang W, Chen C, Ding G, Zhu L, Zhu Z, Liu H, Zhang Y, Wen J, Kang X, Zhu J, Feng Z, Liu B (2016) Prognostic value of decreased expression of RBM4 in human gastric cancer. Sci Rep. https://doi.org/10.1038/srep28222

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This study was partially supported by ABLife (ABL-7702098).

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  1. Wei-Yang Wang and Weili Quan have contributed equally to this work and are joint first authors.

Authors and Affiliations

  1. Trama Center/Department of Emergency and Trauma Surgery, Tongji Hospital Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China

    Wei-Yang Wang, Fan Yang, Jia-Jun Chen, Jie Xie & Zhan-Fei Li

  2. Center for Genome Analysis, ABLife Inc., Wuhan, 430075, Hubei, China

    Weili Quan, Ya-Xun Wei & Yi Zhang

  3. Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, 430075, Hubei, China

    Weili Quan, Han Yu & Yi Zhang

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  1. Wei-Yang Wang
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Wang, WY., Quan, W., Yang, F. et al. RBM4 modulates the proliferation and expression of inflammatory factors via the alternative splicing of regulatory factors in HeLa cells. Mol Genet Genomics 295, 95–106 (2020). https://doi.org/10.1007/s00438-019-01606-3

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