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Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts

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Abstract

Beta-microseminoprotein (MSP)/MSMB is an immunoglobulin superfamily protein synthesized by prostate epithelial cells and secreted into seminal plasma. Variants in the promoter of the MSMB gene have been associated with the risk of prostate cancer (PCa) in several independent genome-wide association studies. Both MSMB and an adjacent gene, NCOA4, are subjected to transcriptional control via androgen response elements. The gene product of NCOA4 interacts directly with the androgen receptor as a co-activator to enhance AR transcriptional activity. Here, we provide evidence for the expression of full-length MSMB-NCOA4 fusion transcripts regulated by the MSMB promoter. The predominant MSMB-NCOA4 transcript arises by fusion of the 5′UTR and exons 1–2 of the MSMB pre-mRNA, with exons 2–10 of the NCOA4 pre-mRNA, producing a stable fusion protein, comprising the essential domains of NCOA4. Analysis of the splice sites of this transcript shows an unusually strong splice acceptor at NCOA4 exon 2 and the presence of Alu repeats flanking the exons potentially involved in the splicing event. Transfection experiments using deletion clones of the promoter coupled with luciferase reporter assays define a core MSMB promoter element located between −27 and −236 of the gene, and a negative regulatory element immediately upstream of the start codon. Computational network analysis reveals that the MSMB gene is functionally connected to NCOA4 and the androgen receptor signaling pathway. The data provide an example of how GWAS-associated variants may have multiple genetic and epigenetic effects.

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Abbreviations

ARE:

Androgen response element

AR:

Androgen receptor

GWAS:

Genome-wide association studies

PCa:

Prostate cancer

References

  • Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, Novik A, Sorek R (2006) Transcription-mediated gene fusion in the human genome. Genome Res 16:30–36

    Article  PubMed  CAS  Google Scholar 

  • Al-Balool HH, Weber D, Liu Y, Wade M, Guleria K, Nam PL, Clayton J, Rowe W, Coxhead J, Irving J, Elliott DJ, Hall AG, Santibanez-Koref M, Jackson MS (2011) Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Res 21:1788–1799

    Article  PubMed  CAS  Google Scholar 

  • Alen P, Claessens F, Schoenmakers E, Swinnen JV, Verhoeven G, Rombauts W, Peeters B (1999) Interaction of the putative androgen receptor-specific coactivator ARA70/ELE1alpha with multiple steroid receptors and identification of an internally deleted ELE1beta isoform. Mol Endocrinol 13:117–128

    Article  PubMed  CAS  Google Scholar 

  • Bjartell AS, Al-Ahmadie H, Serio AM, Eastham JA, Eggener SE, Fine SW, Udby L, Gerald WL, Vickers AJ, Lilja H, Reuter VE, Scardino PT (2007) Association of cysteine-rich secretory protein 3 and beta-microseminoprotein with outcome after radical prostatectomy. Clin Cancer Res 13:4130–4138

    Article  PubMed  CAS  Google Scholar 

  • Chang BL, Cramer SD, Wiklund F, Isaacs SD, Stevens VL, Sun J, Smith S, Pruett K, Romero LM, Wiley KE, Kim ST, Zhu Y, Zhang Z, Hsu FC, Turner AR, Adolfsson J, Liu W, Kim JW, Duggan D, Carpten J, Zheng SL, Rodriguez C, Isaacs WB, Gronberg H, Xu J (2009) Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum Mol Genet 18:1368–1375

    Article  PubMed  CAS  Google Scholar 

  • Choi YL, Takeuchi K, Soda M, Inamura K, Togashi Y, Hatano S, Enomoto M, Hamada T, Haruta H, Watanabe H, Kurashina K, Hatanaka H, Ueno T, Takada S, Yamashita Y, Sugiyama Y, Ishikawa Y, Mano H (2008) Identification of novel isoforms of the EML4-ALK transforming gene in non-small cell lung cancer. Cancer Res 68:4971–4976

    Article  PubMed  CAS  Google Scholar 

  • Chung CC, Chanock SJ (2011) Current status of genome-wide association studies in cancer. Hum Genet 130:59–78

    Article  PubMed  Google Scholar 

  • Crawford ED (2003) Epidemiology of prostate cancer. Urology 62:3–12

    Article  PubMed  Google Scholar 

  • Denayer S, Helsen C, Thorrez L, Haelens A, Claessens F (2010) The rules of DNA recognition by the androgen receptor. Mol Endocrinol 24:898–913

    Article  PubMed  CAS  Google Scholar 

  • Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigo R, Gingeras TR, Antonarakis SE, Reymond A (2007) Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17:746–759

    Article  PubMed  CAS  Google Scholar 

  • Eeles RA, Kote-Jarai Z, Giles GG, Olama AA, Guy M, Jugurnauth SK, Mulholland S, Leongamornlert DA, Edwards SM, Morrison J, Field HI, Southey MC, Severi G, Donovan JL, Hamdy FC, Dearnaley DP, Muir KR, Smith C, Bagnato M, Ardern-Jones AT, Hall AL, O’Brien LT, Gehr-Swain BN, Wilkinson RA, Cox A, Lewis S, Brown PM, Jhavar SG, Tymrakiewicz M, Lophatananon A, Bryant SL, Horwich A, Huddart RA, Khoo VS, Parker CC, Woodhouse CJ, Thompson A, Christmas T, Ogden C, Fisher C, Jamieson C, Cooper CS, English DR, Hopper JL, Neal DE, Easton DF (2008) Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 40:316–321

    Article  PubMed  CAS  Google Scholar 

  • Fabre S, Manin M, Pailhoux E, Veyssiere G, Jean C (1994) Identification of a functional androgen response element in the promoter of the gene for the androgen-regulated aldose reductase-like protein specific to the mouse vas deferens. J Biol Chem 269:5857–5864

    PubMed  CAS  Google Scholar 

  • Fears S, Mathieu C, Zeleznik-Le N, Huang S, Rowley JD, Nucifora G (1996) Intergenic splicing of MDS1 and EVI1 occurs in normal tissues as well as in myeloid leukemia and produces a new member of the PR domain family. Proc Natl Acad Sci USA 93:1642–1647

    Article  PubMed  CAS  Google Scholar 

  • Gray TA, Saitoh S, Nicholls RD (1999) An imprinted, mammalian bicistronic transcript encodes two independent proteins. Proc Natl Acad Sci USA 96:5616–5621

    Article  PubMed  CAS  Google Scholar 

  • Horiuchi T, Aigaki T (2006) Alternative trans-splicing: a novel mode of pre-mRNA processing. Biol Cell 98:135–140

    Article  PubMed  CAS  Google Scholar 

  • Kaye FJ (2009) Mutation-associated fusion cancer genes in solid tumors. Mol Cancer Ther 8:1399–1408

    Article  PubMed  CAS  Google Scholar 

  • Koivunen JP, Mermel C, Zejnullahu K, Murphy C, Lifshits E, Holmes AJ, Choi HG, Kim J, Chiang D, Thomas R, Lee J, Richards WG, Sugarbaker DJ, Ducko C, Lindeman N, Marcoux JP, Engelman JA, Gray NS, Lee C, Meyerson M, Janne PA (2008) EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer. Clin Cancer Res 14:4275–4283

    Article  PubMed  CAS  Google Scholar 

  • Kumar AR, Li Q, Hudson WA, Chen W, Sam T, Yao Q, Lund EA, Wu B, Kowal BJ, Kersey JH (2009) A role for MEIS1 in MLL-fusion gene leukemia. Blood 113:1756–1758

    Article  PubMed  CAS  Google Scholar 

  • Li H, Wang J, Mor G, Sklar J (2008) A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 321:1357–1361

    Article  PubMed  CAS  Google Scholar 

  • Lou H, Yeager M, Li H, Bosquet JG, Hayes RB, Orr N, Yu K, Hutchinson A, Jacobs KB, Kraft P, Wacholder S, Chatterjee N, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Ma J, Gaziano JM, Stampfer M, Schumacher FR, Giovannucci E, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Anderson SK, Tucker M, Hoover RN, Fraumeni JF Jr, Thomas G, Hunter DJ, Dean M, Chanock SJ (2009) Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility. Proc Natl Acad Sci USA 106:7933–7938

    Article  PubMed  CAS  Google Scholar 

  • Mitelman F, Johansson B, Mertens F (2004) Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet 36:331–334

    Article  PubMed  CAS  Google Scholar 

  • Mitelman F, Mertens F, Johansson B (2005) Prevalence estimates of recurrent balanced cytogenetic aberrations and gene fusions in unselected patients with neoplastic disorders. Genes Chromosom Cancer 43:350–366

    Article  PubMed  CAS  Google Scholar 

  • Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S, Wu TD (2011) Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics 4:11

    Google Scholar 

  • Niu Y, Yeh S, Miyamoto H, Li G, Altuwaijri S, Yuan J, Han R, Ma T, Kuo HC, Chang C (2008) Tissue prostate-specific antigen facilitates refractory prostate tumor progression via enhancing ARA70-regulated androgen receptor transactivation. Cancer Res 68:7110–7119

    Article  PubMed  CAS  Google Scholar 

  • Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, Antonarakis SE, Guigo R (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res 16:37–44

    Article  PubMed  CAS  Google Scholar 

  • Peng Y, Li CX, Chen F, Wang Z, Ligr M, Melamed J, Wei J, Gerald W, Pagano M, Garabedian MJ, Lee P (2008) Stimulation of prostate cancer cellular proliferation and invasion by the androgen receptor co-activator ARA70. Am J Pathol 172:225–235

    Article  PubMed  CAS  Google Scholar 

  • Perner S, Wagner PL, Demichelis F, Mehra R, Lafargue CJ, Moss BJ, Arbogast S, Soltermann A, Weder W, Giordano TJ, Beer DG, Rickman DS, Chinnaiyan AM, Moch H, Rubin MA (2008) EML4-ALK fusion lung cancer: a rare acquired event. Neoplasia 10:298–302

    PubMed  CAS  Google Scholar 

  • Pomerantz MM, Shrestha Y, Flavin RJ, Regan MM, Penney KL, Mucci LA, Stampfer MJ, Hunter DJ, Chanock SJ, Schafer EJ, Chan JA, Tabernero J, Baselga J, Richardson AL, Loda M, Oh WK, Kantoff PW, Hahn WC, Freedman ML (2010) Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis. PLoS Genet 6:e1001204

    Article  PubMed  Google Scholar 

  • Qi W, Gao S, Chu J, Zhou L, Wang Z (2012) Negative androgen-response elements mediate androgen-dependent transcriptional inhibition of TGF-beta1 and CDK2 promoters in the prostate gland. J Androl 33:27–36

    Article  PubMed  CAS  Google Scholar 

  • Rabbitts TH (1994) Chromosomal translocations in human cancer. Nature 372:143–149

    Article  PubMed  CAS  Google Scholar 

  • Reeves JR, Dulude H, Panchal C, Daigneault L, Ramnani DM (2006) Prognostic value of prostate secretory protein of 94 amino acids and its binding protein after radical prostatectomy. Clin Cancer Res 12:6018–6022

    Article  PubMed  CAS  Google Scholar 

  • Rickman DS, Pflueger D, Moss B, VanDoren VE, Chen CX, de la Taille A, Kuefer R, Tewari AK, Setlur SR, Demichelis F, Rubin MA (2009) SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer. Cancer Res 69:2734–2738

    Article  PubMed  CAS  Google Scholar 

  • Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131:1190–1203

    Article  PubMed  CAS  Google Scholar 

  • Rogan PK, Faux BM, Schneider TD (1998) Information analysis of human splice site mutations. Hum Mutat 12:153–171

    Article  PubMed  CAS  Google Scholar 

  • Rowley JD (2001) Chromosome translocations: dangerous liaisons revisited. Nat Rev Cancer 1:245–250

    Article  PubMed  CAS  Google Scholar 

  • Santoro M, Dathan NA, Berlingieri MT, Bongarzone I, Paulin C, Grieco M, Pierotti MA, Vecchio G, Fusco A (1994) Molecular characterization of RET/PTC3; a novel rearranged version of the RETproto-oncogene in a human thyroid papillary carcinoma. Oncogene 9:509–516

    PubMed  CAS  Google Scholar 

  • Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, Bando M, Ohno S, Ishikawa Y, Aburatani H, Niki T, Sohara Y, Sugiyama Y, Mano H (2007) Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 448:561–566

    Article  PubMed  CAS  Google Scholar 

  • Thierry MD, Thierry MJ (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol 7:S12–S14

    Article  Google Scholar 

  • Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, Orr N, Yu K, Chatterjee N, Welch R, Hutchinson A, Crenshaw A, Cancel-Tassin G, Staats BJ, Wang Z, Gonzalez-Bosquet J, Fang J, Deng X, Berndt SI, Calle EE, Feigelson HS, Thun MJ, Rodriguez C, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Giovannucci E, Willett WC, Cussenot O, Valeri A, Andriole GL, Crawford ED, Tucker M, Gerhard DS, Fraumeni JF Jr, Hoover R, Hayes RB, Hunter DJ, Chanock SJ (2008) Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 40:310–315

    Article  PubMed  CAS  Google Scholar 

  • Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310:644–648

    Article  PubMed  CAS  Google Scholar 

  • Tomlins SA, Laxman B, Dhanasekaran SM, Helgeson BE, Cao X, Morris DS, Menon A, Jing X, Cao Q, Han B, Yu J, Wang L, Montie JE, Rubin MA, Pienta KJ, Roulston D, Shah RB, Varambally S, Mehra R, Chinnaiyan AM (2007) Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 448:595–599

    Article  PubMed  CAS  Google Scholar 

  • Valtonen-Andre C, Savblom C, Fernlund P, Lilja H, Giwercman A, Lundwall A (2008) Beta-microseminoprotein in serum correlates with the levels in seminal plasma of young, healthy males. J Androl 29:330–337

    Article  PubMed  CAS  Google Scholar 

  • Yeh S, Chang C (1996) Cloning and characterization of a specific coactivator, ARA70, for the androgen receptor in human prostate cells. Proc Natl Acad Sci USA 93:5517–5521

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors would like to thank Allison Bierly and Wei Tan for critical reading of the manuscript and helpful comments. The project was supported in part by the Intramural Research Program of the National Institutes of Health, National Cancer Institute, Center for Cancer Research, and from SAIC-Frederick under contract #NO1-CO-12400. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments comply with the current laws of the United States of America.

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Authors and Affiliations

  1. Human Genetics Section, Basic Research Program, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD, 21702, USA

    Hong Lou

  2. Molecular Immunology Section, Basic Research Program, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD, 21702, USA

    Hongchuan Li & Stephen K. Anderson

  3. Core Genotyping Facility, Advanced Technology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD, 21702, USA

    Meredith Yeager

  4. Cancer and Inflammation Program, Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702, USA

    Kate Im, Bert Gold, Stephen K. Anderson & Michael Dean

  5. Gene Regulation and Chromosome Biology Laboratory, Molecular Information Theory Group, Frederick, MD, 21702, USA

    Thomas D. Schneider

  6. Division of Cancer Epidemiology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA

    Joseph F. Fraumeni Jr. & Stephen J. Chanock

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  1. Hong Lou
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  10. Michael Dean
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Correspondence to Stephen K. Anderson or Michael Dean.

Additional information

H. Lou and H. Li contributed equally to this work.

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Figure S1. Representation of the junction sites of the MSMB-NCOA4 transcripts. The MSMB-NCOA4 fusions are colored, numbered and arrowed from the original reference sequences. Line graphs show the position and cDNA sequence of the fusion points. Bottom-left panel shows the sequencing result of the 5′ RACE assay for MSMB-NCOA4 1 fusion transcript, including MSMB exon 1, MSMB exon 2, partial of NCOA4 exon 2 and 5′RACE primer sites.

Figure S2. Comparison of several concensus published androgen response elements (ARE) sequences and the four MSMB-NCO4 region ARE-like motifs.

Figure S3. BiblioSphere Pathway view network of the MSMB gene co-citated with the NCOA4 gene. A network of 21 genes was identified by analysis of MSMB-related genes with the BiblioSpherePathwayEdition software package based on co-citations with transcription factors, functional co-citations, and co-citations with other genes in the network. The nodes represent the genes. The BLACK edges indicate co-citation of two genes in the PubMed database; the GREEN edges indicate the presence of a significant TFBS on the promoter of the given gene for the specific interacting transcription factor.

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Lou, H., Li, H., Yeager, M. et al. Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts. Hum Genet 131, 1453–1466 (2012). https://doi.org/10.1007/s00439-012-1182-2

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