Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma

Sunniva Stordal Bjørklund ¹, Anshuman Panda ¹, Surendra Kumar ², Michael Seiler ¹, Doug Robinson ³, Jinesh Gheeya ¹, Ming Yao ¹, Grethe I Grenaker Alnæs ², Deborah Toppmeyer ¹, Margit Riis ⁴, Bjørn Naume ⁵, Anne-Lise Børresen-Dale ², Vessela N Kristensen ², Shridar Ganesan ⁶, Gyan Bhanot ⁷

Affiliations

¹ Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.
² Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.
³ BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA.
⁴ Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway.
⁵ Department of Oncology, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
⁶ Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA. ganesash@cinj.rutgers.edu.
⁷ Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA. gyanbhanot@gmail.com.

PMID: 28717182
66 References
8 citations

Abstract

Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort. Alternative exon usage was widespread, and although common events were shared among three subtypes, ER+ HER2-, ER- HER2-, and HER2+, many events on the exon level were subtype specific. Additional RNA-seq analysis was carried out in an independent cohort of 43 ER+ HER2- and ER- HER2- primary breast tumors, confirming many of the exon events identified in the TCGA cohort. Alternative splicing and transcriptional events detected in five genes, MYO6, EPB41L1, TPD52, IQCG, and ACOX2 were validated by qRT-PCR in a third cohort of 40 ER+ HER2- and ER- HER2- patients, showing that these events were truly subtype specific.

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References
Identification of alternative splicing markers for breast cancer. Julian P Venables, Roscoe Klinck, +17 authors, Sherif Abou Elela. less Cancer Res, 2008 Nov 18; 68(22). PMID: 19010929
CD44 enhances tumor aggressiveness by promoting tumor cell plasticity. Yvette W J Paulis, Elisabeth J M Huijbers, +4 authors, Arjan W Griffioen. less Oncotarget, 2015 Jul 21; 6(23). PMID: 26189059 Free PMC article.
Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer. Bjørn Naume, Xi Zhao, +10 authors, Therese Sørlie. less Mol Oncol, 2007 Sep 01; 1(2). PMID: 19383292 Free PMC article.
Rho GTPases in cancer cell biology. Francisco M Vega, Anne J Ridley. FEBS Lett, 2008 May 08; 582(14). PMID: 18460342 Highly Cited. Review.
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nicole Cloonan, Alistair R R Forrest, +16 authors, Sean M Grimmond. less Nat Methods, 2008 Jun 03; 5(7). PMID: 18516046 Highly Cited.
Function of alternative splicing. Olga Kelemen, Paolo Convertini, +4 authors, Stefan Stamm. less Gene, 2012 Aug 23; 514(1). PMID: 22909801 Free PMC article. Highly Cited. Review.
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bo Li, Colin N Dewey. BMC Bioinformatics, 2011 Aug 06; 12. PMID: 21816040 Free PMC article. Highly Cited.
Genotoxic stress modulates CDC25C phosphatase alternative splicing in human breast cancer cell lines. Hélène Albert, Eric Battaglia, Carolino Monteiro, Denyse Bagrel. Mol Oncol, 2012 Aug 09; 6(5). PMID: 22871320 Free PMC article.
Exon-level microarray analyses identify alternative splicing programs in breast cancer. Anna Lapuk, Henry Marr, +22 authors, Joe W Gray. less Mol Cancer Res, 2010 Jul 08; 8(7). PMID: 20605923 Free PMC article.
Determination of the specific activity of CDK1 and CDK2 as a novel prognostic indicator for early breast cancer. S J Kim, S Nakayama, +8 authors, S Noguchi. less Ann Oncol, 2007 Oct 25; 19(1). PMID: 17956886
Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. Stéphanie Cornen, Arnaud Guille, +16 authors, Max Chaffanet. less PLoS One, 2014 Jan 15; 9(1). PMID: 24416132 Free PMC article.
Role of the splicing factor SRSF4 in cisplatin-induced modifications of pre-mRNA splicing and apoptosis. Maude Gabriel, Yves Delforge, +7 authors, Charles Lambert. less BMC Cancer, 2015 Apr 18; 15. PMID: 25884497 Free PMC article.
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Ali Mortazavi, Brian A Williams, +2 authors, Kenneth McCue, Lorian Schaeffer, Barbara Wold. less Nat Methods, 2008 Jun 03; 5(7). PMID: 18516045 Highly Cited.
CD44 attenuates metastatic invasion during breast cancer progression. Jose I Lopez, Todd D Camenisch, +3 authors, Joyce A Schroeder. less Cancer Res, 2005 Aug 03; 65(15). PMID: 16061657
Molecular portraits of human breast tumours. C M Perou, T Sørlie, +15 authors, D Botstein. less Nature, 2000 Aug 30; 406(6797). PMID: 10963602 Highly Cited.
Expression of different tenascin isoforms in normal, hyperplastic and neoplastic human breast tissues. L Borsi, B Carnemolla, +3 authors, G Nicolò, B Spina, G Tanara, L Zardi. less Int J Cancer, 1992 Nov 11; 52(5). PMID: 1385335
Tamoxifen for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists' Collaborative Group. Lancet, 1998 May 30; 351(9114). PMID: 9605801 Highly Cited.
Protein 4.1, a component of the erythrocyte membrane skeleton and its related homologue proteins forming the protein 4.1/FERM superfamily. Witold Diakowski, Michał Grzybek, Aleksander F Sikorski. Folia Histochem Cytobiol, 2007 Jan 16; 44(4). PMID: 17219717 Review.
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Jing Chen, Eric E Bardes, Bruce J Aronow, Anil G Jegga. Nucleic Acids Res, 2009 May 26; 37(Web Server issue). PMID: 19465376 Free PMC article. Highly Cited.
High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Gabriela Alexe, Gul S Dalgin, +9 authors, Gyan Bhanot. less Cancer Res, 2007 Nov 17; 67(22). PMID: 18006808
Aberrant and alternative splicing in cancer. Julian P Venables. Cancer Res, 2004 Nov 03; 64(21). PMID: 15520162 Highly Cited. Review.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Cole Trapnell, Brian A Williams, +6 authors, Lior Pachter. less Nat Biotechnol, 2010 May 04; 28(5). PMID: 20436464 Free PMC article. Highly Cited.
Detecting differential usage of exons from RNA-seq data. Simon Anders, Alejandro Reyes, Wolfgang Huber. Genome Res, 2012 Jun 23; 22(10). PMID: 22722343 Free PMC article. Highly Cited.
Epigenetics in cancer. Manel Esteller. N Engl J Med, 2008 Mar 14; 358(11). PMID: 18337604 Highly Cited. Review.
The Rho guanine nucleotide exchange factor ARHGEF5 promotes tumor malignancy via epithelial-mesenchymal transition. Y Komiya, Y Onodera, +8 authors, M Okada. less Oncogenesis, 2016 Sep 13; 5(9). PMID: 27617642 Free PMC article.
Hallmarks of cancer: the next generation. Douglas Hanahan, Robert A Weinberg. Cell, 2011 Mar 08; 144(5). PMID: 21376230 Highly Cited. Review.
Insulin receptor activation by IGF-II in breast cancers: evidence for a new autocrine/paracrine mechanism. L Sciacca, A Costantino, +7 authors, A Belfiore. less Oncogene, 1999 May 06; 18(15). PMID: 10229198
Increased expression and activity of CDC25C phosphatase and an alternatively spliced variant in prostate cancer. Mustafa Ozen, Michael Ittmann. Clin Cancer Res, 2005 Jul 08; 11(13). PMID: 16000564
Protein kinase C-dependent mobilization of the alpha6beta4 integrin from hemidesmosomes and its association with actin-rich cell protrusions drive the chemotactic migration of carcinoma cells. I Rabinovitz, A Toker, A M Mercurio. J Cell Biol, 1999 Sep 09; 146(5). PMID: 10477766 Free PMC article.
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Kai Wang, Darshan Singh, +11 authors, Jinze Liu. less Nucleic Acids Res, 2010 Aug 31; 38(18). PMID: 20802226 Free PMC article. Highly Cited.
Analysis of integrin beta4 expression in human breast cancer: association with basal-like tumors and prognostic significance. Shaolei Lu, Karl Simin, Ashraf Khan, Arthur M Mercurio. Clin Cancer Res, 2008 Feb 19; 14(4). PMID: 18281537
A new mathematical model for relative quantification in real-time RT-PCR. M W Pfaffl. Nucleic Acids Res, 2001 May 09; 29(9). PMID: 11328886 Free PMC article. Highly Cited.
Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Thomas Fleischer, Arnoldo Frigessi, +12 authors, Vessela N Kristensen. less Genome Biol, 2014 Aug 26; 15(8). PMID: 25146004 Free PMC article. Highly Cited.
RNA sequencing of cancer reveals novel splicing alterations. Jeyanthy Eswaran, Anelia Horvath, +9 authors, Rakesh Kumar. less Sci Rep, 2013 Apr 23; 3. PMID: 23604310 Free PMC article. Highly Cited.
Negative regulation of DNMT3A de novo DNA methylation by frequently overexpressed UHRF family proteins as a mechanism for widespread DNA hypomethylation in cancer. Yuanhui Jia, Pishun Li, +17 authors, Jiemin Wong. less Cell Discov, 2016 Jul 28; 2. PMID: 27462454 Free PMC article.
Epidermal growth factor receptor coexpression modulates susceptibility to Herceptin in HER2/neu overexpressing breast cancer cells via specific erbB-receptor interaction and activation. Simone Diermeier, Gábor Horváth, +3 authors, Gero Brockhoff. less Exp Cell Res, 2005 Mar 08; 304(2). PMID: 15748904
Exonic expression profiling of breast cancer and benign lesions: a retrospective analysis. Fabrice André, Stefan Michiels, +9 authors, Suzette Delaloge. less Lancet Oncol, 2009 Mar 03; 10(4). PMID: 19249242
Clinical significance of the integrin α6β4 in human malignancies. Rachel L Stewart, Kathleen L O'Connor. Lab Invest, 2015 Jun 30; 95(9). PMID: 26121317 Free PMC article. Highly Cited. Review.
Release of cAMP gating by the alpha6beta4 integrin stimulates lamellae formation and the chemotactic migration of invasive carcinoma cells. K L O'Connor, L M Shaw, A M Mercurio. J Cell Biol, 1998 Dec 16; 143(6). PMID: 9852165 Free PMC article.
t(3;11)(q12;p15)/NUP98-LOC348801 fusion transcript in acute myeloid leukemia. Paolo Gorello, Lucia Brandimarte, +7 authors, Cristina Mecucci. less Haematologica, 2008 Jul 08; 93(9). PMID: 18603550
In IGF-I receptor-deficient leiomyosarcoma cells autocrine IGF-II induces cell invasion and protection from apoptosis via the insulin receptor isoform A. Laura Sciacca, Rossana Mineo, +3 authors, Antonino Belfiore. less Oncogene, 2002 Nov 26; 21(54). PMID: 12447687
Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. Soonmyung Paik, Gong Tang, +11 authors, Norman Wolmark. less J Clin Oncol, 2006 May 25; 24(23). PMID: 16720680 Highly Cited.
Functional and molecular features of the calmodulin-interacting protein IQCG required for haematopoiesis in zebrafish. Li-Ting Chen, Wen-Xue Liang, +11 authors, Sai-Juan Chen. less Nat Commun, 2014 May 03; 5. PMID: 24787902
Delta-lactoferrin, an intracellular lactoferrin isoform that acts as a transcription factor. Christophe Mariller, Stephan Hardivillé, +3 authors, Annick Pierce. less Biochem Cell Biol, 2012 Feb 11; 90(3). PMID: 22320386 Review.
Cyclin D3 predicts disease-free survival in breast cancer. Yayun Chi, Sheng Huang, +3 authors, Mengying Liu, Liang Guo, Xuxia Shen, Jiong Wu. less Cancer Cell Int, 2015 Sep 29; 15. PMID: 26412984 Free PMC article.
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Yixin Wang, Jan G M Klijn, +11 authors, John A Foekens. less Lancet, 2005 Feb 22; 365(9460). PMID: 15721472 Highly Cited.
Vav3 oncogene activates estrogen receptor and its overexpression may be involved in human breast cancer. Kiwon Lee, Yin Liu, +3 authors, Shan Lu. less BMC Cancer, 2008 Jun 04; 8. PMID: 18518979 Free PMC article.
Molecular classification of tamoxifen-resistant breast carcinomas by gene expression profiling. Maurice P H M Jansen, John A Foekens, +9 authors, Els M J J Berns. less J Clin Oncol, 2005 Feb 01; 23(4). PMID: 15681518
Genome-wide analysis of alternative transcripts in human breast cancer. Ji Wen, Kevin H Toomer, Zhibin Chen, Xiaodong Cai. Breast Cancer Res Treat, 2015 Apr 29; 151(2). PMID: 25913416 Free PMC article.
Steroid receptors in human breast cancer. W L McGuire. Cancer Res, 1978 Nov 01; 38(11 Pt 2). PMID: 698967
TPD52 represents a survival factor in ERBB2-amplified breast cancer cells. Nuruliza Roslan, Ivan Bièche, +3 authors, Jennifer A Byrne. less Mol Carcinog, 2013 May 11; 53(10). PMID: 23661506
PrLZ, a novel prostate-specific and androgen-responsive gene of the TPD52 family, amplified in chromosome 8q21.1 and overexpressed in human prostate cancer. Ruoxiang Wang, Jianchun Xu, +13 authors, Leland W K Chung. less Cancer Res, 2004 Mar 05; 64(5). PMID: 14996714
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Christina Curtis, Sohrab P Shah, +29 authors, Samuel Aparicio. less Nature, 2012 Apr 24; 486(7403). PMID: 22522925 Free PMC article. Highly Cited.
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Mitchell Guttman, Manuel Garber, +10 authors, Aviv Regev. less Nat Biotechnol, 2010 May 04; 28(5). PMID: 20436462 Free PMC article. Highly Cited.
Splicing imbalances in basal-like breast cancer underpin perturbation of cell surface and oncogenic pathways and are associated with patients' survival. Filipe Gracio, Brian Burford, +8 authors, Emanuele de Rinaldis. less Sci Rep, 2017 Jan 07; 7. PMID: 28059167 Free PMC article.
Dynamic exchange of myosin VI on endocytic structures. Lisa M Bond, Susan D Arden, +2 authors, John Kendrick-Jones, Folma Buss, James R Sellers. less J Biol Chem, 2012 Sep 21; 287(46). PMID: 22992744 Free PMC article.
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Cole Trapnell, Adam Roberts, +7 authors, Lior Pachter. less Nat Protoc, 2012 Mar 03; 7(3). PMID: 22383036 Free PMC article. Highly Cited.
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Liana F Lareau, Maki Inada, +2 authors, Richard E Green, Jordan C Wengrod, Steven E Brenner. less Nature, 2007 Mar 16; 446(7138). PMID: 17361132 Highly Cited.
Expression analysis of DNA methyltransferases 1, 3A, and 3B in sporadic breast carcinomas. Igor Girault, Sengül Tozlu, Rosette Lidereau, Ivan Bièche. Clin Cancer Res, 2003 Oct 14; 9(12). PMID: 14555514 Highly Cited.
The hD52 (TPD52) gene is a candidate target gene for events resulting in increased 8q21 copy number in human breast carcinoma. R L Balleine, M S Fejzo, +3 authors, P Sathasivam, P Basset, C L Clarke, J A Byrne. less Genes Chromosomes Cancer, 2000 Aug 05; 29(1). PMID: 10918393
A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen. Stephen K Chia, Vivien H Bramwell, +12 authors, Torsten O Nielsen. less Clin Cancer Res, 2012 Jun 20; 18(16). PMID: 22711706 Free PMC article. Highly Cited.
Integrin α6A splice variant regulates proliferation and the Wnt/β-catenin pathway in human colorectal cancer cells. Jean-François Groulx, Véronique Giroux, +4 authors, Jean-François Beaulieu. less Carcinogenesis, 2014 Jan 10; 35(6). PMID: 24403311 Free PMC article.
Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data. Miriam Ragle Aure, Israel Steinfeld, +9 authors, Zohar Yakhini. less PLoS One, 2013 Feb 06; 8(1). PMID: 23382830 Free PMC article.
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. T Sørlie, C M Perou, +14 authors, A L Børresen-Dale. less Proc Natl Acad Sci U S A, 2001 Sep 13; 98(19). PMID: 11553815 Free PMC article. Highly Cited.
Ultraconserved elements in the human genome. Gill Bejerano, Michael Pheasant, +4 authors, David Haussler. less Science, 2004 May 08; 304(5675). PMID: 15131266 Highly Cited.
Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas. Sunniva Stordal Bjørklund, Vessela N Kristensen, +9 authors, Shridar Ganesan. less BMC Cancer, 2015 Jul 18; 15. PMID: 26183823 Free PMC article.

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