title: Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression.
abstract: Breast cancer, the second leading cause of cancer death of women worldwide, is a heterogenous disease with multiple different subtypes. These subtypes carry important implications for prognosis and therapy. Interestingly, it is known that these different subtypes not only have different biological behaviors, but also have distinct gene expression profiles. However, it has not been rigorously explored whether particular transcriptional isoforms are also differentially expressed among breast cancer subtypes, or whether transcript isoforms from the same sets of genes can be used to differentiate subtypes. To address these questions, we analyzed the patterns of transcript isoform expression using a small set of RNA-sequencing data for eleven Estrogen Receptor positive (ER+) subtype and fourteen triple negative (TN) subtype tumors. We identified specific sets of isoforms that distinguish these tumor subtypes with higher fidelity than standard mRNA expression profiles. We found that alternate promoter usage, alternative splicing, and alternate 3'UTR usage are differentially regulated in breast cancer subtypes. Profiling of isoform expression in a second, independent cohort of 68 tumors confirmed that expression of splice isoforms differentiates breast cancer subtypes. Furthermore, analysis of RNAseq data from 594 cases from the TCGA cohort confirmed the ability of isoform usage to distinguish breast cancer subtypes. Also using our expression data, we identified several RNA processing factors that were differentially expressed between tumor subtypes and/or regulated by estrogen receptor, including YBX1, YBX2, MAGOH, MAGOHB, and PCBP2. RNAi knock-down of these RNA processing factors in MCF7 cells altered isoform expression. These results indicate that global dysregulation of splicing in breast cancer occurs in a subtype-specific and reproducible manner and is driven by specific differentially expressed RNA processing factors.
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Stricker
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States of America.
authors.forename: Christopher D
authors.identifier: 0000-0002-3785-5008
authors.initials: CD
authors.lastname: Brown
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.
authors.forename: Chaitanya
authors.initials: C
authors.lastname: Bandlamudi
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Department of Pathology, University of Chicago, Chicago, IL, United States of America.
authors.forename: Megan
authors.identifier: 0000-0002-8260-3598
authors.initials: M
authors.lastname: McNerney
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|McDermott Center for Human Growth and Development, University of Texas Southwestern, Dallas, TX, United States of America.
authors.forename: Ralf
authors.initials: R
authors.lastname: Kittler
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Cancer Biology and Epigenomics Program, Ann and Robert H. Lurie Children's Hospital of Chicago Research Center, Chicago, IL, United States of America.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Montoya
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Laboratory of Genetics, University of Wisconsin, Madison, WI, United States of America.
authors.forename: April
authors.initials: A
authors.lastname: Peterson
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Department of Medicine, University of Chicago, Chicago, IL, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Grossman
authors.affiliation: Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, United States of America.|Department of Medicine, University of Chicago, Chicago, IL, United States of America.|Department of Human Genetics, University of Chicago, Chicago, IL, United States of America.|Tempus Labs, Inc. Chicago, IL 60654, United States of America.
authors.forename: Kevin P
authors.identifier: 0000-0003-0079-419X
authors.initials: KP
authors.lastname: White
mesh_terms: D020413:3' Untranslated Regions; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D017398:Alternative Splicing; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism*; D015331:Cohort Studies; D047628:Estrogen Receptor alpha / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D061986:MCF-7 Cells; D008875:Middle Aged; D011379:Prognosis; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D017423:Sequence Analysis, RNA; D064726:Triple Negative Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; D020033:Protein Isoforms; D012333:RNA, Messenger