title: Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications.
abstract: Advances in genomic and transcriptome sequencing are revealing the massive scale of previously unrecognised alterations occurring during neoplastic transformation. Breast cancers are genetically and phenotypically heterogeneous. Each of the three major subtypes [ERBB2 amplified, estrogen receptor (ESR)-positive and triple-negative] poses diagnostic and therapeutic challenges. Here we show, using high-resolution next-generation transcriptome sequencing, that in all three breast cancer subtypes, but not matched controls, there was significant overexpression of transcripts from intronic and untranslated regions in addition to exons from specific genes, particularly amplified oncogenes and hormone receptors. For key genes ERBB2 and ESR1, we demonstrate that overexpression is linked to the production of highly modified and truncated splice variants in tumours, but not controls, correlated with tumour subtype. Translation of these tumour-specific splice variants generates truncated proteins with altered subcellular locations and functions, modifying the phenotype, affecting tumour biology, and targeted antitumour therapies. In contrast, tumour suppressors TP53, BRCA1/2 and NF1 did not show intronic overexpression or truncated splice variants in cancers. These findings emphasize the detection of intronic as well as exonic changes in the transcriptional landscapes of cancers have profound therapeutic implications.
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Shiva Seyed
authors.initials: SS
authors.lastname: Forootan
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Joe M
authors.initials: JM
authors.lastname: Butler
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Derek
authors.initials: D
authors.lastname: Gardener
authors.forename: Dawn
authors.initials: D
authors.lastname: Jones
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Alison E
authors.initials: AE
authors.lastname: Baird
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Dodson
authors.affiliation: Center for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Alistair
authors.initials: A
authors.lastname: Darby
authors.affiliation: Center for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: John
authors.initials: J
authors.lastname: Kenny
authors.affiliation: Center for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.affiliation: Center for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Cossins
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Foster
authors.affiliation: Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Gosden
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D019313:BRCA1 Protein / Q000096:biosynthesis; D024682:BRCA2 Protein / Q000096:biosynthesis; D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology; D047628:Estrogen Receptor alpha / Q000096:biosynthesis* / Q000235:genetics; D005091:Exons; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns / Q000235:genetics; D009154:Mutation; D025542:Neurofibromin 1 / Q000096:biosynthesis; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000096:biosynthesis* / Q000235:genetics; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*; D016159:Tumor Suppressor Protein p53 / Q000096:biosynthesis
chemical_list: D019313:BRCA1 Protein; D024682:BRCA2 Protein; D047628:Estrogen Receptor alpha; D025542:Neurofibromin 1; D018719:Erb-b2 Receptor Tyrosine Kinases; D016159:Tumor Suppressor Protein p53; C506487:ESR1 protein, human; C495901:TP53 protein, human; C508053:ERBB2 protein, human