title: Splicing imbalances in basal-like breast cancer underpin perturbation of cell surface and oncogenic pathways and are associated with patients' survival.
abstract: Despite advancements in the use of transcriptional information to understand and classify breast cancers, the contribution of splicing to the establishment and progression of these tumours has only recently starting to emerge. Our work explores this lesser known landscape, with special focus on the basal-like breast cancer subtype where limited therapeutic opportunities and no prognostic biomarkers are currently available. Using ExonArray analysis of 176 breast cancers and 9 normal breast tissues we demonstrate that splicing levels significantly contribute to the diversity of breast cancer molecular subtypes and explain much of the differences compared with normal tissues. We identified pathways specifically affected by splicing imbalances whose perturbation would be hidden from a conventional gene-centric analysis of gene expression. We found that a large fraction of them involve cell-to-cell communication, extracellular matrix and transport, as well as oncogenic and immune-related pathways transduced by plasma membrane receptors. We identified 247 genes in which splicing imbalances are associated with clinical patients' outcome, whilst no association was detectable at the gene expression level. These include the signaling gene TGFBR1, the proto-oncogene MYB as well as many immune-related genes such as CCR7 and FCRL3, reinforcing evidence for a role of immune components in influencing breast cancer patients' prognosis.
authors.affiliation: Guy's and St Thomas' NHS Foundation Trust and King's College London NIHR Biomedical Research Centre - Translational Bioinformatics Platform, Guy's Hospital, London, UK.
authors.forename: Filipe
authors.initials: F
authors.lastname: Gracio
authors.affiliation: Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.
authors.forename: Brian
authors.initials: B
authors.lastname: Burford
authors.affiliation: Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.|Research Oncology, King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London, UK.
authors.forename: Patrycja
authors.initials: P
authors.lastname: Gazinska
authors.affiliation: Cancer Epidemiology Group, King's Health Partners AHSC, King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London, UK.
authors.forename: Anca
authors.initials: A
authors.lastname: Mera
authors.affiliation: Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.
authors.forename: Aisyah
authors.initials: A
authors.lastname: Mohd Noor
authors.affiliation: Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.
authors.forename: Pierfrancesco
authors.initials: P
authors.lastname: Marra
authors.affiliation: Research Oncology, King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London, UK.|King's Health Partners Cancer Biobank, King's College London Faculty of Life Sciences &Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London, UK.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Gillett
authors.affiliation: Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.
authors.forename: Anita
authors.initials: A
authors.lastname: Grigoriadis
authors.affiliation: Research Oncology, King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London, UK.|King's Health Partners Cancer Biobank, King's College London Faculty of Life Sciences &Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: Pinder
authors.affiliation: Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.|Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, 237 Fulham Road, London.
authors.forename: Andrew
authors.initials: A
authors.lastname: Tutt
authors.affiliation: Guy's and St Thomas' NHS Foundation Trust and King's College London NIHR Biomedical Research Centre - Translational Bioinformatics Platform, Guy's Hospital, London, UK.|Breast Cancer Now Research Unit King's College London, School of Medicine, Division of Cancer Studies, Bermondsey Wing, Guy's Hospital, London.
authors.forename: Emanuele
authors.initials: E
authors.lastname: de Rinaldis
mesh_terms: D017398:Alternative Splicing; D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics* / Q000401:mortality*; D063646:Carcinogenesis / Q000235:genetics*; D005091:Exons; D005260:Female; D015870:Gene Expression; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics*; D000090063:Proto-Oncogene Mas; D015398:Signal Transduction
chemical_list: C000715470:MAS1 protein, human; D008565:Membrane Proteins; D000090063:Proto-Oncogene Mas