title: Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model.
abstract: The initiation and progression of breast cancer from the transformation of the normal epithelium to ductal carcinoma in situ (DCIS) and invasive disease is a complex process involving the acquisition of genetic alterations and changes in gene expression, alongside microenvironmental and recognized histological alterations. Here, we sought to comprehensively characterise the genomic and transcriptomic features of the MCF10 isogenic model of breast cancer progression, and to functionally validate potential driver alterations in three-dimensional (3D) spheroids that may provide insights into breast cancer progression, and identify targetable alterations in conditions more similar to those encountered in vivo. We performed whole genome, exome and RNA sequencing of the MCF10 progression series to catalogue the copy number and mutational and transcriptomic landscapes associated with progression. We identified a number of predicted driver mutations (including PIK3CA and TP53) that were acquired during transformation of non-malignant MCF10A cells to their malignant counterparts that are also present in analysed primary breast cancers from The Cancer Genome Atlas (TCGA). Acquisition of genomic alterations identified MYC amplification and previously undescribed RAB3GAP1-HRAS and UBA2-PDCD2L expressed in-frame fusion genes in malignant cells. Comparison of pathway aberrations associated with progression showed that, when cells are grown as 3D spheroids, they show perturbations of cancer-relevant pathways. Functional interrogation of the dependency on predicted driver events identified alterations in HRAS, PIK3CA and TP53 that selectively decreased cell growth and were associated with progression from preinvasive to invasive disease only when cells were grown as spheroids. Our results have identified changes in the genomic repertoire in cell lines representative of the stages of breast cancer progression, and demonstrate that genetic dependencies can be uncovered when cells are grown in conditions more like those in vivo. The MCF10 progression series therefore represents a good model with which to dissect potential biomarkers and to evaluate therapeutic targets involved in the progression of breast cancer. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.
authors: Sarah L
authors: SL
authors: Maguire
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
authors: Barrie
authors: B
authors: Peck
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
authors: Patty T
authors: PT
authors: Wai
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
authors: James
authors: J
authors: Campbell
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
authors: Holly
authors: H
authors: Barker
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
authors: Aditi
authors: A
authors: Gulati
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.
authors: Frances
authors: F
authors: Daley
authors: Division of Cancer Biology, The Institute of Cancer Research, London, UK.
authors: Simon
authors: S
authors: Vyse
authors: Division of Cancer Biology, The Institute of Cancer Research, London, UK.
authors: Paul
authors: P
authors: Huang
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
authors: Christopher J
authors: CJ
authors: Lord
authors: Institute of Cancer Sciences, University of Manchester, Manchester, UK.
authors: Gillian
authors: G
authors: Farnie
authors: Faculty of Life Sciences, University of Manchester, Manchester, UK.
authors: Keith
authors: K
authors: Brennan
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK. rachael.natrajan@icr.ac.uk.|Division of Molecular Pathology, The Institute of Cancer Research, London, UK. rachael.natrajan@icr.ac.uk.
authors: Rachael
authors: R
authors: Natrajan
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D018270:Carcinoma, Ductal, Breast / Q000235:genetics* / Q000473:pathology; D002285:Carcinoma, Intraductal, Noninfiltrating / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D002471:Cell Transformation, Neoplastic; D058534:Class I Phosphatidylinositol 3-Kinases; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics; D018450:Disease Progression; D059472:Exome / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008954:Models, Biological; D009154:Mutation; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D018874:Spheroids, Cellular; D059467:Transcriptome; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D004273:DNA, Neoplasm; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D019869:Phosphatidylinositol 3-Kinases; D058534:Class I Phosphatidylinositol 3-Kinases; C484760:PIK3CA protein, human
keywords: 3D spheroid assays; breast cancer progression; next-generation sequencing