title: In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers.
abstract: Translocations contribute to the genesis and progression of epithelial tumours and in particular to prostate cancer development. To better understand the contribution of fusion transcripts and visualize the clonal composition of multifocal tumours, we have developed a technology for multiplex in situ detection and identification of expressed fusion transcripts. When compared to immunohistochemistry, TMPRSS2-ERG fusion-negative and fusion-positive prostate tumours were correctly classified. The most prevalent TMPRSS2-ERG fusion variants were visualized, identified, and quantitated in human prostate cancer tissues, and the ratio of the variant fusion transcripts could for the first time be directly determined by in situ sequencing. Further, we demonstrate concurrent in situ detection of gene expression, point mutations, and gene fusions of the prostate cancer relevant targets AMACR, AR, TP53, and TMPRSS2-ERG. This unified approach to in situ analyses of somatic mutations can empower studies of intra-tumoural heterogeneity and future tissue-based diagnostics of mutations and translocations.
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Sara
authors.initials: S
authors.lastname: Kiflemariam
authors.forename: Marco
authors.initials: M
authors.lastname: Mignardi
authors.forename: Muhammad Akhtar
authors.initials: MA
authors.lastname: Ali
authors.forename: Anders
authors.initials: A
authors.lastname: Bergh
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
authors.forename: Tobias
authors.initials: T
authors.lastname: Sjöblom
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D015870:Gene Expression / Q000502:physiology; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008297:Male; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D017354:Point Mutation / Q000235:genetics*; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology; D012697:Serine Endopeptidases / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism; D000071230:Transcriptional Regulator ERG; D014178:Translocation, Genetic / Q000502:physiology
chemical_list: D014408:Biomarkers, Tumor; C072312:ERG protein, human; D015514:Oncogene Proteins, Fusion; D015534:Trans-Activators; D000071230:Transcriptional Regulator ERG; D012697:Serine Endopeptidases; C421305:TMPRSS2 protein, human
keywords: TMPRSS2-ERG; in situ sequencing; padlock probes; prostate cancer; somatic mutations