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Genomic evolution and chemoresistance in germ-cell tumours



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Taylor-Weiner A1,2, Zack T1,3, O’Donnell E4,5, Guerriero JL4, Bernard B4, Reddy A6, Han GC2,4, AlDubayan S7,8, Amin-Mansour A2, Schumacher SE2, Litchfield K9,10, Turnbull C9,10, Gabriel S2, Beroukhim R2,4, Getz G2,11, Carter SL2,12,13,14, Hirsch MS15, Letai A4, Sweeney C4, Van Allen EM2,4,12.


1Division of Medical Sciences, Harvard University, Boston, Massachusetts 02115, USA.
2Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
3Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts 02115, USA.
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
5Department of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
6Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
7Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Massachusetts 02115, USA.
8Department of Medicine, King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia.
9Division of Genetics and Epidemiology, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
10William Harvey Research Institute, Queen Mary University London, Charterhouse Square, London EC1M 6BQ, UK.
11Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
12Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
13Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 , USA.
14Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.
15Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts 02115, USA.

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Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types. These tumours also acquire KRAS mutations during the development from precursor to primary disease, and primary testicular GCTs (TGCTs) are uniformly wild type for TP53. In addition, by functional measurement of apoptotic signalling (BH3 profiling) of fresh tumour and adjacent tissue, we find that primary TGCTs have high mitochondrial priming that facilitates chemotherapy-induced apoptosis. Finally, by phylogenetic analysis of serial TGCTs that emerge with chemotherapy resistance, we show how TGCTs gain additional reciprocal loss of heterozygosity and that this is associated with loss of pluripotency markers (NANOG and POU5F1) in chemoresistant teratomas or transformed carcinomas. Our results demonstrate the distinct genomic features underlying the origins of this disease and associated with the chemosensitivity phenotype, as well as the rare progression to chemoresistance. These results identify the convergence of cancer genomics, mitochondrial priming and GCT evolution, and may provide insights into chemosensitivity and resistance in other cancers.