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      The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

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          Abstract

          Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.

          Abstract

          Hepatocellular carcinoma has one of the poorest survival rates amongst cancers. Here, the authors highlight the intra-tumour heterogeneity of this disease, finding that spatially closer tumour sectors are genetically more similar and that intra-hepatic metastasis is accompanied by rapid genetic diversification.

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          Most cited references23

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          A genetic model for colorectal tumorigenesis.

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            Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft

            Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumor progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumor, a brain metastasis, and a xenograft derived from the primary tumor. The metastasis contained two de novo mutations and a large deletion not present in the primary tumor, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumor mutations, and displayed a mutation enrichment pattern that paralleled the metastasis (16 of 20 genes). Two overlapping large deletions, encompassing CTNNA1, were present in all three tumor samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared to the primary tumor suggest that secondary tumors may arise from a minority of cells within the primary.
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              Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.

              Liver cancer, which is most often associated with virus infection, is prevalent worldwide, and its underlying etiology and genomic structure are heterogeneous. Here we provide a whole-genome landscape of somatic alterations in 300 liver cancers from Japanese individuals. Our comprehensive analysis identified point mutations, structural variations (STVs), and virus integrations, in noncoding and coding regions. We discovered mutational signatures related to liver carcinogenesis and recurrently mutated coding and noncoding regions, such as long intergenic noncoding RNA genes (NEAT1 and MALAT1), promoters, CTCF-binding sites, and regulatory regions. STV analysis found a significant association with replication timing and identified known (CDKN2A, CCND1, APC, and TERT) and new (ASH1L, NCOR1, and MACROD2) cancer-related genes that were recurrently affected by STVs, leading to altered expression. These results emphasize the value of whole-genome sequencing analysis in discovering cancer driver mutations and understanding comprehensive molecular profiles of liver cancer, especially with regard to STVs and noncoding mutations.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                27 February 2017
                2017
                : 8
                : 4565
                Affiliations
                [1 ]Department of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research , 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
                [2 ]Department of Pathology, Singapore General Hospital , Singapore 169608, Singapore
                [3 ]Division of Surgical Oncology, National Cancer Centre , Singapore 169610, Singapore
                [4 ]School of Biological Sciences, Nanyang Technological University , Singapore 637551, Singapore
                [5 ]Department of Hepato-Pancreato-Biliary and Transplant Surgery, Singapore General Hospital , Singapore 169608, Singapore
                [6 ]Division of Medical Oncology, National Cancer Centre , Singapore 169610, Singapore
                [7 ]School of Computing, National University of Singapore, 13 Computing Drive , Singapore 117417, Singapore
                [8 ]Cardiovascular Research Institute, National University of Singapore, National University Healthcare System , Singapore 119228, Singapore
                [9 ]Office of Clinical Sciences, Duke-NUS Graduate Medical School , Singapore 169857, Singapore
                Author notes
                [*]

                These authors contributed equally to this work.

                [†]

                These authors jointly supervised this work.

                Author information
                http://orcid.org/0000-0003-1182-0023
                http://orcid.org/0000-0002-7060-2213
                Article
                ncomms14565
                10.1038/ncomms14565
                5333358
                28240289
                dc24a651-369c-44b1-8001-bb8e8ad93e97
                Copyright © 2017, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 11 October 2016
                : 12 January 2017
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