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Southworth E, Thomson JP, Croy I, Churchman M, Arends MJ, Hollis RL, Gourley C, Herrington CS. Whole exome sequencing reveals diverse genomic relatedness between paired concurrent endometrial and ovarian carcinomas. Eur J Cancer 2024; 208:114205. [PMID: 38986422 DOI: 10.1016/j.ejca.2024.114205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
INTRODUCTION Concurrent non-serous endometrial and ovarian tumours are often managed clinically as two separate primary tumours, but almost all exhibit evidence of a genomic relationship. METHODOLOGY This study investigates the extent of relatedness using whole exome sequencing, which was performed on paired non-serous endometrial and ovarian carcinomas from 27 patients with concurrent tumours in a cohort with detailed clinicopathological annotation. Four whole exome sequencing-derived parameters (mutation, mutational burden, mutational signatures and mutant allele tumour heterogeneity scores) were used to develop a novel unsupervised model for the assessment of genomic similarity to infer genomic relatedness of paired tumours. RESULTS This novel model demonstrated genomic relatedness across all four parameters in all tumour pairs. Mutations in PTEN, ARID1A, CTNNB1, KMT2D and PIK3CA occurred most frequently and 24 of 27 (89 %) tumour pairs shared identical mutations in at least one of these genes, with all pairs sharing mutations in a number of other genes. Ovarian endometriosis, CTNNB1 exon 3 mutation, and progression and death from disease were present across the similarity ranking. Mismatch repair deficiency was associated with less genomically similar pairs. DISCUSSION Although there was diversity across the cohort, the presence of genomic similarity in all paired tumours supports the hypothesis that concurrent non-serous endometrial and ovarian carcinomas are genomically related and may have arisen from a common origin.
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Affiliation(s)
- Emily Southworth
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - John P Thomson
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ian Croy
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Mark J Arends
- Edinburgh Pathology, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert L Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - C Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Edinburgh Pathology, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
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Zhao Y, Zhang B, Ma Y, Guo M, Zhao F, Chen J, Wang B, Jin H, Zhou F, Guan J, Zhao Q, Liu Q, Wang H, Zhao F, Wang X. Distinct molecular profiles drive multifaceted characteristics of colorectal cancer metastatic seeds. J Exp Med 2024; 221:e20231359. [PMID: 38502057 PMCID: PMC10949939 DOI: 10.1084/jem.20231359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/20/2024] Open
Abstract
Metastasis of primary tumors remains a challenge for early diagnosis and prevention. The cellular properties and molecular drivers of metastatically competent clones within primary tumors remain unclear. Here, we generated 10-16 single cell-derived lines from each of three colorectal cancer (CRC) tumors to identify and characterize metastatic seeds. We found that intrinsic factors conferred clones with distinct metastatic potential and cellular communication capabilities, determining organ-specific metastasis. Poorly differentiated or highly metastatic clones, rather than drug-resistant clones, exhibited poor clinical prognostic impact. Personalized genetic alterations, instead of mutation burden, determined the occurrence of metastatic potential during clonal evolution. Additionally, we developed a gene signature for capturing metastatic potential of primary CRC tumors and demonstrated a strategy for identifying metastatic drivers using isogenic clones with distinct metastatic potential in primary tumors. This study provides insight into the origin and mechanisms of metastasis and will help develop potential anti-metastatic therapeutic targets for CRC patients.
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Affiliation(s)
- Yuanyuan Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, China
| | - Bing Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiming Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fuqiang Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianan Chen
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingzhi Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Jin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fulai Zhou
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiawei Guan
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qian Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, China
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Elgun T, Yurttas AG, Cinar K, Ozcelik S, Gul A. Effect of aza-BODIPY-photodynamic therapy on the expression of carcinoma-associated genes and cell death mode. Photodiagnosis Photodyn Ther 2023; 44:103849. [PMID: 37863378 DOI: 10.1016/j.pdpdt.2023.103849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
BACKGROUND Breast cancer is the most common cancer affecting women worldwide.Photodynamic therapy(PDT) has now proven to be a promising form of cancer therapy due to its targeted and low cytotoxicity to healthy cells and tissues.PDT is a technique used to create cell death localized by light after application of a light-sensitive agent.Aza-BODIPY is a promising photosensitizer for use in PDT. Our results showed that aza-BODIPY-PDT induced apoptosis, probably through p53 and caspase3 in MCF-7 cells. Future studies should delineate the molecular mechanisms underlying aza-BODIPY-PDT-induced cell death for a better understanding of the signaling pathways modulated by the therapy so that this novel technology could be implemented in the clinic for treating breast cancer. AIM In this study,we aimed to determine the change in the expression levels of 88 carcinoma-associated genes induced by aza-BODIPY-PDT were analyzed so as to understand the specific pathways that are modulated by aza-BODIPY-PDT. MATERIAL METHOD In this study,the molecular basis of the anti-cancer activity of aza-BODIPY-PDT was investigated.Induction of apoptosis and necrosis in MCF-7 breast cancer cells after treatment with aza- BODIPY derivative with phthalonitrile substituents (aza-BODIPY) followed by light exposure was evaluated by Annexin V 7- Aminoactinomycin D (7-AAD) flow cytometry. RESULTS Aza-BODIPY-PDT induced cell death in MCF-7 cells treated with aza-BODIPY-PDT; flow cytometry revealed that 28 % of the cells died by apoptosis. Seven of the 88 carcinoma-associated genes that were assayed were differentially expressed -EGF, LEF1, WNT1, TCF7, and TGFBR2 were downregulated, and CASP3 and TP53 were upregulated - in cells subjected to aza-BODIPY-PDT.This made us think that the aza-BODIPY-PDT induced caspase 3 and p53-mediated apoptosis in MCF7 cells. CONCLUSION In our study,it was determined that the application of aza-BODIPY-PDT to MCF7 cells had a negative effect on cell connectivity and cell cycle.The fact that the same effect was not observed in control cells and MCF7 cells in the dark field of aza-BODIPY indicates that aza-BODIPY has a strong phodynamic anticancer effect.
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Affiliation(s)
- Tugba Elgun
- Department of Medical Biology, Faculty of Medicine, Biruni University, Istanbul, Turkey
| | - Asiye Gok Yurttas
- Department of Biochemistry, Faculty of Pharmacy, Istanbul Health and Technology University, Istanbul, Turkey.
| | - Kamil Cinar
- Department of Physics, Faculty of Basic Sciences, Gebze Technical University, Istanbul, Turkey
| | - Sennur Ozcelik
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | - Ahmet Gul
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
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Hühns M, Ameziane N, Holzmann C, Al-Ali R, Prall F. Clonal and "Intrinsic" Heterogeneity of Somatic Variants in Microsatellite-Stable Colorectal Carcinomas and Their Metastases. J Transl Med 2023; 103:100132. [PMID: 36966951 DOI: 10.1016/j.labinv.2023.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/07/2023] [Accepted: 03/19/2023] [Indexed: 04/21/2023] Open
Abstract
To test the traditional model of tumor progression, Darwinian-type evolution, against the more recent Big Bang model, we selected 6 microsatellite-stable colorectal standard-type adenocarcinomas and their synchronous lymph node and liver metastases. Somatic genomic variants were identified by whole-exome sequencing (WES) of large tumor fragments from the primaries and 1 liver metastasis each, and used to design targeted resequencing next-generation sequencing (NGS) panels, 1 per case. Targeted deep resequencing (mean coverage, 2725; median, 2222) was performed with DNA from punch samples (1-mm tissue microarrayer needles) obtained from different regions of the primaries and their metastases. In total, 255 genomic variants were interrogated in 108 punch samples. Clonal heterogeneity was infrequent: a pattern of clonal heterogeneity consistent with a role in metastasis formation was observed only in 1 case in a single gene (p. Asp604Tyr of the PTPRT gene). However, when comparing variant allele frequencies (VAFs) of genomic variants in adjacent positions on chromosomes ("matched genomic variant loci") across punch samples, differences that exceeded 2 SD of the NGS assay variations (ad hoc dubbed VAF dysbalance) were observed in 7.1% of the punch samples (2.6%-12.0% per case), which indicates an intricate intermixing of mutated and nonmutated tumor cells ("intrinsic heterogeneity"). Additional OncoScan array analyses on a subset of the punch samples (31 in total) showed gross genomic aberrations as a possible explanation in only some (39.2%) of the matched genomic variant loci with VAF dysbalance. Our study provides a fairly direct (statistical model-free) view of the genomic states of microsatellite-stable colorectal carcinomas and their metastases, and suggests that Darwinian-type tumor evolution is not the key pathway of the metastasizing disease; instead, we recorded an "intrinsic" genomic heterogeneity, which may echo an initial Big Bang-like event.
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Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, Strempelstraße, Rostock, Germany
| | - Najim Ameziane
- Centogene AG, Am Strande, Rostock, Germany; Arcensus GmbH, Goethestraße, Rostock, Germany
| | - Carsten Holzmann
- Institute of Medical Genetics, Rostock University Medical Center, Ernst-Heydemann-Straße, Rostock, Germany
| | | | - Friedrich Prall
- Institute of Pathology, University Medicine of Rostock, Strempelstraße, Rostock, Germany.
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5
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Guzman G, Pellot K, Reed MR, Rodriguez A. CAR T-cells to treat brain tumors. Brain Res Bull 2023; 196:76-98. [PMID: 36841424 DOI: 10.1016/j.brainresbull.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023]
Abstract
Tremendous success using CAR T therapy in hematological malignancies has garnered significant interest in developing such treatments for solid tumors, including brain tumors. This success, however, has yet to be mirrored in solid organ neoplasms. CAR T function has shown limited efficacy against brain tumors due to several factors including the immunosuppressive tumor microenvironment, blood-brain barrier, and tumor-antigen heterogeneity. Despite these considerations, CAR T-cell therapy has the potential to be implemented as a treatment modality for brain tumors. Here, we review adult and pediatric brain tumors, including glioblastoma, diffuse midline gliomas, and medulloblastomas that continue to portend a grim prognosis. We describe insights gained from different preclinical models using CAR T therapy against various brain tumors and results gathered from ongoing clinical trials. Furthermore, we outline the challenges limiting CAR T therapy success against brain tumors and summarize advancements made to overcome these obstacles.
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Affiliation(s)
- Grace Guzman
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Megan R Reed
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR, United States; Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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6
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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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Wang Z, Xing L, Huang Y, Han P. FAT2 mutation is associated with better prognosis and responsiveness to immunotherapy in uterine corpus endometrial carcinoma. Cancer Med 2022; 12:3797-3811. [PMID: 36812126 PMCID: PMC9939103 DOI: 10.1002/cam4.5119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Uterine corpus endometrial carcinoma (UCEC) ranks sixth among malignant tumors in women and the mortality is still rising. FAT2 gene has been considered to be related to the survival and prognosis of some certain diseases in previous studies, but the FAT2 mutation status in UCEC and its prognostic value has been rarely studied. Hence, the purpose of our study was to explore the role of FAT2 mutations for predicting prognosis and responsiveness to immunotherapy in patients with UCEC. METHODS UCEC samples from the Cancer Genome Atlas database were analyzed. We evaluated the impact of FAT2 gene mutation status and clinicopathological characteristics on the prognosis of UCEC patients and used univariate and multivariate Cox analysis risk scores to independently predict patient overall survival (OS). Tumor mutation burden (TMB) values of the FAT2 mutant and non-mutant groups were computed by Wilcoxon rank sum test. The correlation of FAT2 mutation and half maximal inhibitory concentration (IC50) values of various anticancer drugs was analyzed. Gene Ontology data and Gene Set Enrichment Analysis (GSEA) were employed to examine the differential expression of genes between the two groups. Finally, a single-sample GSEA arithmetic was utilized to measure the abundance of tumor-infiltrating immune cells in UCEC patients. RESULTS FAT2 mutations suggested better OS (p < 0.001) and disease-free survival (DFS) (p = 0.007) in UCEC. The IC50 values of 18 anticancer drugs were upregulated in FAT2 mutation patients (p < 0.05). The TMB and microsatellite instability values of patients with FAT2 mutations were significantly higher (p < 0.001). Next, the Kyoto Encyclopedia of Genes and Genomes functional analysis and GSEA revealed the potential mechanism of FAT2 mutation on the tumorigenesis and progression of UCEC. In addition, in reference to the UCEC microenvironment, the infiltration levels of activated CD4/CD8 T cells (p < 0.001/p = 0.001) and plasmacytoid dendritic cells (p = 0.006) were upregulated in the non-FAT2 mutation group, and Type 2 T helper cells (p = 0.001) were downregulated in the FAT2 mutation group. CONCLUSIONS UCEC patients with FAT2 mutations have better prognosis and are more likely to respond to immunotherapy. FAT2 mutation may be a valuable predictor for prognosis and responsiveness to immunotherapy in UCEC patients.
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Affiliation(s)
- Zhe Wang
- Department of Gynecology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouPeople's Republic of China
| | - Linan Xing
- Department of Gynecology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouPeople's Republic of China
| | - Yujie Huang
- Department of Gynecology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouPeople's Republic of China
| | - Peilin Han
- Department of Gynecology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouPeople's Republic of China
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8
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Wang Q, Cui L, Li P, Wang Y. Somatic Mutation of FAT Family Genes Implicated Superior Prognosis in Patients With Stomach Adenocarcinoma. Front Med (Lausanne) 2022; 9:873836. [PMID: 35836939 PMCID: PMC9273734 DOI: 10.3389/fmed.2022.873836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
FAT family genes encode protocadherin, which regulates tumor cell proliferation and migration. Although transcriptional levels of FAT family members had been reported in multiple malignant tumors, the association between mutation and prognosis of the FAT family in stomach adenocarcinoma (STAD) has not been investigated. Herein, we performed a multi-omics integrative bioinformatics analysis using genomic and mRNA expression data to explore the role of gene mutations across the FAT family on clinical outcomes of STAD. The results showed that FAT mutations occurred in 174 of 435 (40%) of the samples. Patients with FAT mutations possessed significantly better progression-free survival (P = 0.019) and overall survival (P = 0.034) than those with non-FAT mutations, and FAT mutations exhibited significantly higher tumor mutational burden (TMB) and microsatellite instability. Notably, FAT mutations had a greater effect on somatic single-nucleotide variation than copy number variation and resulted in more abundant DNA damage repair (DDR) mutations. Further investigation demonstrated that FAT mutations contributed to an inflammatory tumor microenvironment (TME), as indicated by significantly increased numbers of activated CD4 and CD8 T cells, and significantly decreased numbers of mast cell, plasmacytoid dendritic cell, type 2 T helper cell, and high expression of immune-promoting genes. Moreover, biological process antigen processing and presentation, DNA replication, and DDR-related pathways were significantly upregulated in patients with FAT mutations. Collectively, FAT mutations significantly improved the survival of patients with STAD by enhancing tumor immunogenicity (e.g., TMB and DDR mutations) and an inflamed TME, indicating that the FAT family might be a potential prognostic and therapeutic biomarker for STAD.
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Affiliation(s)
- Qingjun Wang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Liang Cui
- GenePlus-Beijing Institute, Beijing, China
| | - Pansong Li
- GenePlus-Beijing Institute, Beijing, China
| | - Yuanyuan Wang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
- *Correspondence: Yuanyuan Wang,
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9
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Ding RF, Zhang Y, Wu LY, You P, Fang ZX, Li ZY, Zhang ZY, Ji ZL. Discovering Innate Driver Variants for Risk Assessment of Early Colorectal Cancer Metastasis. Front Oncol 2022; 12:898117. [PMID: 35795065 PMCID: PMC9252167 DOI: 10.3389/fonc.2022.898117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
Metastasis is the main fatal cause of colorectal cancer (CRC). Although enormous efforts have been made to date to identify biomarkers associated with metastasis, there is still a huge gap to translate these efforts into effective clinical applications due to the poor consistency of biomarkers in dealing with the genetic heterogeneity of CRCs. In this study, a small cohort of eight CRC patients was recruited, from whom we collected cancer, paracancer, and normal tissues simultaneously and performed whole-exome sequencing. Given the exomes, a novel statistical parameter LIP was introduced to quantitatively measure the local invasion power for every somatic and germline mutation, whereby we affirmed that the innate germline mutations instead of somatic mutations might serve as the major driving force in promoting local invasion. Furthermore, via bioinformatic analyses of big data derived from the public zone, we identified ten potential driver variants that likely urged the local invasion of tumor cells into nearby tissue. Of them, six corresponding genes were new to CRC metastasis. In addition, a metastasis resister variant was also identified. Based on these eleven variants, we constructed a logistic regression model for rapid risk assessment of early metastasis, which was also deployed as an online server, AmetaRisk (http://www.bio-add.org/AmetaRisk). In summary, we made a valuable attempt in this study to exome-wide explore the genetic driving force to local invasion, which provides new insights into the mechanistic understanding of metastasis. Furthermore, the risk assessment model can assist in prioritizing therapeutic regimens in clinics and discovering new drug targets, and thus substantially increase the survival rate of CRC patients.
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Affiliation(s)
- Ruo-Fan Ding
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yun Zhang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lv-Ying Wu
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Pan You
- Department of Clinical Laboratory, Xiamen Xianyue Hospital, Xiamen, China
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
- *Correspondence: Zhi-Liang Ji, ; Pan You,
| | - Zan-Xi Fang
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
| | - Zhi-Yuan Li
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
| | - Zhong-Ying Zhang
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- *Correspondence: Zhi-Liang Ji, ; Pan You,
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10
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Liu X, Zhang Y, Zhou CX, Li TJ. Salivary gland papillary adenocarcinoma with intestinal-like features: Clinicopathologic, immunohistochemical, and genetic study of six cases. J Oral Pathol Med 2022; 51:172-179. [PMID: 34982488 DOI: 10.1111/jop.13271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/29/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Salivary gland tumors with papillary architecture and intestinal-like mucinous cytologic features are rare. Their clinicopathologic and genetic features are not fully understood, and whether they represent one separate entity remains unclear. METHODS Six salivary adenocarcinomas with papillary architecture and intestinal-like mucinous cytologic features were reported. Immunostaining was done for CK7, CK20, CDX2, SOX10, S100, MUC1, MUC2 and MUC5AC. Tumor DNA samples were extracted for Sanger sequencing. Previously reported morphology-analogous cases were reviewed. RESULTS Six cases involved the palate (2), retromolar region (1), submandibular region (1), tongue (1), and mandible (1). Five cases were followed up, with one case of recurrence one year after surgery, one death from cerebral infarction seven days after surgery, and three cases without signs of recurrence or metastasis over five years. All cases had abundant mucinous production and presented a typical immunophenotype common to salivary primaries, CK7 & MUC1 positive, CK20 & CDX-2 negative. Sanger sequencing demonstrated recurrent AKT1 E17K mutations in four cases (4/6, 66.7%). A review of reported salivary intestinal-like tumors revealed 3 out of 13 cases presented with papillary morphology and CDX-2 negative. Some salivary papillary neoplasms with mucinous cytologic features termed as intraductal papillary neoplasms or mucinous adenocarcinomas were also reported with AKT1 E17K mutations. CONCLUSION We describe 6 cases of salivary gland papillary adenocarcinoma with intestinal-like mucinous cytologic features, which are different from conventional intestinal-type adenocarcinoma, presenting a consistent immunophenotype of CK7 & MUC1 positive, CK20 & CDX-2 negative and exhibiting recurrent AKT1 E17K mutations.
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Affiliation(s)
- Xiaoxiao Liu
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, 22 South Avenue Zhongguancun, Haidian District, Beijing, 100081, PR China
| | - Ye Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, 22 South Avenue Zhongguancun, Haidian District, Beijing, 100081, PR China
| | - Chuan-Xiang Zhou
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, 22 South Avenue Zhongguancun, Haidian District, Beijing, 100081, PR China.,National Engineering Laboratory for Digital and Material Technology of Stomatology, Peking University School and Hospital of Stomatology.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, PR China
| | - Tie-Jun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, 22 South Avenue Zhongguancun, Haidian District, Beijing, 100081, PR China.,National Engineering Laboratory for Digital and Material Technology of Stomatology, Peking University School and Hospital of Stomatology.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, PR China
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11
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Xu K, Jiang X, Ariston Gabriel AN, Li X, Wang Y, Xu S. Evolving Landscape of Long Non-coding RNAs in Cerebrospinal Fluid: A Key Role From Diagnosis to Therapy in Brain Tumors. Front Cell Dev Biol 2021; 9:737670. [PMID: 34692695 PMCID: PMC8529119 DOI: 10.3389/fcell.2021.737670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/31/2021] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a type of non-coding RNAs that act as molecular fingerprints and modulators of many pathophysiological processes, particularly in cancer. Specifically, lncRNAs can be involved in the pathogenesis and progression of brain tumors, affecting stemness/differentiation, replication, invasion, survival, DNA damage response, and chromatin dynamics. Furthermore, the aberrations in the expressions of these transcripts can promote treatment resistance, leading to tumor recurrence. The development of next-generation sequencing technologies and the creation of lncRNA-specific microarrays have boosted the study of lncRNA etiology. Cerebrospinal fluid (CSF) directly mirrors the biological fluid of biochemical processes in the brain. It can be enriched for small molecules, peptides, or proteins released by the neurons of the central nervous system (CNS) or immune cells. Therefore, strategies that identify and target CSF lncRNAs may be attractive as early diagnostic and therapeutic options. In this review, we have reviewed the studies on CSF lncRNAs in the context of brain tumor pathogenesis and progression and discuss their potential as biomarkers and therapeutic targets.
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Affiliation(s)
- Kanghong Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Xinquan Jiang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | | | - Xiaomeng Li
- Department of Hematology, Jining First People's Hospital, Jining, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Shuo Xu
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
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12
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Zhou L, Yang Y, Liu M, Gan Y, Liu R, Ren M, Zheng Y, Wang Y, Zhou Y. Identification of the RP11-21C4.1/SVEP1 gene pair associated with FAT2 mutations as a potential biomarker in gastric cancer. Bioengineered 2021; 12:4361-4373. [PMID: 34308747 PMCID: PMC8806586 DOI: 10.1080/21655979.2021.1953211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Gastric cancer (GC) is one of the most common malignancies worldwide. Despite rapid advances in systemic therapy, GC remains the third leading cause of cancer-related deaths. We aimed to identify a novel prognostic signature associated with FAT2 mutations in GC. We analyzed the expression levels of FAT2-mutant and FAT2-wildtype GC samples obtained from The Cancer Genome Atlas (TCGA). The Kaplan–Meier survival curve showed that patients with FAT2 mutations showed better prognosis than those without the mutation. Sixteen long non-coding RNAs (lncRNAs) and 62 messenger RNAs (mRNAs) associated with FAT2 mutations were correlated with the prognosis of GC. We then constructed a 4-mRNA signature and a 5-lncRNA signature for GC. Finally, we identified the most relevant RP11-21 C4.1/SVEP1 gene pair as a prognostic signature of GC that exhibited superior predictive performance in comparison with the 4-mRNA or 5-lncRNA signature by weighted gene correlation network analysis (WGCNA) and Cox proportional hazards regression analysis. In this study, we constructed a prognostic signature of GC by integrative genomics analysis, which also provided insights into the molecular mechanisms linked to FAT2 mutations in GC.
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Affiliation(s)
- Lingshan Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Department of Geriatrics Ward 2, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuan Yang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Min Liu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuling Gan
- Department 1nd Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Rong Liu
- Department of Geriatrics Ward 2, The First Hospital of Lanzhou University, Lanzhou, China
| | - Man Ren
- Department of Geriatrics Ward 2, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
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13
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Okamoto T, duVerle D, Yaginuma K, Natsume Y, Yamanaka H, Kusama D, Fukuda M, Yamamoto M, Perraudeau F, Srivastava U, Kashima Y, Suzuki A, Kuze Y, Takahashi Y, Ueno M, Sakai Y, Noda T, Tsuda K, Suzuki Y, Nagayama S, Yao R. Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer. Stem Cell Reports 2021; 16:954-967. [PMID: 33711267 PMCID: PMC8072036 DOI: 10.1016/j.stemcr.2021.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
Metastasis is the major cause of cancer-related death, but whether metastatic lesions exhibit the same cellular composition as primary tumors has yet to be elucidated. To investigate the cellular heterogeneity of metastatic colorectal cancer (CRC), we established 72 patient-derived organoids (PDOs) from 21 patients. Combined bulk transcriptomic and single-cell RNA-sequencing analysis revealed decreased gene expression of markers for differentiated cells in PDOs derived from metastatic lesions. Paradoxically, expression of potential intestinal stem cell markers was also decreased. We identified OLFM4 as the gene most strongly correlating with a stem-like cell cluster, and found OLFM4+ cells to be capable of initiating organoid culture growth and differentiation capacity in primary PDOs. These cells were required for the efficient growth of primary PDOs but dispensable for metastatic PDOs. These observations demonstrate that metastatic lesions have a cellular composition distinct from that of primary tumors; patient-matched PDOs are a useful resource for analyzing metastatic CRC. Seventy-two PDOs were established from 21 stage IV CRC patients Forty-one DEGs were identified between primary and corresponding metastatic PODs scRNA-seq analysis identified OLFM4 as a potential cancer stem cell marker Different roles of OLFM4+ cells in primary and metastatic PDOs were demonstrated
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Affiliation(s)
- Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - David duVerle
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Katsuyuki Yaginuma
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Daisuke Kusama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mayuko Fukuda
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mayuko Yamamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Fanny Perraudeau
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Upasna Srivastava
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yukie Kashima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yuuta Kuze
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yu Takahashi
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masashi Ueno
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoshiharu Sakai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tetsuo Noda
- Director's Room, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Koji Tsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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14
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Sugai T, Osakabe M, Sugimoto R, Eizuka M, Tanaka Y, Yanagawa N, Otsuka K, Sasaki A, Matsumoto T, Suzuki H. A genome-wide study of the relationship between chromosomal abnormalities and gene expression in colorectal tumors. Genes Chromosomes Cancer 2020; 60:250-262. [PMID: 33258187 PMCID: PMC7898915 DOI: 10.1002/gcc.22924] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
The role of somatic copy number alterations (SCNAs) that occur in colorectal tumors is poorly understood. SCNAs are correlated with corresponding gene expression changes that may contribute to neoplastic progression. Thus, we examined SCNAs and the expression of messenger RNAs (mRNAs) located at corresponding loci in colorectal neoplasia, a progression model of human neoplasm. We used 42 colorectal neoplastic samples, including adenomas, intramucosal cancers (IMC) and invasive colorectal cancers (CRC) that were microsatellite stable (MSS) using a genome-wide SNP array and gene expression array (first cohort). In addition, validation analyses were examined (37 colorectal neoplasias). None of the mRNAs with a corresponding SCNA was found in the adenomas. However, three mRNAs, including ARFGEF2 at 20q13.13, N4BP2L2 at 13q13.1 and OLFM4 at 13q14.3 with a copy number (CN) gain at the corresponding locus were upregulated in IMCs of the first cohort. Moreover, upregulated expression of ARFGEF2 and OLFM4 was upregulated in the validation analysis. Finally, 28 mRNAs with gains of corresponding loci were pooled in invasive CRC of the first cohort. The mRNAs, including ACSS2 (20q11.22), DDX27 (20q13.13), MAPRE1 (20q11.21), OSBPL2 (20q11.22) and PHF20 (20q11.22-q11.23) with CN gains of the corresponding loci were identified in 28 mRNAs. Four of these mRNAs (DDX27, MAPRE1, OSBPL2 and PHF20) were upregulated in the invasive CRC in the validation analysis. We conclude that specific 13q and 22q CN gains with gene expression changes in the corresponding loci may play an important role in IMC cells' progression into invasive CRC.
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Affiliation(s)
- Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Ryo Sugimoto
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Yoshihito Tanaka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Naoki Yanagawa
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Koki Otsuka
- Department of Surgery, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Akira Sasaki
- Department of Surgery, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, Iwate Medical University, Morioka, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
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15
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Seo H, Cho DH. Feature selection algorithm based on dual correlation filters for cancer-associated somatic variants. BMC Bioinformatics 2020; 21:486. [PMID: 33121438 PMCID: PMC7596964 DOI: 10.1186/s12859-020-03767-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
Background Since the development of sequencing technology, an enormous amount of genetic information has been generated, and human cancer analysis using this information is drawing attention. As the effects of variants on human cancer become known, it is important to find cancer-associated variants among countless variants. Results We propose a new filter-based feature selection method applicable for extracting cancer-associated somatic variants considering correlations of data. Both variants associated with the activation and deactivation of cancer’s characteristics are analyzed using dual correlation filters. The multiobjective optimization is utilized to consider two types of variants simultaneously without redundancy. To overcome high computational complexity problem, we calculate the correlation-based weight to select significant variants instead of directly searching for the optimal subset of variants. The proposed algorithm is applied to the identification of melanoma metastasis or breast cancer stage, and the classification results of the proposed method are compared with those of conventional single correlation filter-based method. Conclusions We verified that the proposed dual correlation filter-based method can extract cancer-associated variants related to the characteristics of human cancer.
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Affiliation(s)
- Hyein Seo
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, 34141, Daejeon, Republic of Korea
| | - Dong-Ho Cho
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, 34141, Daejeon, Republic of Korea.
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16
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González-González M, Gutiérrez ML, Sayagués JM, Muñoz-Bellvís L, Orfao A. Genomic profiling of sporadic liver metastatic colorectal cancer. Semin Cancer Biol 2020; 71:98-108. [PMID: 32485312 DOI: 10.1016/j.semcancer.2020.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Sporadic colorectal cancer (sCRC) is the third leading cause of cancer death in the Western world. Approximately, a quarter of sCRC patients present metastatic dissemination at the moment of diagnosis, the liver being the most frequently affected organ. Additionally, this group of CRC patients is characterized by a worse prognosis. In the last decades, significant technological developments for genome analysis have fostered the identification and characterization of genetic alterations involved in the pathogenesis of sCRC. However, genetic alterations involved in the metastatic process through which tumor cells are able to colonize other tissues with a different microenvironment, still remain to be fully identified. Here, we review current knowledge about the most relevant genomic alterations involved in the liver metastatic process of sCRC, including detailed information about the genetic profile of primary colorectal tumors vs. their paired liver metastases.
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Affiliation(s)
- María González-González
- Department of Medicine and Cytometry Service (NUCLEUS), University of Salamanca, Salamanca, Spain; Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain
| | - María Laura Gutiérrez
- Department of Medicine and Cytometry Service (NUCLEUS), University of Salamanca, Salamanca, Spain; Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain
| | - José María Sayagués
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain; Department of Pathology, Universidad de Salamanca, Salamanca, Spain
| | - Luis Muñoz-Bellvís
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain; Department of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and Cytometry Service (NUCLEUS), University of Salamanca, Salamanca, Spain; Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Spain.
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17
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Long Y, Zhu Y. Identification of FBXW7α-regulated genes in M1-polarized macrophages in colorectal cancer by RNA sequencing. Saudi Med J 2020; 40:766-773. [PMID: 31423512 PMCID: PMC6718864 DOI: 10.15537/smj.2019.8.24361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To determine the FBXW7α-regulated genes in tumor-polarized macrophages in colorectal cancer. METHODS This experimental study was performed between June 2017 and March 2019. FBXW7α siRNA transfected RAW264.7 cells, together with the control group, were co-cultured with the colon cancer cell line, Colon-26. M1 marker production from the macrophages was determined by ELISA and quantitative reverse transcription-polymerase chain reaction. Whole genomic differential expression between the FBXW7α siRNA group and the control group were determined by RNA-sequencing analysis. The target site of the microRNA-205 gene was predicted using Targetscan and was verified by the luciferase assay. By transfecting mimics or inhibitors of microRNA-205, we explored the role of FBXW7α/microRNA-205 axis in regulating the polarization of tumor-associated macrophages (TAM). RESULTS FBXW7α knockdown in RAW264.7 enhanced the expression of cyclooxigenase (COX)-2 and inducible nitric oxide synthase (iNOS), mRNA expression and IL6, IL12, p40, and tumor necrosis factor-α (TNFα) production upon co-culture with Colon-26 cells in vitro. Further, compared with the control group, 648 genes in total were enhanced and 416 targets were downregulated in FBXW7α siRNA transfected cells, among which miR-205 was the most significantly upregulated. SMAD1 was identified as an miR-205 target. The FBXW7α/miR-205 axis might regulate TAM polarization by affecting SMAD1 expression. CONCLUSION These results prove that the FBXW7α/miR-205 axis plays an important role in TAM polarization and could facilitate further exploration of its molecular mechanism.
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Affiliation(s)
- Yupeng Long
- Department of Clinical Laboratory, Army 958 Hospital of the Chinese People's Liberation Army, Chongqing, China. E-mail.
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18
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Bach DH, Zhang W, Sood AK. Chromosomal Instability in Tumor Initiation and Development. Cancer Res 2019; 79:3995-4002. [PMID: 31350294 PMCID: PMC7694409 DOI: 10.1158/0008-5472.can-18-3235] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022]
Abstract
Chromosomal instability (CIN) is one of the major forms of genomic instability in various human cancers and is recognized as a common hallmark of tumorigenesis and heterogeneity. However, some malignant tumors show a paucity of chromosomal alterations, suggesting that tumor progression and evolution can occur in the absence of CIN. It is unclear whether CIN is stable between precursor lesions, primary tumor, and metastases or if it evolves during these steps. In this review, we describe the influence of CIN on the various steps in tumor initiation and development. Given the recognized significant effects of CIN in cancer, CIN-targeted therapeutics could have a major impact on improving clinical outcomes.
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Affiliation(s)
- Duc-Hiep Bach
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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19
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Zheng G, Ma Y, Zou Y, Yin A, Li W, Dong D. HCMDB: the human cancer metastasis database. Nucleic Acids Res 2019; 46:D950-D955. [PMID: 29088455 PMCID: PMC5753185 DOI: 10.1093/nar/gkx1008] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/13/2017] [Indexed: 12/20/2022] Open
Abstract
Metastasis is the main event leading to death in cancer patients. Over the past decade, high-throughput technologies have provided genome-wide view of transcriptomic changes associated with cancer metastases. Many microarray and RNA sequencing studies have addressed metastases-related expression patterns in various types of cancer, and the number of relevant works continues to increase rapidly. These works have characterized genes that orchestrate the metastatic phenotype of cancer cells. However, these expression data have been deposited in various repositories, and efficiently analyzing these data is still difficult because of the lack of an integrated data mining platform. To facilitate the in-depth analyses of transcriptome data on metastasis, it is quite important to make a comprehensive integration of these metastases-related expression data. Here, we presented a database, HCMDB (the human cancer metastasis database, http://hcmdb.i-sanger.com/index), which is freely accessible to the research community query cross-platform transcriptome data on metastases. HCMDB is developed and maintained as a useful resource for building the systems-biology understanding of metastasis.
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Affiliation(s)
- Guantao Zheng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.,Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Yijie Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yang Zou
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - An Yin
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Wushuang Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
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20
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Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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21
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Hu Z, Ding J, Ma Z, Sun R, Seoane JA, Scott Shaffer J, Suarez CJ, Berghoff AS, Cremolini C, Falcone A, Loupakis F, Birner P, Preusser M, Lenz HJ, Curtis C. Quantitative evidence for early metastatic seeding in colorectal cancer. Nat Genet 2019; 51:1113-1122. [PMID: 31209394 PMCID: PMC6982526 DOI: 10.1038/s41588-019-0423-x] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
Abstract
Both the timing and molecular determinants of metastasis are unknown, hindering treatment and prevention efforts. Here we characterize the evolutionary dynamics of this lethal process by analyzing exome-sequencing data from 118 biopsies from 23 patients with colorectal cancer with metastases to the liver or brain. The data show that the genomic divergence between the primary tumor and metastasis is low and that canonical driver genes were acquired early. Analysis within a spatial tumor growth model and statistical inference framework indicates that early disseminated cells commonly (81%, 17 out of 21 evaluable patients) seed metastases while the carcinoma is clinically undetectable (typically, less than 0.01 cm3). We validated the association between early drivers and metastasis in an independent cohort of 2,751 colorectal cancers, demonstrating their utility as biomarkers of metastasis. This conceptual and analytical framework provides quantitative in vivo evidence that systemic spread can occur early in colorectal cancer and illuminates strategies for patient stratification and therapeutic targeting of the canonical drivers of tumorigenesis.
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Affiliation(s)
- Zheng Hu
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jie Ding
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Veracyte Inc, South San Francisco, CA, USA
| | - Zhicheng Ma
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ruping Sun
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jose A Seoane
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - J Scott Shaffer
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna S Berghoff
- Comprehensive Cancer Center CNS Tumor Unit, Medical University of Vienna, Vienna, Austria
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Chiara Cremolini
- Department of Oncology, University Hospital of Pisa, Pisa, Italy
| | - Alfredo Falcone
- Department of Oncology, University Hospital of Pisa, Pisa, Italy
| | - Fotios Loupakis
- Unit of Medical Oncology 1, Department of Clinical and Experimental Oncology, Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - Peter Birner
- Comprehensive Cancer Center CNS Tumor Unit, Medical University of Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Comprehensive Cancer Center CNS Tumor Unit, Medical University of Vienna, Vienna, Austria
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Heinz-Josef Lenz
- Department of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
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22
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McCoach CE, Bivona TG. Engineering Multidimensional Evolutionary Forces to Combat Cancer. Cancer Discov 2019; 9:587-604. [PMID: 30992280 PMCID: PMC6497542 DOI: 10.1158/2159-8290.cd-18-1196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/28/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
With advances in technology and bioinformatics, we are now positioned to view and manage cancer through an evolutionary lens. This perspective is critical as our appreciation for the role of tumor heterogeneity, tumor immune compartment, and tumor microenvironment on cancer pathogenesis and evolution grows. Here, we explore recent knowledge on the evolutionary basis of cancer pathogenesis and progression, viewing tumors as multilineage, multicomponent organisms whose growth is regulated by subcomponent fitness relationships. We propose reconsidering some current tenets of the cancer management paradigm in order to take better advantage of crucial fitness relationships to improve outcomes of patients with cancer. SIGNIFICANCE: Tumor and tumor immune compartment and microenvironment heterogeneity, and their evolution, are critical disease features that affect treatment response. The impact and interplay of these components during treatment are viable targets to improve clinical response. In this article, we consider how tumor cells, the tumor immune compartment and microenvironment, and epigenetic factors interact and also evolve during treatment. We evaluate the convergence of these factors and suggest innovative treatment concepts that leverage evolutionary relationships to limit tumor growth and drug resistance.
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Affiliation(s)
- Caroline E McCoach
- Department of Medicine, University of California, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
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23
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High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer. Nat Commun 2018; 9:5079. [PMID: 30498242 PMCID: PMC6265294 DOI: 10.1038/s41467-018-07406-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/30/2018] [Indexed: 12/31/2022] Open
Abstract
Most triple negative breast cancers (TNBCs) are aggressively metastatic with a high degree of intra-tumoral heterogeneity (ITH), but how ITH contributes to metastasis is unclear. Here, clonal dynamics during metastasis were studied in vivo using two patient-derived xenograft (PDX) models established from the treatment-naive primary breast tumors of TNBC patients diagnosed with synchronous metastasis. Genomic sequencing and high-complexity barcode-mediated clonal tracking reveal robust alterations in clonal architecture between primary tumors and corresponding metastases. Polyclonal seeding and maintenance of heterogeneous populations of low-abundance subclones is observed in each metastasis. However, lung, liver, and brain metastases are enriched for an identical population of high-abundance subclones, demonstrating that primary tumor clones harbor properties enabling them to seed and thrive in multiple organ sites. Further, clones that dominate multi-organ metastases share a genomic lineage. Thus, intrinsic properties of rare primary tumor subclones enable the seeding and colonization of metastases in secondary organs in these models. It is unclear how intra-tumoral heterogeneity contributes to metastasis. Here the authors study the clonal dynamics of triple negative breast cancer metastasis using patient derived xenografts and demonstrate that primary tumor clones harbor properties that support seeding and colonization of multiple organs.
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24
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Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nat Commun 2018; 9:4782. [PMID: 30429477 PMCID: PMC6235880 DOI: 10.1038/s41467-018-07041-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
Incomplete understanding of the metastatic process hinders personalized therapy. Here we report the most comprehensive whole-genome study of colorectal metastases vs. matched primary tumors. 65% of somatic mutations originate from a common progenitor, with 15% being tumor- and 19% metastasis-specific, implicating a higher mutation rate in metastases. Tumor- and metastasis-specific mutations harbor elevated levels of BRCAness. We confirm multistage progression with new components ARHGEF7/ARHGEF33. Recurrently mutated non-coding elements include ncRNAs RP11-594N15.3, AC010091, SNHG14, 3’ UTRs of FOXP2, DACH2, TRPM3, XKR4, ANO5, CBL, CBLB, the latter four potentially dual protagonists in metastasis and efferocytosis-/PD-L1 mediated immunosuppression. Actionable metastasis-specific lesions include FAT1, FGF1, BRCA2, KDR, and AKT2-, AKT3-, and PDGFRA-3’ UTRs. Metastasis specific mutations are enriched in PI3K-Akt signaling, cell adhesion, ECM and hepatic stellate activation genes, suggesting genetic programs for site-specific colonization. Our results put forward hypotheses on tumor and metastasis evolution, and evidence for metastasis-specific events relevant for personalized therapy. The evolution and genetic nature of metastatic lesions is not completely characterized. Here the authors perform a comprehensive whole-genome study of colorectal metastases in comparison to matched primary tumors and define a multistage progression model and metastasis-specific changes that, in part, are therapeutically actionable.
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25
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The gene mutational discrepancies between primary and paired metastatic colorectal carcinoma detected by next-generation sequencing. J Cancer Res Clin Oncol 2018; 144:2149-2159. [DOI: 10.1007/s00432-018-2742-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/21/2018] [Indexed: 01/22/2023]
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26
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Liu M, Di J, Liu Y, Su Z, Jiang B, Wang Z, Su X. Comparison of EpCAM highCD44 + cancer stem cells with EpCAM highCD44 - tumor cells in colon cancer by single-cell sequencing. Cancer Biol Ther 2018; 19:939-947. [PMID: 29580161 DOI: 10.1080/15384047.2018.1456605] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cancer stem cells (CSCs) are considered to be responsible for tumorigenesis and cancer relapse. EpCAMhighCD44+ tumor cells are putative colorectal CSCs that express high levels of stem cell genes, while the EpCAMhighCD44- population mostly contains differentiated tumor cells (DTCs). This study aims to determine whether single CSC (EpCAMhighCD44+) and DTC (EpCAMhighCD44-) can be distinguished in terms of somatic copy number alterations (SCNAs). We applied fluorescence-activated cell sorting to isolate the CD45-EpCAMhighCD44+ and CD45-EpCAMhighCD44- populations from two primary colon tumors, on which low-coverage single-cell whole-genome sequencing (WGS) was then performed ∼0.1x depth. We compared the SCNAs of the CSCs and DTCs at single-cell resolution. In total, 47 qualified single cells of the two populations underwent WGS. The single-cell SCNA profiles showed that there were obvious SCNAs in both the CSCs and DTCs of each patient, and each patient had a specific copy number alteration pattern. Hierarchical clustering and correlation analysis both showed that the SCNA profiles of CSCs and DTCs from the same patient had similar SCNA pattern, while there were regional differences in the CSCs and DTCs in certain patient. SCNAs of CSCs in the same patient were highly reproducible. Our data suggest that major SCNAs occurred at an early stage and were inherited steadily. The similarity of ubiquitous SCNAs between the CSCs and DTCs might have arisen from lineage differentiation. CSCs from the same patient had reproducible SCNA profiles, indicating that gain or loss in certain chromosome is required for colon cancer development.
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Affiliation(s)
- Mingshan Liu
- a Biodynamics Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing , China
| | - Jiabo Di
- b Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) , Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute , Beijing , China
| | - Yang Liu
- a Biodynamics Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing , China
| | - Zhe Su
- a Biodynamics Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing , China
| | - Beihai Jiang
- b Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) , Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute , Beijing , China
| | - Zaozao Wang
- b Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) , Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute , Beijing , China
| | - Xiangqian Su
- b Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) , Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute , Beijing , China
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27
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Abstract
Tumour heterogeneity poses a substantial problem for the clinical management of cancer. Somatic evolution of the cancer genome results in genetically distinct subclones in the primary tumour with different biological properties and therapeutic sensitivities. The problem of heterogeneity is compounded in metastatic disease owing to the complexity of the metastatic process and the multiple biological hurdles that the tumour cell must overcome to establish a clinically overt metastatic lesion. New advances in sequencing technology and clinical sample acquisition are providing insights into the phylogenetic relationship of metastases and primary tumours at the level of somatic tumour genetics while also illuminating fundamental mechanisms of the metastatic process. In addition to somatically acquired genetic heterogeneity in the tumour cells, inherited population-based genetic heterogeneity can profoundly modify metastatic biology and further complicate the development of effective, broadly applicable antimetastatic therapies. Here, we examine how genetic heterogeneity impacts metastatic disease and the implications of current knowledge for future research endeavours and therapeutic interventions.
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28
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Hühns M, Krohn S, Murua Escobar H, Prall F. Genomic heterogeneity in primary colorectal carcinomas and their metastases: born bad or brought up a villain? Hum Pathol 2018; 74:54-63. [PMID: 29307628 DOI: 10.1016/j.humpath.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022]
Abstract
Progression of solid cancers, colorectal carcinomas among them, from their primaries to metastatic lesions traditionally is thought to proceed by a stepwise acquisition of and selection for genomic aberrations. To test if patterns of genomic aberrations would be consistent with this model, we studied 10 colorectal carcinoma primary-metastasis pairs, 9 with 1 liver metastasis each and 1 with 2 metastases. Next-generation targeted sequencing (50-gene panel) with samples obtained from different regions of the primaries and their metastases demonstrated 1-11 gene mutations per lesion. But only in 2 tumors were there seen mutations in all samples from the metastasis and not any of the primaries (BRAFD594N and SMARCB1R377C mutation, respectively). However, allelotyping the multiregional samples with polymorphous microsatellite markers (17p13.1, D9S942, D9S1748, D5S346, D5S1385) and DNA methylation studies with a marker panel (MLH1, CDNK2A, NEUROG1, CRABP1, CACNA1G, IGF2, RUNX3, SOCS1) showed remarkably "insular" genomic aberrations in all cases for at least some of the analyses. The marked preponderance of mutations shared by the primaries and their metastases throughout the lesions over mutations private to metastases suggests that, at least in many cases, colorectal carcinomas might be endowed with a mutational load sufficient for fully fledged metastases even at a very early stage ("born bad"). But the very focal allelic imbalances and methylations observed here, hypothetically, could play a role in clinically metastasizing disease, a process of years rather than months and very much a matter of tumor-host interactions when tumor cells adapt to the host microenvironment.
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Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, 18055 Rostock, Germany.
| | - Saskia Krohn
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, University of Rostock, D-18057 Rostock, Germany.
| | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, University of Rostock, D-18057 Rostock, Germany.
| | - Friedrich Prall
- Institute of Pathology, University Medicine of Rostock, 18055 Rostock, Germany.
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29
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Sutton PA, Jithesh PV, Jones RP, Evans JP, Vimalachandran D, Malik HZ, Park BK, Goldring CE, Palmer DH, Kitteringham NR. Exome sequencing of synchronously resected primary colorectal tumours and colorectal liver metastases to inform oncosurgical management. Eur J Surg Oncol 2017; 44:115-121. [PMID: 29174709 DOI: 10.1016/j.ejso.2017.10.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Next generation sequencing technology has facilitated mapping of the colorectal cancer genotype and furthered our understanding of metastogenesis. The aim of this study was to investigate for conserved and different mutations in the exomes of synchronously resected primary colorectal tumour and liver metastases. This information could potentially be utilised to guide the treatment of advanced disease with the help of biological information from the primary tumour. METHODS We performed exome sequencing of synchronously resected primary colorectal cancer and colorectal liver metastases as well as normal colonic mucosa and liver parenchyma, from four patients who had received neo-adjuvant chemotherapy, at a depth of 50X using the Ion Proton platform. Raw data was mapped to the reference genome prior to variant calling, annotation and downstream analysis. RESULTS Exome sequencing identified 585 non-synonymous missense single nucleotide variants (SNVs), of which 215 (36.8%) were unique to the primary tumour, 226 (38.6%) unique to the metastasis and 81 (13.8%) present in patient matched pairs. SNVs identified in the ErbB pathway appear to be concordant between primary and metastatic tumours. CONCLUSION Only 13.8% of the metastatic exome can be predicted by the genotype of the primary tumour. We have demonstrated concordance of a number of SNVs in the ErbB pathway, which may inform selection of therapeutic agents in advanced colorectal cancer.
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Affiliation(s)
- P A Sutton
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK.
| | - P V Jithesh
- Sidra Medical and Research Centre, Doha, Qatar
| | - R P Jones
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - J P Evans
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - D Vimalachandran
- Countess of Chester NHS Foundation Trust, Liverpool Road, Chester, CH2 1UL, UK
| | - H Z Malik
- Aintree University Hospital NHS Foundation Trust, Longmoor Lane, Liverpool, L9 7AL, UK
| | - B K Park
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - C E Goldring
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - D H Palmer
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - N R Kitteringham
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
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30
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Østrup O, Dagenborg VJ, Rødland EA, Skarpeteig V, Silwal-Pandit L, Grzyb K, Berstad AE, Fretland ÅA, Mælandsmo GM, Børresen-Dale AL, Ree AH, Edwin B, Nygaard V, Flatmark K. Molecular signatures reflecting microenvironmental metabolism and chemotherapy-induced immunogenic cell death in colorectal liver metastases. Oncotarget 2017; 8:76290-76304. [PMID: 29100312 PMCID: PMC5652706 DOI: 10.18632/oncotarget.19350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
Background Metastatic colorectal cancer (CRC) is associated with highly variable clinical outcome and response to therapy. The recently identified consensus molecular subtypes (CMS1-4) have prognostic and therapeutic implications in primary CRC, but whether these subtypes are valid for metastatic disease is unclear. We performed multi-level analyses of resectable CRC liver metastases (CLM) to identify molecular characteristics of metastatic disease and evaluate the clinical relevance. Methods In this ancillary study to the Oslo-CoMet trial, CLM and tumor-adjacent liver tissue from 46 patients were analyzed by profiling mutations (targeted sequencing), genome-wide copy number alteration (CNAs), and gene expression. Results Somatic mutations and CNAs detected in CLM were similar to reported primary CRC profiles, while CNA profiles of eight metastatic pairs suggested intra-patient divergence. A CMS classifier tool applied to gene expression data, revealed the cohort to be highly enriched for CMS2. Hierarchical clustering of genes with highly variable expression identified two subgroups separated by high or low expression of 55 genes with immune-related and metabolic functions. Importantly, induction of genes and pathways associated with immunogenic cell death (ICD) was identified in metastases exposed to neoadjuvant chemotherapy (NACT). Conclusions The uniform classification of CLM by CMS subtyping may indicate that novel class discovery approaches need to be explored to uncover clinically useful stratification of CLM. Detected gene expression signatures support the role of metabolism and chemotherapy in shaping the immune microenvironment of CLM. Furthermore, the results point to rational exploration of immune modulating strategies in CLM, particularly by exploiting NACT-induced ICD.
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Affiliation(s)
- Olga Østrup
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Vegar Johansen Dagenborg
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Einar Andreas Rødland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Veronica Skarpeteig
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Laxmi Silwal-Pandit
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Krzysztof Grzyb
- Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Audun Elnæs Berstad
- Department of Radiology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Åsmund Avdem Fretland
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- The Intervention Centre, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gunhild Mari Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Pharmacy, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Hansen Ree
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjørn Edwin
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- The Intervention Centre, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vigdis Nygaard
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Gastroenterological Surgery, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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31
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Chukwueke UN, Brastianos PK. Sequencing brain metastases and opportunities for targeted therapies. Pharmacogenomics 2017; 18:585-594. [PMID: 28290769 DOI: 10.2217/pgs-2016-0170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
CNS metastases have long been recognized as a common and late complication of systemic malignancies. They represent the most common tumor of the brain. As outcomes and overall survival improve with better tolerated and more durable responses from therapies for systemic cancers, the incidence and prevalence of brain metastases is likely to increase. Among the most common systemic cancers leading to brain metastases include lung, melanoma, breast (triple-negative histology) and renal cell cancers. To date, there has been infrequent involvement of gastrointestinal and gynecologic malignancies; however, this may also change, reflecting improvement in overall survival and therapeutic regimens. Traditional therapy of brain metastases has focused on surgery, radiation therapy or best supportive/palliative care. The advent of modern genomic techniques, including next-generation and whole-exome sequencing, has allowed for the identification of unique markers and potential drivers of metastatic pathways. This review aims to discuss and highlight the known drivers of disease and the opportunities for ultimate development of targeted therapies.
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Affiliation(s)
- Ugonma N Chukwueke
- Division of Hematology & Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Division of Neuro-Oncology, Department of Neurology Massachusetts General Hospital, Boston, MA 02114, USA
| | - Priscilla K Brastianos
- Division of Hematology & Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Division of Neuro-Oncology, Department of Neurology Massachusetts General Hospital, Boston, MA 02114, USA
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32
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Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
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Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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Amaro A, Chiara S, Pfeffer U. Molecular evolution of colorectal cancer: from multistep carcinogenesis to the big bang. Cancer Metastasis Rev 2016; 35:63-74. [PMID: 26947218 DOI: 10.1007/s10555-016-9606-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Colorectal cancer is characterized by exquisite genomic instability either in the form of microsatellite instability or chromosomal instability. Microsatellite instability is the result of mutation of mismatch repair genes or their silencing through promoter methylation as a consequence of the CpG island methylator phenotype. The molecular causes of chromosomal instability are less well characterized. Genomic instability and field cancerization lead to a high degree of intratumoral heterogeneity and determine the formation of cancer stem cells and epithelial-mesenchymal transition mediated by the TGF-β and APC pathways. Recent analyses using integrated genomics reveal different phases of colorectal cancer evolution. An initial phase of genomic instability that yields many clones with different mutations (big bang) is followed by an important, previously not detected phase of cancer evolution that consists in the stabilization of several clones and a relatively flat outgrowth. The big bang model can best explain the coexistence of several stable clones and is compatible with the fact that the analysis of the bulk of the primary tumor yields prognostic information.
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Affiliation(s)
- Adriana Amaro
- Molecular Pathology, IRCCS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Silvana Chiara
- Medical Oncology, IRCCS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Ulrich Pfeffer
- Molecular Pathology, IRCCS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi 10, 16132, Genoa, Italy.
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34
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Chen Z, Gowan K, Leach SM, Viboolsittiseri SS, Mishra AK, Kadoishi T, Diener K, Gao B, Jones K, Wang JH. Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing. BMC Genomics 2016; 17:823. [PMID: 27769169 PMCID: PMC5075209 DOI: 10.1186/s12864-016-3153-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/11/2016] [Indexed: 01/05/2023] Open
Abstract
Background Whole genome next generation sequencing (NGS) is increasingly employed to detect genomic rearrangements in cancer genomes, especially in lymphoid malignancies. We recently established a unique mouse model by specifically deleting a key non-homologous end-joining DNA repair gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in germinal center B cells. This mouse model spontaneously develops mature B cell lymphomas (termed G1XP lymphomas). Results Here, we attempt to employ whole genome NGS to identify novel structural rearrangements, in particular inter-chromosomal translocations (CTXs), in these G1XP lymphomas. We sequenced six lymphoma samples, aligned our NGS data with mouse reference genome (in C57BL/6J (B6) background) and identified CTXs using CREST algorithm. Surprisingly, we detected widespread CTXs in both lymphomas and wildtype control samples, majority of which were false positive and attributable to different genetic backgrounds. In addition, we validated our NGS pipeline by sequencing multiple control samples from distinct tissues of different genetic backgrounds of mouse (B6 vs non-B6). Lastly, our studies showed that widespread false positive CTXs can be generated by simply aligning sequences from different genetic backgrounds of mouse. Conclusions We conclude that mapping and alignment with reference genome might not be a preferred method for analyzing whole-genome NGS data obtained from a genetic background different from reference genome. Given the complex genetic background of different mouse strains or the heterogeneity of cancer genomes in human patients, in order to minimize such systematic artifacts and uncover novel CTXs, a preferred method might be de novo assembly of personalized normal control genome and cancer cell genome, instead of mapping and aligning NGS data to mouse or human reference genome. Thus, our studies have critical impact on the manner of data analysis for cancer genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3153-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA.,Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
| | - Katherine Gowan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA.,Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Sawanee S Viboolsittiseri
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Ameet K Mishra
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Tanya Kadoishi
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Katrina Diener
- Genomic and Microarray Core, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Bifeng Gao
- Genomic and Microarray Core, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kenneth Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA. .,Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA.
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35
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Kovaleva V, Geissler AL, Lutz L, Fritsch R, Makowiec F, Wiesemann S, Hopt UT, Passlick B, Werner M, Lassmann S. Spatio-temporal mutation profiles of case-matched colorectal carcinomas and their metastases reveal unique de novo mutations in metachronous lung metastases by targeted next generation sequencing. Mol Cancer 2016; 15:63. [PMID: 27756406 PMCID: PMC5069823 DOI: 10.1186/s12943-016-0549-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/06/2016] [Indexed: 12/13/2022] Open
Abstract
Background Targeted next generation sequencing (tNGS) has become part of molecular pathology diagnostics for determining RAS mutation status in colorectal cancer (CRC) patients as predictive tool for decision on EGFR-targeted therapy. Here, we investigated mutation profiles of case-matched tissue specimens throughout the disease course of CRC, to further specify RAS-status dynamics and to identify de novo mutations associated with distant metastases. Methods Case-matched formalin-fixed and paraffin-embedded (FFPE) resection specimens (n = 70; primary tumours, synchronous and/or metachronous liver and/or lung metastases) of 14 CRC cases were subjected to microdissection of normal colonic epithelial, primary and metastatic tumour cells, their DNA extraction and an adapted library protocol for limited DNA using the 48 gene TruSeq Amplicon Cancer PanelTM, MiSeq sequencing and data analyses (Illumina). Results By tNGS primary tumours were RAS wildtype in 5/14 and mutated in 9/14 (8/9 KRAS exon 2; 1/9 NRAS Exon 3) of cases. RAS mutation status was maintained in case-matched metastases throughout the disease course, albeit with altered allele frequencies. Case-matched analyses further identified a maximum of three sequence variants (mainly in APC, KRAS, NRAS, TP53) shared by all tumour specimens throughout the disease course per individual case. In addition, further case-matched de novo mutations were detected in synchronous and/or metachronous liver and/or lung metastases (e.g. in APC, ATM, FBXW7, FGFR3, GNAQ, KIT, PIK3CA, PTEN, SMAD4, SMO, STK11, TP53, VHL). Moreover, several de novo mutations were more frequent in synchronous (e.g. ATM, KIT, PIK3CA, SMAD4) or metachronous (e.g. FBXW7, SMO, STK11) lung metastases. Finally, some de novo mutations occurred only in metachronous lung metastases (CDKN2A, FGFR2, GNAS, JAK3, SRC). Conclusion Together, this study employs an adapted FFPE-based tNGS approach to confirm conservation of RAS mutation status in primary and metastatic tissue specimens of CRC patients. Moreover, it identifies genes preferentially mutated de novo in late disease stages of metachronous CRC lung metastases, several of which might be actionable by targeted therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12943-016-0549-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valentina Kovaleva
- Institute for Surgical Pathology, Medical Center-Faculty of Medicine, University of Freiburg, Breisacherstr. 115A, 79106, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna-Lena Geissler
- Institute for Surgical Pathology, Medical Center-Faculty of Medicine, University of Freiburg, Breisacherstr. 115A, 79106, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lisa Lutz
- Institute for Surgical Pathology, Medical Center-Faculty of Medicine, University of Freiburg, Breisacherstr. 115A, 79106, Freiburg, Germany
| | - Ralph Fritsch
- Department of Medicine I, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Makowiec
- Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of General and Visceral Surgery, Medical Center- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Wiesemann
- Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Thoracic Surgery, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrich T Hopt
- Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of General and Visceral Surgery, Medical Center- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernward Passlick
- Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Thoracic Surgery, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center-Faculty of Medicine, University of Freiburg, Breisacherstr. 115A, 79106, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center-Faculty of Medicine, University of Freiburg, Breisacherstr. 115A, 79106, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Comprehensive Cancer Center Freiburg, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
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Barøy T, Chilamakuri CSR, Lorenz S, Sun J, Bruland ØS, Myklebost O, Meza-Zepeda LA. Genome Analysis of Osteosarcoma Progression Samples Identifies FGFR1 Overexpression as a Potential Treatment Target and CHM as a Candidate Tumor Suppressor Gene. PLoS One 2016; 11:e0163859. [PMID: 27685995 PMCID: PMC5042545 DOI: 10.1371/journal.pone.0163859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/15/2016] [Indexed: 12/25/2022] Open
Abstract
Osteosarcoma (OS) is the most common primary malignant tumor of bone, showing complex chromosomal rearrangements but with few known consistent changes. Deeper biological understanding is crucial to find new therapies to improve patient survival. We have sequenced the whole exome of two primary tumors (before and after chemotherapy), one metastatic tumor and a matched normal sample from two OS patients, to identify mutations involved in cancer biology. The metastatic samples were also RNA sequenced. By RNA sequencing we identified dysregulated expression levels of drug resistance- and apoptosis-related genes. Two fusion transcripts were identified in one patient (OS111); the first resulted in p53 inactivation by fusing the first exon of TP53 to the fifth exon of FAM45A. The second fusion joined the two first exons of FGFR1 to the second exon of ZNF343. Furthermore, FGFR1 was amplified and highly expressed, representing a potential treatment target in this patient. Whole exome sequencing revealed large intertumor heterogeneity, with surprisingly few shared mutations. Careful evaluation and validation of the data sets revealed a number of artefacts, but one recurrent mutation was validated, a nonsense mutation in CHM (patient OS106), which also was the mutation with the highest expression frequency (53%). The second patient (OS111) had wild-type CHM, but a downregulated expression level. In a panel of 71 clinical samples, we confirmed significant low expression of CHM compared to the controls (p = 0.003). Furthermore, by analyzing public datasets, we identified a significant association between low expression and poor survival in two other cancer types. Together, these results suggest CHM as a candidate tumor suppressor gene that warrants further investigation.
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Affiliation(s)
- Tale Barøy
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Chandra S. R. Chilamakuri
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Susanne Lorenz
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Jinchang Sun
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Øyvind S. Bruland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, NO-0310 Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Leonardo A. Meza-Zepeda
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- Norwegian Cancer Genomics Consortium, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, NO-0310 Oslo, Norway
- * E-mail:
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37
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Lim B, Mun J, Kim JH, Kim CW, Roh SA, Cho DH, Kim YS, Kim SY, Kim JC. Genome-wide mutation profiles of colorectal tumors and associated liver metastases at the exome and transcriptome levels. Oncotarget 2016; 6:22179-90. [PMID: 26109429 PMCID: PMC4673155 DOI: 10.18632/oncotarget.4246] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/18/2015] [Indexed: 01/06/2023] Open
Abstract
To characterize the mutation profiles of colorectal cancer (CRC) primary tumors (PTs) and liver metastases (CLMs), we performed both whole-exome and RNA sequencing. Ten significantly mutated genes, including BMI1, CARD11, and NRG1, were found in 34 CRCs with CLMs. We defined three mutation classes (Class 1 to 3) based on the absence or presence of mutations during liver metastasis. Most mutations were classified into Class 1 (shared between PTs and CLMs), suggesting the common clonal origin of PTs and CLMs. Class 1 was more strongly associated with the clinical characteristics of advanced cancer and was more frequently superimposed with chromosomal deletions in CLMs than Class 2 (PT-specific). The integration of exome and RNA sequencing revealed that variant-allele frequencies (VAFs) of mutations in the transcriptome tended to have stronger functional implications than those in the exome. For instance, VAFs of the TP53 and APC mutations in the transcriptome significantly correlated with the expression level of their target genes. Additionally, mutations with high functional impact were enriched with high VAFs in the CLM transcriptomes. We identified 11 mutation-associated splicing events in the CRC transcriptomes. Thus, the integration of the exome and the transcriptome may elucidate the underlying molecular events responsible for CLMs.
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Affiliation(s)
- Byungho Lim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jihyeob Mun
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Chan Wook Kim
- Department of Surgery, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seon Ae Roh
- Department of Surgery, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Institute of Innovative Cancer Research and Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Dong-Hyung Cho
- Institute of Innovative Cancer Research and Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.,Graduate School of East-West Medical Science, Kyung Hee University, Gyeonggi-do, Republic of Korea
| | - Yong Sung Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Institute of Innovative Cancer Research and Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Seon-Young Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Jin Cheon Kim
- Department of Surgery, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Institute of Innovative Cancer Research and Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
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38
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Lemoine L, Sugarbaker P, Van der Speeten K. Pathophysiology of colorectal peritoneal carcinomatosis: Role of the peritoneum. World J Gastroenterol 2016; 22:7692-7707. [PMID: 27678351 PMCID: PMC5016368 DOI: 10.3748/wjg.v22.i34.7692] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/28/2016] [Accepted: 08/01/2016] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the fourth most common cause of cancer-related death worldwide. Besides the lymphatic and haematogenous routes of dissemination, CRC frequently gives rise to transcoelomic spread of tumor cells in the peritoneal cavity, which ultimately leads to peritoneal carcinomatosis (PC). PC is associated with a poor prognosis and bad quality of life for these patients in their terminal stages of disease. A loco-regional treatment modality for PC combining cytoreductive surgery and hyperthermic intraperitoneal peroperative chemotherapy has resulted in promising clinical results. However, this novel approach is associated with significant morbidity and mortality. A comprehensive understanding of the molecular events involved in peritoneal disease spread is paramount in avoiding unnecessary toxicity. The emergence of PC is the result of a molecular crosstalk between cancer cells and host elements, involving several well-defined steps, together known as the peritoneal metastatic cascade. Individual or clumps of tumor cells detach from the primary tumor, gain access to the peritoneal cavity and become susceptible to the regular peritoneal transport. They attach to the distant peritoneum, subsequently invade the subperitoneal space, where angiogenesis sustains proliferation and enables further metastatic growth. These molecular events are not isolated events but rather a continuous and interdependent process. In this manuscript, we review current data regarding the molecular mechanisms underlying the development of colorectal PC, with a special focus on the peritoneum and the role of the surgeon in peritoneal disease spread.
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Lee M, Crawford NPS. Defining the Influence of Germline Variation on Metastasis Using Systems Genetics Approaches. Adv Cancer Res 2016; 132:73-109. [PMID: 27613130 DOI: 10.1016/bs.acr.2016.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer is estimated to be responsible for 8 million deaths worldwide and over half a million deaths every year in the United States. The majority of cancer-related deaths in solid tumors is directly associated with the effects of metastasis. While the influence of germline factors on cancer risk and development has long been recognized, the contribution of hereditary variation to tumor progression and metastasis has only gained acceptance more recently. A variety of approaches have been used to define how hereditary variation influences tumor progression and metastasis. One approach that garnered much early attention was epidemiological studies of cohorts of cancer patients, which demonstrated that specific loci within the human genome are associated with a differential propensity for aggressive tumor development. However, a powerful, and somewhat underutilized approach has been the use of systems genetics approaches in transgenic mouse models of human cancer. Such approaches are typically multifaceted, and involve integration of multiple lines of evidence derived, for example, from genetic and transcriptomic screens of genetically diverse mouse models of cancer, coupled with bioinformatics analysis of human cancer datasets, and functional analysis of candidate genes. These methodologies have allowed for the identification of multiple hereditary metastasis susceptibility genes, with wide-ranging cellular functions including regulation of gene transcription, cell proliferation, and cell-cell adhesion. In this chapter, we review how each of these approaches have facilitated the identification of these hereditary metastasis modifiers, the molecular functions of these metastasis-associated genes, and the implications of these findings upon patient survival.
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Affiliation(s)
- M Lee
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, United States
| | - N P S Crawford
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, United States.
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Tanenbaum DG, Hall WA, Colbert LE, Bastien AJ, Brat DJ, Kong J, Kim S, Dwivedi B, Kowalski J, Landry JC, Yu DS. TNFRSF10C copy number variation is associated with metastatic colorectal cancer. J Gastrointest Oncol 2016; 7:306-14. [PMID: 27284460 DOI: 10.21037/jgo.2015.11.04] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Genetic markers for distant metastatic disease in patients with colorectal cancer (CRC) are not well defined. Identification of genetic alterations associated with metastatic CRC could help to guide systemic and local treatment strategies. We evaluated the association of tumor necrosis factor receptor superfamily member 10C (TNFRSF10C) copy number variation (CNV) with distant metastatic disease in patients with CRC using The Cancer Genome Atlas (TCGA). METHODS Genetic sequencing data and clinical characteristics were obtained from TCGA for all available patients with CRC. There were 515 CRC patient samples with CNV and clinical outcome data, including a subset of 144 rectal adenocarcinoma patient samples. Using the TCGA CRC dataset, CNV of TNFRSF10C was evaluated for association with distant metastatic disease (M1 vs. M0). Multivariate logistic regression analysis with odds ratio (OR) using a 95% confidence interval (CI) was performed adjusting for age, T stage, N stage, adjuvant chemotherapy, gender, microsatellite instability (MSI), location, and surgical margin status. RESULTS TNFRSF10C CNV in patients with CRC was associated with distant metastatic disease [OR 4.81 (95% CI, 2.13-10.85) P<0.001] and positive lymph nodes [OR 18.83 (95% CI, 8.42-42.09)]; P<0.001) but not MSI (OR P=0.799). On multivariate analysis, after adjusting for pathologic T stage, N stage, adjuvant chemotherapy, gender, and MSI, TNFRSF10C CNV remained significantly associated with distant metastatic disease (OR P=0.018). Subset analysis revealed that TNFRSF10C CNV was also significantly associated with distant metastatic disease in patients with rectal adenocarcinoma (OR P=0.016). CONCLUSIONS TNFRSF10C CNV in patients with CRC is associated with distant metastatic disease. With further validation, such genetic profiles could be used clinically to support optimal systemic treatment strategies versus more aggressive local therapies in patients with CRC, including radiation therapy for rectal adenocarcinoma.
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Affiliation(s)
- Daniel G Tanenbaum
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - William A Hall
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lauren E Colbert
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amanda J Bastien
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel J Brat
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jun Kong
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungjin Kim
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bhakti Dwivedi
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeanne Kowalski
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jerome C Landry
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David S Yu
- 1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Whom to blame for metastasis, the epithelial-mesenchymal transition or the tumor microenvironment? Cancer Lett 2016; 380:359-68. [PMID: 26791236 DOI: 10.1016/j.canlet.2015.12.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/22/2015] [Accepted: 12/25/2015] [Indexed: 02/06/2023]
Abstract
Changes in the tumor microenvironment (TME) can trigger the activation of otherwise non-malignant cells to become highly aggressive and motile. This is evident during initial tumor growth when the poor vascularization in tumors generates hypoxic regions that trigger the latent embryonic program, epithelial-to-mesenchymal transition (EMT), in epithelial carcinoma cells (e-cars) leading to highly motile mesenchymal-like carcinoma cells (m-cars), which also acquire cancer stem cell properties. After that, specific bidirectional interactions take place between m-cars and the cellular components of TME at different stages of metastasis. These interactions include several vicious positive feedback loops in which m-cars trigger a phenotypic switch, causing normal stromal cells to become pro-tumorigenic, which then further promote the survival, motility, and proliferation of m-cars. Accordingly, there is not a single culprit accounting for metastasis. Instead both m-cars and the TME dynamically interact, evolve and promote metastasis. In this review, we discuss the current status of the known interactions between m-cars and the TME during different stages of metastasis and how these interactions promote the metastatic activity of highly malignant m-cars by promoting their invasive mesenchymal phenotype and CSC properties.
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Sylvester BE, Vakiani E. Tumor evolution and intratumor heterogeneity in colorectal carcinoma: insights from comparative genomic profiling of primary tumors and matched metastases. J Gastrointest Oncol 2015; 6:668-75. [PMID: 26697200 DOI: 10.3978/j.issn.2078-6891.2015.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metastatic colorectal cancer (CRC) is one of the leading causes of cancer-related mortality among men and women worldwide. Over the past few decades, advances in our understanding of the genetic and epigenetic underpinnings of CRC have led to important insights into the pathogenesis of invasive tumors and have identified different molecular subgroups. Nonetheless, the events that might facilitate dissemination of tumor cells to distant sites giving rise to metastatic disease are not well characterized. Furthermore, in contrast to intertumor heterogeneity the extent of intratumor heterogeneity in different types of CRC has not been fully defined. In this paper, we review studies that have compared the genetic profile of primary invasive carcinomas to that of matched metastases and discuss the implications of their findings for our understanding of tumor evolution and for the clinical management of patients with advanced CRC.
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Affiliation(s)
- Brooke E Sylvester
- 1 Human Oncology and Pathogenesis Program, 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- 1 Human Oncology and Pathogenesis Program, 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Xie T, Musteanu M, Lopez-Casas PP, Shields DJ, Olson P, Rejto PA, Hidalgo M. Whole Exome Sequencing of Rapid Autopsy Tumors and Xenograft Models Reveals Possible Driver Mutations Underlying Tumor Progression. PLoS One 2015; 10:e0142631. [PMID: 26555578 PMCID: PMC4640827 DOI: 10.1371/journal.pone.0142631] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is a highly lethal malignancy due to its propensity to invade and rapidly metastasize and remains very difficult to manage clinically. One major hindrance towards a better understanding of PDAC is the lack of molecular data sets and models representative of end stage disease. Moreover, it remains unclear how molecularly similar patient-derived xenograft (PDX) models are to the primary tumor from which they were derived. To identify potential molecular drivers in metastatic pancreatic cancer progression, we obtained matched primary tumor, metastases and normal (peripheral blood) samples under a rapid autopsy program and performed whole exome sequencing (WES) on tumor as well as normal samples. PDX models were also generated, sequenced and compared to tumors. Across the matched data sets generated for three patients, there were on average approximately 160 single-nucleotide mutations in each sample. The majority of mutations in each patient were shared among the primary and metastatic samples and, importantly, were largely retained in the xenograft models. Based on the mutation prevalence in the primary and metastatic sites, we proposed possible clonal evolution patterns marked by functional mutations affecting cancer genes such as KRAS, TP53 and SMAD4 that may play an important role in tumor initiation, progression and metastasis. These results add to our understanding of pancreatic tumor biology, and demonstrate that PDX models derived from advanced or end-stage likely closely approximate the genetics of the disease in the clinic and thus represent a biologically and clinically relevant pre-clinical platform that may enable the development of effective targeted therapies for PDAC.
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Affiliation(s)
- Tao Xie
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
- * E-mail: (TX); (MH)
| | - Monica Musteanu
- CNIO (Spanish National Cancer Research Centre), E-28029, Madrid, Madrid, Spain
| | | | - David J. Shields
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Peter Olson
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Paul A. Rejto
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Manuel Hidalgo
- CNIO (Spanish National Cancer Research Centre), E-28029, Madrid, Madrid, Spain
- * E-mail: (TX); (MH)
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Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL, Tabernero J, Seoane J, Martinez-Saez E, Curry WT, Dunn IF, Paek SH, Park SH, McKenna A, Chevalier A, Rosenberg M, Barker FG, Gill CM, Van Hummelen P, Thorner AR, Johnson BE, Hoang MP, Choueiri TK, Signoretti S, Sougnez C, Rabin MS, Lin NU, Winer EP, Stemmer-Rachamimov A, Meyerson M, Garraway L, Gabriel S, Lander ES, Beroukhim R, Batchelor TT, Baselga J, Louis DN, Getz G, Hahn WC. Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov 2015; 5:1164-1177. [PMID: 26410082 PMCID: PMC4916970 DOI: 10.1158/2159-8290.cd-15-0369] [Citation(s) in RCA: 719] [Impact Index Per Article: 79.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022]
Abstract
UNLABELLED Brain metastases are associated with a dismal prognosis. Whether brain metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. We performed whole-exome sequencing of 86 matched brain metastases, primary tumors, and normal tissue. In all clonally related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found potentially clinically informative alterations in the brain metastases not detected in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were genetically homogenous. Distal extracranial and regional lymph node metastases were highly divergent from brain metastases. We detected alterations associated with sensitivity to PI3K/AKT/mTOR, CDK, and HER2/EGFR inhibitors in the brain metastases. Genomic analysis of brain metastases provides an opportunity to identify potentially clinically informative alterations not detected in clinically sampled primary tumors, regional lymph nodes, or extracranial metastases. SIGNIFICANCE Decisions for individualized therapies in patients with brain metastasis are often made from primary-tumor biopsies. We demonstrate that clinically actionable alterations present in brain metastases are frequently not detected in primary biopsies, suggesting that sequencing of primary biopsies alone may miss a substantial number of opportunities for targeted therapy.
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Affiliation(s)
- Priscilla K. Brastianos
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Scott L. Carter
- Joint Center for Cancer Precision Medicine, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Sandro Santagata
- Department of Cancer Biology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Amaro Taylor-Weiner
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Robert T. Jones
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Michael S. Lawrence
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Peleg M. Horowitz
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Kristian Cibulskis
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Keith L. Ligon
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Josep Tabernero
- Department of Medical Oncology, Department of Pathology, Barcelona - all in Spain
| | - Joan Seoane
- Department of Medical Oncology, Department of Pathology, Barcelona - all in Spain
| | - Elena Martinez-Saez
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Barcelona - all in Spain
| | - William T. Curry
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Ian F. Dunn
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Sun Ha Paek
- Department of Neurosurgery and Department of Pathology, Seoul National University College of Medicine - all in Korea
| | - Sung-Hye Park
- Department of Neurosurgery and Department of Pathology, Seoul National University College of Medicine - all in Korea
| | - Aaron McKenna
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Aaron Chevalier
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Mara Rosenberg
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Frederick G. Barker
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Corey M. Gill
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Paul Van Hummelen
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Aaron R. Thorner
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Bruce E. Johnson
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Mai P. Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Toni K. Choueiri
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Carrie Sougnez
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Michael S. Rabin
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Nancy U. Lin
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Eric P. Winer
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Anat Stemmer-Rachamimov
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Matthew Meyerson
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Levi Garraway
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Joint Center for Cancer Precision Medicine, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Stacey Gabriel
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Eric S. Lander
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Rameen Beroukhim
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Cancer Biology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Tracy T. Batchelor
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Jose Baselga
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York City
| | - David N. Louis
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Gad Getz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - William C. Hahn
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
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Gemoll T, Meyer R, Habermann JK. Applying Genomics and Proteomics in Translational Surgical Oncology Research. Eur Surg Res 2015; 55:184-97. [PMID: 26339997 DOI: 10.1159/000438860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Translational surgical research can range from investigating clinically oriented basic pathophysiological research via the correlation of molecular findings with a patient's clinical outcome to conducting treatment response studies. Herein, the specialist's opinion as a 'surgeon scientist' plays a pivotal role, e.g. in planning experimental setups focusing on the clinically most relevant needs. SUMMARY AND KEY MESSAGES: This review provides a survey of genomic and proteomic technologies and gives an up-to-date overview of those studies applying these technologies exemplarily in colorectal cancer-based biomarker research. Although current results are promising, future validation studies within multicenter networks are required to promote the translation of 'omics' from bench to bedside. In this endeavor, departments of surgery and institutes of experimental surgery together should play a fundamental role. The program for 'clinician scientists' recently launched by the German Research Society (DFG) could be one tool to promote interdisciplinary networks and surgeons' impact on translational research.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lx00FC;beck and University Medical Center Schleswig-Holstein (UKSH), Lx00FC;beck, Germany
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Wang H, Liang L, Fang JY, Xu J. Somatic gene copy number alterations in colorectal cancer: new quest for cancer drivers and biomarkers. Oncogene 2015; 35:2011-9. [PMID: 26257062 DOI: 10.1038/onc.2015.304] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/07/2015] [Accepted: 07/12/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) results from the accumulation of genetic alterations, and somatic copy number alterations (CNAs) are crucial for the development of CRC. Genome-wide survey of CNAs provides opportunities for identifying cancer driver genes in an unbiased manner. The detection of aberrant CNAs may provide novel markers for the early diagnosis and personalized treatment of CRC. A major challenge in array-based profiling of CNAs is to distinguish the alterations that play causative roles from the random alterations that accumulate during colorectal carcinogenesis. In this view, we systematically discuss the frequent CNAs in CRC, focusing on functional genes that have potential diagnostic, prognostic and therapeutic significance.
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Affiliation(s)
- H Wang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - L Liang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J-Y Fang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J Xu
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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Distinctive Spatiotemporal Stability of Somatic Mutations in Metastasized Microsatellite-stable Colorectal Cancer. Am J Surg Pathol 2015; 39:1140-7. [DOI: 10.1097/pas.0000000000000423] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Hutchinson RA, Adams RA, McArt DG, Salto-Tellez M, Jasani B, Hamilton PW. Epidermal growth factor receptor immunohistochemistry: new opportunities in metastatic colorectal cancer. J Transl Med 2015; 13:217. [PMID: 26149458 PMCID: PMC4492076 DOI: 10.1186/s12967-015-0531-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/12/2015] [Indexed: 02/06/2023] Open
Abstract
The treatment of cancer is becoming more precise, targeting specific oncogenic drivers with targeted molecular therapies. The epidermal growth factor receptor has been found to be over-expressed in a multitude of solid tumours. Immunohistochemistry is widely used in the fields of diagnostic and personalised medicine to localise and visualise disease specific proteins. To date the clinical utility of epidermal growth factor receptor immunohistochemistry in determining monoclonal antibody efficacy has remained somewhat inconclusive. The lack of an agreed reproducible scoring criteria for epidermal growth factor receptor immunohistochemistry has, in various clinical trials yielded conflicting results as to the use of epidermal growth factor receptor immunohistochemistry assay as a companion diagnostic. This has resulted in this test being removed from the licence for the drug panitumumab and not performed in clinical practice for cetuximab. In this review we explore the reasons behind this with a particular emphasis on colorectal cancer, and to suggest a way of resolving the situation through improving the precision of epidermal growth factor receptor immunohistochemistry with quantitative image analysis of digitised images complemented with companion molecular morphological techniques such as in situ hybridisation and section based gene mutation analysis.
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Affiliation(s)
- Ryan A Hutchinson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK.
- Waring Laboratory, Department of Pathology, Centre for Translational Pathology, University of Melbourne, Parkville, 3010, VIC, Australia.
| | - Richard A Adams
- Institute of Cancer and Genetics, Cardiff University School of Medicine, Institute of Medical Genetics Building, Heath Park, Cardiff, CF14 4XN, UK.
| | - Darragh G McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK.
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK.
| | - Bharat Jasani
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 010000, Kazakhstan.
| | - Peter W Hamilton
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK.
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Cardone C, Martini G, Troiani T, Napolitano S, Selvaggi F, Ciardiello F, Martinelli E. Genetic Landscape of Primary Versus Metastatic Colorectal Cancer: to What Extent Are They Concordant? CURRENT COLORECTAL CANCER REPORTS 2015. [DOI: 10.1007/s11888-015-0278-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sanz-Pamplona R, Lopez-Doriga A, Paré-Brunet L, Lázaro K, Bellido F, Alonso MH, Aussó S, Guinó E, Beltrán S, Castro-Giner F, Gut M, Sanjuan X, Closa A, Cordero D, Morón-Duran FD, Soriano A, Salazar R, Valle L, Moreno V. Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer. Clin Cancer Res 2015; 21:4709-18. [PMID: 26071483 DOI: 10.1158/1078-0432.ccr-15-0159] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/17/2015] [Indexed: 12/30/2022]
Abstract
PURPOSE Somatic mutations occur at early stages of adenoma and accumulate throughout colorectal cancer progression. The aim of this study was to characterize the mutational landscape of stage II tumors and to search for novel recurrent mutations likely implicated in colorectal cancer tumorigenesis. EXPERIMENTAL DESIGN The exomic DNA of 42 stage II, microsatellite-stable colon tumors and their paired mucosae were sequenced. Other molecular data available in the discovery dataset [gene expression, methylation, and copy number variations (CNV)] were used to further characterize these tumors. Additional datasets comprising 553 colorectal cancer samples were used to validate the discovered mutations. RESULTS As a result, 4,886 somatic single-nucleotide variants (SNV) were found. Almost all SNVs were private changes, with few mutations shared by more than one tumor, thus revealing tumor-specific mutational landscapes. Nevertheless, these diverse mutations converged into common cellular pathways, such as cell cycle or apoptosis. Among this mutational heterogeneity, variants resulting in early stop codons in the AMER1 (also known as FAM123B or WTX) gene emerged as recurrent mutations in colorectal cancer. Losses of AMER1 by other mechanisms apart from mutations such as methylation and copy number aberrations were also found. Tumors lacking this tumor suppressor gene exhibited a mesenchymal phenotype characterized by inhibition of the canonical Wnt pathway. CONCLUSIONS In silico and experimental validation in independent datasets confirmed the existence of functional mutations in AMER1 in approximately 10% of analyzed colorectal cancer tumors. Moreover, these tumors exhibited a characteristic phenotype.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Paré-Brunet
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kira Lázaro
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fernando Bellido
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Henar Alonso
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sergi Beltrán
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | | | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Xavier Sanjuan
- Pathology Service, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adria Closa
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - David Cordero
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco D Morón-Duran
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Soriano
- Gastroenterology Service, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ramón Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain. Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain.
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