1
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Song Y, Kerr TD, Sanders C, Dai L, Baxter SS, Somerville B, Baugher RN, Mellott SD, Young TB, Lawhorn HE, Plona TM, Xu B, Wei L, Hu Q, Liu S, Hutson A, Karim B, Burkett S, Difilippantonio S, Pinto L, Gebert J, Kloor M, Lipkin SM, Sei S, Shoemaker RH. Organoids and metastatic orthotopic mouse model for mismatch repair-deficient colorectal cancer. Front Oncol 2023; 13:1223915. [PMID: 37746286 PMCID: PMC10516605 DOI: 10.3389/fonc.2023.1223915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Background Genome integrity is essential for the survival of an organism. DNA mismatch repair (MMR) genes (e.g., MLH1, MSH2, MSH6, and PMS2) play a critical role in the DNA damage response pathway for genome integrity maintenance. Germline mutations of MMR genes can lead to Lynch syndrome or constitutional mismatch repair deficiency syndrome, resulting in an increased lifetime risk of developing cancer characterized by high microsatellite instability (MSI-H) and high mutation burden. Although immunotherapy has been approved for MMR-deficient (MMRd) cancer patients, the overall response rate needs to be improved and other management options are needed. Methods To better understand the biology of MMRd cancers, elucidate the resistance mechanisms to immune modulation, and develop vaccines and therapeutic testing platforms for this high-risk population, we generated organoids and an orthotopic mouse model from intestine tumors developed in a Msh2-deficient mouse model, and followed with a detailed characterization. Results The organoids were shown to be of epithelial origin with stem cell features, to have a high frameshift mutation frequency with MSI-H and chromosome instability, and intra- and inter-tumor heterogeneity. An orthotopic model using intra-cecal implantation of tumor fragments derived from organoids showed progressive tumor growth, resulting in the development of adenocarcinomas mixed with mucinous features and distant metastasis in liver and lymph node. Conclusions The established organoids with characteristics of MSI-H cancers can be used to study MMRd cancer biology. The orthotopic model, with its distant metastasis and expressing frameshift peptides, is suitable for evaluating the efficacy of neoantigen-based vaccines or anticancer drugs in combination with other therapies.
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Affiliation(s)
- Yurong Song
- Frederick National Laboratory for Cancer Research, Vaccine, Immunity, and Cancer Directorate, Frederick, MD, United States
| | - Travis D. Kerr
- Frederick National Laboratory for Cancer Research, Vaccine, Immunity, and Cancer Directorate, Frederick, MD, United States
| | - Chelsea Sanders
- Frederick National Laboratory for Cancer Research, Laboratory Animal Sciences Program, Frederick, MD, United States
| | - Lisheng Dai
- Frederick National Laboratory for Cancer Research, Vaccine, Immunity, and Cancer Directorate, Frederick, MD, United States
| | - Shaneen S. Baxter
- Frederick National Laboratory for Cancer Research, Vaccine, Immunity, and Cancer Directorate, Frederick, MD, United States
| | - Brandon Somerville
- Frederick National Laboratory for Cancer Research, Vaccine, Immunity, and Cancer Directorate, Frederick, MD, United States
| | - Ryan N. Baugher
- Frederick National Laboratory for Cancer Research, Clinical Laboratory Improvement Amendments (CLIA) Molecular Diagnostics Laboratory, Frederick, MD, United States
| | - Stephanie D. Mellott
- Frederick National Laboratory for Cancer Research, Clinical Laboratory Improvement Amendments (CLIA) Molecular Diagnostics Laboratory, Frederick, MD, United States
| | - Todd B. Young
- Frederick National Laboratory for Cancer Research, Clinical Laboratory Improvement Amendments (CLIA) Molecular Diagnostics Laboratory, Frederick, MD, United States
| | - Heidi E. Lawhorn
- Frederick National Laboratory for Cancer Research, Clinical Laboratory Improvement Amendments (CLIA) Molecular Diagnostics Laboratory, Frederick, MD, United States
| | - Teri M. Plona
- Frederick National Laboratory for Cancer Research, Clinical Laboratory Improvement Amendments (CLIA) Molecular Diagnostics Laboratory, Frederick, MD, United States
| | - Bingfang Xu
- Frederick National Laboratory for Cancer Research, Genomics Laboratory, Frederick, MD, United States
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, Frederick, MD, United States
| | - Simone Difilippantonio
- Frederick National Laboratory for Cancer Research, Laboratory Animal Sciences Program, Frederick, MD, United States
| | - Ligia Pinto
- Frederick National Laboratory for Cancer Research, Vaccine, Immunity, and Cancer Directorate, Frederick, MD, United States
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Steven M. Lipkin
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Shizuko Sei
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, United States
| | - Robert H. Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, United States
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2
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Song Y, Baxter SS, Dai L, Sanders C, Burkett S, Baugher RN, Mellott SD, Young TB, Lawhorn HE, Difilippantonio S, Karim B, Kadariya Y, Pinto LA, Testa JR, Shoemaker RH. Mesothelioma Mouse Models with Mixed Genomic States of Chromosome and Microsatellite Instability. Cancers (Basel) 2022; 14:3108. [PMID: 35804881 PMCID: PMC9264972 DOI: 10.3390/cancers14133108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
Malignant mesothelioma (MMe) is a rare malignancy originating from the linings of the pleural, peritoneal and pericardial cavities. The best-defined risk factor is exposure to carcinogenic mineral fibers (e.g., asbestos). Genomic studies have revealed that the most frequent genetic lesions in human MMe are mutations in tumor suppressor genes. Several genetically engineered mouse models have been generated by introducing the same genetic lesions found in human MMe. However, most of these models require specialized breeding facilities and long-term exposure of mice to asbestos for MMe development. Thus, an alternative model with high tumor penetrance without asbestos is urgently needed. We characterized an orthotopic model using MMe cells derived from Cdkn2a+/-;Nf2+/- mice chronically injected with asbestos. These MMe cells were tumorigenic upon intraperitoneal injection. Moreover, MMe cells showed mixed chromosome and microsatellite instability, supporting the notion that genomic instability is relevant in MMe pathogenesis. In addition, microsatellite markers were detectable in the plasma of tumor-bearing mice, indicating a potential use for early cancer detection and monitoring the effects of interventions. This orthotopic model with rapid development of MMe without asbestos exposure represents genomic instability and specific molecular targets for therapeutic or preventive interventions to enable preclinical proof of concept for the intervention in an immunocompetent setting.
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Affiliation(s)
- Yurong Song
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (S.S.B.); (L.D.); (L.A.P.)
| | - Shaneen S. Baxter
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (S.S.B.); (L.D.); (L.A.P.)
| | - Lisheng Dai
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (S.S.B.); (L.D.); (L.A.P.)
| | - Chelsea Sanders
- Animal Research Technical Support of Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.S.); (S.D.)
| | - Sandra Burkett
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD 21702, USA;
| | - Ryan N. Baugher
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.N.B.); (S.D.M.); (T.B.Y.); (H.E.L.)
| | - Stephanie D. Mellott
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.N.B.); (S.D.M.); (T.B.Y.); (H.E.L.)
| | - Todd B. Young
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.N.B.); (S.D.M.); (T.B.Y.); (H.E.L.)
| | - Heidi E. Lawhorn
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.N.B.); (S.D.M.); (T.B.Y.); (H.E.L.)
| | - Simone Difilippantonio
- Animal Research Technical Support of Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.S.); (S.D.)
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Yuwaraj Kadariya
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.K.); (J.R.T.)
| | - Ligia A. Pinto
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (S.S.B.); (L.D.); (L.A.P.)
| | - Joseph R. Testa
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.K.); (J.R.T.)
| | - Robert H. Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA;
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3
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Golas MM, Gunawan B, Cakir M, Cameron S, Enders C, Liersch T, Füzesi L, Sander B. Evolutionary patterns of chromosomal instability and mismatch repair deficiency in proximal and distal colorectal cancer. Colorectal Dis 2022; 24:157-176. [PMID: 34623739 DOI: 10.1111/codi.15946] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/04/2021] [Accepted: 09/28/2021] [Indexed: 12/27/2022]
Abstract
AIM Colorectal carcinomas (CRCs) progress through heterogeneous pathways. The aim of this study was to analyse whether or not the cytogenetic evolution of CRC is linked to tumour site, level of chromosomal imbalance and metastasis. METHOD A set of therapy-naïve pT3 CRCs comprising 26 proximal and 49 distal pT3 CRCs was studied by combining immunohistochemistry of mismatch repair (MMR) proteins, microsatellite analyses and molecular karyotyping as well as clinical parameters. RESULTS A MMR deficient/microsatellite-unstable (dMMR/MSI-H) status was associated with location of the primary tumour proximal to the splenic flexure, and dMMR/MSI-H tumours presented with significantly lower levels of chromosomal imbalances compared with MMR proficient/microsatellite-stable (pMMR/MSS) tumours. Oncogenetic tree modelling suggested two evolutionary clusters characterized by dMMR/MSI-H and chromosomal instability (CIN), respectively, for both proximal and distal CRCs. In CIN cases, +13q, -18q and +20q were predicted as preferentially early events, and -1p, -4 -and -5q as late events. Separate oncogenetic tree models of proximal and distal cases indicated similar early events independent of tumour site. However, in cases with high CIN defined by more than 10 copy number aberrations, loss of 17p occurred earlier in cytogenetic evolution than in cases showing low to moderate CIN. Differences in the oncogenetic trees were observed for CRCs with lymph node and distant metastasis. Loss of 8p was modelled as an early event in node-positive CRC, while +7p and +8q comprised early events in CRC with distant metastasis. CONCLUSION CRCs characterized by CIN follow multiple, interconnected genetic pathways in line with the basic 'Vogelgram' concept proposed for the progression of CRC that places the accumulation of genetic changes at centre of tumour evolution. However, the timing of specific genetic events may favour metastatic potential.
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Affiliation(s)
- Mariola Monika Golas
- Department of Hematology and Medical Oncology, Comprehensive Cancer Center Augsburg, University Medical Center Augsburg, Augsburg, Germany
| | - Bastian Gunawan
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Meliha Cakir
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Cameron
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Christina Enders
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Torsten Liersch
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Laszlo Füzesi
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.,Institute of Pathology and Molecular Diagnostics, University Medical Center Augsburg, Augsburg, Germany
| | - Bjoern Sander
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.,Institute of Pathology, Hannover Medical School, Hannover, Germany
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4
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Shin G, Greer SU, Hopmans E, Grimes SM, Lee H, Zhao L, Miotke L, Suarez C, Almeda AF, Haraldsdottir S, Ji HP. Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8. Genome Med 2021; 13:145. [PMID: 34488871 PMCID: PMC8420050 DOI: 10.1186/s13073-021-00958-z] [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] [Received: 12/24/2020] [Accepted: 08/23/2021] [Indexed: 11/10/2022] Open
Abstract
We developed a sensitive sequencing approach that simultaneously profiles microsatellite instability, chromosomal instability, and subclonal structure in cancer. We assessed diverse repeat motifs across 225 microsatellites on colorectal carcinomas. Our study identified elevated alterations at both selected tetranucleotide and conventional mononucleotide repeats. Many colorectal carcinomas had a mix of genomic instability states that are normally considered exclusive. An MSH3 mutation may have contributed to the mixed states. Increased copy number of chromosome arm 8q was most prevalent among tumors with microsatellite instability, including a case of translocation involving 8q. Subclonal analysis identified co-occurring driver mutations previously known to be exclusive.
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Affiliation(s)
- GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Stephanie U Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Erik Hopmans
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Susan M Grimes
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Lan Zhao
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Carlos Suarez
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Alison F Almeda
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Sigurdis Haraldsdottir
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA. .,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
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5
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Patil S, Sengupta K. Role of A- and B-type lamins in nuclear structure-function relationships. Biol Cell 2021; 113:295-310. [PMID: 33638183 DOI: 10.1111/boc.202000160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022]
Abstract
Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A- and B-type lamins localizes in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilises protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organisation, the mechanical stability of the nucleus, genome organisation, transcriptional regulation, genome stability and cellular differentiation. Here, we review recent research on nuclear lamins and unique roles of A- and B-type lamins in modulating various nuclear processes and their impact on cell function.
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Affiliation(s)
- Shalaka Patil
- Biology, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Kundan Sengupta
- Biology, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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6
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Li Y, Li J, Guo E, Huang J, Fang G, Chen S, Yang B, Fu Y, Li F, Wang Z, Xiao R, Liu C, Huang Y, Wu X, Lu F, You L, Feng L, Xi L, Wu P, Ma D, Sun C, Wang B, Chen G. Integrating pathology, chromosomal instability and mutations for risk stratification in early-stage endometrioid endometrial carcinoma. Cell Biosci 2020; 10:122. [PMID: 33110489 PMCID: PMC7583263 DOI: 10.1186/s13578-020-00486-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Background Risk stratifications for endometrial carcinoma (EC) depend on histopathology and molecular pathology. Histopathological risk stratification lacks reproducibility, neglects heterogeneity and contributes little to surgical procedures. Existing molecular stratification is useless in patients with specific pathological or molecular characteristics and cannot guide postoperative adjuvant radiotherapies. Chromosomal instability (CIN), the numerical and structural alterations of chromosomes resulting from ongoing errors of chromosome segregation, is an intrinsic biological mechanism for the evolution of different prognostic factors of histopathology and molecular pathology and may be applicable to the risk stratification of EC. Results By analyzing CIN25 and CIN70, two reliable gene expression signatures for CIN, we found that EC with unfavorable prognostic factors of histopathology or molecular pathology had serious CIN. However, the POLE mutant, as a favorable prognostic factor, had elevated CIN signatures, and the CTNNB1 mutant, as an unfavorable prognostic factor, had decreased CIN signatures. Only if these two mutations were excluded were CIN signatures strongly prognostic for outcomes in different adjuvant radiotherapy subgroups. Integrating pathology, CIN signatures and POLE/CTNNB1 mutation stratified stageIendometrioid EC into four groups with improved risk prognostication and treatment recommendations. Conclusions We revealed the possibility of integrating histopathology and molecular pathology by CIN for risk stratification in early-stage EC. Our integrated risk model deserves further improvement and validation.
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Affiliation(s)
- Yuan Li
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Jiaqi Li
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ensong Guo
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Jia Huang
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Guangguang Fang
- Department of Gynecology,Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen Dapeng New District Maternity & Child Health Hospital, Shenzhen, 518038 China
| | - Shaohua Chen
- Department of Gynecology and Obstetrics, The People's Hospital of Macheng City, Macheng, 438300 China
| | - Bin Yang
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Yu Fu
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Fuxia Li
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Zizhuo Wang
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Rourou Xiao
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Chen Liu
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Yuhan Huang
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Xue Wu
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Funian Lu
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Lixin You
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Ling Feng
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Xi
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Peng Wu
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Ding Ma
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Chaoyang Sun
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Beibei Wang
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
| | - Gang Chen
- National Clinical Research Center of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Anv, Wuhan, 430030 Hubei China
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7
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Kolenčík D, Shishido SN, Pitule P, Mason J, Hicks J, Kuhn P. Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges. Cancers (Basel) 2020; 12:E1376. [PMID: 32471160 PMCID: PMC7352156 DOI: 10.3390/cancers12061376] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/16/2020] [Accepted: 05/25/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal carcinoma (CRC) is characterized by wide intratumor heterogeneity with general genomic instability and there is a need for improved diagnostic, prognostic, and therapeutic tools. The liquid biopsy provides a noninvasive route of sample collection for analysis of circulating tumor cells (CTCs) and genomic material, including cell-free DNA (cfDNA), as a complementary biopsy to the solid tumor tissue. The solid biopsy is critical for molecular characterization and diagnosis at the time of collection. The liquid biopsy has the advantage of longitudinal molecular characterization of the disease, which is crucial for precision medicine and patient-oriented treatment. In this review, we provide an overview of CRC and the different methodologies for the detection of CTCs and cfDNA, followed by a discussion on the potential clinical utility of the liquid biopsy in CRC patient care, and lastly, current challenges in the field.
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Affiliation(s)
- Drahomír Kolenčík
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (P.P.)
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
| | - Pavel Pitule
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (P.P.)
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
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8
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Franch-Expósito S, Bassaganyas L, Vila-Casadesús M, Hernández-Illán E, Esteban-Fabró R, Díaz-Gay M, Lozano JJ, Castells A, Llovet JM, Castellví-Bel S, Camps J. CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications. eLife 2020; 9:e50267. [PMID: 31939734 PMCID: PMC7010409 DOI: 10.7554/elife.50267] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
Somatic copy number alterations (CNAs) are a hallmark of cancer, but their role in tumorigenesis and clinical relevance remain largely unclear. Here, we developed CNApp, a web-based tool that allows a comprehensive exploration of CNAs by using purity-corrected segmented data from multiple genomic platforms. CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to the TCGA pan-cancer dataset of 10,635 genomes showing that CNAs classify cancer types according to their tissue-of-origin, and that each cancer type shows specific ranges of broad and focal CNA scores. Moreover, CNApp reproduces recurrent CNAs in hepatocellular carcinoma and predicts colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and discrete genomic imbalances. In summary, CNApp facilitates CNA-driven research by providing a unique framework to identify relevant clinical implications. CNApp is hosted at https://tools.idibaps.org/CNApp/.
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Affiliation(s)
- Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology TeamInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | - Laia Bassaganyas
- Liver Cancer Translational Research Group, Liver UnitInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | | | - Eva Hernández-Illán
- Gastrointestinal and Pancreatic Oncology TeamInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | - Roger Esteban-Fabró
- Liver Cancer Translational Research Group, Liver UnitInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | - Marcos Díaz-Gay
- Gastrointestinal and Pancreatic Oncology TeamInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | | | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology TeamInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | - Josep Maria Llovet
- Liver Cancer Translational Research Group, Liver UnitInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Sergi Castellví-Bel
- Gastrointestinal and Pancreatic Oncology TeamInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology TeamInstitut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de BarcelonaBarcelonaSpain
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de MedicinaUniversitat Autònoma de BarcelonaBellaterraSpain
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9
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Methotrexate-induced senescence of human colon cancer cells depends on p53 acetylation, but not genomic aberrations. Anticancer Drugs 2019; 30:374-382. [DOI: 10.1097/cad.0000000000000731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Namba S, Sato K, Kojima S, Ueno T, Yamamoto Y, Tanaka Y, Inoue S, Nagae G, Iinuma H, Hazama S, Ishihara S, Aburatani H, Mano H, Kawazu M. Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer. Cancer Sci 2019; 110:1096-1104. [PMID: 30637877 PMCID: PMC6398885 DOI: 10.1111/cas.13937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 12/11/2022] Open
Abstract
The silencing of tumor suppressor genes by promoter CpG island (CGI) methylation is an important cause of oncogenesis. Silencing of MLH1 and BRCA1, two examples of oncogenic events, results from promoter CGI methylation. Interestingly, both MLH1 and BRCA1 have a divergent promoter, from which another gene on the opposite strand is also transcribed. Although studies have shown that divergent transcription is an important factor in transcriptional regulation, little is known about its implication in aberrant promoter methylation in cancer. In this study, we analyzed the methylation status of CGI in divergent promoters using a recently enriched transcriptome database. We measured the extent of CGI methylation in 119 colorectal cancer (CRC) clinical samples (65 microsatellite instability high [MSI‐H] CRC with CGI methylator phenotype, 28 MSI‐H CRC without CGI methylator phenotype and 26 microsatellite stable CRC) and 21 normal colorectal tissues using Infinium MethylationEPIC BeadChip. We found that CGI within divergent promoters are less frequently methylated than CGI within unidirectional promoters in normal cells. In the genome of CRC cells, CGI within unidirectional promoters are more vulnerable to aberrant methylation than CGI within divergent promoters. In addition, we identified three DNA sequence motifs that correlate with methylated CGI. We also showed that methylated CGI are associated with genes whose expression is low in normal cells. Thus, we here provide fundamental observations regarding the methylation of divergent promoters that are essential for the understanding of carcinogenesis and development of cancer prevention strategies.
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Affiliation(s)
- Shinichi Namba
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhito Sato
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Inoue
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hisae Iinuma
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Shoichi Hazama
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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11
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Zhang TM, Huang T, Wang RF. Cross talk of chromosome instability, CpG island methylator phenotype and mismatch repair in colorectal cancer. Oncol Lett 2018; 16:1736-1746. [PMID: 30008861 PMCID: PMC6036478 DOI: 10.3892/ol.2018.8860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/22/2018] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer is a severe cancer associated with a high prevalence and fatality rate. There are three major mechanisms for colorectal cancer: (1) Chromosome instability (CIN), (2) CpG island methylator phenotype (CIMP) and (3) mismatch repair (MMR), of which CIN is the most common type. However, these subtypes are not exclusive and overlap. To investigate their biological mechanisms and cross talk, the gene expression profiles of 585 colorectal cancer patients with CIN, CIMP and MMR status records were collected. By comparing the CIN+ and CIN-samples, CIMP+ and CIMP-samples, MMR+ and MMR-samples with minimal redundancy maximal relevance (mRMR) and incremental feature selection (IFS) methods, the CIN, CIMP and MMR associated genes were selected. Unfortunately, there was little direct overlap among them. To investigate their indirect interactions, downstream genes of CIN, CIMP and MMR were identified using the random walk with restart (RWR) method and a greater overlap of downstream genes was indicated. The common downstream genes were involved in biosynthetic and metabolic pathways. These findings were consistent with the clinical observation of wide range metabolite aberrations in colorectal cancer. To conclude, the present study gave a gene level explanation of CIN, CIMP and MMR, but also showed the network level cross talk of CIN, CIMP and MMR. The common genes of CIN, CIMP and MMR may be useful for cross-subtype general colorectal cancer drug development.
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Affiliation(s)
- Tian-Ming Zhang
- Department of Colorectal and Anal Surgery, Jinhua Hospital of Zhejiang University, Jinhua, Zhejiang 321000, P.R. China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Rong-Fei Wang
- Department of Colorectal and Anal Surgery, Jinhua People's Hospital, Jinhua, Zhejiang 321000, P.R. China
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12
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Abstract
Microsatellite instability (MSI) refers to the hypermutator phenotype secondary to frequent polymorphism in short repetitive DNA sequences and single nucleotide substitution, as consequence of DNA mismatch repair (MMR) deficiency. MSI secondary to germline mutation in DNA MMR proteins is the molecular fingerprint of Lynch syndrome (LS), while epigenetic inactivation of these genes is more commonly found in sporadic MSI tumors. MSI occurs at different frequencies across malignancies, although original methods to assess MSI or MMR deficiency have been developed mostly in LS related cancers. Here we will discuss the current methods to detect MSI/MMR deficiency with a focus of new tools which are emerging as highly sensitive detector for MSI across multiple tumor types. Due to high frequencies of non-synonymous mutations, the presence of frameshift-mutated neoantigens, which can trigger a more robust and long-lasting immune response and strong TIL infiltration with tumor eradication, MSI has emerged as an important predictor of sensitivity for immunotherapy-based strategies, as showed by the recent FDA's first histology agnostic-accelerated approval to immune checkpoint inhibitors for refractory, adult and pediatric, MMR deficient (dMMR) or MSI high (MSI-H) tumors. Moreover, it is known that MSI status may predict cancer response/resistance to certain chemotherapies. Here we will describe the complex interplay between the genetic and clinical-pathological features of MSI/dMMR tumors and the cancer immunotherapy, with a focus on the predictive and prognostic role of MMR status for immune checkpoint inhibitors (ICIs) and providing some suggestions on how to conceive better predictive markers for immunotherapy in the next future.
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Affiliation(s)
- Marina Baretti
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, United States
| | - Dung T Le
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, United States.
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13
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Fan Z, Mackey L. Empirical Bayesian analysis of simultaneous changepoints in multiple data sequences. Ann Appl Stat 2017. [DOI: 10.1214/17-aoas1075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Ahmad F, Patrick S, Sheikh T, Sharma V, Pathak P, Malgulwar PB, Kumar A, Joshi SD, Sarkar C, Sen E. Telomerase reverse transcriptase (TERT) - enhancer of zeste homolog 2 (EZH2) network regulates lipid metabolism and DNA damage responses in glioblastoma. J Neurochem 2017; 143:671-683. [PMID: 28833137 DOI: 10.1111/jnc.14152] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/29/2017] [Accepted: 08/11/2017] [Indexed: 12/27/2022]
Abstract
Elevated expression of enhancer of zeste homolog 2 (EZH2), a histone H3K27 methyltransferase, was observed in gliomas harboring telomerase reverse transcriptase (TERT) promoter mutations. Given the known involvement of TERT and EZH2 in glioma progression, the correlation between the two and subsequently its involvement in metabolic programming was investigated. Inhibition of human telomerase reverse transcriptase either pharmacologically or through genetic manipulation not only decreased EZH2 expression, but also (i) abrogated FASN levels, (ii) decreased de novo fatty acid accumulation, and (iii) increased ataxia-telangiectasia-mutated (ATM) phosphorylation levels. Conversely, diminished TERT and FASN levels upon siRNA-mediated EZH2 knockdown indicated a positive correlation between TERT and EZH2. Interestingly, ATM kinase inhibitor rescued TERT inhibition-mediated decrease in FASN and EZH2 levels. Importantly, TERT promoter mutant tumors exhibited greater microsatellite instability, heightened FASN levels and lipid accumulation. Coherent with in vitro findings, pharmacological inhibition of TERT by costunolide decreased lipid accumulation and elevated ATM expression in heterotypic xenograft glioma mouse model. By bringing TERT-EZH2 network at the forefront as driver of dysregulated metabolism, our findings highlight the non-canonical but distinct role of TERT in metabolic reprogramming and DNA damage responses in glioblastoma.
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Affiliation(s)
- Fahim Ahmad
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Shruti Patrick
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Touseef Sheikh
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Anupam Kumar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Shanker Datt Joshi
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ellora Sen
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
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15
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Alonso MH, Aussó S, Lopez-Doriga A, Cordero D, Guinó E, Solé X, Barenys M, de Oca J, Capella G, Salazar R, Sanz-Pamplona R, Moreno V. Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component. Br J Cancer 2017; 117:421-431. [PMID: 28683472 PMCID: PMC5537504 DOI: 10.1038/bjc.2017.208] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/11/2017] [Accepted: 06/09/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression. METHODS Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes. All analyses were adjusted for the quantity of stroma in each sample, which was inferred from gene expression data. RESULTS High heterogeneity among samples was observed; the proportion of altered genome ranged between 0.04 and 26.6%. Recurrent CNA regions with gains were frequent in chromosomes 7p, 8q, 13q, and 20, whereas 8p, 17p, and 18 cumulated losses. A significant positive correlation was observed between the number of somatic mutations and total CNA (Spearman's r=0.42, P=0.006). Approximately 37% of genes located in CNA regions changed their level of expression and the average partial correlation (adjusted for stromal content) with copy number was 0.54 (interquartile range 0.20 to 0.81). Altered genes showed enrichment in pathways relevant for CRC. Tumours classified as CMS2 and CMS4 by the consensus molecular subtyping showed higher frequency of CNA. Losses of one small region in 1p36.33, with gene CDK11B, were associated with poor prognosis. More than 66% of the recurrent CNA were validated in the The Cancer Genome Atlas (TCGA) data when analysed with the same procedure. Furthermore, 79% of the genes with altered expression in our data were validated in the TCGA. CONCLUSIONS Although CNA are frequent events in microsatellite stable CRC, few focal recurrent regions were found. These aberrations have strong effects on gene expression and contribute to deregulate relevant cancer pathways. Owing to the diploid nature of stromal cells, it is important to consider the purity of tumour samples to accurately calculate CNA events in CRC.
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Affiliation(s)
- M Henar Alonso
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - David Cordero
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Xavier Solé
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Mercè Barenys
- Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Gastroenterology Service, Hospital de Viladecans, Barcelona, Spain.,Faculty of Medicine, Department of Clinical Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Javier de Oca
- Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Faculty of Medicine, Department of Clinical Sciences, University of Barcelona (UB), Barcelona, Spain.,Department of General and Digestive Surgery, Bellvitge University Hospital, Barcelona, Spain
| | - Gabriel Capella
- Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Faculty of Medicine, Department of Clinical Sciences, University of Barcelona (UB), Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO) and CIBERONC, Barcelona, Spain
| | - Ramón Salazar
- Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Faculty of Medicine, Department of Clinical Sciences, University of Barcelona (UB), Barcelona, Spain.,Oncology Department, Catalan Institute of Oncology (ICO) and CIBERONC, Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), CIBERESP, Gran Via 199, Hospitalet Llobregat, 08908 Barcelona, Spain.,Molecular Mechanisms and Experimental Therapy Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Faculty of Medicine, Department of Clinical Sciences, University of Barcelona (UB), Barcelona, Spain
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16
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Ali H, Bitar MS, Al Madhoun A, Marafie M, Al-Mulla F. Functionally-focused algorithmic analysis of high resolution microarray-CGH genomic landscapes demonstrates comparable genomic copy number aberrations in MSI and MSS sporadic colorectal cancer. PLoS One 2017; 12:e0171690. [PMID: 28231327 PMCID: PMC5322957 DOI: 10.1371/journal.pone.0171690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/23/2017] [Indexed: 12/25/2022] Open
Abstract
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers. We utilized aCGH to characterize genomic CNAs in 116 well-defined sets of colorectal cancer (CRC) cases. We further applied the significance testing for aberrant copy number (STAC) and Genomic Identification of Significant Targets in Cancer (GISTIC) algorithms to identify functionally relevant (nonrandom) chromosomal aberrations in the analyzed colorectal cancer samples. Our results produced high resolution genomic landscapes of both, MSI and MSS sporadic CRC. We found that CNAs in MSI and MSS CRCs are heterogeneous in nature but may be divided into 3 distinct genomic patterns. Moreover, we show that although CNAs in MSI and MSS CRCs differ with respect to their size, number and chromosomal distribution, the functional copy number aberrations obtained from MSI and MSS CRCs were in fact comparable but not identical. These unifying CNAs were verified by MLPA tumor-loss gene panel, which spans 15 different chromosomal locations and contains 50 probes for at least 20 tumor suppressor genes. Consistently, deletion/amplification in these frequently cancer altered genes were identical in MSS and MSI CRCs. Our results suggest that MSI and MSS copy number aberrations driving CRC may be functionally comparable.
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Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Jabriya, Kuwait
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- * E-mail: (HA); (FA)
| | - Milad S. Bitar
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ashraf Al Madhoun
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | | | - Fahd Al-Mulla
- Molecular Pathology Unit, Department of Pathology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- Research Division, Genomics Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- * E-mail: (HA); (FA)
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17
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Sefrioui D, Vermeulin T, Blanchard F, Chapusot C, Beaussire L, Armengol-Debeir L, Sesboué R, Gangloff A, Hebbar M, Copin MC, Houivet E, Schwarz L, Clatot F, Tuech JJ, Bénichou J, Martin L, Bouvier AM, Sabourin JC, Sarafan-Vasseur N, Frébourg T, Lepage C, Michel P, Di Fiore F. Copy number variations inDCC/18q andERBB2/17q are associated with disease-free survival in microsatellite stable colon cancer. Int J Cancer 2017; 140:1653-1661. [DOI: 10.1002/ijc.30584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/10/2016] [Accepted: 11/23/2016] [Indexed: 01/05/2023]
Affiliation(s)
- David Sefrioui
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Thomas Vermeulin
- Department of Biostatistics; Rouen University Hospital; Rouen France
| | - France Blanchard
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
- Department of Pathology; Rouen University Hospital; Rouen France
| | - Caroline Chapusot
- Department of Pathology; Dijon University Hospital, University of Burgundy; Dijon France
| | - Ludivine Beaussire
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
| | - Laura Armengol-Debeir
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
| | - Richard Sesboué
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Alice Gangloff
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Mohamed Hebbar
- Department of Medical Oncology; Lille University Hospital; Lille France
| | | | - Estelle Houivet
- Department of Biostatistics; Rouen University Hospital; Rouen France
| | - Lilian Schwarz
- Department of Surgery; Rouen University Hospital; Rouen France
| | - Florian Clatot
- Department of Medical Oncology; Centre Henri Becquerel; Rouen France
| | | | - Jacques Bénichou
- Department of Biostatistics; Rouen University Hospital; Rouen France
| | - Laurent Martin
- Department of Pathology; Dijon University Hospital, University of Burgundy; Dijon France
| | - Anne-Marie Bouvier
- Digestive Cancer Registry of Burgundy, INSERM U866, University Hospital Dijon, University of Burgundy; Dijon France
| | - Jean-Christophe Sabourin
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
- Department of Pathology; Rouen University Hospital; Rouen France
| | - Nasrin Sarafan-Vasseur
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Thierry Frébourg
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
| | - Côme Lepage
- Digestive Cancer Registry of Burgundy, INSERM U866, University Hospital Dijon, University of Burgundy; Dijon France
| | - Pierre Michel
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Frédéric Di Fiore
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
- Department of Medical Oncology; Centre Henri Becquerel; Rouen France
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18
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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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19
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Barresi V, Castorina S, Musso N, Capizzi C, Luca T, Privitera G, Condorelli DF. Chromosomal instability analysis and regional tumor heterogeneity in colon cancer. Cancer Genet 2016; 210:9-21. [PMID: 28212810 DOI: 10.1016/j.cancergen.2016.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/11/2016] [Accepted: 11/14/2016] [Indexed: 01/24/2023]
Abstract
Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively). In 15 tumors, two samples, separated by at least 1 cm, were taken from the same tumor mass (double-sampling pairs) in order to evaluate differences in detection of chromosomal abnormalities between distant regions of the same tumor and their influence on CIN quantitative and qualitative analysis. Our data show a high degree of correlation of the quantitative CIN index (somatic BCNA number) between distant tumor regions. On the contrary, a lower correlation is observed in terms of chromosomal distribution of BCNAs, as summarized by a simplified cytogenetic table. Quantitative or qualitative analysis of FCNAs, including homozygous deletions and high level amplifications, did not add further information on the CIN status. The use of the index "somatic BCNA number" can be proposed for a robust classification of tumors as CIN positive or negative even in the presence of a significant tumor regional heterogeneity.
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Affiliation(s)
- Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Italy; Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy
| | - Sergio Castorina
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, University of Catania, Italy; Fondazione Mediterranea G.B. Morgagni, Catania, Italy
| | - Nicolò Musso
- Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy
| | - Carmela Capizzi
- Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy
| | - Tonia Luca
- Fondazione Mediterranea G.B. Morgagni, Catania, Italy
| | | | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Italy; Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy.
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20
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Abstract
Genome-wide studies are increasingly becoming a must, especially for complex diseases such as cancer where multiple genes and diverse molecular mechanisms are known to be involved in genes' function alteration. In this review, we report our latest genomic and epigenomic findings in African-American colorectal cancer patients. This population suffers a higher burden of the disease and most investigators in this field are looking for the underlying genetic and epigenetic targets that might be responsible for this disparity. We here report genome-wide copy number variations, single nucleotide mutations and DNA methylation findings that might be specific to this population.
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Affiliation(s)
- Hassan Brim
- Pathology Department, Howard University College of Medicine, Gastroenterology Division and Cancer Center, Washington DC, USA
| | - Hassan Ashktorab
- Howard University College of Medicine, Department of Medicine and Cancer Center, 2041 Georgia Avenue, Washington, DC, 20060, USA
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21
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Mlecnik B, Bindea G, Angell HK, Maby P, Angelova M, Tougeron D, Church SE, Lafontaine L, Fischer M, Fredriksen T, Sasso M, Bilocq AM, Kirilovsky A, Obenauf AC, Hamieh M, Berger A, Bruneval P, Tuech JJ, Sabourin JC, Le Pessot F, Mauillon J, Rafii A, Laurent-Puig P, Speicher MR, Trajanoski Z, Michel P, Sesboüe R, Frebourg T, Pagès F, Valge-Archer V, Latouche JB, Galon J. Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability. Immunity 2016; 44:698-711. [PMID: 26982367 DOI: 10.1016/j.immuni.2016.02.025] [Citation(s) in RCA: 712] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/12/2015] [Accepted: 11/25/2015] [Indexed: 02/07/2023]
Abstract
Microsatellite instability in colorectal cancer predicts favorable outcomes. However, the mechanistic relationship between microsatellite instability, tumor-infiltrating immune cells, Immunoscore, and their impact on patient survival remains to be elucidated. We found significant differences in mutational patterns, chromosomal instability, and gene expression that correlated with patient microsatellite instability status. A prominent immune gene expression was observed in microsatellite-instable (MSI) tumors, as well as in a subgroup of microsatellite-stable (MSS) tumors. MSI tumors had increased frameshift mutations, showed genetic evidence of immunoediting, had higher densities of Th1, effector-memory T cells, in situ proliferating T cells, and inhibitory PD1-PDL1 cells, had high Immunoscores, and were infiltrated with mutation-specific cytotoxic T cells. Multivariate analysis revealed that Immunoscore was superior to microsatellite instability in predicting patients' disease-specific recurrence and survival. These findings indicate that assessment of the immune status via Immunoscore provides a potent indicator of tumor recurrence beyond microsatellite-instability staging that could be an important guide for immunotherapy strategies.
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Affiliation(s)
- Bernhard Mlecnik
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Gabriela Bindea
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Helen K Angell
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France; Innovative Medicines and Early Development, Oncology, AstraZeneca, CB4 OWG Cambridge, UK
| | - Pauline Maby
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, U1079, Faculté de Médecine, Université de Rouen and the Institute for Research and Innovation in Biomedecine (IRIB), 76000 Rouen, France
| | - Mihaela Angelova
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France; Biocenter, Division of Bioinformatics, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - David Tougeron
- INSERM, U1079, Faculté de Médecine, Université de Rouen and the Institute for Research and Innovation in Biomedecine (IRIB), 76000 Rouen, France; Department of Gastroenterology, Rouen University Hospital, 76000 Rouen, France; Department of Genetics, Rouen University Hospital, 76000 Rouen, France
| | - Sarah E Church
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Lucie Lafontaine
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Maria Fischer
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Tessa Fredriksen
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Maristella Sasso
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Amélie M Bilocq
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Amos Kirilovsky
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France
| | - Anna C Obenauf
- Institute of Human Genetics, Medical University of Graz, 8010 Graz, Austria
| | - Mohamad Hamieh
- INSERM, U1079, Faculté de Médecine, Université de Rouen and the Institute for Research and Innovation in Biomedecine (IRIB), 76000 Rouen, France
| | - Anne Berger
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; Department of General and Digestive Surgery, Hôpital Européen Georges-Pompidou, Assistance Publique-Hopitaux de Paris, 75015 Paris, France
| | - Patrick Bruneval
- Department of Anatomopathology, Hôpital Européen Georges-Pompidou, Assistance Publique-Hopitaux de Paris, 75015 Paris, France
| | - Jean-Jacques Tuech
- Department of Digestive Surgery, Rouen University Hospital, 76000 Rouen, France
| | | | - Florence Le Pessot
- Department of Anatomopathology, Rouen University Hospital, 76000 Rouen, France
| | - Jacques Mauillon
- Department of Anatomopathology, Rouen University Hospital, 76000 Rouen, France; Department of Gastroenterology, Le Havre Hospital, 76600 Le Havre, France
| | - Arash Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, 3263 Doha, Qatar
| | - Pierre Laurent-Puig
- UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; INSERM, UMRS775, Bases Moléculaires de la Réponse aux Xénobiotiques, 75006 Paris, France
| | - Michael R Speicher
- Institute of Human Genetics, Medical University of Graz, 8010 Graz, Austria
| | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Pierre Michel
- Department of Gastroenterology, Rouen University Hospital, 76000 Rouen, France
| | - Richard Sesboüe
- INSERM, U1079, Faculté de Médecine, Université de Rouen and the Institute for Research and Innovation in Biomedecine (IRIB), 76000 Rouen, France
| | - Thierry Frebourg
- INSERM, U1079, Faculté de Médecine, Université de Rouen and the Institute for Research and Innovation in Biomedecine (IRIB), 76000 Rouen, France; INSERM, UMRS775, Bases Moléculaires de la Réponse aux Xénobiotiques, 75006 Paris, France
| | - Franck Pagès
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France; Department of Immunology, Hôpital Européen Georges-Pompidou, Assistance Publique-Hopitaux de Paris, 75015 Paris, France
| | - Viia Valge-Archer
- Innovative Medicines and Early Development, Oncology, AstraZeneca, CB4 OWG Cambridge, UK; MedImmune, CB21 GGH Cambridge, UK
| | - Jean-Baptiste Latouche
- INSERM, U1079, Faculté de Médecine, Université de Rouen and the Institute for Research and Innovation in Biomedecine (IRIB), 76000 Rouen, France; Department of Genetics, Rouen University Hospital, 76000 Rouen, France
| | - Jérôme Galon
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, 75006 Paris, France; UMRS1138, Université Paris Descartes - Sorbonne Paris Cité, 75006 Paris, France; UMRS1138, Pierre and Marie Curie University (Paris 6) - Sorbonne Paris Cité, Centre de Recherche des Cordeliers, 75006 Paris, France.
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22
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Maby P, Tougeron D, Hamieh M, Mlecnik B, Kora H, Bindea G, Angell HK, Fredriksen T, Elie N, Fauquembergue E, Drouet A, Leprince J, Benichou J, Mauillon J, Le Pessot F, Sesboüé R, Tuech JJ, Sabourin JC, Michel P, Frébourg T, Galon J, Latouche JB. Correlation between Density of CD8+ T-cell Infiltrate in Microsatellite Unstable Colorectal Cancers and Frameshift Mutations: A Rationale for Personalized Immunotherapy. Cancer Res 2015; 75:3446-55. [PMID: 26060019 DOI: 10.1158/0008-5472.can-14-3051] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 05/14/2015] [Indexed: 01/30/2023]
Abstract
Colorectal cancers with microsatellite instability (MSI) represent 15% of all colorectal cancers, including Lynch syndrome as the most frequent hereditary form of this disease. Notably, MSI colorectal cancers have a higher density of tumor-infiltrating lymphocytes (TIL) than other colorectal cancers. This feature is thought to reflect the accumulation of frameshift mutations in sequences that are repeated within gene coding regions, thereby leading to the synthesis of neoantigens recognized by CD8(+) T cells. However, there has yet to be a clear link established between CD8(+) TIL density and frameshift mutations in colorectal cancer. In this study, we examined this link in 103 MSI colorectal cancers from two independent cohorts where frameshift mutations in 19 genes were analyzed and CD3(+), CD8(+), and FOXP3(+) TIL densities were quantitated. We found that CD8(+) TIL density correlated positively with the total number of frameshift mutations. TIL densities increased when frameshift mutations were present within the ASTE1, HNF1A, or TCF7L2 genes, increasing even further when at least one of these frameshift mutations was present in all tumor cells. Through in vitro assays using engineered antigen-presenting cells, we were able to stimulate peripheral cytotoxic T cells obtained from colorectal cancer patients with peptides derived from frameshift mutations found in their tumors. Taken together, our results highlight the importance of a CD8(+) T cell immune response against MSI colorectal cancer-specific neoantigens, establishing a preclinical rationale to target them as a personalized cellular immunotherapy strategy, an especially appealing goal for patients with Lynch syndrome.
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Affiliation(s)
- Pauline Maby
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - David Tougeron
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France. Department of Gastroenterology, Poitiers University Hospital, Poitiers, France. Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Poitiers University, Poitiers, France
| | - Mohamad Hamieh
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Bernhard Mlecnik
- Inserm U1138, Laboratory of Integrative Cancer Immunology, Paris, France. Université Paris Descartes, Paris, France. Cordeliers Research Centre, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Hafid Kora
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Gabriela Bindea
- Inserm U1138, Laboratory of Integrative Cancer Immunology, Paris, France. Université Paris Descartes, Paris, France. Cordeliers Research Centre, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Helen K Angell
- Inserm U1138, Laboratory of Integrative Cancer Immunology, Paris, France. Université Paris Descartes, Paris, France. Cordeliers Research Centre, Université Pierre et Marie Curie, Paris 6, Paris, France. AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Tessa Fredriksen
- Inserm U1138, Laboratory of Integrative Cancer Immunology, Paris, France. Université Paris Descartes, Paris, France. Cordeliers Research Centre, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Nicolas Elie
- Imaging Core Facility, CMABIO, Caen University Hospital, Caen, France
| | - Emilie Fauquembergue
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Aurélie Drouet
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Jérôme Leprince
- Inserm U982, Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, France
| | - Jacques Benichou
- Biostatistics Unit, Inserm U657, Rouen University Hospital, Rouen University, Rouen, France
| | - Jacques Mauillon
- Department of Genetics, Rouen University Hospital, Rouen, France. Department of Gastroenterology, Le Havre Hospital, Le Havre, France
| | | | - Richard Sesboüé
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Jean-Jacques Tuech
- Department of Digestive Surgery, Rouen University Hospital, Rouen, France
| | - Jean-Christophe Sabourin
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France. Department of Pathology, Rouen University Hospital, Rouen, France
| | - Pierre Michel
- Department of Gastroenterology, Rouen University Hospital, Rouen, France
| | - Thierry Frébourg
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France. Department of Genetics, Rouen University Hospital, Rouen, France
| | - Jérôme Galon
- Inserm U1138, Laboratory of Integrative Cancer Immunology, Paris, France. Université Paris Descartes, Paris, France. Cordeliers Research Centre, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Jean-Baptiste Latouche
- Inserm U1079, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France. Department of Genetics, Rouen University Hospital, Rouen, France.
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23
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Berg M, Nordgaard O, Kørner H, Oltedal S, Smaaland R, Søreide JA, Søreide K. Molecular subtypes in stage II-III colon cancer defined by genomic instability: early recurrence-risk associated with a high copy-number variation and loss of RUNX3 and CDKN2A. PLoS One 2015; 10:e0122391. [PMID: 25879218 PMCID: PMC4399912 DOI: 10.1371/journal.pone.0122391] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/20/2015] [Indexed: 01/02/2023] Open
Abstract
Objective We sought to investigate various molecular subtypes defined by genomic instability that may be related to early death and recurrence in colon cancer. Methods We sought to investigate various molecular subtypes defined by instability at microsatellites (MSI), changes in methylation patterns (CpG island methylator phenotype, CIMP) or copy number variation (CNV) in 8 genes. Stage II-III colon cancers (n = 64) were investigated by methylation-specific multiplex ligated probe amplification (MS-MLPA). Correlation of CNV, CIMP and MSI, with mutations in KRAS and BRAFV600E were assessed for overlap in molecular subtypes and early recurrence risk by uni- and multivariate regression. Results The CIMP phenotype occurred in 34% (22/64) and MSI in 27% (16/60) of the tumors, with noted CIMP/MSI overlap. Among the molecular subtypes, a high CNV phenotype had an associated odds ratio (OR) for recurrence of 3.2 (95% CI 1.1-9.3; P = 0.026). Losses of CACNA1G (OR of 2.9, 95% CI 1.4-6.0; P = 0.001), IGF2 (OR of 4.3, 95% CI 1.1-15.8; P = 0.007), CDKN2A (p16) (OR of 2.0, 95% CI 1.1-3.6; P = 0.024), and RUNX3 (OR of 3.4, 95% CI 1.3-8.7; P = 0.002) were associated with early recurrence, while MSI, CIMP, KRAS or BRAF V600E mutations were not. The CNV was significantly higher in deceased patients (CNV in 6 of 8) compared to survivors (CNV in 3 of 8). Only stage and loss of RUNX3 and CDKN2A were significant in the multivariable risk-model for early recurrence. Conclusions A high copy number variation phenotype is a strong predictor of early recurrence and death, and may indicate a dose-dependent relationship between genetic instability and outcome. Loss of tumor suppressors RUNX3 and CDKN2A were related to recurrence-risk and warrants further investigation.
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Affiliation(s)
- Marianne Berg
- Centre of Organelle Research (CORE), University of Stavanger, Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
| | - Oddmund Nordgaard
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Hartwig Kørner
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Satu Oltedal
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Rune Smaaland
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Jon Arne Søreide
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kjetil Søreide
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- * E-mail:
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24
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Shivakumar BM, Rotti H, Vasudevan TG, Balakrishnan A, Chakrabarty S, Bhat G, Rao L, Pai CG, Satyamoorthy K. Copy number variations are progressively associated with the pathogenesis of colorectal cancer in ulcerative colitis. World J Gastroenterol 2015; 21:616-622. [PMID: 25605985 PMCID: PMC4296023 DOI: 10.3748/wjg.v21.i2.616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/10/2014] [Accepted: 07/22/2014] [Indexed: 02/07/2023] Open
Abstract
AIM: To evaluate the association of known copy number variations (CNVs) in ulcerative colitis (UC) progressing to colorectal cancer.
METHODS: Microsatellite instability analysis using the National Cancer Institute’s panel of markers, and CNV association studies using Agilent 2 × 105 k arrays were done in tissue samples from four patient groups with UC: those at low risk (LR) or high risk of developing colorectal cancer, those with premalignant dysplastic lesions, and those with colitis-associated colorectal cancer (CAC). DNA from tissue samples of these groups were independently hybridized on arrays and analyzed. The data obtained were further subjected to downstream bioinformatics enrichment analysis to examine the correlation with CAC progression.
RESULTS: Microarray analysis highlighted a progressive increase in the total number of CNVs [LR (n = 178) vs CAC (n = 958), 5.3-fold], gains and losses [LR (n = 37 and 141) vs CAC (n = 495 and 463), 13.4- and 3.3-fold, respectively], size [LR (964.2 kb) vs CAC (10540 kb), 10.9-fold] and the number of genes in such regions [LR (n = 119) vs CAC (n = 455), 3.8-fold]. Chromosome-wise analysis of CNVs also showed an increase in the number of CNVs across each chromosome. There were 38 genes common to all four groups in the study; 13 of these were common to cancer genes from the Genetic Disease Association dataset. The gene set enrichment analysis and ontology analysis highlighted many cancer-associated genes. All the samples in the different groups were microsatellite stable.
CONCLUSION: Increasing numbers of CNVs are associated with the progression of UC to CAC, and warrant further detailed exploration.
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Eichenmüller M, Trippel F, Kreuder M, Beck A, Schwarzmayr T, Häberle B, Cairo S, Leuschner I, von Schweinitz D, Strom TM, Kappler R. The genomic landscape of hepatoblastoma and their progenies with HCC-like features. J Hepatol 2014; 61:1312-20. [PMID: 25135868 DOI: 10.1016/j.jhep.2014.08.009] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 07/15/2014] [Accepted: 08/07/2014] [Indexed: 02/01/2023]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is the most common childhood liver cancer and occasionally presents with histological and clinical features reminiscent of hepatocellular carcinoma (HCC). Identification of molecular mechanisms that drive the neoplastic continuation towards more aggressive HCC phenotypes may help to guide the new stage of targeted therapies. METHODS We performed comprehensive studies on genetic and chromosomal alterations as well as candidate gene function and their clinical relevance. RESULTS Whole-exome sequencing identified HB as a genetically very simple tumour (2.9 mutations per tumour) with recurrent mutations in ß-catenin (CTNNB1) (12/15 cases) and the transcription factor NFE2L2 (2/15 cases). Their HCC-like progenies share the common CTNNB1 mutation, but additionally exhibit a significantly increased mutation number and chromosomal instability due to deletions of the genome guardians RAD17 and TP53, accompanied by telomerase reverse-transcriptase (TERT) promoter mutations. Targeted genotyping of 33 primary tumours and cell lines revealed CTNNB1, NFE2L2, and TERT mutations in 72.5%, 9.8%, and 5.9% of cases, respectively. All NFE2L2 mutations affected residues of the NFE2L2 protein that are recognized by the KEAP1/CUL3 complex for proteasomal degradation. Consequently, cells transfected with mutant NFE2L2 were insensitive to KEAP1-mediated downregulation of NFE2L2 signalling. Clinically, overexpression of the NFE2L2 target gene NQO1 in tumours was significantly associated with metastasis, vascular invasion, the adverse prognostic C2 gene signature, as well as poor outcome. CONCLUSIONS Our study demonstrates the importance of CTNNB1 mutations and NFE2L2-KEAP1 pathway activation in HB development and defines loss of genomic stability and TERT promoter mutations as prominent characteristics of aggressive HB with HCC features.
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Affiliation(s)
- Melanie Eichenmüller
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Franziska Trippel
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michaela Kreuder
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexander Beck
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Beate Häberle
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | | | - Ivo Leuschner
- Institute of Paidopathology, Pediatric Tumor Registry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dietrich von Schweinitz
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Kaiser JC, Meckbach R, Jacob P. Genomic instability and radiation risk in molecular pathways to colon cancer. PLoS One 2014; 9:e111024. [PMID: 25356998 PMCID: PMC4214691 DOI: 10.1371/journal.pone.0111024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 09/28/2014] [Indexed: 01/28/2023] Open
Abstract
Colon cancer is caused by multiple genomic alterations which lead to genomic instability (GI). GI appears in molecular pathways of microsatellite instability (MSI) and chromosomal instability (CIN) with clinically observed case shares of about 15–20% and 80–85%. Radiation enhances the colon cancer risk by inducing GI, but little is known about different outcomes for MSI and CIN. Computer-based modelling can facilitate the understanding of the phenomena named above. Comprehensive biological models, which combine the two main molecular pathways to colon cancer, are fitted to incidence data of Japanese a-bomb survivors. The preferred model is selected according to statistical criteria and biological plausibility. Imprints of cell-based processes in the succession from adenoma to carcinoma are identified by the model from age dependences and secular trends of the incidence data. Model parameters show remarkable compliance with mutation rates and growth rates for adenoma, which has been reported over the last fifteen years. Model results suggest that CIN begins during fission of intestinal crypts. Chromosomal aberrations are generated at a markedly elevated rate which favors the accelerated growth of premalignant adenoma. Possibly driven by a trend of Westernization in the Japanese diet, incidence rates for the CIN pathway increased notably in subsequent birth cohorts, whereas rates pertaining to MSI remained constant. An imbalance between number of CIN and MSI cases began to emerge in the 1980s, whereas in previous decades the number of cases was almost equal. The CIN pathway exhibits a strong radio-sensitivity, probably more intensive in men. Among young birth cohorts of both sexes the excess absolute radiation risk related to CIN is larger by an order of magnitude compared to the MSI-related risk. Observance of pathway-specific risks improves the determination of the probability of causation for radiation-induced colon cancer in individual patients, if their exposure histories are known.
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Affiliation(s)
- Jan Christian Kaiser
- Institute of Radiation Protection, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- * E-mail:
| | - Reinhard Meckbach
- Institute of Radiation Protection, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Peter Jacob
- Institute of Radiation Protection, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
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Establishing a biological profile for interval colorectal cancers. Dig Dis Sci 2014; 59:2390-402. [PMID: 24839919 DOI: 10.1007/s10620-014-3210-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/07/2014] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) remains the second leading cause of cancer-related deaths in North America. Screening for CRC and its precursor lesions is highly effective in reducing the incidence and deaths due to the disease. However, there remain a substantial number of individuals who are diagnosed with CRC soon after a negative/clearing colonoscopy with no documented evidence of CRC. The occurrence of these interval CRCs (I-CRCs) reduces the effectiveness of CRC screening and detection tests and has only recently attracted wide spread attention. I-CRCs can be subdivided into those that occur most likely due to the failure of the colonoscopy examination (missed CRC and CRC that developed from missed or incompletely resected precursor lesions) and those that develop rapidly after the colonoscopy (de novo I-CRCs). In this review, we discuss the current literature and present both the clinical and biological factors that have been identified to account for I-CRCs, with a particular focus on the aberrant molecular features that are candidate causative agents for I-CRCs. We conclude additional studies are required to fully understand the molecular features that lead to the development of I-CRCs, which in turn is essential to develop measures to prevent the occurrence of this group of CRCs and thereby improve CRC screening and detection strategies.
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Abstract
Subclonal cancer populations change spatially and temporally during the disease course. Studies are revealing branched evolutionary cancer growth with low-frequency driver events present in subpopulations of cells, providing escape mechanisms for targeted therapeutic approaches. Despite such complexity, evidence is emerging for parallel evolution of subclones, mediated through distinct somatic events converging on the same gene, signal transduction pathway, or protein complex in different subclones within the same tumor. Tumors may follow gradualist paths (microevolution) as well as major shifts in evolutionary trajectories (macroevolution). Although macroevolution has been subject to considerable controversy in post-Darwinian evolutionary theory, we review evidence that such nongradual, saltatory leaps, driven through chromosomal rearrangements or genome doubling, may be particularly relevant to tumor evolution. Adapting cancer care to the challenges imposed by tumor micro- and macroevolution and developing deeper insight into parallel evolutionary events may prove central to improving outcome and reducing drug development costs.
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Affiliation(s)
- Marco Gerlinger
- Cancer Research UK London Research Institute, London, United Kingdom WC2A 3LY;
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Gender-associated genomic differences in colorectal cancer: clinical insight from feminization of male cancer cells. Int J Mol Sci 2014; 15:17344-65. [PMID: 25268611 PMCID: PMC4227166 DOI: 10.3390/ijms151017344] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 12/19/2022] Open
Abstract
Gender-related differences in colorectal cancer (CRC) are not fully understood. Recent studies have shown that CRC arising in females are significantly associated with CpG island methylator phenotype (CIMP-high). Using array comparative genomic hybridization, we analyzed a cohort of 116 CRCs (57 males, 59 females) for chromosomal copy number aberrations (CNA) and found that CRC in females had significantly higher numbers of gains involving chromosome arms 1q21.2–q21.3, 4q13.2, 6p21.1 and 16p11.2 and copy number losses of chromosome arm 11q25 compared to males. Interestingly, a subset of male CRCs (46%) exhibited a “feminization” phenomenon in the form of gains of X chromosomes (or an arm of X) and/or losses of the Y chromosome. Feminization of cancer cells was significantly associated with microsatellite-stable CRCs (p-value 0.003) and wild-type BRAF gene status (p-value 0.009). No significant association with other clinicopathological parameters was identified including disease-free survival. In summary, our data show that some CNAs in CRC may be gender specific and that male cancers characterized by feminization may constitute a specific subset of CRCs that warrants further investigation.
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Lee JS. Expression of Microsatellite Instability (MSI) from Colorectal Carcinoma Patients. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2014. [DOI: 10.15324/kjcls.2014.46.2.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jae-Sik Lee
- Department of Clinical Laboratory Science, Hyejeon College, Hongseong 350-702, Korea
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31
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Bellido F, Pineda M, Sanz-Pamplona R, Navarro M, Nadal M, Lázaro C, Blanco I, Moreno V, Capellá G, Valle L. Comprehensive molecular characterisation of hereditary non-polyposis colorectal tumours with mismatch repair proficiency. Eur J Cancer 2014; 50:1964-72. [PMID: 24841217 DOI: 10.1016/j.ejca.2014.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/12/2014] [Accepted: 04/23/2014] [Indexed: 02/01/2023]
Abstract
BACKGROUND Hereditary non-polyposis colorectal cancer (CRC) without mismatch repair (MMR) defects occurs in almost half of high-risk CRC families, but its genetic cause(s) is(are) still unknown. We aimed to identify unique molecular features that differentiate hereditary from sporadic MMR-proficient colorectal tumours. METHODS Genomic alterations in 16 tumours from 14 Amsterdam I-II families were studied using the genome-wide copy number OncoScan™ FFPE microarray. Somatic mutation hotspots in BRAF, KRAS, PIK3CA and TP53 were analysed in 37 colorectal tumours from 26 families and in 99 sporadic MMR-proficient CRCs, using direct automated sequencing and KASPar genotyping assays. CpG methylation index was studied in 25 tumours from 19 families by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). RESULTS Our findings indicate that hereditary MMR-proficient tumours have overlapping genomic profiles to those obtained in sporadic cases, both suggestive of high chromosomal instability, and no high CpG methylation index. Nevertheless, we identified a significant increase in the frequency of chromosome 2p and 2q gains, and of 10 q loss in Amsterdam I families, as well as low frequency of >2 Mb copy-neutral or -gained loss of heterozygosity (LOH). No statistically significant differences in the frequency of BRAF, KRAS, PIK3CA and TP53 mutations or in the gene mutation patterns were observed. However, TP53 mutations appeared almost twice more frequently in sporadic tumours. CONCLUSIONS Overall, hereditary MMR-proficient CRCs display similar molecular characteristics than their sporadic counterparts. However, the differences identified, such as the chromosome 2 gain, 10 q loss, or the under-representation of TP53 mutations, if validated in larger series, might be of relevance in the clinical setting and/or in the identification of germline defects underlying some of these familial cases.
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Affiliation(s)
- Fernando Bellido
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Marga Nadal
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain.
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Lee SY, Haq F, Kim D, Jun C, Jo HJ, Ahn SM, Lee WS. Comparative genomic analysis of primary and synchronous metastatic colorectal cancers. PLoS One 2014; 9:e90459. [PMID: 24599305 PMCID: PMC3944022 DOI: 10.1371/journal.pone.0090459] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/30/2014] [Indexed: 12/30/2022] Open
Abstract
Approximately 50% of patients with primary colorectal carcinoma develop liver metastases. Understanding the genetic differences between primary colon cancer and their metastases to the liver is essential for devising a better therapeutic approach for this disease. We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss. The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar somatic copy number alteration patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number alterations. Our results suggest that about half of the metastatic colorectal carcinoma had the same clonal origin with their primary colorectal carcinomas, whereas remaining cases were genetically distinct from their primary carcinomas. These findings underscore the need to evaluate metastatic lesions separately for optimized therapy, rather than to extrapolate from primary tumor data.
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Affiliation(s)
- Sun Young Lee
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Farhan Haq
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Deokhoon Kim
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Cui Jun
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Hui-Jong Jo
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
| | - Sung-Min Ahn
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
- Department of Biomedical Informatics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
- * E-mail: (SMA); (WSL)
| | - Won-Suk Lee
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
- Department of Surgery, Gil Medical Center, Gachon University, Incheon, Korea
- * E-mail: (SMA); (WSL)
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Orsetti B, Selves J, Bascoul-Mollevi C, Lasorsa L, Gordien K, Bibeau F, Massemin B, Paraf F, Soubeyran I, Hostein I, Dapremont V, Guimbaud R, Cazaux C, Longy M, Theillet C. Impact of chromosomal instability on colorectal cancer progression and outcome. BMC Cancer 2014; 14:121. [PMID: 24559140 PMCID: PMC4233623 DOI: 10.1186/1471-2407-14-121] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/07/2014] [Indexed: 01/16/2023] Open
Abstract
Background It remains presently unclear whether disease progression in colorectal carcinoma (CRC), from early, to invasive and metastatic forms, is associated to a gradual increase in genetic instability and to a scheme of sequentially occurring Copy Number Alterations (CNAs). Methods In this work we set to determine the existence of such links between CRC progression and genetic instability and searched for associations with patient outcome. To this aim we analyzed a set of 162 Chromosomal Instable (CIN) CRCs comprising 131 primary carcinomas evenly distributed through stage 1 to 4, 31 metastases and 14 adenomas by array-CGH. CNA profiles were established according to disease stage and compared. We, also, asked whether the level of genomic instability was correlated to disease outcome in stage 2 and 3 CRCs. Two metrics of chromosomal instability were used; (i) Global Genomic Index (GGI), corresponding to the fraction of the genome involved in CNA, (ii) number of breakpoints (nbBP). Results Stage 1, 2, 3 and 4 tumors did not differ significantly at the level of their CNA profiles precluding the conventional definition of a progression scheme based on increasing levels of genetic instability. Combining GGI and nbBP,we classified genomic profiles into 5 groups presenting distinct patterns of chromosomal instability and defined two risk classes of tumors, showing strong differences in outcome and hazard risk (RFS: p = 0.012, HR = 3; OS: p < 0.001, HR = 9.7). While tumors of the high risk group were characterized by frequent fractional CNAs, low risk tumors presented predominantly whole chromosomal arm CNAs. Searching for CNAs correlating with negative outcome we found that losses at 16p13.3 and 19q13.3 observed in 10% (7/72) of stage 2–3 tumors showed strong association with early relapse (p < 0.001) and death (p < 0.007, p < 0.016). Both events showed frequent co-occurrence (p < 1x10-8) and could, therefore, mark for stage 2–3 CRC susceptible to negative outcome. Conclusions Our data show that CRC disease progression from stage 1 to stage 4 is not paralleled by increased levels of genetic instability. However, they suggest that stage 2–3 CRC with elevated genetic instability and particularly profiles with fractional CNA represent a subset of aggressive tumors.
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An integrative CGH, MSI and candidate genes methylation analysis of colorectal tumors. PLoS One 2014; 9:e82185. [PMID: 24475022 PMCID: PMC3903472 DOI: 10.1371/journal.pone.0082185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/21/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Different DNA aberrations processes can cause colorectal cancer (CRC). Herein, we conducted a comprehensive molecular characterization of 27 CRCs from Iranian patients. MATERIALS AND METHODS Array CGH was performed. The MSI phenotype and the methylation status of 15 genes was established using MSP. The CGH data was compared to two established lists of 41 and 68 cancer genes, respectively, and to CGH data from African Americans. A maximum parsimony cladogram based on global aberrations was established. RESULTS The number of aberrations seem to depend on the MSI status. MSI-H tumors displayed the lowest number of aberrations. MSP revealed that most markers were methylated, except RNF182 gene. P16 and MLH1 genes were primarily methylated in MSI-H tumors. Seven markers with moderate to high frequency of methylation (SYNE1, MMP2, CD109, EVL, RET, LGR and PTPRD) had very low levels of chromosomal aberrations. All chromosomes were targeted by aberrations with deletions more frequent than amplifications. The most amplified markers were CD248, ERCC6, ERGIC3, GNAS, MMP2, NF1, P2RX7, SFRS6, SLC29A1 and TBX22. Most deletions were noted for ADAM29, CHL1, CSMD3, FBXW7, GALNS, MMP2, NF1, PRKD1, SMAD4 and TP53. Aberrations targeting chromosome X were primarily amplifications in male patients and deletions in female patients. A finding similar to what we reported for African American CRC patients. CONCLUSION This first comprehensive analysis of CRC Iranian tumors reveals a high MSI rate. The MSI tumors displayed the lowest level of chromosomal aberrations but high frequency of methylation. The MSI-L were predominantly targeted with chromosomal instability in a way similar to the MSS tumors. The global chromosomal aberration profiles showed many similarities with other populations but also differences that might allow a better understanding of CRC's clinico-pathological specifics in this population.
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Casper M, Weber SN, Kloor M, Müllenbach R, Grobholz R, Lammert F, Zimmer V. Hepatocellular carcinoma as extracolonic manifestation of Lynch syndrome indicates SEC63 as potential target gene in hepatocarcinogenesis. Scand J Gastroenterol 2013; 48:344-51. [PMID: 23537056 DOI: 10.3109/00365521.2012.752030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Lynch syndrome is a cancer predisposition syndrome caused by germline mutations in DNA mismatch repair (MMR) genes with microsatellite instability (MSI) as its molecular hallmark. Hepatocellular carcinoma (HCC) has not been considered part of the tumor spectrum. The aim was to provide a detailed molecular characterization of an HCC associated with Lynch Syndrome (Muir-Torre variant). MATERIALS AND METHODS HCC samples were analyzed for MSI, MMR protein expression and coding microsatellite instability (cMSI). Since cMSI also affected SEC63 coding for an endoplasmic reticulum membrane protein with implications for intracellular protein translocation, its impact on hepatocyte growth control was assessed in an established short-term model. Recombinant inbred mouse lines (BXD) showing different basal SEC63 expression levels were treated with the chemocarcinogen diethylnitrosamine (DEN) intraperitoneally. Proliferation and apoptosis of hepatocytes were determined after 48 h using Ki67 and TUNEL assays. RESULTS The HCC was high-grade microsatellite unstable with loss of MSH2 expression. cMSI was detected in four genes (ASTE1, SEC63, TAF1B, TGFBR2). However, only TGFBR2 is known to be involved in hepatocarcinogenesis. When investigating the impact of SEC63 expression on hepatocyte growth control in the murine model, low hepatic expression correlated significantly (p < 0.05) with a decrease in apoptosis and increased proliferative activity. CONCLUSIONS For the first time, an HCC with characteristic molecular features of association with Lynch syndrome is described. The pro-carcinogenic growth behavior of hepatocytes with low SEC63 expression in the murine model indicates a potential role for SEC63 in hepatocarcinogenesis in general, but this needs further functional validation.
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Affiliation(s)
- Markus Casper
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany.
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Loo LWM, Tiirikainen M, Cheng I, Lum-Jones A, Seifried A, Church JM, Gryfe R, Weisenberger DJ, Lindor NM, Gallinger S, Haile RW, Duggan DJ, Thibodeau SN, Casey G, Le Marchand L. Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer. Genes Chromosomes Cancer 2013; 52:450-66. [PMID: 23341073 DOI: 10.1002/gcc.22043] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/04/2012] [Accepted: 12/16/2012] [Indexed: 12/11/2022] Open
Abstract
Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)-negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome-wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12-11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15-12, 4q12-35, 5q21-22, 6q26, 8p, 14q, 15q11-12, 17p, 18p, 18q, 21q21-22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P < 0.0001 and ±1.5-fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11-20q13 contained several cancer-related genes (AHCY, POFUT1, RPN2, TH1L, and PRPF6) that were upregulated and demonstrated a significant linear correlation (P < 0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer.
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Affiliation(s)
- Lenora W M Loo
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
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Sengupta N, Yau C, Sakthianandeswaren A, Mouradov D, Gibbs P, Suraweera N, Cazier JB, Polanco-Echeverry G, Ghosh A, Thaha M, Ahmed S, Feakins R, Propper D, Dorudi S, Sieber O, Silver A, Lai C. Analysis of colorectal cancers in British Bangladeshi identifies early onset, frequent mucinous histotype and a high prevalence of RBFOX1 deletion. Mol Cancer 2013; 12:1. [PMID: 23286373 PMCID: PMC3544714 DOI: 10.1186/1476-4598-12-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022] Open
Abstract
Background Prevalence of colorectal cancer (CRC) in the British Bangladeshi population (BAN) is low compared to British Caucasians (CAU). Genetic background may influence mutations and disease features. Methods We characterized the clinicopathological features of BAN CRCs and interrogated their genomes using mutation profiling and high-density single nucleotide polymorphism (SNP) arrays and compared findings to CAU CRCs. Results Age of onset of BAN CRC was significantly lower than for CAU patients (p=3.0 x 10-5) and this difference was not due to Lynch syndrome or the polyposis syndromes. KRAS mutations in BAN microsatellite stable (MSS) CRCs were comparatively rare (5.4%) compared to CAU MSS CRCs (25%; p=0.04), which correlates with the high percentage of mucinous histotype observed (31%) in the BAN samples. No BRAF mutations was seen in our BAN MSS CRCs (CAU CRCs, 12%; p=0.08). Array data revealed similar patterns of gains (chromosome 7 and 8q), losses (8p, 17p and 18q) and LOH (4q, 17p and 18q) in BAN and CAU CRCs. A small deletion on chromosome 16p13.2 involving the alternative splicing factor RBFOX1 only was found in significantly more BAN (50%) than CAU CRCs (15%) cases (p=0.04). Focal deletions targeting the 5’ end of the gene were also identified. Novel RBFOX1 mutations were found in CRC cell lines and tumours; mRNA and protein expression was reduced in tumours. Conclusions KRAS mutations were rare in BAN MSS CRC and a mucinous histotype common. Loss of RBFOX1 may explain the anomalous splicing activity associated with CRC.
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Affiliation(s)
- Neel Sengupta
- Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, London, E1 2AT, UK
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Lotze MT, Robinson BW, June CH, Whiteside TL. Tumor immunotherapy. Clin Immunol 2013. [DOI: 10.1016/b978-0-7234-3691-1.00091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Therkildsen C, Jönsson G, Dominguez-Valentin M, Nissen A, Rambech E, Halvarsson B, Bernstein I, Borg K, Nilbert M. Gain of chromosomal region 20q and loss of 18 discriminates between Lynch syndrome and familial colorectal cancer. Eur J Cancer 2012; 49:1226-35. [PMID: 23245329 DOI: 10.1016/j.ejca.2012.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 06/07/2012] [Accepted: 11/09/2012] [Indexed: 12/24/2022]
Abstract
Lynch syndrome and familial colorectal cancer type X, FCCTX, represent the two predominant colorectal cancer syndromes. Whereas Lynch syndrome is clinically and genetically well defined, the genetic cause of FCCTX is unknown and genomic differences between Lynch syndrome and FCCTX tumours are largely unknown. We applied array-based comparative genomic hybridisation to 23 colorectal cancers from FCCTX with comparison to 23 Lynch syndrome tumours and to 45 sporadic colorectal cancers. FCCTX tumours showed genomic complexity with frequent gains on chromosomes 20q, 19 and 17 and losses of 18, 8p and 15. Gain of genetic material in two separate regions encompassing, 20q12-13.12 and 20q13.2-13.32, was identified in 65% of the FCCTX tumours. Gain of material on chromosome 20q and loss on chromosome 18 significantly discriminated colorectal cancers associated with FCCTX from Lynch syndrome, which likely signifies different preferred tumourigenic pathways.
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Affiliation(s)
- Christina Therkildsen
- The Danish HNPCC Register, Clinical Research Centre and Department of Gastroenterology, Copenhagen University Hospital, Hvidovre, Denmark.
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Rübben A, Nordhoff O. A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution. Biol Open 2012; 2:49-62. [PMID: 23336076 PMCID: PMC3545268 DOI: 10.1242/bio.20122543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/15/2012] [Indexed: 12/22/2022] Open
Abstract
Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment. It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution. The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome architecture have multiple and possibly opposed effects which manifest themselves at disparate times and progression stages. Dissection of putative mechanisms mediating constraints exerted by the genome architecture on somatic cancer evolution may provide an algorithm for understanding and predicting as well as modifying somatic cancer evolution in individual patients.
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Affiliation(s)
- Albert Rübben
- Independent Institute of Systems Sciences Aachen , 52064 Aachen , Germany ; Department of Dermatology, RWTH Aachen University , 52074 Aachen , Germany
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Chromosomal instability in BRAF mutant, microsatellite stable colorectal cancers. PLoS One 2012; 7:e47483. [PMID: 23110075 PMCID: PMC3478278 DOI: 10.1371/journal.pone.0047483] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/12/2012] [Indexed: 01/05/2023] Open
Abstract
The BRAF oncogene is mutated in 15% of sporadic colorectal cancers. Approximately half of these BRAF mutant cancers demonstrate frequent frameshift mutations termed microsatellite instability (MSI), but are diploid and chromosomally stable. BRAF wild type cancers are typically microsatellite stable (MSS) and instead acquire chromosomal instability (CIN). In these cancers, CIN is associated with a poor outcome. BRAF mutant cancers that are MSS, typically present at an advanced stage and have a particularly poor prognosis. We have previously demonstrated clinical and molecular similarities between MSS cancers with or without a BRAF mutation, and therefore hypothesised that CIN may also be frequent in BRAF mutant/MSS cancers. BRAF mutant/MSS (n = 60), and BRAF wild type/MSS CRCs (n = 90) were investigated for CIN using loss of heterozygosity analysis over twelve loci encompassing chromosomal regions 5q, 8p, 17p and 18q. CIN was frequent in BRAF mutant/MSS cancers (41/57, 72%), which was comparable to the rate found in BRAF wild type/MSS cancers (74/90, 82%). The greatest loss in BRAF mutant/MSS cancers occurred at 8p (26/44, 59%), and the least at 5q (19/49, 39%). CIN in BRAF mutant/MSS cancers correlated with advanced stage (AJCC III/IV: 15/17, 88%; p = 0.02); showed high rates of co-occurrence with the CpG Island Methylator Phenotype (17/23, 74%); and CIN at 18q and 8p associated with worse survival (p = 0.02, p<0.05). This study demonstrates that CIN commonly occurs in advanced BRAF mutant/MSS colorectal cancers where it may contribute to poorer survival, and further highlights molecular similarities occurring between these and BRAF wild type cancers.
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Gaiser T, Meinhardt S, Hirsch D, Killian JK, Gaedcke J, Jo P, Ponsa I, Miró R, Rüschoff J, Seitz G, Hu Y, Camps J, Ried T. Molecular patterns in the evolution of serrated lesion of the colorectum. Int J Cancer 2012; 132:1800-10. [PMID: 23011871 DOI: 10.1002/ijc.27869] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 09/03/2012] [Indexed: 12/22/2022]
Abstract
Colorectal cancer (CRC) mostly develops from a variety of polyps following mainly three different molecular pathways: chromosomal instability (CIN), microsatellite instability (MSI) and CpG island methylation (CIMP). Polyps are classified histologically as conventional adenomas, hyperplastic polyps, sessile serrated adenomas/polyps (SSA/P) and traditional serrated adenomas (TSA). However, the association of these polyps with the different types of CRCs and the underlying genetic and epigenetic aberrations has yet to be resolved. In order to address this question we analyzed 140 tumors and 20 matched mucosae by array comparative genomic hybridization, by sequence analysis of the oncogenes BRAF, KRAS, PI3K3CA and by methylation arrays. MSI was tested indirectly by immunohistochemistry (IHC) and a loss of MLH1, MSH2, MSH6 or PMS2 was assigned as high microsatellite instability (MSI-H), while low microsatellite instability (MSI-L) was defined as MGMT IHC negativity only. CIN was detected in 78% of all MSI-H CRCs, most commonly as a gain of chromosome 8. Methylation data analyses allowed classification of samples into four groups and detected similar methylation profiles in SSA/P and MSI-H CRC. TSA also revealed aberrant methylation pattern, but clustered more heterogeneously and closer to microsatellite stable (MSS) CRCs. SSA/P, TSA and MSI-H CRCs had the highest degree of promotor methylation (CIMP pathway). Chromosomal instability, in contrast to the established doctrine, is a common phenomenon in MSI CRCs, yet to a lower extent and at later stages than in MSS CRCs. Methylation analyses suggest that SSA/P are precursors for MSI-H CRCs and follow the CIMP pathway.
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Affiliation(s)
- Timo Gaiser
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Genomic aberrations in an African American colorectal cancer cohort reveals a MSI-specific profile and chromosome X amplification in male patients. PLoS One 2012; 7:e40392. [PMID: 22879877 PMCID: PMC3412863 DOI: 10.1371/journal.pone.0040392] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/06/2012] [Indexed: 02/06/2023] Open
Abstract
Objective DNA aberrations that cause colorectal cancer (CRC) occur in multiple steps that involve microsatellite instability (MSI) and chromosomal instability (CIN). Herein, we studied CRCs from AA patients for their CIN and MSI status. Experimental Design Array CGH was performed on 30 AA colon tumors. The MSI status was established. The CGH data from AA were compared to published lists of 41 TSG and oncogenes in Caucasians and 68 cancer genes, proposed via systematic sequencing for somatic mutations in colon and breast tumors. The patient-by-patient CGH profiles were organized into a maximum parsimony cladogram to give insights into the tumors' aberrations lineage. Results The CGH analysis revealed that CIN was independent of age, gender, stage or location. However, both the number and nature of aberrations seem to depend on the MSI status. MSI-H tumors clustered together in the cladogram. The chromosomes with the highest rates of CGH aberrations were 3, 5, 7, 8, 20 and X. Chromosome X was primarily amplified in male patients. A comparison with Caucasians revealed an overall similar aberration profile with few exceptions for the following genes; THRB, RAF1, LPL, DCC, XIST, PCNT, STS and genes on the 20q12-q13 cytoband. Among the 68 CAN genes, all showed some level of alteration in our cohort. Conclusion Chromosome X amplification in male patients with CRC merits follow-up. The observed CIN may play a distinctive role in CRC in AAs. The clustering of MSI-H tumors in global CGH data analysis suggests that chromosomal aberrations are not random.
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Bläker H, Warth A, Kloor M, Schirmacher P. [Chromosomal instability, microsatellite instability and CpG island methylator phenotype: roles in small intestinal carcinogenesis]. DER PATHOLOGE 2012; 32 Suppl 2:181-4. [PMID: 21915661 DOI: 10.1007/s00292-011-1509-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AIMS Intestinal carcinogenesis is associated with genetic instability affecting either the chromosomal level (CIN) or microsatellite DNA sequences (MIN). In addition, epigenetic alterations, such as aberrant CpG island methylation (CIMP) may contribute to tumor development. While these single genetic alterations have frequently been addressed in intestinal carcinogenesis little is known about the interaction of the epigenetics and genetics in tumorigenesis. This investigation therefore aimed to define the synergistic effects of CIN, MSI and CIMP in small bowel adenocarcinomas. METHODS A total of 37 primary small bowel adenocarcinomas were investigated for CIN, MSI, CIMP, KRAS and BRAF mutations. The results showed that CIN was found in 22 out of 37 (57%) tumors (3 out of 9 microsatellite instable and 19 out of 28 microsatellite stable carcinomas) and 9 carcinomas (24%) were microsatellite and chromosomally stable. Aberrant CIMP was detected in 16% of chromosomal instable tumors and in 44% of both microsatellite instable and microsatellite and chromosomally stable carcinomas, KRAS was mutated in 55%, 0% and 10% of chromosomal instable, microsatellite instable and microsatellite and chromosomal stable tumors, respectively, while BRAF mutations occurred in 6% of chromosomal instable and 22% of both microsatellite instable and microsatellite and chromosomal stable carcinomas. CONCLUSION Chromosomal instable carcinomas of the small intestine are distinguished from microsatellite instable and microsatellite and chromosomal stable tumors by a high frequency of KRAS mutations and low frequencies of CIMP and BRAF mutations. In microsatellite instable and microsatellite and chromosomally stable cancers, CIMP and BRAF/KRAS mutations are similarly distributed indicating common mechanisms of tumor initiation or progression in the molecular pathogenesis.
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Affiliation(s)
- H Bläker
- Pathologisches Institut, Universitätsklinik Heidelberg, Heidelberg, Deutschland.
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van Dyk E, Pretorius P. Impaired DNA repair and genomic stability in hereditary tyrosinemia type 1. Gene 2012; 495:56-61. [DOI: 10.1016/j.gene.2011.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 11/18/2011] [Accepted: 12/06/2011] [Indexed: 11/26/2022]
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de Miranda NFCC, Hes FJ, van Wezel T, Morreau H. Role of the microenvironment in the tumourigenesis of microsatellite unstable and MUTYH-associated polyposis colorectal cancers. Mutagenesis 2012; 27:247-53. [DOI: 10.1093/mutage/ger077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Kovac M, Laczko E, Haider R, Jiricny J, Mueller H, Heinimann K, Marra G. Familial colorectal cancer: eleven years of data from a registry program in Switzerland. Fam Cancer 2012; 10:605-16. [PMID: 21671081 DOI: 10.1007/s10689-011-9458-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Deleterious germ-line variants involving the DNA mismatch repair (MMR) genes have been identified as the cause of the hereditary nonpolyposis colorectal cancer syndrome known as the Lynch syndrome, but in numerous familial clusters of colon cancer, the cause remains obscure. We analyzed data for 235 German-speaking Swiss families with nonpolyposis forms of colorectal cancer (one of the largest and most ethnically homogeneous cohorts of its kind) to identify the phenotypic features of forms that cannot be explained by MMR deficiency. Based on the results of microsatellite instability analysis and immunostaining of proband tumor samples, the kindreds were classified as MMR-proficient (n = 134, 57%) or MMR-deficient (n = 101, 43%). In 81 of the latter kindreds, deleterious germ-line MMR-gene variants have already been found (62 different variants, including 13 that have not been previously reported), confirming the diagnosis of Lynch syndrome. Compared with MMR-deficient kindreds, the 134 who were MMR proficient were less likely to meet the Amsterdam Criteria II regarding autosomal dominant transmission. They also had primary cancers with later onset and colon-segment distribution patterns resembling those of sporadic colorectal cancers, and they had lower frequencies of metachronous colorectal cancers and extracolonic cancers in general. Although the predisposition to colorectal cancer in these kindreds is probably etiologically heterogeneous, we were unable to identify distinct phenotypic subgroups solely on the basis of the clinical data collected in this study. Further insight, however, is expected to emerge from the molecular characterization of their tumors.
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Affiliation(s)
- Michal Kovac
- Research Group Human Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
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Brosens RPM, Belt EJTH, Haan JC, Buffart TE, Carvalho B, Grabsch H, Quirke P, Cuesta MA, Engel AF, Ylstra B, Meijer GA. Deletion of chromosome 4q predicts outcome in stage II colon cancer patients. Cell Oncol (Dordr) 2011; 34:215-23. [PMID: 21717218 PMCID: PMC3149118 DOI: 10.1007/s13402-011-0042-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2010] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Around 30% of all stage II colon cancer patients will relapse and die of their disease. At present no objective parameters to identify high-risk stage II colon cancer patients, who will benefit from adjuvant chemotherapy, have been established. With traditional histopathological features definition of high-risk stage II colon cancer patients is inaccurate. Therefore more objective and robust markers for prediction of relapse are needed. DNA copy number aberrations have proven to be robust prognostic markers, but have not yet been investigated for this specific group of patients. The aim of the present study was to identify chromosomal aberrations that can predict relapse of tumor in patients with stage II colon cancer. MATERIALS AND METHODS DNA was isolated from 40 formaldehyde fixed paraffin embedded stage II colon cancer samples with extensive clinicopathological data. Samples were hybridized using Comparative Genomic Hybridization (CGH) arrays to determine DNA copy number changes and microsatellite stability was determined by PCR. To analyze differences between stage II colon cancer patients with and without relapse of tumor a Wilcoxon rank-sum test was implemented with multiple testing correction. RESULTS Stage II colon cancers of patients who had relapse of disease showed significantly more losses on chromosomes 4, 5, 15q, 17q and 18q. In the microsatellite stable (MSS) subgroup (n = 28), only loss of chromosome 4q22.1-4q35.2 was significantly associated with disease relapse (P < 0.05, FDR < 0.15). No differences in clinicopathological characteristics between patients with and without relapse were observed. CONCLUSION In the present series of MSS stage II colon cancer patients losses on 4q22.1-4q35.2 were associated with worse outcome and these genomic alterations may aid in selecting patients for adjuvant therapy.
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Affiliation(s)
- R. P. M. Brosens
- Department of Surgery, VU University Medical Centre, Amsterdam, the Netherlands
| | - E. J. T. H. Belt
- Department of Surgery, VU University Medical Centre, Amsterdam, the Netherlands
| | - J. C. Haan
- Department of Pathology, VU University Medical Centre, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - T. E. Buffart
- Department of Pathology, VU University Medical Centre, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - B. Carvalho
- Department of Pathology, VU University Medical Centre, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - H. Grabsch
- Department of Pathology and Tumour Biology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
| | - P. Quirke
- Department of Pathology and Tumour Biology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
| | - M. A. Cuesta
- Department of Surgery, VU University Medical Centre, Amsterdam, the Netherlands
| | - A. F. Engel
- Department of Surgery, Zaans Medical Centre, Zaandam, the Netherlands
| | - B. Ylstra
- Department of Pathology, VU University Medical Centre, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - G. A. Meijer
- Department of Pathology, VU University Medical Centre, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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miRNA expression in colon polyps provides evidence for a multihit model of colon cancer. PLoS One 2011; 6:e20465. [PMID: 21694772 PMCID: PMC3111419 DOI: 10.1371/journal.pone.0020465] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 04/26/2011] [Indexed: 02/06/2023] Open
Abstract
Changes in miRNA expression are a common feature in colon cancer. Those changes occurring in the transition from normal to adenoma and from adenoma to carcinoma, however, have not been well defined. Additionally, miRNA changes among tumor subgroups of colon cancer have also not been adequately evaluated. In this study, we examined the global miRNA expression in 315 samples that included 52 normal colonic mucosa, 41 tubulovillous adenomas, 158 adenocarcinomas with proficient DNA mismatch repair (pMMR) selected for stage and age of onset, and 64 adenocarcinomas with defective DNA mismatch repair (dMMR) selected for sporadic (n = 53) and inherited colon cancer (n = 11). Sporadic dMMR tumors all had MLH1 inactivation due to promoter hypermethylation. Unsupervised PCA and cluster analysis demonstrated that normal colon tissue, adenomas, pMMR carcinomas and dMMR carcinomas were all clearly discernable. The majority of miRNAs that were differentially expressed between normal and polyp were also differentially expressed with a similar magnitude in the comparison of normal to both the pMMR and dMMR tumor groups, suggesting a stepwise progression for transformation from normal colon to carcinoma. Among the miRNAs demonstrating the largest fold up- or down-regulated changes (≥4), four novel (miR-31, miR-1, miR-9 and miR-99a) and two previously reported (miR-137 and miR-135b) miRNAs were identified in the normal/adenoma comparison. All but one of these (miR-99a) demonstrated similar expression differences in the two normal/carcinoma comparisons, suggesting that these early tumor changes are important in both the pMMR- and dMMR-derived cancers. The comparison between pMMR and dMMR tumors identified four miRNAs (miR-31, miR-552, miR-592 and miR-224) with statistically significant expression differences (≥2-fold change).
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Genetics and epigenetics of small bowel adenocarcinoma: the interactions of CIN, MSI, and CIMP. Mod Pathol 2011; 24:564-70. [PMID: 21297586 DOI: 10.1038/modpathol.2010.223] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Characterization of tumor genetics and epigenetics allows to stratify a tumor entity according to molecular pathways and may shed light on the interactions of different types of DNA alterations during tumorigenesis. Small intestinal adenocarcinoma is rare, and to date the interrelation of genomic instability and epigenetics has not been investigated in this tumor type. We therefore analyzed 37 primary small bowel carcinomas with known microsatellite instability and KRAS status for chromosomal instability using comparative genomic hybridization, for the presence of aberrant methylation (CpG island methylation phenotype) by methylation-specific polymerase chain reaction, and for BRAF mutations. Chromosomal instability was detected in 22 of 37 (59%) tumors (3 of 9 microsatellite instable, and 19 of 28 microsatellite stable carcinomas). Nine carcinomas (24%) were microsatellite and chromosomally stable. High-level DNA methylation was found in 16% of chromosomal instable tumors and in 44% of both microsatellite instable and microsatellite and chromosomally stable carcinomas. KRAS was mutated in 55, 0, and 10% of chromosomal instable, microsatellite instable, and microsatellite and chromosomally stable tumors, respectively whereas the frequencies of BRAF mutations were 6% for chromosomal instable and 22% for both microsatellite instable and microsatellite and chromosomally stable carcinomas. In conclusion, in this study we show that chromosomal instable carcinomas of the small intestine are distinguished from microsatellite instable and microsatellite and chromosomally stable tumors by a high frequency of KRAS mutations, low frequencies of CpG island methylation phenotype, and BRAF mutations. In microsatellite instable and microsatellite and chromosomally stable cancers, CpG island methylation phenotype and BRAF/KRAS mutations are similarly distributed, indicating common mechanisms of tumor initiation or progression in their molecular pathogenesis.
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