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Dhakras P, Uboha N, Horner V, Reinig E, Matkowskyj KA. Gastrointestinal cancers: current biomarkers in esophageal and gastric adenocarcinoma. Transl Gastroenterol Hepatol 2020; 5:55. [PMID: 33073050 DOI: 10.21037/tgh.2020.01.08] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/15/2020] [Indexed: 12/29/2022] Open
Abstract
Esophageal and gastric adenocarcinomas are frequently diagnosed at an advanced stage and have a dismal prognosis. Even in patients with potentially curative cancer, nearly 50% will develop recurrent disease despite aggressive treatments. A number of biomarkers currently guide treatment decisions for patients with esophageal and gastric adenocarcinoma and include human epidermal growth factor receptor 2 (HER2) amplification, mismatch repair deficiency/microsatellite instability (dMMR/MSI-H) and program death-ligand 1 (PD-L1) expression. This review will focus on the function, testing and FDA-approved targeted therapies for HER2, dMMR/MSI-H and PD-L1. In addition, a number of novel targets in esophageal and gastric cancer are being studied in clinical trials. Neurotrophic-tropomyosin receptor kinase (NTRK), claudin-18 (CLDN18)/Rho GTPase activating protein 26 (ARHGAP26) gene fusion, fibroblast growth factor receptor (FGFR), lymphocyte-activation gene 3 (LAG3) and T cell immunoglobulin and mucin-domain containing-3 (TIM3) will be briefly reviewed. Despite several biomarkers used in the selection of treatment therapies, treatment outcomes remain poor. Future research efforts will focus on the identification of new biomarkers, moving existing biomarkers into earlier lines of therapy, and evaluating new combinations of existing biomarkers and therapies.
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Affiliation(s)
- Purabi Dhakras
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - Nataliya Uboha
- Division of Hematology, Medical Oncology and Palliative Care, Department of Medicine, University of Wisconsin, Madison, WI, USA.,UW Carbone Cancer Center, Madison, WI, USA.,William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Vanessa Horner
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA.,Wisconsin State Lab of Hygiene, Madison, WI, USA
| | - Erica Reinig
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - Kristina A Matkowskyj
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA.,UW Carbone Cancer Center, Madison, WI, USA.,William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
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102
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Gao A, Guo M. Epigenetic based synthetic lethal strategies in human cancers. Biomark Res 2020; 8:44. [PMID: 32974031 PMCID: PMC7493427 DOI: 10.1186/s40364-020-00224-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023] Open
Abstract
Over the past decades, it is recognized that loss of DNA damage repair (DDR) pathways is an early and frequent event in tumorigenesis, occurring in 40-50% of many cancer types. The basis of synthetic lethality in cancer therapy is DDR deficient cancers dependent on backup DNA repair pathways. In cancer, the concept of synthetic lethality has been extended to pairs of genes, in which inactivation of one by deletion or mutation and pharmacological inhibition of the other leads to death of cancer cells whereas normal cells are spared the effect of the drug. The paradigm study is to induce cell death by inhibiting PARP in BRCA1/2 defective cells. Since the successful application of PARP inhibitor, a growing number of developed DDR inhibitors are ongoing in preclinical and clinical testing, including ATM, ATR, CHK1/2 and WEE1 inhibitors. Combination of PARP inhibitors and other DDR inhibitors, or combination of multiple components of the same pathway may have great potential synthetic lethality efficiency. As epigenetics joins Knudson’s two hit theory, silencing of DDR genes by aberrant epigenetic changes provide new opportunities for synthetic lethal therapy in cancer. Understanding the causative epigenetic changes of loss-of-function has led to the development of novel therapeutic agents in cancer. DDR and related genes were found frequently methylated in human cancers, including BRCA1/2, MGMT, WRN, MLH1, CHFR, P16 and APC. Both genetic and epigenetic alterations may serve as synthetic lethal therapeutic markers.
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Affiliation(s)
- Aiai Gao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052 Henan China.,State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
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103
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Are Microsatellite Patterns Specific for Tumor Types? A Pilot Investigation. JOURNAL OF MOLECULAR PATHOLOGY 2020. [DOI: 10.3390/jmp1010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microsatellite testing is an emerging field of molecular pathology, as microsatellite instability (MSI) appears to be a predictive biomarker for some cancers. Although multiple studies on microsatellites have been published, recent observations suggest that the microsatellites that define instability differ between tumor entities. This assumption is confirmed by the present study that compared different MSI assays validated for colorectal cancer. Whilst all assays deliver the same MSI/MSS status for colorectal cancers, they differ for tonsillar tumors, leading to the hypothesis that MSI patterns are tumor-type specific.
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104
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P53 expression and micro-vessel density in relation with 5-year survival in patients with colorectal cancer. Ann Med Surg (Lond) 2020; 57:311-314. [PMID: 32874562 PMCID: PMC7452034 DOI: 10.1016/j.amsu.2020.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancers are among the commonest causes of cancer related morbidity and mortality worldwide. Adenomatous polyps which develop dysplastic changes are the main cause of invasive cancer. P53 inactivation is a key genetic step in the occurrence of cancer. The degree of the formation of the blood vessels inside the tumor (microvessel density) increases the ability of the tumor to have local infiltration, metastatic potential and may reflect the tumor metabolic activity. A total number of 104 patients who underwent surgeries for colorectal adenocarcinoma followed for 5 years. Patients were categorized into 4 categories based on tumor expression of P53 and micro-vessel density, 64.42% of patients were females, 58.7% died from colorectal cancer during the 5-year period, 37.5% had 5-years survival free from cancer, and 16.3% survived with recurrence, 28.8% had over expression of both P53 and MVD. A significant correlation was found between: P53 and MVD with the site of tumor occurrence being more significant with left-sided colonic tumors, the clinical stage being more significant with stage III disease, and with the survival rate being more significant in patients who died during this period, P values 0.025, 0.01, and 0.001 respectively. Overexpression of P53 and MVD are associated with higher mortality and more advanced disease. We advise a more aggressive form of therapy for colorectal adenocarcinomas expressing high level of both factors and tumors with high expression of both factors may need modification in the chemotherapeutic drugs or radiation therapy with closer follow up than tumors having lower expression.
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105
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Zhang Y, Li CC, Zhang X, Xu Q, Zhang CY. Development of Oxidation Damage Base-Based Fluorescent Probe for Direct Detection of DNA Methylation. Anal Chem 2020; 92:10223-10227. [PMID: 32664718 DOI: 10.1021/acs.analchem.0c01880] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation has become a promising epigenetic biomarker for cancer diagnosis, prognosis, and therapy monitoring. Herein, we demonstrate for the first time the development of a new oxidation damage base (8-oxo-7,8-dihydroguanine (8-oxoG))-modified fluorescent probe for direct detection of DNA methylation. This fluorescent probe is labeled with carboxy-X-rhodamine (ROX) and black hole quencher 2 (BHQ2) at the 5' and 3' termini, respectively, with one 8-oxoG base modification in the middle position, and it can discriminate the methylated cytosine from the unmethylated cytosine. The presence of target methylated DNA may induce the recycle cleavage of fluorescent probes with the assistance of human 8-oxoG DNA glycosylase 1 (hOGG1) enzyme, resulting in an enhanced fluorescence signal. In comparison with the reported bisulfite treatment-based indirect approaches, this fluorescent probe can be used for direct detection of DNA methylation under isothermal conditions without the requirement of a stringent primer/template design, any thermal cycling, and ligation procedures, greatly simplifying the experimental processes. Moreover, this fluorescent probe exhibits good specificity and high sensitivity, and it can distinguish a 0.01% methylation level even in the presence of excess unmethylated DNA. Furthermore, this fluorescent probe can be used to detect DNA methylation in genomic DNA extracted from human colon cancer cells, holding great potential in epigenetic study and early clinical diagnosis.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xuechong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
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106
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Eriksson J, Amonkar M, Al-Jassar G, Lambert J, Malmenäs M, Chase M, Sun L, Kollmar L, Vichnin M. Experience of mismatch repair/microsatellite instability (MMR/MSI) testing among patients with advanced/metastatic colorectal cancer in the US. Curr Med Res Opin 2020; 36:1355-1361. [PMID: 32468869 DOI: 10.1080/03007995.2020.1776235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Objective: We assessed knowledge and awareness of MMR/MSI testing among advanced/metastatic CRC patients in the US who had previously taken the test.Methods: A non-interventional, cross-sectional online survey was conducted among 150 US CRC patients invited through a research panel. Eligible patients had to be ≥18 years, with stage III or IV CRC (self-reported), had undergone MMR/MSI testing for CRC in past 12 months and could recall the test, and provided informed consent. Descriptive analyses were performed.Results: 81.3% of patients received MMR/MSI testing information from their doctor. Of 64.7% of patients who were a member of a patient support group, 86.6% received information from their groups. Most patients (82.7%) also searched for information on their own (internet searches). Most patients (93.5 to 96.9%) were satisfied with information received from these sources. Reasons for having testing done included increasing knowledge about their cancer (69.3%), being beneficial to determining treatment options (60.7%), and doctor recommendation (62.7%). Key barriers to testing included personal reservations regarding benefits of the test (29.3%), insurance coverage (27.3%), and out-of-pocket costs (18.7%); 45.3% reported no barriers.Conclusions: Patients were well informed about MMR/MSI testing. Increased education of testing benefits and addressing financial barriers may help to further improve testing rates.
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107
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Russell H, Kedzierska K, Buchanan DD, Thomas R, Tham E, Mints M, Keränen A, Giles GG, Southey MC, Milne RL, Tomlinson I, Church D, Spurdle AB, O'Mara TA, Lewis A. The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability. Clin Epigenetics 2020; 12:102. [PMID: 32641106 PMCID: PMC7346630 DOI: 10.1186/s13148-020-00889-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Both colorectal (CRC, 15%) and endometrial cancers (EC, 30%) exhibit microsatellite instability (MSI) due to MLH1 hypermethylation and silencing. The MLH1 promoter polymorphism, rs1800734 is associated with MSI CRC risk, increased methylation and reduced MLH1 expression. In EC samples, we investigated rs1800734 risk using MSI and MSS cases and controls. We found no evidence that rs1800734 or other MLH1 SNPs were associated with the risk of MSI EC. We found the rs1800734 risk allele had no effect on MLH1 methylation or expression in ECs. We propose that MLH1 hypermethylation occurs by different mechanisms in CRC and EC.
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Affiliation(s)
- Holly Russell
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Katarzyna Kedzierska
- Cancer Genomics and Immunology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, 3010, Australia
| | - Rachael Thomas
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Miriam Mints
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Anne Keränen
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
| | - Melissa C Southey
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - David Church
- Cancer Genomics and Immunology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, QLD, Brisbane, 4006, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, QLD, Brisbane, 4006, Australia
| | - Annabelle Lewis
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University, Kingston Lane, Uxbridge, UB8 3PH, UK.
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108
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Singh AK, Talseth-Palmer B, McPhillips M, Lavik LAS, Xavier A, Drabløs F, Sjursen W. Targeted sequencing of genes associated with the mismatch repair pathway in patients with endometrial cancer. PLoS One 2020; 15:e0235613. [PMID: 32634176 PMCID: PMC7340288 DOI: 10.1371/journal.pone.0235613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/19/2020] [Indexed: 01/28/2023] Open
Abstract
Germline variants inactivating the mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 cause Lynch syndrome that implies an increased cancer risk, where colon and endometrial cancer are the most frequent. Identification of these pathogenic variants is important to identify endometrial cancer patients with inherited increased risk of new cancers, in order to offer them lifesaving surveillance. However, several other genes are also part of the MMR pathway. It is therefore relevant to search for variants in additional genes that may be associated with cancer risk by including all known genes involved in the MMR pathway. Next-generation sequencing was used to screen 22 genes involved in the MMR pathway in constitutional DNA extracted from full blood from 199 unselected endometrial cancer patients. Bioinformatic pipelines were developed for identification and functional annotation of variants, using several different software tools and custom programs. This facilitated identification of 22 exonic, 4 UTR and 9 intronic variants that could be classified according to pathogenicity. This study has identified several germline variants in genes of the MMR pathway that potentially may be associated with an increased risk for cancer, in particular endometrial cancer, and therefore are relevant for further investigation. We have also developed bioinformatics strategies to analyse targeted sequencing data, including low quality data and genomic regions outside of the protein coding exons of the relevant genes.
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Affiliation(s)
- Ashish Kumar Singh
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology, Trondheim, Norway
| | - Bente Talseth-Palmer
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
- School of Biomedical Science and Pharmacy, Faculty of Health and Medicine, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
- Department of Research and Development, Møre og Romsdal Hospital Trust, Molde, Norway
| | - Mary McPhillips
- NSW Health Pathology, Molecular Medicine, John Hunter Hospital, Newcastle, NSW, Australia
| | | | - Alexandre Xavier
- School of Biomedical Science and Pharmacy, Faculty of Health and Medicine, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology, Trondheim, Norway
| | - Wenche Sjursen
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology, Trondheim, Norway
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109
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Implications of Hereditary Origin on the Immune Phenotype of Mismatch Repair-Deficient Cancers: Systematic Literature Review. J Clin Med 2020; 9:jcm9061741. [PMID: 32512823 PMCID: PMC7357024 DOI: 10.3390/jcm9061741] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023] Open
Abstract
Microsatellite instability (MSI) represents one of the major types of genomic instability in human cancers and is most common in colorectal cancer (CRC) and endometrial cancer (EC). MSI develops as a consequence of DNA mismatch repair (MMR) deficiency, which can occur sporadically or in the context of Lynch syndrome (LS), the most common inherited tumor syndrome. MMR deficiency triggers the accumulation of high numbers of somatic mutations in the affected cells, mostly indel mutations at microsatellite sequences. MSI tumors are among the most immunogenic human tumors and are often characterized by pronounced local immune responses. However, so far, little is known about immunological differences between sporadic and hereditary MSI tumors. Therefore, a systematic literature search was conducted to comprehensively collect data on the differences in local T cell infiltration and immune evasion mechanisms between sporadic and LS-associated MSI tumors. The vast majority of collected studies were focusing on CRC and EC. Generally, more pronounced T cell infiltration and a higher frequency of B2M mutations were reported for LS-associated compared to sporadic MSI tumors. In addition, phenotypic features associated with enhanced lymphocyte recruitment were reported to be specifically associated with hereditary MSI CRCs. The quantitative and qualitative differences clearly indicate a distinct biology of sporadic and hereditary MSI tumors. Clinically, these findings underline the need for differentiating sporadic and hereditary tumors in basic science studies and clinical trials, including trials evaluating immune checkpoint blockade therapy in MSI tumors.
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110
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Puccini A, Battaglin F, Iaia ML, Lenz HJ, Salem ME. Overcoming resistance to anti-PD1 and anti-PD-L1 treatment in gastrointestinal malignancies. J Immunother Cancer 2020; 8:e000404. [PMID: 32393474 PMCID: PMC7223273 DOI: 10.1136/jitc-2019-000404] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 12/14/2022] Open
Abstract
In the last few years, the unprecedented results of immune checkpoint inhibitors have led to a paradigm shift in clinical practice for the treatment of several cancer types. However, the vast majority of patients with gastrointestinal cancer do not benefit from immunotherapy. To date, microsatellite instability high and DNA mismatch repair deficiency are the only robust predictive biomarkers of response to immune checkpoint inhibitors. Unfortunately, these patients comprise only 5%-10% of all gastrointestinal cancers. Several mechanisms of both innate and adaptive resistance to immunotherapy have been recognized that may be at least in part responsible for the failure of immune checkpoint inhibitors in this population of patients. In the first part of this review article, we provide an overview of the main clinical trials with immune checkpoint inhibitors in patients with gastrointestinal cancer and the role of predictive biomarkers. In the second part, we discuss the actual body of knowledge in terms of mechanisms of resistance to immunotherapy and the most promising approach that are currently under investigation in order to expand the population of patients with gastrointestinal cancer who could benefit from immune checkpoint inhibitors.
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Affiliation(s)
- Alberto Puccini
- University of Genoa, Medical Oncology Unit 1, Ospedale Policlinico San Martino IRCCS, Genova, Italy
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Maria Laura Iaia
- University of Genoa, Medical Oncology Unit 1, Ospedale Policlinico San Martino IRCCS, Genova, Italy
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Mohamed E Salem
- Department of Medical Oncology, Levine Cancer Institute, Atrium Health, Charlotte, North Carolina, USA
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111
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Kaur J, Daoud A, Eblen ST. Targeting Chromatin Remodeling for Cancer Therapy. Curr Mol Pharmacol 2020; 12:215-229. [PMID: 30767757 PMCID: PMC6875867 DOI: 10.2174/1874467212666190215112915] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Background: Epigenetic alterations comprise key regulatory events that dynamically alter gene expression and their deregulation is commonly linked to the pathogenesis of various diseases, including cancer. Unlike DNA mutations, epigenetic alterations involve modifications to proteins and nucleic acids that regulate chromatin structure without affecting the underlying DNA sequence, altering the accessibility of the transcriptional machinery to the DNA, thus modulating gene expression. In cancer cells, this often involves the silencing of tumor suppressor genes or the increased expression of genes involved in oncogenesis. Advances in laboratory medicine have made it possible to map critical epigenetic events, including histone modifications and DNA methylation, on a genome-wide scale. Like the identification of genetic mutations, mapping of changes to the epigenetic landscape has increased our understanding of cancer progression. However, in contrast to irreversible genetic mutations, epigenetic modifications are flexible and dynamic, thereby making them promising therapeutic targets. Ongoing studies are evaluating the use of epigenetic drugs in chemotherapy sensitization and immune system modulation. With the preclinical success of drugs that modify epigenetics, along with the FDA approval of epigenetic drugs including the DNA methyltransferase 1 (DNMT1) inhibitor 5-azacitidine and the histone deacetylase (HDAC) inhibitor vorinostat, there has been a rise in the number of drugs that target epigenetic modulators over recent years. Conclusion: We provide an overview of epigenetic modulations, particularly those involved in cancer, and discuss the recent advances in drug development that target these chromatin-modifying events, primarily focusing on novel strategies to regulate the epigenome.
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Affiliation(s)
- Jasmine Kaur
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Abdelkader Daoud
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Scott T Eblen
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
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112
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Machnik M, Oleksiewicz U. Dynamic Signatures of the Epigenome: Friend or Foe? Cells 2020; 9:cells9030653. [PMID: 32156057 PMCID: PMC7140607 DOI: 10.3390/cells9030653] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
Highly dynamic epigenetic signaling is influenced mainly by (micro)environmental stimuli and genetic factors. The exact mechanisms affecting particular epigenomic patterns differ dependently on the context. In the current review, we focus on the causes and effects of the dynamic signatures of the human epigenome as evaluated with the high-throughput profiling data and single-gene approaches. We will discuss three different aspects of phenotypic outcomes occurring as a consequence of epigenetics interplaying with genotype and environment. The first issue is related to the cases of environmental impacts on epigenetic profile, and its adverse and advantageous effects related to human health and evolutionary adaptation. The next topic will present a model of the interwoven co-evolution of genetic and epigenetic patterns exemplified with transposable elements (TEs) and their epigenetic repressors Krüppel-associated box zinc finger proteins (KRAB–ZNFs). The third aspect concentrates on the mitosis-based microevolution that takes place during carcinogenesis, leading to clonal diversity and expansion of tumor cells. The whole picture of epigenome plasticity and its role in distinct biological processes is still incomplete. However, accumulating data define epigenomic dynamics as an essential co-factor driving adaptation at the cellular and inter-species levels with a benefit or disadvantage to the host.
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Affiliation(s)
- Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
- Correspondence:
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113
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Cercek A, Dos Santos Fernandes G, Roxburgh CS, Ganesh K, Ng S, Sanchez-Vega F, Yaeger R, Segal NH, Reidy-Lagunes DL, Varghese AM, Markowitz A, Wu C, Szeglin B, Sauvé CEG, Salo-Mullen E, Tran C, Patel Z, Krishnan A, Tkachuk K, Nash GM, Guillem J, Paty PB, Shia J, Schultz N, Garcia-Aguilar J, Diaz LA, Goodman K, Saltz LB, Weiser MR, Smith JJ, Stadler ZK. Mismatch Repair-Deficient Rectal Cancer and Resistance to Neoadjuvant Chemotherapy. Clin Cancer Res 2020; 26:3271-3279. [PMID: 32144135 DOI: 10.1158/1078-0432.ccr-19-3728] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/31/2020] [Accepted: 03/02/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE Evaluate response of mismatch repair-deficient (dMMR) rectal cancer to neoadjuvant chemotherapy. EXPERIMENTAL DESIGN dMMR rectal tumors at Memorial Sloan Kettering Cancer Center (New York, NY) were retrospectively reviewed for characteristics, treatment, and outcomes. Fifty patients with dMMR rectal cancer were identified by IHC and/or microsatellite instability analysis, with initial treatment response compared with a matched MMR-proficient (pMMR) rectal cancer cohort. Germline and somatic mutation analyses were evaluated. Patient-derived dMMR rectal tumoroids were assessed for chemotherapy sensitivity. RESULTS Of 21 patients receiving neoadjuvant chemotherapy (fluorouracil/oxaliplatin), six (29%) had progression of disease. In comparison, no progression was noted in 63 pMMR rectal tumors (P = 0.0001). Rectal cancer dMMR tumoroids reflected this resistance to chemotherapy. No genomic predictors of chemotherapy response were identified. Of 16 patients receiving chemoradiation, 13 (93%) experienced tumor downstaging; one patient had stable disease, comparable with 48 pMMR rectal cancers. Of 13 patients undergoing surgery, 12 (92%) had early-stage disease. Forty-two (84%) of the 50 patients tested positive for Lynch syndrome with enrichment of germline MSH2 and MSH6 mutations when compared with 193 patients with Lynch syndrome-associated colon cancer (MSH2, 57% vs 36%; MSH6, 17% vs 9%; P < 0.003). CONCLUSIONS Over one-fourth of dMMR rectal tumors treated with neoadjuvant chemotherapy exhibited disease progression. Conversely, dMMR rectal tumors were sensitive to chemoradiation. MMR status should be performed upfront in all locally advanced rectal tumors with careful monitoring for response on neoadjuvant chemotherapy and genetic testing for Lynch syndrome in patients with dMMR rectal cancer.
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Affiliation(s)
- Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Campbell S Roxburgh
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Karuna Ganesh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shu Ng
- Alfred Health Radiation Oncology, Melbourne, Victoria, Australia
| | - Francisco Sanchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neil H Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arnold Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chao Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bryan Szeglin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Tran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zalak Patel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Asha Krishnan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Garrett M Nash
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jose Guillem
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip B Paty
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karyn Goodman
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, Colorado
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - J Joshua Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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Zaanan A, Shi Q, Taieb J, Alberts SR, Meyers JP, Smyrk TC, Julie C, Zawadi A, Tabernero J, Mini E, Goldberg RM, Folprecht G, Van Laethem JL, Le Malicot K, Sargent DJ, Laurent-Puig P, Sinicrope FA. Clinical Outcomes in Patients With Colon Cancer With Microsatellite Instability of Sporadic or Familial Origin Treated With Adjuvant FOLFOX With or Without Cetuximab: A Pooled Analysis of the PETACC8 and N0147 Trials. JCO Precis Oncol 2020; 4:1900237. [PMID: 32923882 PMCID: PMC7446392 DOI: 10.1200/po.19.00237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/31/2022] Open
Abstract
PURPOSE The microsatellite instability (MSI) or deficient mismatch repair (dMMR) phenotype is usually regarded as a single biologic entity, given the absence of comparative analyses regarding prognosis and response to chemotherapy between sporadic and familial dMMR cancers. PATIENTS AND METHODS Patients with stage III colon cancers were randomly assigned to FOLFOX (leucovorin, fluorouracil, and oxaliplatin) with or without cetuximab in 2 large adjuvant phase III trials (N = 5,577). Among patients with MSI and KRAS exon 2 wild-type (WT) tumors, the prognostic and predictive impacts of sporadic versus familial dMMR cancers and BRAF V600E mutational status were determined. Multivariable Cox proportional hazards models were used to assess disease-free survival (DFS) by treatment arm, adjusting for age, sex, tumor grade, Eastern Cooperative Oncology Group performance status, pT/pN stage, and primary tumor location. RESULTS Among patients with MSI status with complete data for dMMR mechanism analysis (n = 354), 255 (72%) had sporadic (BRAF mutation and/or MLH1 methylation) and 99 (28%) had familial tumors (BRAF WT and unmethylated MLH1 or loss of MSH2/MSH6/PMS2 protein expression). A large proportion of dMMR sporadic tumors were mutated for BRAF (n = 200). In patients treated with FOLFOX, DFS did not differ statistically by dMMR mechanism, whereas in patients treated with FOLFOX plus cetuximab, those with sporadic tumors had worse DFS than those with familial cancers (multivariable hazard ratio, 2.69; 95% CI, 1.02 to 7.08; P = .04). Considering the predictive utility, the interaction between treatment and dMMR mechanism was significant (P = .03). Furthermore, a nonsignificant trend toward a deleterious effect of adding cetuximab to FOLFOX was observed in patients with BRAF-mutant but not BRAF WT tumors. CONCLUSION The addition of cetuximab to adjuvant FOLFOX was associated with shorter DFS in patients with sporadic dMMR colon cancer. Additional studies are needed to validate these results in metastatic disease.
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Affiliation(s)
- Aziz Zaanan
- Department of Medicine, Mayo Clinic,
Rochester, MN,Department of Gastroenterology and
Digestive Oncology, European Georges Pompidou Hospital, Assistance Publique
Hôpitaux de Paris (APHP), Paris, France,Aziz Zaanan, MD, PhD, Department of Gastroenterology and
Digestive Oncology, European Georges Pompidou Hospital, Paris Descartes
University, Paris, France; e-mail:
| | - Qian Shi
- Alliance Statistics and Data Center, Mayo
Clinic, Rochester, MN
| | - Julien Taieb
- Centre de Recherche des Cordeliers,
INSERM, Sorbonne Université, Université Paris Descartes,
Université Paris Diderot, Université Sorbonne Paris Cité,
Paris, France,Department of Gastroenterology and
Digestive Oncology, European Georges Pompidou Hospital, Assistance Publique
Hôpitaux de Paris (APHP), Paris, France
| | | | | | - Thomas C. Smyrk
- Laboratory Medicine and Pathology, Mayo
Clinic, Rochester, MN
| | - Catherine Julie
- Department of Pathology, Ambroise
Paré Hospital, APHP, Boulogne-Billancourt, France,Versailles Saint-Quentin-en-Yvelines
University, Boulogne-Billancourt, France
| | - Ayman Zawadi
- Radiotherapy Unit, Departmental Hospital
Center, La Roche-Sur-Yon, France
| | - Josep Tabernero
- Medical Oncology Department, Vall
d‘Hebron University Hospital, Barcelona, Spain,Vall d‘Hebron Institute of
Oncology, University of Vic, IOB-Quiron, Barcelona, Spain
| | - Enrico Mini
- Section of Clinical Pharmacology and
Oncology, Department of Health Sciences, University of Florence, Florence,
Italy,DENOTHE Excellence Center, University of
Florence, Florence, Italy
| | | | - Gunnar Folprecht
- First Medical Department, University
Hospital Carl Gustav Carus, Dresden, Germany
| | | | - Karine Le Malicot
- Department of Statistics,
Fédération Francophone de Cancérologie Digestive, Dijon,
France
| | | | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers,
INSERM, Sorbonne Université, Université Paris Descartes,
Université Paris Diderot, Université Sorbonne Paris Cité,
Paris, France,Department of Biology, European Georges
Pompidou Hospital, APHP, Paris, France
| | - Frank A. Sinicrope
- Department of Medicine, Mayo Clinic,
Rochester, MN,Mayo Comprehensive Cancer Center,
Rochester, MN
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115
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Zhou N, Hofstetter WL. Prognostic and therapeutic molecular markers in the clinical management of esophageal cancer. Expert Rev Mol Diagn 2020; 20:401-411. [PMID: 32067548 DOI: 10.1080/14737159.2020.1731307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Esophageal cancer is a deadly disease with high mortality. Treatment with chemotherapy, radiation, and surgery continues to leave many patients with disease progression and recurrence. Novel treatments are needed for this patient population. The development of molecular markers are important for identifying therapeutic targets, as well as prognosis.Areas covered: This review evaluates three molecular markers in esophageal cancer: HER2, PD-L1, and MSI. The fundamentals of these markers, diagnosis, and rates of occurrence in esophageal cancer are explored. The prognostic potential of these markers is based on existing literature as well as application in clinical trials. Key trial findings pertaining to the therapeutic targets for HER2 and PD-1 as well as the role of MSI are discussed.Expert commentary: Molecular markers are changing the practice for esophageal cancer. Therapeutic targeting for HER2 and PD-L1 have shown positive results in recent clinical trials. Trials evaluating immunotherapy as first-line agents are currently underway.
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Affiliation(s)
- Nicolas Zhou
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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116
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Jung G, Hernández-Illán E, Moreira L, Balaguer F, Goel A. Epigenetics of colorectal cancer: biomarker and therapeutic potential. Nat Rev Gastroenterol Hepatol 2020; 17:111-130. [PMID: 31900466 PMCID: PMC7228650 DOI: 10.1038/s41575-019-0230-y] [Citation(s) in RCA: 383] [Impact Index Per Article: 95.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2019] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC), a leading cause of cancer-related death worldwide, evolves as a result of the stepwise accumulation of a series of genetic and epigenetic alterations in the normal colonic epithelium, leading to the development of colorectal adenomas and invasive adenocarcinomas. Although genetic alterations have a major role in a subset of CRCs, the pathophysiological contribution of epigenetic aberrations in this malignancy has attracted considerable attention. Data from the past couple of decades has unequivocally illustrated that epigenetic marks are important molecular hallmarks of cancer, as they occur very early in disease pathogenesis, involve virtually all key cancer-associated pathways and, most importantly, can be exploited as clinically relevant disease biomarkers for diagnosis, prognostication and prediction of treatment response. In this Review, we summarize the current knowledge on the best-studied epigenetic modifications in CRC, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators. We focus on the emerging potential for the bench-to-bedside translation of some of these epigenetic alterations into clinical practice and discuss the burgeoning evidence supporting the potential of emerging epigenetic therapies in CRC as we usher in the era of precision medicine.
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Affiliation(s)
- Gerhard Jung
- Gastroenterology Department, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Eva Hernández-Illán
- Gastroenterology Department, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.,;
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA.,Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, California, USA.,;
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117
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Nano A, Bailis JM, Mariano NF, Pham ED, Threatt SD, Barton JK. Cell-Selective Cytotoxicity of a Fluorescent Rhodium Metalloinsertor Conjugate Results from Irreversible DNA Damage at Base Pair Mismatches. Biochemistry 2020; 59:717-726. [DOI: 10.1021/acs.biochem.9b01037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Adela Nano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Julie M. Bailis
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Natalie F. Mariano
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Elizabeth D. Pham
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Stephanie D. Threatt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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118
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A DNA methylation signature to improve survival prediction of gastric cancer. Clin Epigenetics 2020; 12:15. [PMID: 31959204 PMCID: PMC6972030 DOI: 10.1186/s13148-020-0807-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/02/2020] [Indexed: 02/08/2023] Open
Abstract
Background The current Union International Committee on Cancer or the American Joint Committee on Cancer TNM stage system has shown valuable but insufficient estimation for subsets of gastric cancer and prediction for prognosis patients. Thus, there is an urgent need to identify diagnostic, prognostic, and predictive biomarkers to improve patients’ outcomes. Our aim was to perform an integrative analysis on publicly available datasets to identify epigenetic changes that may play key role in the initiation and progression of gastric cancer, based on which we set to develop a DNA methylation signature to improve survival prediction of gastric cancer. Results A total of 340 methylation-related differentially expression genes (mrDEGs) were screened in gastric cancer patients from The Cancer Genome Atlas (TCGA) project. Pathway enrichment analysis revealed that they were involved in the biological process related to initiation and progression of gastric cancer. Based on the mrDEGs identified, we developed a DNA methylation signature consisting of ten gene members (SCNN1B, NFE2L3, CLDN2, RBPMS2, JPH2, GBP6, COL4A5, SMKR1, PPP1R14A, and ARL4D) according to their methylation β value. This innovative DNA methylation signature was associated with cancer recurrence, while it showed independence of cancer recurrence and TNM stage for survival prediction. Combination of this DNA methylation signature and TNM stage improved overall survival prediction in the receiver operating characteristic analysis. We also verified that two individual genes (PPP1R14A and SCNN1B) of the identified prognostic signature were regulated by promoter region methylation in a panel of gastric cell lines. Conclusions This study presents a powerful DNA methylation signature by performing analyses integrating multi-source data including transcriptome, methylome, and clinical outcome of gastric cancer patients from TCGA. The identified DNA methylation signature may be used to refine the current prognostic model and facilitate further stratification of patients in the future clinical trials. Further experimental studies are warranted to unveil the regulatory mechanism and functional role of all the individual genes of the DNA methylation signature. Also, clinical investigations in large GC patient cohorts are greatly needed to validate our findings.
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119
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Mohammad G, Radhakrishnan R, Kowluru RA. Epigenetic Modifications Compromise Mitochondrial DNA Quality Control in the Development of Diabetic Retinopathy. Invest Ophthalmol Vis Sci 2020; 60:3943-3951. [PMID: 31546260 PMCID: PMC6759036 DOI: 10.1167/iovs.19-27602] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Purpose Diabetes causes dysfunction in the retinal mitochondria and increases base mismatches in their DNA (mtDNA). The enzyme responsible for repairing the base mismatches, MutL homolog 1 (Mlh1), is compromised. Diabetes also favors many epigenetic modifications and activates DNA methylation machinery, and Mlh1 has a CpG-rich promoter. Our aim is to identify the molecular mechanism responsible for impaired mtDNA mismatch repair in the pathogenesis of diabetic retinopathy. Methods Human retinal endothelial cells, incubated in 20 mM glucose, were analyzed for mitochondrial localization of Mlh1 by an immunofluorescence technique, Mlh1 promoter DNA methylation by the methylated DNA capture method, and the binding of Dnmt1 and transcriptional factor Sp1 by chromatin immunoprecipitation. The results were confirmed in retinal microvessels from streptozotocin-induced diabetic mice, with or without Dnmt inhibitors, and from human donors with diabetic retinopathy. Results Compared with cells in 5 mM glucose, high glucose decreased Mlh1 mitochondrial localization, and its promoter DNA was hypermethylated with increased Dnmt-1 binding and decreased Sp1 binding. Dnmt inhibitors attenuated Mlh1 promoter hypermethylation and prevented a decrease in its gene transcripts and an increase in mtDNA mismatches. The administration of Dnmt inhibitors in mice ameliorated a diabetes-induced increase in Mlh1 promoter hypermethylation and a decrease in its gene transcripts. Similar decreases in Mlh1 gene transcripts and its promoter DNA hypermethylation were observed in human donors. Conclusions Thus, as a result of the epigenetic modifications of the Mlh1 promoter, its transcription is decreased, and decreased mitochondrial accumulation fails to repair mtDNA mismatches. Therapies targeted to halt DNA methylation have the potential to prevent/halt mtDNA damage and the development of diabetic retinopathy.
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Affiliation(s)
- Ghulam Mohammad
- Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, Michigan, United States
| | - Rakesh Radhakrishnan
- Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, Michigan, United States
| | - Renu A Kowluru
- Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, Michigan, United States
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120
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Fridman WH, Miller I, Sautès-Fridman C, Byrne AT. Therapeutic Targeting of the Colorectal Tumor Stroma. Gastroenterology 2020; 158:303-321. [PMID: 31622621 DOI: 10.1053/j.gastro.2019.09.045] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/05/2019] [Accepted: 09/08/2019] [Indexed: 02/07/2023]
Abstract
Colorectal tumors have been classified based on histologic factors, genetic factors, and consensus molecular subtypes, all of which affect the tumor microenvironment. Elements of the tumor microenvironment serve as therapeutic targets and might be used as prognostic factors. For example, immune checkpoint inhibitors are used to treat tumors with microsatellite instability, and anti-angiogenic agents may be used in combination with other drugs to slow or inhibit tumor growth. We review the features of the colorectal tumor stroma that are associated with patient outcomes and discuss potential therapeutic agents that target these features.
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Affiliation(s)
- Wolf H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Inflammation, Complement and Cancer Team, Paris, France.
| | - Ian Miller
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Inflammation, Complement and Cancer Team, Paris, France
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Benhamida JK, Hechtman JF, Nafa K, Villafania L, Sadowska J, Wang J, Wong D, Zehir A, Zhang L, Bale T, Arcila ME, Ladanyi M. Reliable Clinical MLH1 Promoter Hypermethylation Assessment Using a High-Throughput Genome-Wide Methylation Array Platform. J Mol Diagn 2019; 22:368-375. [PMID: 31881335 DOI: 10.1016/j.jmoldx.2019.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 12/21/2022] Open
Abstract
Clinical testing for MLH1 promoter hypermethylation status is important in the workup of patients with MLH1-deficient colorectal and uterine carcinomas when evaluating patients for Lynch syndrome. Current assays use single gene-based methods to assess promoter hypermethylation. Herein, we describe the development and report the performance of a clinical assay for MLH1 promoter hypermethylation using the Infinium methylationEPIC (850k) bead-array platform. Using four cytosine-guanine dinucleotide (CpG) sites within the MLH1 gene promoter, a qualitative MLH1 promoter hypermethylation assay was developed and validated using 63 gastrointestinal and uterine carcinoma samples of known hypermethylation status based on a pyrosequencing reference test. The array-based method achieves clinically robust and reproducible results at an analytical sensitivity level of 8%. Of importance, the 850k array contains probes targeting >850,000 additional CpG sites across the genome, covering sites in most known genes as well as important enhancer regions provided by the Encyclopedia of DNA Elements and Functional Annotation of The Mammalian Genome projects. Thus, the testing modality presented may also be applied to determine the methylation status of other clinically relevant genes or regulatory regions, potentially providing a single laboratory testing workflow for all clinical methylation assays. Furthermore, the concomitant acquisition of genome-wide methylation information provides a workflow that seamlessly enables wider translational epigenetic research.
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Affiliation(s)
- Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liliana Villafania
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jiajing Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Donna Wong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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122
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Paredes SR, Chan C, Rickard MJFX. Immunohistochemistry in screening for heritable colorectal cancer: what to do with an abnormal result. ANZ J Surg 2019; 90:702-707. [PMID: 31828933 DOI: 10.1111/ans.15586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 02/06/2023]
Abstract
Recent developments in our understanding of molecular genetics have transformed screening and diagnostic practices for Lynch syndrome. The current standard involves universal tumour analysis of resected colorectal cancer (and ideally polypectomy) specimens using immunohistochemistry and molecular techniques. Patients with abnormal immunohistochemical findings are subsequently referred for definitive mutational testing. This review relates the molecular pathogenesis of Lynch syndrome to current immunohistochemistry-based screening strategies and discusses the interpretation and clinical implications of screening results.
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Affiliation(s)
- Steven R Paredes
- Discipline of Surgery, School of Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Concord Clinical School, School of Medicine, The University of Sydney, Sydney, New South Wales, Australia
| | - Charles Chan
- Concord Clinical School, School of Medicine, The University of Sydney, Sydney, New South Wales, Australia.,Anatomical Pathology Department, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
| | - Matthew J F X Rickard
- Discipline of Surgery, School of Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Division of Colorectal Surgery, Department of Surgery, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.,Division of Colorectal Surgery, Department of Surgery, Macquarie University Hospital, Macquarie University, Sydney, New South Wales, Australia
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Ben Sghaier R, Jansen AML, Bdioui A, Van Wezel T, Ksiaa M, Elgolli L, Ben Fatma L, Ben Ahmed S, Azzouz MM, Hellara O, Elghali A, Darbel F, Skandrani K, Mokkni M, Gdissa A, Ltaief R, Saad A, Hmila F, Gribaa M, Morreau H. Targeted next generation sequencing screening of Lynch syndrome in Tunisian population. Fam Cancer 2019; 18:343-348. [PMID: 31114938 DOI: 10.1007/s10689-019-00130-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A high colorectal cancer (CRC) incidence is observed in Tunisia, with a relatively high proportion of patients developing CRC before the age of 40. While this suggests a genetic susceptibility, only a few Tunisian Lynch Syndrome families have been described. In this study we aimed to identify the underlying genetic cause in 32 patients with early onset CRC and/or a positive family history. Of twenty-four patients' tumor or biopsies could be analyzed with immunohistochemical staining to detect loss of expression of one of the MMR proteins. Ten tumors showed loss of expression, of which one tumor was from a patient where a germline pathogenic MSH2 variant was detected previously with Sanger sequencing. Next generation sequencing of the MMR, POLE and POLD1 genes was performed in leukocyte and tumor DNA of the remaining nine patients, as well as in two patients with MMR-proficient tumors, but with severe family history. In six of 11 patients a germline variant was detected in MLH1 (n = 5) or MSH2 (n = 1). Two of six patients were from the same family and both were found to carry a novel in-frame MLH1 deletion, predicted to affect MLH1 function. All MLH1 variant carriers had loss of heterozygosity with retention of the variant in the tumors, while a somatic pathogenic variant was detected in the patient with the germline MSH2 variant.
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Affiliation(s)
- Rihab Ben Sghaier
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia.
| | | | - Ahlem Bdioui
- Cytology and Anatomopathology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Tom Van Wezel
- Pathology Department, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - Mehdi Ksiaa
- Gastroenterology Department, Sahloul Hospital, Sousse, Tunisia
| | | | - Leila Ben Fatma
- Carcinology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Slim Ben Ahmed
- Carcinology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | | | - Olfa Hellara
- Gastroenterology Department, Fatouma Bourguiba Hospital, Monastir, Tunisia
| | - Amine Elghali
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | | | | | - Moncef Mokkni
- Cytology and Anatomopathology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Ameni Gdissa
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Rached Ltaief
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Ali Saad
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Fahmi Hmila
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Moez Gribaa
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Hans Morreau
- Pathology Department, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
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124
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Kientz C, Prieur F, Clemenson A, Joly MO, Stachowicz ML, Auclair J, Attignon V, Schiappa R, Wang Q. MLH1 promoter hypermethylation: are you absolutely sure about the absence of MLH1 germline mutation? About a new case. Fam Cancer 2019; 19:11-14. [PMID: 31745674 DOI: 10.1007/s10689-019-00151-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/12/2019] [Indexed: 11/30/2022]
Abstract
Lynch syndrome accounts for 3-5% of colorectal cancers and is due to a germline mutation in one of the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. Somatic hypermethylation of the MLH1 promoter is commonly associated to sporadic cases. Strategies have been developed to identify patients with Lynch Syndrome based on clinical findings, tumoral phenotype, family history and immunohistochemistry analysis. However, there still are some pitfalls in this strategy, possibly responsible for an underdiagnosis of Lynch syndrome. Here we report the case of a 37 years-old man presenting with two concomitant tumors located in the rectosigmoid and in the ileocecal angle. Both tumors were microsatellites instability-high (MSI-H) and showed a loss of MLH1 and PMS2 protein expression, but only one had MLH1 promoter hypermethylation. Constitutional analysis of mismatch repair genes could not be performed from a blood sample, because of the early death of the patient. However, tumoral tissue analyses revealed in both tumors a pathogenic variant in the MLH1 gene. Further analysis of the surrounding tumor-free tissue also showed the presence of this alteration of the MHL1 gene. Finally, the same pathogenic variant was present constitutionally in one of the siblings of the patient, confirming its hereditary nature. This new case of concomitant presence of MLH1 promoter hypermethylation and MLH1 germline mutation demonstrates that the presence of MLH1 promoter hypermethylation should not rule out the diagnosis of Lynch Syndrome.
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Affiliation(s)
- Caroline Kientz
- Department of Genetics, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne Cedex 2, France.
| | - Fabienne Prieur
- Department of Genetics, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne Cedex 2, France
| | - Alix Clemenson
- Department of Pathology, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne cedex 2, France
| | - Marie-Odile Joly
- Hospices Civils de Lyon, Molecular Biopathology, Centre of Pathology, GHE Hospital, Bron, France.,Claude Bernard University Lyon 1, University of Lyon, 69622, Villeurbanne cedex, France
| | - Marie-Laure Stachowicz
- Department of Pathology, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne cedex 2, France
| | - Jessie Auclair
- Centre Léon Bérard, Cancer Genomics Platform, 69272, Lyon cedex 08, France
| | - Valéry Attignon
- Centre Léon Bérard, Cancer Genomics Platform, 69272, Lyon cedex 08, France
| | - Renaud Schiappa
- Epidemiology and Biostatistics Unit, Centre Antoine Lacassagne, University of Cote d'Azur, 33 avenue de valombrose, 06189, Nice, France
| | - Qing Wang
- Centre Léon Bérard, Cancer Genomics Platform, 69272, Lyon cedex 08, France.,Centre Léon Bérard, Joint laboratory for constitutional genetics HCL-CLB, 69272, Lyon cedex 08, France
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125
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Wang SM, Jiang B, Deng Y, Huang SL, Fang MZ, Wang Y. Clinical significance of MLH1/ MSH2 for stage II/III sporadic colorectal cancer. World J Gastrointest Oncol 2019; 11:1065-1080. [PMID: 31798786 PMCID: PMC6883179 DOI: 10.4251/wjgo.v11.i11.1065] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/10/2019] [Accepted: 09/10/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The development of colorectal cancer (CRC) is a complicated multistep process that involves an accumulation of mutations in tumor suppressor genes and oncogenes. In the process of DNA replication, base mismatch often occurs due to various factors leading to abnormal expression of mismatch repair genes (MMR), among which MLH1 and MSH2 are the most important. Recently, numerous studies indicated that MLH1/MSH2 phenotype is associated with CRC. We wanted to elucidate the role of MLH1/MSH2 in the prediction and prognosis of CRC through long-term clinical observation.
AIM To evaluate the prognostic and predictive significance of MLH1/MSH2 in patients with stage II-III CRC using immunohistochemical analysis and GeneScan.
METHODS Specimens from 681 patients with CRC (395 stage II and 286 stage III, 387 males and 294 females) who underwent curative surgical resection from 2013 to 2016 were tested. Immunohistochemistry was used to analyze MMR status and the microsatellite status of 133 patients was determined by GeneScan analysis.
RESULTS Five hundred and fifty (80.76%) patients were MLH1/MSH2 positive and 131 (19.24%) were negative by immunohistochemistry. MLH1/MSH2-positive tumors were significantly more frequent in the colon than in the rectum, and had poor differentiation and less mucin production (P < 0.05). Patients of different groups did not differ in terms of age, gender, tumor size, tumor stage, lymphocytic infiltration, or circumscribed margin. MLH1/MSH2-negative patients had a more favorable OS than MLH1/MSH2-positive patients (P < 0.001). Univariate and multivariate analyses demonstrated MLH1/MSH2 expression as an independent prognostic and predictive factor for stage II/III CRC. MLH1/MSH2 expression was a strong prognostic factor in all patients [P < 0.001, hazard ratio (HR) = 4.064, 95%CI: 2.241–7.369]. Adjuvant chemotherapy had a greater correlation with survival advantage in MLH1/MSH2-negative patients with stage III disease (P < 0.001, HR = 7.660, 95%CI: 2.974–15.883). However, patients with stage II disease or MLH1/MSH2-positive patients with stage III disease did not benefit from adjuvant chemotherapy. GeneScan analysis demonstrated that among 133 patients, 105 (78.95%) were microsatellite stable, and 28 (21.05%) had microsatellite instability (MSI), including 18 (13.53%) with high MSI and 10 (7.52%) with low MSI. This is consistent with the immunohistochemical results.
CONCLUSION MLH1/MSH2 phenotype constitutes a pathologically and clinically distinct subtype of sporadic CRC. MLH1/MSH2 is an independent prognostic and predictive factor for outcome of stage II-III CRC.
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Affiliation(s)
- Shui-Ming Wang
- National Center of Colorectal Disease, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210022, Jiangsu Province, China
| | - Bin Jiang
- National Center of Colorectal Disease, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210022, Jiangsu Province, China
| | - Youping Deng
- Bioinformatics Core, Department of Complementary and Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI 96813, United States
| | - Shu-Liang Huang
- Department of Pathology, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210022, Jiangsu Province, China
| | - Ming-Zhi Fang
- Department of Oncology, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210022, Jiangsu Province, China
| | - Yu Wang
- Bioinformatics Core, Department of Complementary and Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI 96813, United States
- Department of Oncology, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210022, Jiangsu Province, China
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126
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Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KYC, Ross JP. DNA Methylation Cancer Biomarkers: Translation to the Clinic. Front Genet 2019; 10:1150. [PMID: 31803237 PMCID: PMC6870840 DOI: 10.3389/fgene.2019.01150] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
Carcinogenesis is accompanied by widespread DNA methylation changes within the cell. These changes are characterized by a globally hypomethylated genome with focal hypermethylation of numerous 5’-cytosine-phosphate-guanine-3’ (CpG) islands, often spanning gene promoters and first exons. Many of these epigenetic changes occur early in tumorigenesis and are highly pervasive across a tumor type. This allows DNA methylation cancer biomarkers to be suitable for early detection and also to have utility across a range of areas relevant to cancer detection and treatment. Such tests are also simple in construction, as only one or a few loci need to be targeted for good test coverage. These properties make cancer-associated DNA methylation changes very attractive for development of cancer biomarker tests with substantive clinical utility. Across the patient journey from initial detection, to treatment and then monitoring, there are several points where DNA methylation assays can inform clinical practice. Assays on surgically removed tumor tissue are useful to determine indicators of treatment resistance, prognostication of outcome, or to molecularly characterize, classify, and determine the tissue of origin of a tumor. Cancer-associated DNA methylation changes can also be detected with accuracy in the cell-free DNA present in blood, stool, urine, and other biosamples. Such tests hold great promise for the development of simple, economical, and highly specific cancer detection tests suitable for population-wide screening, with several successfully translated examples already. The ability of circulating tumor DNA liquid biopsy assays to monitor cancer in situ also allows for the ability to monitor response to therapy, to detect minimal residual disease and as an early biomarker for cancer recurrence. This review will summarize existing DNA methylation cancer biomarkers used in clinical practice across the application domains above, discuss what makes a suitable DNA methylation cancer biomarker, and identify barriers to translation. We discuss technical factors such as the analytical performance and product-market fit, factors that contribute to successful downstream investment, including geography, and how this impacts intellectual property, regulatory hurdles, and the future of the marketplace and healthcare system.
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Affiliation(s)
- Warwick J Locke
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Dominic Guanzon
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Chenkai Ma
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Yi Jin Liew
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Konsta R Duesing
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Kim Y C Fung
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Jason P Ross
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
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127
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Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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128
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Nakanishi Y, Diaz-Meco MT, Moscat J. Serrated Colorectal Cancer: The Road Less Travelled? Trends Cancer 2019; 5:742-754. [PMID: 31735291 DOI: 10.1016/j.trecan.2019.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 02/06/2023]
Abstract
Studies of colorectal cancer (CRC) originating through the conventional adenoma-carcinoma sequence have provided insight into the molecular mechanisms controlling its initiation and progression. Less is known about the alternative 'serrated' pathway, which has been associated with BRAF mutation and microsatellite instability. Recent transcriptomics approaches to classify human CRC revealed that mesenchymal and/or desmoplastic features combined with an immunosuppressive microenvironment are key determinants of CRC with the poorest prognosis. Importantly, these aggressive CRCs harbor the characteristics of serrated tumors, suggesting that initiation through this alternative pathway determines how aggressive the CRC becomes. Here, we review recent evidence on how serrated carcinogenesis contributes to the subtype of CRC with the poorest prognosis.
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Affiliation(s)
- Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Maria T Diaz-Meco
- Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jorge Moscat
- Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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129
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Yoshioka KI, Matsuno Y, Hyodo M, Fujimori H. Genomic-Destabilization-Associated Mutagenesis and Clonal Evolution of Cells with Mutations in Tumor-Suppressor Genes. Cancers (Basel) 2019; 11:cancers11111643. [PMID: 31653100 PMCID: PMC6895985 DOI: 10.3390/cancers11111643] [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: 10/11/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
The development of cancer is driven by genomic instability and mutations. In general, cancer develops via multiple steps. Each step involves the clonal evolution of cells with abrogated defense systems, such as cells with mutations in cancer-suppressor genes. However, it remains unclear how cellular defense systems are abrogated and the associated clonal evolution is triggered and propagated. In this manuscript, we review current knowledge regarding mutagenesis associated with genomic destabilization and its relationship with the clonal evolution of cells over the course of cancer development, focusing especially on mechanistic aspects.
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Affiliation(s)
- Ken-Ichi Yoshioka
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
| | - Yusuke Matsuno
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Mai Hyodo
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
- Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Haruka Fujimori
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
- Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
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130
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Jácome AA, Eng C. Role of immune checkpoint inhibitors in the treatment of colorectal cancer: focus on nivolumab. Expert Opin Biol Ther 2019; 19:1247-1263. [DOI: 10.1080/14712598.2019.1680636] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alexandre A. Jácome
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cathy Eng
- Gastrointestinal Oncology department, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
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131
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Scalea S, Maresca C, Catalanotto C, Marino R, Cogoni C, Reale A, Zampieri M, Zardo G. Modifications of H3K4 methylation levels are associated with DNA hypermethylation in acute myeloid leukemia. FEBS J 2019; 287:1155-1175. [PMID: 31599112 DOI: 10.1111/febs.15086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/02/2019] [Accepted: 10/06/2019] [Indexed: 01/07/2023]
Abstract
The 'instructive model' of aberrant DNA methylation in human tumors is based on the observation that CpG islands prone to hypermethylation in cancers are embedded in chromatin enriched in H3K27me3 in human embryonic stem cells (hESC). Recent studies also link methylation of CpG islands to the methylation status of H3K4, where H3K4me3 is inversely correlated with DNA methylation. To provide insight into these conflicting findings, we generated DNA methylation profiles for acute myeloid leukemia samples from patients and leukemic cell lines and integrated them with publicly available ChIp-seq data, containing H3K4me3 and H3K27me3 CpG island occupation in hESC, or hematopoietic stem or progenitor cells (hHSC/MPP). Hypermethylated CpG islands in AML samples displayed H3K27me3 enrichments in hESC and hHSC/MPP; however, ChIp analysis of specific hypermethylated CpG islands revealed a significant reduction in H3K4me3 signal with a concomitant increase in H3K4me0 levels as opposed to a nonsignificant increase in H3K27me3 marks. The integration of AML DNA methylation profiles with the ChIp-seq data in hESC and hHSC/MPP also led to the identification of Iroquois homeobox 2 (IRX2) as a previously unknown factor promoting differentiation of leukemic cells. Our results indicate that in contrast to the 'instructive model', H3K4me3 levels are strongly associated with DNA methylation patterns in AML and have a role in the regulation of critical genes, such as the putative tumor suppressor IRX2.
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Affiliation(s)
- Stefania Scalea
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Carmen Maresca
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Rachele Marino
- Department of Molecular Medicine, University of Rome, Sapienza, Italy
| | - Carlo Cogoni
- Department of Molecular Medicine, University of Rome, Sapienza, Italy
| | - Anna Reale
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
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132
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Liu GC, Liu RY, Yan JP, An X, Jiang W, Ling YH, Chen JW, Bei JX, Zuo XY, Cai MY, Liu ZX, Zuo ZX, Liu JH, Pan ZZ, Ding PR. The Heterogeneity Between Lynch-Associated and Sporadic MMR Deficiency in Colorectal Cancers. J Natl Cancer Inst 2019; 110:975-984. [PMID: 29471527 DOI: 10.1093/jnci/djy004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/04/2018] [Indexed: 11/12/2022] Open
Abstract
Background Previous studies demonstrated that prognosis of germline deficiency in mismatch repair protein (dMMR) was different from that of sporadic dMMR. The underlying mechanism has not been studied. Methods From a prospectively maintained database, we collected dMMR colorectal cancer (CRC) patients identified by postoperative immunohistochemistry screening. According to genetic test, patients were grouped as Lynch-associated or sporadic dMMR. We compared the clinical-pathological features, prognosis, and immunoreactive differences between the two groups. By whole-exome sequencing and neoantigen detection pipeline, mutational frequencies and neoantigen burdens were also compared. All statistical tests were two-sided. Results Sixty-seven sporadic dMMR and 85 Lynch-associated CRC patients were included in the study. Sporadic dMMR patients were older (P < .001) and their tumors were poorly differentiated (P = .03). The survival was better in the Lynch-associated group (P = .001). After adjustment, the difference still remained statistically significant (hazard ratio = 0.29, 95% confidence interval = 0.09 to 0.95, P = .04). The scores of Crohn's-like reaction (CRO; P < .001), immunoreactions in the invasive margin (IM; P = .01), tumor stroma (TS; P = .009), and cancer nest (CN; P = .02) of the Lynch-associated group were statistically significantly higher. The numbers of CD3+, CD8+, Foxp3+ tumor-infiltrating lymphocytes (TILs) in IM; CD3+, CD4+ TILs in TS; and CD3+, CD4+, CD8+ TILs in CN were statistically significantly higher in Lynch-associated dMMR patients. Based on the 16 patients who under went whole-exome sequencing, there were also more somatic mutations and neoantigen burdens in the Lynch-associated group compared with the sporadic dMMR group (439/pt vs 68/pt, P = .006; 628/pt vs 97/pt, P = .009). Conclusions There are heterogeneities in dMMR CRCs. Lynch-associated dMMR patients present with more somatic mutations and neoantigens compared with sporadic dMMR, which probably results in stronger immunoreactions and survival improvement.
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Affiliation(s)
- Guo-Chen Liu
- Department of Gynecologic Oncology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Ran-Yi Liu
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Jun-Ping Yan
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, P. R. China
| | - Xin An
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Wu Jiang
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Yi-Hong Ling
- Department of Pathology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Jie-Wei Chen
- Department of Pathology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Jin-Xin Bei
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Xiao-Yu Zuo
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Mu-Yan Cai
- Department of Pathology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Ze-Xian Liu
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Zhi-Xiang Zuo
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Ji-Hong Liu
- Department of Gynecologic Oncology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Zhi-Zhong Pan
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Pei-Rong Ding
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
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133
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Wang Y, Zhang B, Gao G, Zhang Y, Xia Q. GEFT protein expression in digestive tract malignant tumors and its clinical significance. Oncol Lett 2019; 18:5577-5590. [PMID: 31620201 DOI: 10.3892/ol.2019.10915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/13/2019] [Indexed: 01/23/2023] Open
Abstract
Guanine nucleotide exchange factor T (GEFT), a member of the Rho guanine nucleotide exchange factor family, is expressed in a variety of tumors. In the present study, the expression and clinical significance of GEFT in malignant digestive tract tumors was assessed. Tumor and adjacent control samples from 180 patients were tested. Positive GEFT expression rates were 80, 83.33 and 86.67% in esophageal squamous carcinoma (ESCC), gastric carcinoma (GC) and colorectal cancer (CRC), respectively. GEFT expression was associated with diffuse type carcinoma according to the Lauren classification (χ2=12.525, P=0.002) and tumor-node-metastasis (TNM) stages III/IV (χ2=4.033, P=0.045) in GC, and with vessel carcinoma embolus (χ2=7.890, P=0.005) and lymph node metastasis (χ2=5.455, P=0.020) in CRC, but was not associated with other clinicopathological parameters. Patients with high levels of GEFT protein expression had a less favorable outcome compared with patients with low levels of GEFT expression in patients with CRC (χ2=3.876, P=0.049). However, a significant association was not found between GEFT expression and overall survival in patients with ESCC (χ2=0.040, P=0.842) or GC (χ2=0.501, P=0.479). The rate of human epidermal growth factor receptor 2 upregulation in patients with GC was 13.33% and it was associated with nerve invasion (χ2=4.005, P=0.045) and TNM stages III/IV (χ2=5.600, P=0.018). Mismatch repair protein (MMRP) defect was observed in six cases, and the KRAS mutation rate was 26.67% in patients with CRC. GEFT expression was significantly correlated with MMRP (r=-0.285, P=0.027) and KRAS mutation in patients with CRC (r=0.697, P<0.001). These findings revealed frequent GEFT upregulation in malignant digestive tract tumors, which may have promoted tumor development. GEFT expression in CRC may be associated with microsatellite instability and KRAS mutation status, suggesting that GEFT may be a potential therapeutic target for patients with CRC.
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Affiliation(s)
- Yuanyuan Wang
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Bing Zhang
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Ge Gao
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Yinping Zhang
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Qingxin Xia
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
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134
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The emerging role of epigenetic therapeutics in immuno-oncology. Nat Rev Clin Oncol 2019; 17:75-90. [PMID: 31548600 DOI: 10.1038/s41571-019-0266-5] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
The past decade has seen the emergence of immunotherapy as a prime approach to cancer treatment, revolutionizing the management of many types of cancer. Despite the promise of immunotherapy, most patients do not have a response or become resistant to treatment. Thus, identifying combinations that potentiate current immunotherapeutic approaches will be crucial. The combination of immune-checkpoint inhibition with epigenetic therapy is one such strategy that is being tested in clinical trials, encompassing a variety of cancer types. Studies have revealed key roles of epigenetic processes in regulating immune cell function and mediating antitumour immunity. These interactions make combined epigenetic therapy and immunotherapy an attractive approach to circumvent the limitations of immunotherapy alone. In this Review, we highlight the basic dynamic mechanisms underlying the synergy between immunotherapy and epigenetic therapies and detail current efforts to translate this knowledge into clinical benefit for patients.
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135
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Taghbalout A, Du M, Jillette N, Rosikiewicz W, Rath A, Heinen CD, Li S, Cheng AW. Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways. Nat Commun 2019; 10:4296. [PMID: 31541098 PMCID: PMC6754513 DOI: 10.1038/s41467-019-12339-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
Here we develop a methylation editing toolbox, Casilio-ME, that enables not only RNA-guided methylcytosine editing by targeting TET1 to genomic sites, but also by co-delivering TET1 and protein factors that couple methylcytosine oxidation to DNA repair activities, and/or promote TET1 to achieve enhanced activation of methylation-silenced genes. Delivery of TET1 activity by Casilio-ME1 robustly alters the CpG methylation landscape of promoter regions and activates methylation-silenced genes. We augment Casilio-ME1 to simultaneously deliver the TET1-catalytic domain and GADD45A (Casilio-ME2) or NEIL2 (Casilio-ME3) to streamline removal of oxidized cytosine intermediates to enhance activation of targeted genes. Using two-in-one effectors or modular effectors, Casilio-ME2 and Casilio-ME3 remarkably boost gene activation and methylcytosine demethylation of targeted loci. We expand the toolbox to enable a stable and expression-inducible system for broader application of the Casilio-ME platforms. This work establishes a platform for editing DNA methylation to enable research investigations interrogating DNA methylomes.
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Affiliation(s)
- Aziz Taghbalout
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Menghan Du
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Nathaniel Jillette
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Wojciech Rosikiewicz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Abhijit Rath
- Center for Molecular Oncology, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Christopher D Heinen
- Center for Molecular Oncology, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Albert W Cheng
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health, 400 Farmington Avenue, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, UConn Health Science Center, 400 Farmington Avenue, Farmington, CT, 06030, USA.
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136
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Court F, Le Boiteux E, Fogli A, Müller-Barthélémy M, Vaurs-Barrière C, Chautard E, Pereira B, Biau J, Kemeny JL, Khalil T, Karayan-Tapon L, Verrelle P, Arnaud P. Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms. Genome Res 2019; 29:1605-1621. [PMID: 31533980 PMCID: PMC6771409 DOI: 10.1101/gr.249219.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylation–dependent and –independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found that most transcriptional alterations in tumor samples were DNA methylation–independent. Instead, altered histone H3 trimethylation at lysine 27 (H3K27me3) was the predominant molecular defect at deregulated genes. Our results also suggest that the presence of a bivalent chromatin signature at CpG island promoters in stem cells predisposes not only to hypermethylation, as widely documented, but more generally to all types of transcriptional alterations in transformed cells. In addition, the gene expression strength in healthy brain cells influences the choice between DNA methylation- and H3K27me3-associated silencing in glioma. Highly expressed genes were more likely to be repressed by H3K27me3 than by DNA methylation. Our findings support a model in which altered H3K27me3 dynamics, more specifically defects in the interplay between polycomb protein complexes and the brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells. Our study provides the first comprehensive description of epigenetic changes in glioma and their relative contribution to transcriptional changes. It may be useful for the design of drugs targeting cancer-related epigenetic defects.
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Affiliation(s)
- Franck Court
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Elisa Le Boiteux
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Anne Fogli
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Mélanie Müller-Barthélémy
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France.,Pathology Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Catherine Vaurs-Barrière
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, Clermont-Ferrand 63011, France.,Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France
| | - Bruno Pereira
- Biostatistics Department, Délégation à la Recherche Clinique et à l'Innovation, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Julian Biau
- Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Jean-Louis Kemeny
- Pathology Department, Université Clermont Auvergne and Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Toufic Khalil
- Department of Neurosurgery, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Lucie Karayan-Tapon
- INSERM, U1084, Poitiers 86021, France.,Poitiers University, Poitiers 86000, France.,Department of Cancer Biology, Poitiers Hospital, Poitiers 86021, France
| | - Pierre Verrelle
- INSERM, U1196 CNRS UMR9187, Curie Institute, Orsay 91405, France.,Radiotherapy Department Curie Institute, Paris 75005, France.,Université Clermont Auvergne, Clermont-Ferrand 63000, France
| | - Philippe Arnaud
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
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137
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The Impact of the Epigenetic Cancer Drug Azacitidine on Host Immunity: The Role of Myelosuppression, Iron Overload and tp53 Mutations in a Zebrafish Model. Cancers (Basel) 2019; 11:cancers11091294. [PMID: 31480804 PMCID: PMC6770285 DOI: 10.3390/cancers11091294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022] Open
Abstract
The unsatisfactory real-world efficacy of the hypomethylating agent azacitidine in treating myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) has prompted us to investigate the hematological adverse events and host variables that may compromise the use of this epigenetic drug. Using the zebrafish, we found that azacitidine destroyed their myeloid precursors and impaired myeloid function by inhibiting antigen processing, allogeneic response and phagocytic activity, resulting in increased susceptibility to infection even by the normal flora E. coli. In addition, iron overload, a MDS-associated condition following repeated transfusions, exacerbated bacterial infection especially by V. vulnificus with known iron dependence. Furthermore, we show that the tp53M214K mutant zebrafish survived longer than the wild-type (WT) when challenged with bacteria following azacitidine treatment. This was attributed to the mutant’s hematopoietic cells rather than its general genetic background, since the WT animals reconstituted with the tp53M214K mutant kidney marrow became more resistant to bacterial infection following treatment with azacitidine. The clinical relevance of our findings was indicated by a MDS case with severe azacitidine-induced bone marrow suppression and by the association of hyperferritinemia with bacteremia in azacitidine-treated patients, while tp53M214K-mediated resistance to azacitidine-induced myelosuppression may explain the survival advantage of malignant MDS and AML clones over their normal counterparts under azacitidine treatment. Together, we propose that myelosuppression, iron overload and TP53 mutations may represent the host variables that compromise the azacitidine efficacy.
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138
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139
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Liu X, Yang H, Wu X, Huang K, Ma P, Jiang P, Zheng W, Tang T, Liu D. Molecular mutation characteristics of mismatch and homologous recombination repair genes in gastrointestinal cancer. Oncol Lett 2019; 18:2789-2798. [PMID: 31452757 PMCID: PMC6676647 DOI: 10.3892/ol.2019.10607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 04/12/2019] [Indexed: 11/05/2022] Open
Abstract
Gastrointestinal cancer is one of the most common types of cancer with high mortality rates. Mutations in several genes are reportedly involved in the progression of gastrointestinal cancer, including tumor protein 53 (TP53), APC regulator of WNT signaling pathway (APC), KRAS proto-oncogene GTPase (KRAS) and erb-b2 receptor tyrosine kinase 2 (ERBB2). Most notably, there are numerous mutations in DNA repair genes, including mismatch repair (MMR) and homologous recombination (HR) genes. The focus of the present study was to investigate the effects of MMR and HR gene mutations on genomic instability in gastrointestinal cancer. Using targeted capture and massively parallel genomic sequencing, 137 gastrointestinal cancer patients were analyzed for somatic single-nucleotide variants (SNVs) and insertion-deletion (indel) mutations in the exon regions of 183 cancer driver genes, including 4 MMR genes [MutL homolog MLH1, MLH2, MLH6 and PMS1 homolog 2, mismatch repair system component (PMS2)] and 15 HR genes [BRCA1 DNA repair associated (BRCA1), BRCA2 DNA repair associated (BRCA2), ATM serine/threonine kinase (ATM), phosphatase and tensin homolog, BLM RecQ like helicase, FA complementation group A, FA complementation group C, FA complementation group D2, FA complementation group E, FA complementation group F, FA complementation group G, nibrin, partner and localizer of BRCA2 and Werner syndrome RecQ like helicase]. A number of frequently mutated genes, including but not limited to, mechanistic target of rapamycin kinase, neurofibromin 1, APC and, in particular, DNA repair genes, including PMS2, ATM and BRCA2, were identified. Frequency analysis was performed based on the SNVs and indels in the 183 genes to indirectly indicate the relative status of genomic instability in each patient. Correlation analysis suggested that MMR and HR gene mutations directly affected the count of SNVs and indels. Overall, 56 of the gastrointestinal cancer patients (40%) were found to have an inactivation mutation (stopgain/frameshift/splicing) in one or more of the four MMR genes, whereas 112 patients (82%) harbored at least one HR gene inactivation mutation. In addition, patients with MMR or HR inactivation variants had more SNVs and indels compared with patients with no such mutations. No other clinical characteristics (including sex and age) appeared to have a statistically significant impact. Further analysis indicated that different MMR or HR genes exerted distinct effects on genomic instability. The results obtained in the current study may lay a foundation for investigations into the tumorigenic process and for the development of novel therapeutic strategies for the treatment of gastrointestinal cancer.
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Affiliation(s)
- Xingcun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Haiping Yang
- First Dimension Biosciences (Suzhou) Co., Ltd., Suzhou, Jiangsu 215126, P.R. China
| | - Xiaohong Wu
- First Dimension Biosciences (Suzhou) Co., Ltd., Suzhou, Jiangsu 215126, P.R. China
| | - Kai Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Paul Ma
- First Dimension Biosciences (Suzhou) Co., Ltd., Suzhou, Jiangsu 215126, P.R. China
| | - Pengpeng Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Weiqing Zheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Tom Tang
- First Dimension Biosciences (Suzhou) Co., Ltd., Suzhou, Jiangsu 215126, P.R. China
| | - Dujuan Liu
- First Dimension Biosciences (Suzhou) Co., Ltd., Suzhou, Jiangsu 215126, P.R. China
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140
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Zhao J, Wang L, Kong D, Hu G, Wei B. Construction of Novel DNA Methylation-Based Prognostic Model to Predict Survival in Glioblastoma. J Comput Biol 2019; 27:718-728. [PMID: 31460783 DOI: 10.1089/cmb.2019.0125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is a most aggressive primary cancer in brain with poor prognosis. This study aimed to identify novel tumor biomarkers with independent prognostic values in GBMs. The DNA methylation profiles were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus database. Differential methylated genes (DMGs) were screened from recurrent GBM samples using limma package in R software. Functional enrichment analysis was performed to identify major biological processes and signaling pathways. Furthermore, critical DMGs associated with the prognosis of GBM were screened according to univariate and multivariate cox regression analysis. A risk score-based prognostic model was constructed for these DMGs and prediction ability of this model was validated in training and validation data set. In total, 495 DMGs were identified between recurrent samples and disease-free samples, including 356 significantly hypermethylated and 139 hypomethylated genes. Functional and pathway items for these DMGs were mainly related to sensory organ development, neuroactive ligand-receptor interaction, pathways in cancer, etc. Five genes with abnormal methylation level were significantly correlated with prognosis according to survival analysis, such as ALX1, KANK1, NUDT12, SNED1, and SVOP. Finally, the risk model provided an effective ability for prognosis prediction both in training and validation data set. We constructed a novel prognostic model for survival prediction of GBMs. In addition, we identified five DMGs as critical prognostic biomarkers in GBM progression.
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Affiliation(s)
- Jingwei Zhao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Le Wang
- Department of Ophthalmology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Daliang Kong
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Guozhang Hu
- Department of Emergency Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Bo Wei
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
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141
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Aberrant DNA methylation defines isoform usage in cancer, with functional implications. PLoS Comput Biol 2019; 15:e1007095. [PMID: 31329578 PMCID: PMC6675117 DOI: 10.1371/journal.pcbi.1007095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 08/01/2019] [Accepted: 05/12/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative transcript isoforms are common in tumors and act as potential drivers of cancer. Mechanisms determining altered isoform expression include somatic mutations in splice regulatory sites or altered splicing factors. However, since DNA methylation is known to regulate transcriptional isoform activity in normal cells, we predicted the highly dysregulated patterns of DNA methylation present in cancer also affect isoform activity. We analyzed DNA methylation and RNA-seq isoform data from 18 human cancer types and found frequent correlations specifically within 11 cancer types. Examining the top 25% of variable methylation sites revealed that the location of the methylated CpG site in a gene determined which isoform was used. In addition, the correlated methylation-isoform patterns classified tumors into known subtypes and predicted distinct protein functions between tumor subtypes. Finally, methylation-correlated isoforms were enriched for oncogenes, tumor suppressors, and cancer-related pathways. These findings provide new insights into the functional impact of dysregulated DNA methylation in cancer and highlight the relationship between the epigenome and transcriptome. In eukaryotes, one gene can be transcribed into multiple RNA sequences (or isoforms) that are subsequently translated into proteins with different functions in response to specific cellular needs. Recent studies showed that cancer cells can obtain abnormal functions via expressing different isoforms. In normal cells, isoform expression can be regulated by DNA methylation–a molecular signature with attached methyl groups on DNA sequences. Given that dysregulation of DNA methylation is a cancer hallmark, we suspect the same regulation holds in cancer and contributes to cancer progression. In this study, we analyzed data from 18 human cancer types and found frequent correlations in 11 cancer types between specific isoform usage and DNA methylation depending on the location of the methylated site in a gene. These correlation patterns can classify heterogeneous tumors in a cancer type into homogeneous subtypes and are predicted to change protein functions via isoform switching between subtypes. Finally, we found cancer-related genes often harbored more DNA methylation-isoform correlations than genes not implicated in cancer. This finding could help us to better understand the functional impact of DNA methylation alterations via regulation of isoform expression in tumorigenesis and to further improve the cancer treatment.
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142
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Xie T, Yu J, Fu W, Wang Z, Xu L, Chang S, Wang E, Zhu F, Zeng S, Kang Y, Hou T. Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study. Phys Chem Chem Phys 2019; 21:12931-12947. [PMID: 31165133 DOI: 10.1039/c9cp02024a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA methyltransferases (DNMTs), responsible for the regulation of DNA methylation, have been regarded as promising drug targets for cancer therapy. However, high structural conservation of the catalytic domains of DNMTs poses a big challenge to design selective inhibitors for a specific DNMT isoform. In this study, molecular dynamics (MD) simulations, end-point free energy calculations and umbrella sampling (US) simulations were performed to reveal the molecular basis of the binding selectivity of three representative DNMT inhibitors towards DNMT1 and DNMT3A, including SFG (DNMT1 and DNMT3A dual inhibitors), DC-05 (DNMT1 selective inhibitor) and GSKex1 (DNMT3A selective inhibitor). The binding selectivity of the studied inhibitors reported in previous experiments is reproduced by the MD simulation and binding free energy prediction. The simulation results also suggest that the driving force to determine the binding selectivity of the studied inhibitors stems from the difference in the protein-inhibitor van der Waals interactions. Meanwhile, the per-residue free energy decomposition reveals that the contributions from several non-conserved residues in the binding pocket of DNMT1/DNMT3A, especially Val1580/Trp893, Asn1578/Arg891 and Met1169/Val665, are the key factors responsible for the binding selectivity of DNMT inhibitors. In addition, the binding preference of the studied inhibitors was further validated by the potentials of mean force predicted by the US simulations. This study will provide valuable information for the rational design of novel selective inhibitors targeting DNMT1 and DNMT3A.
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Affiliation(s)
- Tianli Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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143
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Liang JY, Yang QF, Zeng YL, Liu YY, Liu YT, Gu FF, Hu Y, Zhang K, Zhong H, Liu L. Clinical value of MLH1-negative circulating tumor cells in lung cancer patients. Medicine (Baltimore) 2019; 98:e15721. [PMID: 31232917 PMCID: PMC6636948 DOI: 10.1097/md.0000000000015721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Circulating tumor cells (CTCs) serve as valuable biomarkers. However, MutL homolog 1 (MLH1)-negative CTCs and their clinical significance in lung cancer are nearly unknown.Here, bioinformatic analysis of MLH1 expression and its clinical significance was conducted using the Oncomine, Ualcan, and Kaplan-Meier plotter websites. Size-based isolation and RNA in situ hybridization assays were used to identify CTCs and evaluate MLH1 and mesenchymal marker expression in CTCs. MLH1 was downregulated in lung cancer patients. Patients with lower MLH1 expression levels had worse prognoses. In a cohort of 32 randomly selected patients with lung cancer, the patients with poorer treatment responses had more MLH1-negative CTCs. The total CTCs, MLH1-negative CTCs and mesenchymal markers-expressing CTCs levels were negatively correlated with prognosis in the lung cancer patients.Our data showed the clinical significance of MLH1 expression in lung cancer tissues. The characterization and numeration of CTCs based on the expression of MLH1 and mesenchymal markers may be a convenient approach for predicting treatment response and prognosis in lung cancer.
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Affiliation(s)
- Jin-Yan Liang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Qi-Fan Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Yu-Lan Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Yang-Yang Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Yu-Ting Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Fei-Fei Gu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Yue Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Kai Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Hao Zhong
- Department of Surgery, Changsha Hospital for Maternal and Child Health, Changsha, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
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144
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Kumar P, Gupta P, Gupta N, Rajwanshi A, Rai B, Shalini G. Evaluation of DNA Mismatch Repair Protein Deficiency in Primary Endometrial Carcinoma. J Gynecol Surg 2019. [DOI: 10.1089/gyn.2018.0083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Pankaj Kumar
- Department of Cytology and Gynecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Parikshaa Gupta
- Department of Cytology and Gynecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nalini Gupta
- Department of Cytology and Gynecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arvind Rajwanshi
- Department of Cytology and Gynecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bhavana Rai
- Department of Radiotherapy, and Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Gainder Shalini
- Department of Obstetrics and Gynecology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Ahtiainen M, Wirta EV, Kuopio T, Seppälä T, Rantala J, Mecklin JP, Böhm J. Combined prognostic value of CD274 (PD-L1)/PDCDI (PD-1) expression and immune cell infiltration in colorectal cancer as per mismatch repair status. Mod Pathol 2019; 32:866-883. [PMID: 30723299 DOI: 10.1038/s41379-019-0219-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 01/03/2023]
Abstract
The CD274 (programmed cell death ligand-1, PD-L1)/PDCD1 (programmed cell death-1, PD-1) pathway is crucial suppressor of the cytotoxic immune response. Antibodies targeting CD274 or PDCD1 have been revealed to be effective in several malignancies. In colorectal cancer, the response to CD274/PDCD1 blockage is associated with microsatellite instability. However, the value of CD274/PDCD1 for predicting response to treatment or survival benefit is still unclear. The aims of the study were (1) to clarify differences in immune microenvironment and expression of checkpoint proteins (CD274/PDCD1) in DNA mismatch repair-proficient, mismatch repair-deficient, and hereditary Lynch syndrome-associated colorectal cancer, and (2) to assess the prognostic value of these factors and their combinations. Ninety-four mismatch repair-deficient colorectal cancers, 100 age, sex, and AJCC/UICC stage-matched mismatch repair-proficient colorectal cancers, and 48 Lynch syndrome-associated colorectal cancers were analyzed. Using whole section samples, detailed analysis of immune cell score, PDCD1, and CD274 expression was performed. Overlapping of CD274 expression in tumor and immune cells was almost complete (95%). Immune cell score and CD274/PDCD1 positivity were significantly more frequent in mismatch repair-deficient than in mismatch repair-proficient colorectal cancers (70% vs. 41% (high immune cell score); 81% vs. 49% (PDCD1high), 23% vs. 1% (CD274 on tumor cells) and 68% vs. 30% (CD274 on immune cells), P < 0.001), and were associated strongly with each other. Although the independent impact of immune cell score, PDCD1, and CD274 on immune cells was moderate, the immunoprofile parameter combining the above three factors appeared to be a strong independent prognostic factor for disease-specific survival and overall survival (P = 0.001) and had suggestive impact on disease-free survival (P = 0.011). Our results encourage the use of immune cell score analysis together with PDCD1 and CD274 detection to improve the prognostic evaluation of colorectal cancer patients. Particularly, the analyses from whole tissue sections are encouraged to allow reliable and cell-specific analyses of CD274 expression.
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Affiliation(s)
- Maarit Ahtiainen
- Department of Education and Research, Central Finland Central Hospital, Jyväskylä, Finland.
| | - Erkki-Ville Wirta
- Department of Surgery, Central Finland Central Hospital, Jyväskylä, Finland.,Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Teijo Kuopio
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, Finland.,Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Toni Seppälä
- Department of Gastrointestinal Surgery, Abdominal Center, Helsinki University Hospital, and University of Helsinki, Helsinki, Finland
| | | | - Jukka-Pekka Mecklin
- Department of Education and Research, Central Finland Central Hospital, Jyväskylä, Finland.,Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, Finland
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146
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Batista WR, Santos G, Vital FMR, Matos D. Immunoexpression of TS, p53, COX2, EGFR, MSH6 and MLH1 biomarkers and its correlation with degree of differentiation, tumor staging and prognostic factors in colorectal adenocarcinoma: a retrospective longitudinal study. SAO PAULO MED J 2019; 137:33-38. [PMID: 31116268 PMCID: PMC9721211 DOI: 10.1590/1516-3180.2018.0270071218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/07/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND There are cases of colorectal tumors that, although small, show more aggressive evolution than large tumors. This motivated us to study whether there are any proteins capable of alerting about these changes. The aim here was to correlate the immunoexpression of the TS, p53, COX2, EGFR, MSH6 and MLH1 biomarkers in tumors in patients with colorectal adenocarcinoma, with the degree of cell differentiation, tumor staging and clinical-pathological prognostic factors. DESIGN AND SETTING Retrospective observational study at a public tertiary-level hospital. METHODS We analyzed tissue-microarray paraffin blocks of tumor tissues that had been resected from 107 patients. We used Fisher's exact test to study associations between tumor differentiation/staging and the immunoexpression of biomarkers. We also used Kaplan-Meier estimation, the log-rank test and the adjusted Cox regression model to investigate the patients' overall survival (in months) according to biomarkers and disease-free interval. RESULTS The degree of tumor differentiation and tumor staging were not associated with the biomarkers, except in cases of patients in stages III or IV, in which there was a correlation with MLH1 expression (P=0.021). Patient survival and disease-free interval were not associated with the biomarkers. CONCLUSION There were no associations between the degree of tumor differentiation, staging, length of survival or disease-free interval and the immunoexpression of the TS, p53, COX2, EGFR or MSH6 tumor markers. In advanced cases of colorectal adenocarcinoma (stages III and IV), there was a higher percentage of MLH1-negative results.
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Affiliation(s)
- Wilson Roberto Batista
- MD. Coordinator, Oncological Surgery Sector, Muriaé Cancer Hospital, Muriaé (MG), Brazil, and Doctoral Student, Universidade Federal de São Paulo (UNIFESP), São Paulo (SP), Brazil.
| | - Gianni Santos
- MSc. Statistician, Applied Statistics Sector, Pro-Rectorate for Postgraduate Studies and Research, Universidade Federal de São Paulo (UNIFESP), São Paulo (SP), Brazil.
| | | | - Delcio Matos
- MD, MSc, PhD. Associate Professor, Department of Surgery, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo (SP), Brazil.
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147
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Wong KS, Lorch JH, Alexander EK, Nehs MA, Nowak JA, Hornick JL, Barletta JA. Clinicopathologic Features of Mismatch Repair-Deficient Anaplastic Thyroid Carcinomas. Thyroid 2019; 29:666-673. [PMID: 30869569 DOI: 10.1089/thy.2018.0716] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background: Prior studies have reported mutations in mismatch repair (MMR) genes in a small subset of anaplastic thyroid carcinomas (ATC). The aim of this study was to identify MMR-protein-deficient (MMR-D) ATC and investigate their histopathologic features and clinical outcome. Methods: A cohort of 28 ATC diagnosed between 2003 and 2017 with tissue blocks available were evaluated. Immunohistochemistry for MMR proteins was performed to identify MMR-D tumors. Clinicopathologic features, molecular findings (determined by a targeted next-generation sequencing assay), and clinical outcome data for MMR-D tumors were recorded and compared to that of MMR-protein-intact (MMR-I) tumors. Results: There were four (14%) MMR-D ATC, all of which showed complete loss of MSH2 and MSH6 with intact expression of MLH1 and PMS2. Three of these tumors had MSH2 mutations and a hypermutated phenotype by next-generation sequencing. All four patients (two male; Mage at diagnosis = 64 years) presented with stage IVB disease (i.e., gross extrathyroidal extension or a lymph node metastasis at presentation). There were no differences in tumor size or rates of gross extrathyroidal extension, lymph node metastases, or positive resection margins between MMR-D and MMR-I ATC. Patients with MMR-D tumors were less likely to have distant metastatic disease at presentation (p = 0.035), although half did eventually develop distant metastases. MMR-D tumors were not histologically distinct. All four patients with MMR-D tumors lived for more than one year. One patient died of disease at 15 months, while the remaining three were alive at last follow-up, with survival of 19, 38, and 48 months. Patients with MMR-D ATC had significantly better survival compared to those with MMR-I tumors (p = 0.033), which was maintained when considering only patients with stage IVB disease at presentation (p = 0.030). Conclusion: MMR-D tumors comprised 14% of this ATC cohort. Although the findings must be interpreted with caution given the small number of MMR-D ATC in the cohort, the results suggest that MMR status may be prognostically significant in ATC.
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Affiliation(s)
- Kristine S Wong
- 1 Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jochen H Lorch
- 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Erik K Alexander
- 3 Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Nehs
- 4 Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- 1 Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jason L Hornick
- 1 Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Justine A Barletta
- 1 Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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148
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Kaina B, Christmann M. DNA repair in personalized brain cancer therapy with temozolomide and nitrosoureas. DNA Repair (Amst) 2019; 78:128-141. [PMID: 31039537 DOI: 10.1016/j.dnarep.2019.04.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/11/2019] [Accepted: 04/14/2019] [Indexed: 12/16/2022]
Abstract
Alkylating agents have been used since the 60ties in brain cancer chemotherapy. Their target is the DNA and, although the DNA of normal and cancer cells is damaged unselectively, they exert tumor-specific killing effects because of downregulation of some DNA repair activities in cancer cells. Agents exhibiting methylating properties (temozolomide, procarbazine, dacarbazine, streptozotocine) induce at least 12 different DNA lesions. These are repaired by damage reversal mechanisms involving the alkyltransferase MGMT and the alkB homologous protein ALKBH2, and through base excision repair (BER). There is a strong correlation between the MGMT expression level and therapeutic response in high-grade malignant glioma, supporting the notion that O6-methylguanine and, for nitrosoureas, O6-chloroethylguanine are the most relevant toxic damages at therapeutically relevant doses. Since MGMT has a significant impact on the outcome of anti-cancer therapy, it is a predictive marker of the effectiveness of methylating anticancer drugs, and clinical trials are underway aimed at assessing the influence of MGMT inhibition on the therapeutic success. Other DNA repair factors involved in methylating drug resistance are mismatch repair, DNA double-strand break (DSB) repair by homologous recombination (HR) and DSB signaling. Base excision repair and ALKBH2 might also contribute to alkylating drug resistance and their downregulation may have an impact on drug sensitivity notably in cells expressing a high amount of MGMT and at high doses of temozolomide, but the importance in a therapeutic setting remains to be shown. MGMT is frequently downregulated in cancer cells (up to 40% in glioblastomas), which is due to CpG promoter methylation. Astrocytoma (grade III) are frequently mutated in isocitrate dehydrogenase (IDH1). These tumors show a surprisingly good therapeutic response. IDH1 mutation has an impact on ALKBH2 activity thus influencing DNA repair. A master switch between survival and death is p53, which often retains transactivation activity (wildtype) in malignant glioma. The role of p53 in regulating survival via DNA repair and the routes of death are discussed and conclusions as to cancer therapeutic options were drawn.
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Affiliation(s)
- Bernd Kaina
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
| | - Markus Christmann
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
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149
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Fennell L, Dumenil T, Wockner L, Hartel G, Nones K, Bond C, Borowsky J, Liu C, McKeone D, Bowdler L, Montgomery G, Klein K, Hoffmann I, Patch AM, Kazakoff S, Pearson J, Waddell N, Wirapati P, Lochhead P, Imamura Y, Ogino S, Shao R, Tejpar S, Leggett B, Whitehall V. Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals 5 Distinct Subtypes of Colorectal Adenocarcinomas. Cell Mol Gastroenterol Hepatol 2019; 8:269-290. [PMID: 30954552 PMCID: PMC6699251 DOI: 10.1016/j.jcmgh.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer is an epigenetically heterogeneous disease, however, the extent and spectrum of the CpG island methylator phenotype (CIMP) is not clear. METHODS Genome-scale methylation and transcript expression were measured by DNA Methylation and RNA expression microarray in 216 unselected colorectal cancers, and findings were validated using The Cancer Genome Atlas 450K and RNA sequencing data. Mutations in epigenetic regulators were assessed using CIMP-subtyped Cancer Genome Atlas exomes. RESULTS CIMP-high cancers dichotomized into CIMP-H1 and CIMP-H2 based on methylation profile. KRAS mutation was associated significantly with CIMP-H2 cancers, but not CIMP-H1 cancers. Congruent with increasing methylation, there was a stepwise increase in patient age from 62 years in the CIMP-negative subgroup to 75 years in the CIMP-H1 subgroup (P < .0001). CIMP-H1 predominantly comprised consensus molecular subtype 1 cancers (70%) whereas consensus molecular subtype 3 was over-represented in the CIMP-H2 subgroup (55%). Polycomb Repressive Complex-2 (PRC2)-marked loci were subjected to significant gene body methylation in CIMP cancers (P < 1.6 × 10-78). We identified oncogenes susceptible to gene body methylation and Wnt pathway antagonists resistant to gene body methylation. CIMP cluster-specific mutations were observed in chromatin remodeling genes, such as in the SWItch/Sucrose Non-Fermentable and Chromodomain Helicase DNA-Binding gene families. CONCLUSIONS There are 5 clinically and molecularly distinct subgroups of colorectal cancer. We show a striking association between CIMP and age, sex, and tumor location, and identify a role for gene body methylation in the progression of serrated neoplasia. These data support our recent findings that CIMP is uncommon in young patients and that BRAF mutant polyps in young patients may have limited potential for malignant progression.
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Affiliation(s)
- Lochlan Fennell
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia,School of Sports and Health Science, University of the Sunshine Coast, Queensland, Australia,Correspondence Address correspondence to: Lochlan Fennell, BSc, Level 7 Clive Berghofer Cancer Research Centre, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006 Australia. fax: +617 3362 0101.
| | - Troy Dumenil
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Leesa Wockner
- Statistics Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Gunter Hartel
- Statistics Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Katia Nones
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Catherine Bond
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Jennifer Borowsky
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Cheng Liu
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Diane McKeone
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Lisa Bowdler
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Grant Montgomery
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Kerenaftali Klein
- Statistics Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Isabell Hoffmann
- Institute of Medical Biostatistics, Epidemiology and Informatics, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Ann-Marie Patch
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Stephen Kazakoff
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - John Pearson
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Pratyaksha Wirapati
- Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland
| | - Paul Lochhead
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Tokyo, Japan
| | - Shuji Ogino
- Dana-Farber Cancer Institute, Boston, Massachusetts,Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Renfu Shao
- School of Sports and Health Science, University of the Sunshine Coast, Queensland, Australia
| | - Sabine Tejpar
- Digestive Oncology Unit, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Leggett
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia,School of Medicine, University of Queensland, Queensland, Australia,Department of Gastroenterology and Hepatology, Royal Brisbane and Women’s Hospital, Queensland, Australia
| | - Vicki Whitehall
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia,School of Medicine, University of Queensland, Queensland, Australia,Chemical Pathology Department, Pathology Queensland, Queensland, Australia
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150
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Gupta D, Heinen CD. The mismatch repair-dependent DNA damage response: Mechanisms and implications. DNA Repair (Amst) 2019; 78:60-69. [PMID: 30959407 DOI: 10.1016/j.dnarep.2019.03.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/25/2019] [Accepted: 03/16/2019] [Indexed: 12/22/2022]
Abstract
An important role for the DNA mismatch repair (MMR) pathway in maintaining genomic stability is embodied in its conservation through evolution and the link between loss of MMR function and tumorigenesis. The latter is evident as inheritance of mutations within the major MMR genes give rise to the cancer predisposition condition, Lynch syndrome. Nonetheless, how MMR loss contributes to tumorigenesis is not completely understood. In addition to preventing the accumulation of mutations, MMR also directs cellular responses, such as cell cycle checkpoint or apoptosis activation, to different forms of DNA damage. Understanding this MMR-dependent DNA damage response may provide insight into the full tumor suppressing capabilities of the MMR pathway. Here, we delve into the proposed mechanisms for the MMR-dependent response to DNA damaging agents. We discuss how these pre-clinical findings extend to the clinical treatment of cancers, emphasizing MMR status as a crucial variable in selection of chemotherapeutic regimens. Also, we discuss how loss of the MMR-dependent damage response could promote tumorigenesis via the establishment of a survival advantage to endogenous levels of stress in MMR-deficient cells.
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Affiliation(s)
- Dipika Gupta
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030, USA
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