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Boonsanay V, Mosa MH, Looso M, Weichenhan D, Ceteci F, Pudelko L, Lechel A, Michel CS, Künne C, Farin HF, Plass C, Greten FR. Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression. Gastroenterology 2023; 164:214-227. [PMID: 36402192 PMCID: PMC9889219 DOI: 10.1053/j.gastro.2022.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND & AIMS Epigenetic processes regulating gene expression contribute markedly to epithelial cell plasticity in colorectal carcinogenesis. The lysine methyltransferase SUV420H2 comprises an important regulator of epithelial plasticity and is primarily responsible for trimethylation of H4K20 (H4K20me3). Loss of H4K20me3 has been suggested as a hallmark of human cancer due to its interaction with DNMT1. However, the role of Suv4-20h2 in colorectal cancer is unknown. METHODS We examined the alterations in histone modifications in patient-derived colorectal cancer organoids. Patient-derived colorectal cancer organoids and mouse intestinal organoids were genetically manipulated for functional studies in patient-derived xenograft and orthotopic transplantation. Gene expression profiling, micrococcal nuclease assay, and chromatin immunoprecipitation were performed to understand epigenetic regulation of chromatin states and gene expression in patient-derived and mouse intestinal organoids. RESULTS We found that reduced H4K20me3 levels occurred predominantly in right-sided patient-derived colorectal cancer organoids, which were associated with increased chromatin accessibility. Re-compaction of chromatin by methylstat, a histone demethylase inhibitor, resulted in reduced growth selectively in subcutaneously grown tumors derived from right-sided cancers. Using mouse intestinal organoids, we confirmed that Suv4-20h2-mediated H4K20me3 is required for maintaining heterochromatin compaction and to prevent R-loop formation. Cross-species comparison of Suv4-20h2-depleted murine organoids with right-sided colorectal cancer organoids revealed a large overlap of gene signatures involved in chromatin silencing, DNA methylation, and stemness/Wnt signaling. CONCLUSIONS Loss of Suv4-20h2-mediated H4K20me3 drives right-sided colorectal tumorigenesis through an epigenetically controlled mechanism of chromatin compaction. Our findings unravel a conceptually novel approach for subtype-specific therapy of this aggressive form of colorectal cancer.
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Affiliation(s)
- Verawan Boonsanay
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mohammed H. Mosa
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mario Looso
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Fatih Ceteci
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lorenz Pudelko
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Andre Lechel
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Christian S. Michel
- Department of Hematology, Medical Oncology, and Pneumology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Carsten Künne
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany,Correspondence Address correspondence to: Florian R. Greten, MD, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, 60596 Frankfurt am Main, Germany.
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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Lorzadeh A, Romero-Wolf M, Goel A, Jadhav U. Epigenetic Regulation of Intestinal Stem Cells and Disease: A Balancing Act of DNA and Histone Methylation. Gastroenterology 2021; 160:2267-2282. [PMID: 33775639 PMCID: PMC8169626 DOI: 10.1053/j.gastro.2021.03.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
Genetic mutations or regulatory failures underlie cellular malfunction in many diseases, including colorectal cancer and inflammatory bowel diseases. However, mutational defects alone fail to explain the complexity of such disorders. Epigenetic regulation-control of gene action through chemical and structural changes of chromatin-provides a platform to integrate multiple extracellular inputs and prepares the cellular genome for appropriate gene expression responses. Coregulation by polycomb repressive complex 2-mediated trimethylation of lysine 27 on histone 3 and DNA methylation has emerged as one of the most influential epigenetic controls in colorectal cancer and many other diseases, but molecular details remain inadequate. Here we review the molecular interplay of these epigenetic features in relation to gastrointestinal development, homeostasis, and disease biology. We discuss other epigenetic mechanisms pertinent to the balance of trimethylation of lysine 27 on histone 3 and DNA methylation and their actions in gastrointestinal cancers. We also review the current molecular understanding of chromatin control in the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maile Romero-Wolf
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Unmesh Jadhav
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.
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Akimoto N, Zhao M, Ugai T, Zhong R, Lau MC, Fujiyoshi K, Kishikawa J, Haruki K, Arima K, Twombly TS, Zhang X, Giovannucci EL, Wu K, Song M, Chan AT, Cao Y, Meyerhardt JA, Ng K, Giannakis M, Väyrynen JP, Nowak JA, Ogino S. Tumor Long Interspersed Nucleotide Element-1 (LINE-1) Hypomethylation in Relation to Age of Colorectal Cancer Diagnosis and Prognosis. Cancers (Basel) 2021; 13:2016. [PMID: 33922024 PMCID: PMC8122644 DOI: 10.3390/cancers13092016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 12/12/2022] Open
Abstract
Evidence indicates the pathogenic role of epigenetic alterations in early-onset colorectal cancers diagnosed before age 50. However, features of colorectal cancers diagnosed at age 50-54 (hereafter referred to as "intermediate-onset") remain less known. We hypothesized that tumor long interspersed nucleotide element-1 (LINE-1) hypomethylation might be increasingly more common with decreasing age of colorectal cancer diagnosis. In 1356 colorectal cancers, including 28 early-onset and 66 intermediate-onset cases, the tumor LINE-1 methylation level measured by bisulfite-PCR-pyrosequencing (scaled 0 to 100) showed a mean of 63.6 (standard deviation (SD) 10.1). The mean tumor LINE-1 methylation level decreased with decreasing age (mean 64.7 (SD 10.4) in age ≥70, 62.8 (SD 9.4) in age 55-69, 61.0 (SD 10.2) in age 50-54, and 58.9 (SD 12.0) in age <50; p < 0.0001). In linear regression analysis, the multivariable-adjusted β coefficient (95% confidence interval (CI)) (vs. age ≥70) was -1.38 (-2.47 to -0.30) for age 55-69, -2.82 (-5.29 to -0.34) for age 50-54, and -4.54 (-8.24 to -0.85) for age <50 (Ptrend = 0.0003). Multivariable-adjusted hazard ratios (95% CI) for LINE-1 methylation levels of ≤45, 45-55, and 55-65 (vs. >65) were 2.33 (1.49-3.64), 1.39 (1.05-1.85), and 1.29 (1.02-1.63), respectively (Ptrend = 0.0005). In conclusion, tumor LINE-1 hypomethylation is increasingly more common with decreasing age of colorectal cancer diagnosis, suggesting a role of global DNA hypomethylation in colorectal cancer arising in younger adults.
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Affiliation(s)
- Naohiko Akimoto
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
- Department of Gastroenterology, Nippon Medical School, Graduate School of Medicine, Tokyo 1138602, Japan
| | - Melissa Zhao
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Tomotaka Ugai
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA; (E.L.G.); (K.W.)
| | - Rong Zhong
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA; (E.L.G.); (K.W.)
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mai Chan Lau
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Kenji Fujiyoshi
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Junko Kishikawa
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Koichiro Haruki
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Kota Arima
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Tyler S. Twombly
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (X.Z.); (A.T.C.)
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
| | - Edward L. Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA; (E.L.G.); (K.W.)
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (X.Z.); (A.T.C.)
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
| | - Kana Wu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA; (E.L.G.); (K.W.)
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (X.Z.); (A.T.C.)
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew T. Chan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (X.Z.); (A.T.C.)
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA;
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey A. Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; (J.A.M.); (K.N.); (M.G.)
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; (J.A.M.); (K.N.); (M.G.)
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; (J.A.M.); (K.N.); (M.G.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Juha P. Väyrynen
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; (J.A.M.); (K.N.); (M.G.)
- Cancer and Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90220 Oulu, Finland
| | - Jonathan A. Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
| | - Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (N.A.); (M.Z.); (T.U.); (R.Z.); (M.C.L.); (K.F.); (J.K.); (K.H.); (K.A.); (T.S.T.); (J.A.N.)
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA; (E.L.G.); (K.W.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Cancer Immunology and Cancer Epidemiology Programs, Dana-Farber Harvard Cancer Center, Boston, MA 02215, USA
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Impact of Tumor LINE-1 Methylation Level and Neoadjuvant Treatment and Its Association with Colorectal Cancer Survival. J Pers Med 2020; 10:jpm10040219. [PMID: 33187096 PMCID: PMC7712476 DOI: 10.3390/jpm10040219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Recent studies suggest that long-interspersed nucleotide element-1 (LINE-1) hypomethylation is commonly found in colorectal cancer (CRC), and is associated with worse prognosis. However, the utility of LINE-1 methylation on the prognosis of CRC is still controversial, and may be due to the fact that some clinical and pathological features may affect LINE-1 methylation. Thus, the aim of this study was to assess the prognostic value of tumor LINE-1 methylation in CRC, through their association with the CRC clinical and pathological characteristics. Survival of sixty-seven CRC patients was evaluated according to the median of tumor LINE-1 methylation, as well as pathological and oncological variables. We also studied the association between LINE-1 methylation and pathological features, and finally, we assessed the overall and disease-free survival of LINE1 methylation, stratified by neoadjuvant treatment and further checked by multivariate Cox regression to assess the statistical interactions. LINE-1 was hypomethylated in the CRC tumor with respect to the tumor adjacent-free area (p < 0.05), without association with any other clinical and oncological features, nor with overall and disease-free survival rates for CRC. Relevantly, in neoadjuvant treatment, LINE-1 methylation was associated with survival rates. Thus, disease-free and overall survival rates of treated CRC patients were worse in the hypomethylated LINE-1 tumors than those with normal LINE-1 methylation (p = 0.004 and 0.0049, respectively). Indeed, LINE-1 was hypermethylated more in the treated patients than in the non-treated patients (p < 0.05). The present study showed that tumor LINE-1 hypomethylation was associated with worse survival rates in only treated patients. Our data suggest an interactive effect of neoadjuvant treatment and tumor LINE-1 methylation, which could be a specific-tissue biomarker to predict survival of the treated patients, and help to personalize treatment in CRC.
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Kim Y, Rhee YY, Wen X, Cho NY, Bae JM, Kim WH, Kang GH. Combination of L1 methylation and tumor-infiltrating lymphocytes as prognostic marker in advanced gastric cancer. Gastric Cancer 2020; 23:464-472. [PMID: 31691036 DOI: 10.1007/s10120-019-01025-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 10/18/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND High density of tumor-infiltrating lymphocyte (TIL) is known to be associated with prolonged survival time, whereas tumoral-L1 hypomethylation has been associated with shortened survival time in patients with gastric cancer (GC). Since L1-methylation level is high in lymphocytes, higher density of TIL could lead to higher measurement of L1-methylation level in cancer tissues which contain cancer cells as well as non-neoplastic cells, including TIL. Putative interaction of TIL in the relationship between L1-methylation level and survival led us to explore combinatory statuses of tumoral-L1-methylation level and TIL density as a prognostic marker in GC. METHODS TIL and tumoral-L1-methylation level were measured in advanced GC samples (n = 491), using CD3 immunohistochemistry and pyrosequencing-methylation analysis, respectively. TIL density was measured in tumor center and invasive front areas. RESULTS TIL density correlated with tumoral-L1-methylation level but the relationship was weak. Combinatory statuses of L1-methylation level and CD3 TIL density were found to be statistically significant in survival analysis. Multivariate analysis revealed that the relationship between combinatory statuses and survival was independent. Prognostic value of the combinatory statuses at invasive front was significant in an independent set. CONCLUSIONS Our findings indicate that tumoral-L1-methylation level is correlated with TIL density and that combinatory statuses might help to find a subset of GCs with worse clinical outcome in GCs with low-L1-methylation status or a subset of GCs with better clinical outcome in GCs with high-L1-methylation status.
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Affiliation(s)
- Younghoon Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ye-Young Rhee
- Pathology Center, Seegene Medical Foundation, Seoul, Korea
| | - Xianyu Wen
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea. .,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
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Advani SM, Advani PS, Brown DW, DeSantis SM, Korphaisarn K, VonVille HM, Bressler J, Lopez DS, Davis JS, Daniel CR, Sarshekeh AM, Braithwaite D, Swartz MD, Kopetz S. Global differences in the prevalence of the CpG island methylator phenotype of colorectal cancer. BMC Cancer 2019; 19:964. [PMID: 31623592 PMCID: PMC6796359 DOI: 10.1186/s12885-019-6144-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background CpG Island Methylator Phenotype (CIMP) is an epigenetic phenotype in CRC characterized by hypermethylation of CpG islands in promoter regions of tumor suppressor genes, leading to their transcriptional silencing and loss of function. While the prevalence of CRC differs across geographical regions, no studies have compared prevalence of CIMP-High phenotype across regions. The purpose of this project was to compare the prevalence of CIMP across geographical regions after adjusting for variations in methodologies to measure CIMP in a meta-analysis. Methods We searched PubMed, Medline, and Embase for articles focusing on CIMP published from 2000 to 2018. Two reviewers independently identified 111 articles to be included in final meta-analysis. We classified methods used to quantify CIMP into 4 categories: a) Classical (MINT marker) Panel group b) Weisenberg-Ogino (W-O) group c) Human Methylation Arrays group and d) Miscellaneous group. We compared the prevalence of CIMP across geographical regions after correcting for methodological variations using meta-regression techniques. Results The pooled prevalence of CIMP-High across all studies was 22% (95% confidence interval:21–24%; I2 = 94.75%). Pooled prevalence of CIMP-H across Asia, Australia, Europe, North America and South America was 22, 21, 21, 27 and 25%, respectively. Meta-regression analysis identified no significant differences in the prevalence of CIMP-H across geographical regions after correction for methodological variations. In exploratory analysis, we observed variations in CIMP-H prevalence across countries. Conclusion Although no differences were found for CIMP-H prevalence across countries, further studies are needed to compare the influence of demographic, lifestyle and environmental factors in relation to the prevalence of CIMP across geographical regions.
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Affiliation(s)
- Shailesh Mahesh Advani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA. .,Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20007, USA. .,Social Behavioral Research Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, 20892, USA.
| | - Pragati Shailesh Advani
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Institutes of Health, National Cancer Institute, Rockville, MD, 20850, USA
| | - Derek W Brown
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Stacia M DeSantis
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Krittiya Korphaisarn
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA
| | - Helena M VonVille
- Library, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jan Bressler
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - David S Lopez
- Division of Urology- UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Department of Preventive Medicine and Community Health, UTMB Health-School of Medicine, Galveston, TX, 77555-1153, USA
| | - Jennifer S Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carrie R Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Amir Mehrvarz Sarshekeh
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA
| | - Dejana Braithwaite
- Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20007, USA
| | - Michael D Swartz
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA.
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8
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Wang T, McCullough LE, White AJ, Bradshaw PT, Xu X, Cho YH, Terry MB, Teitelbaum SL, Neugut AI, Santella RM, Chen J, Gammon MD. Prediagnosis aspirin use, DNA methylation, and mortality after breast cancer: A population-based study. Cancer 2019; 125:3836-3844. [PMID: 31402456 DOI: 10.1002/cncr.32364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/20/2018] [Accepted: 01/07/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The authors hypothesized that epigenetic changes may help to clarify the underlying biologic mechanism linking aspirin use to breast cancer prognosis. To the authors' knowledge, this is the first epidemiologic study to examine whether global methylation and/or tumor promoter methylation of breast cancer-related genes interact with aspirin use to impact mortality after breast cancer. METHODS Prediagnosis aspirin use was assessed through in-person interviews within a population-based cohort of 1508 women diagnosed with a first primary breast cancer in 1996 and 1997. Global methylation in peripheral blood was assessed by long interspersed elements-1 (LINE-1) and the luminometric methylation assay. Promoter methylation of 13 breast cancer-related genes was measured in tumor by methylation-specific polymerase chain reaction and the MethyLight assay. Vital status was determined by the National Death Index through December 31, 2014 (N = 202/476 breast cancer-specific/all-cause deaths identified among 1266 women with any methylation assessment and complete aspirin data). Cox proportional hazards regression was used to estimate hazard ratios (HRs) and 95% CIs, and the likelihood ratio test was used to evaluate multiplicative interactions. RESULTS All-cause mortality was elevated among aspirin users who had methylated promotor of BRCA1 (HR, 1.67; 95% CI, 1.26-2.22), but not among those with unmethylated promoter of BRCA1 (HR, 0.99; 95% CI, 0.67-1.45; P for interaction ≤.05). Decreased breast cancer-specific mortality was observed among aspirin users who had unmethylated promotor of BRCA1 and PR and global hypermethylation of LINE-1 (HR, 0.60, 0.78, and 0.63, respectively; P for interaction ≤.05), although the 95% CIs included the null. CONCLUSIONS The current study suggests that the LINE-1 global methylation and promoter methylation of BRCA1 and PR in tumor may interact with aspirin use to influence mortality after breast cancer.
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Affiliation(s)
- Tengteng Wang
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | | | - Alexandra J White
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Patrick T Bradshaw
- Division of Epidemiology, University of California, Berkeley, California
| | - Xinran Xu
- Department of Biometrics, Roche Product Development in Asia-Pacific, Shanghai, China
| | - Yoon Hee Cho
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, New York
| | - Susan L Teitelbaum
- Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alfred I Neugut
- Department of Epidemiology, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
| | | | - Jia Chen
- Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
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9
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Zhang Y, Niu Q, Fan W, Huang F, He H. Oral microbiota and gastrointestinal cancer. Onco Targets Ther 2019; 12:4721-4728. [PMID: 31417273 PMCID: PMC6592037 DOI: 10.2147/ott.s194153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/12/2019] [Indexed: 12/16/2022] Open
Abstract
The microbiota inhabiting the oral cavity is a complex ecosystem and responsible for resisting pathogens, maintaining homeostasis, and modulating the immune system. Some components of the oral microbiota contribute to the etiology of some oral diseases. Accumulating evidence suggests that the human oral microbiota is implicated in the development and progression of gastrointestinal cancer. In this review, we described the current understanding of possible roles and mechanisms of oral microbiota in the gastrointestinal cancers studied to date. The perspectives for oral microbiota as the biomarkers for early detection and new therapeutic targets were also discussed.
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Affiliation(s)
- Yangyang Zhang
- Guanghua School of Stomatology, Institute of Stomatological Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, People’s Republic of China
- The Oral Medicine Clinical Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Qiaoli Niu
- The Oral Medicine Clinical Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Wenguo Fan
- Guanghua School of Stomatology, Institute of Stomatological Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Fang Huang
- Guanghua School of Stomatology, Institute of Stomatological Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Hongwen He
- Guanghua School of Stomatology, Institute of Stomatological Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, People’s Republic of China
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10
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Rozek LS, Virani S, Bellile EL, Taylor JMG, Sartor MA, Zarins KR, Virani A, Cote C, Worden FP, Mark MEP, McLean SA, Duffy SA, Yoo GH, Saba NF, Shin DM, Kucuk O, Wolf GT. Soy Isoflavone Supplementation Increases Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Head and Neck Squamous Cell Carcinoma. Nutr Cancer 2019; 71:772-780. [PMID: 30862188 PMCID: PMC6513708 DOI: 10.1080/01635581.2019.1577981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/13/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022]
Abstract
AIM Soy isoflavones have been suggested as epigenetic modulating agents with effects that could be important in carcinogenesis. Hypomethylation of LINE-1 has been associated with head and neck squamous cell carcinoma (HNSCC) development from oral premalignant lesions and with poor prognosis. To determine if neoadjuvant soy isoflavone supplementation could modulate LINE-1 methylation in HNSCC, we undertook a clinical trial. METHODS Thirty-nine patients received 2-3 weeks of soy isoflavone supplements (300 mg/day) orally prior to surgery. Methylation of LINE-1, and 6 other genes was measured by pyrosequencing in biopsy, resection, and whole blood (WB) specimens. Changes in methylation were tested using paired t tests and ANOVA. Median follow up was 45 months. RESULTS LINE-1 methylation increased significantly after soy isoflavone (P < 0.005). Amount of change correlated positively with days of isoflavone taken (P = 0.04). Similar changes were not seen in corresponding WB samples. No significant changes in tumor or blood methylation levels were seen in the other candidate genes. CONCLUSION This is the first demonstration of in vivo increases in tissue-specific global methylation associated with soy isoflavone intake in patients with HNSCC. Prior associations of LINE-1 hypomethylation with genetic instability, carcinogenesis, and prognosis suggest that soy isoflavones maybe potential chemopreventive agents in HNSCC.
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Affiliation(s)
- Laura S Rozek
- a University of Michigan , Ann Arbor , Michigan, USA
| | - Shama Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - A Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | - C Cote
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - George H Yoo
- c Karmanos Cancer Institute , Wayne State University , Detroit , Michigan 48201, USA
| | - Nabil F Saba
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Dong M Shin
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Omer Kucuk
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
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11
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Fouad MA, Salem SE, Hussein MM, Zekri ARN, Hafez HF, El Desouky ED, Shouman SA. Impact of Global DNA Methylation in Treatment Outcome of Colorectal Cancer Patients. Front Pharmacol 2018; 9:1173. [PMID: 30405408 PMCID: PMC6201055 DOI: 10.3389/fphar.2018.01173] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
Background: Global DNA methylation has an impact in cancer pathogenesis and progression. This study aimed at investigating the impact of global DNA methylation in treatment outcome of Colorectal Cancer (CRC). Patients and Methods: Global DNA methylation was measured by LC/MS/MS in peripheral blood leucocytes of 102, 48, and 32 Egyptian CRC patients at baseline and after 3 and 6 months of Fluoropyrimidine (FP) therapy respectively, in addition to 32 normal healthy matched in age and sex. The genetic expressions of DNA methyl transferases (DNMTs) were determined and correlated with patients‘ survival using univariate and multivariate methods of analyses. Results: Egyptian CRC patients had significant global hypomethylation of 5mC level and 5mC % with overexpression of DNMT3A and DNMT3B. Significant higher 5mC levels were shown in patients > 45 years, male gender, T2 tumors, stage II, negative lymph nodes, and absence of metastasis. FP therapy significantly reduced DNA methylation particularly in the subgroups of patients with high DNA methylation level at baseline and good prognostic features. After 3 years of follow up, patients with 5mC % > 8.02% had significant poor overall survival (OS) while, significant better event-free survival (EFS) was found in patients with 5mC level > 0.55. High initial CEA level and presence of metastasis were significantly associated with hazards of disease progression and death. Conclusion: Global DNA methylation has a significant impact on the treatment outcome and survival of Egyptian CRC patients treated with FP- based therapy.
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Affiliation(s)
- Mariam A Fouad
- Pharmacology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Salem E Salem
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa M Hussein
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdel Rahman N Zekri
- Virology and Immunology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hafez F Hafez
- Pharmacology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Eman D El Desouky
- Department of Biostatistics and Epidemiology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Samia A Shouman
- Pharmacology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
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12
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Molnár B, Galamb O, Péterfia B, Wichmann B, Csabai I, Bodor A, Kalmár A, Szigeti KA, Barták BK, Nagy ZB, Valcz G, Patai ÁV, Igaz P, Tulassay Z. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer 2018; 18:695. [PMID: 29945573 PMCID: PMC6020382 DOI: 10.1186/s12885-018-4609-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome methylation and targeted mutation analysis of colorectal cancer (CRC)-related genes and mRNA expression analysis of TP53 pathway genes. Methods Long interspersed nuclear element-1 (LINE-1) BS-PCR followed by pyrosequencing was performed for the estimation of global DNA metlyation levels along the colorectal normal-adenoma-carcinoma sequence. Methyl capture sequencing was done on 6 normal adjacent (NAT), 15 adenomatous (AD) and 9 CRC tissues. Overall quantitative methylation analysis, selection of top hyper/hypomethylated genes, methylation analysis on mutation regions and TP53 pathway gene promoters were performed. Mutations of 12 CRC-related genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53) were evaluated. mRNA expression of TP53 pathway genes was also analyzed. Results According to the LINE-1 methylation results, overall hypomethylation was observed along the normal-adenoma-carcinoma sequence. Within top50 differential methylated regions (DMRs), in AD-N comparison TP73, NGFR, PDGFRA genes were hypermethylated, FMN1, SLC16A7 genes were hypomethylated. In CRC-N comparison DKK2, SDC2, SOX1 genes showed hypermethylation, while ERBB4, CREB5, CNTN1 genes were hypomethylated. In certain mutation hot spot regions significant DNA methylation alterations were detected. The TP53 gene body was addressed by hypermethylation in adenomas. APC, TP53 and KRAS mutations were found in 30, 15, 21% of adenomas, and in 29, 53, 29% of CRCs, respectively. mRNA expression changes were observed in several TP53 pathway genes showing promoter methylation alterations. Conclusions DNA methylation with consecutive phenotypic effect can be observed in a high number of promoter and gene body regions through CRC development. Electronic supplementary material The online version of this article (10.1186/s12885-018-4609-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary. .,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.,Institute of Mathematics and Informatics, Faculty of Sciences, University of Pécs, Ifjúság útja 6, Pécs, H-7624, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Krisztina Andrea Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
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13
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Early onset sporadic colorectal cancer: Worrisome trends and oncogenic features. Dig Liver Dis 2018; 50:521-532. [PMID: 29615301 DOI: 10.1016/j.dld.2018.02.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 02/07/2023]
Abstract
Early onset colorectal cancers, defined as arising before 50 years of age, are a growing health hazard in western and eastern countries alike. The incidence of colon and rectal cancers in young individuals is projected to increase by as much as 90% and 140%, respectively, by 2030. Although several known cancer risk factors (e.g. smoking, alcohol, dietary habits) have been investigated, there is no single compelling explanation for this epidemiological trend. While some early onset colorectal cancers have been associated with germline mutations in cancer predisposition genes, genetic syndromes are implicated in only a fraction of these cancers (20%) and do not explain the rising incidence. Colorectal neoplasms develop through microsatellite instability or chromosomal instability pathways, with most of the early onset colorectal cancers exhibiting microsatellite stable phenotypes. Genome-wide hypomethylation is a feature of a subgroup of early onset cancers, which appears to be correlated with chromosomal instability and poor prognosis.
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14
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Kuan TC, Lin PC, Yang SH, Lin CC, Lan YT, Lin HH, Liang WY, Chen WS, Lin JK, Jiang JK, Chang SC. Impact of LINE-1 hypomethylation on the clinicopathological and molecular features of colorectal cancer patients. PLoS One 2018; 13:e0197681. [PMID: 29795620 PMCID: PMC5993106 DOI: 10.1371/journal.pone.0197681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/07/2018] [Indexed: 12/17/2022] Open
Abstract
Recent studies suggest that aberrant DNA methylation might occur early and commonly in colorectal tumorigenesis. In 111 normal subjects, the mean LINE-1 methylation level of peripheral blood was 81.0 ± 5.7%. Of 143 colorectal cancer (CRC) patients, the mean level of LINE-1 methylation was 60.5 ± 12.5%. We defined below 60% as cut-off value of LINE-1 hypomethylation, and 93 cases (65.0%) had LINE-1 hypomethylation in the tumor tissue. LINE-1 hypomethylation was not associated with any other clinical features. There was a trend that LINE-1 hypomethylation tumors were associated with advanced disease, but it did not reach statistical significance. There was no significant association between mutations of 12 genes, MSI-high, EMAST, and LINE-1 hypomethylation level. The median follow-up was 61.2 months. Five-year disease-free survival (DFS) and overall survival curves of patients with LINE-1 hypomethylation tumors were significantly lower than those of patients with normal LINE-1 methylation tumors (p = 0.032 and 0.001, respectively). Multivariate analysis showed that only TNM staging was an independent prognostic factor for CRC patients including DFS and overall survival (OS). LINE-1 did not impact patients' outcomes in multivariate analysis including DFS and OS. In conclusion, LINE-1 hypomethylation is marginally related to advanced stage CRC and impacts patients' outcomes in univariate analysis.
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Affiliation(s)
- Tai-Chuan Kuan
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Pei-Ching Lin
- Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan
- Department of Health and Welfare, University of Taipei, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Chun-Chi Lin
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Yuan-Tzu Lan
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Hung-Hsin Lin
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Wen-Yi Liang
- Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Wei-Shone Chen
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Jen-Kou Lin
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
| | - Jeng-Kai Jiang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
- * E-mail: (SCC); (JKJ)
| | - Shih-Ching Chang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University,Taipei, Taiwan
- * E-mail: (SCC); (JKJ)
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15
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Cardelli M. The epigenetic alterations of endogenous retroelements in aging. Mech Ageing Dev 2018; 174:30-46. [PMID: 29458070 DOI: 10.1016/j.mad.2018.02.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 02/06/2023]
Abstract
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation. Indeed, most of the genomic CpG sites subjected to DNA methylation in the nuclear DNA are carried by these repetitive elements. As other parts of the genome, endogenous retroelements and other transposable elements are subjected to deep epigenetic alterations during aging, repeatedly observed in the context of organismal and cellular senescence, in human and other species. This review summarizes the current status of knowledge about the epigenetic alterations occurring in this large, non-genic portion of the genome in aging and age-related conditions, with a focus on the causes and the possible functional consequences of these alterations.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, Italian National Research Center on Aging (INRCA), via Birarelli 8, 60121 Ancona, Italy.
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16
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Porcellini E, Laprovitera N, Riefolo M, Ravaioli M, Garajova I, Ferracin M. Epigenetic and epitranscriptomic changes in colorectal cancer: Diagnostic, prognostic, and treatment implications. Cancer Lett 2018; 419:84-95. [PMID: 29360561 DOI: 10.1016/j.canlet.2018.01.049] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
A cancer cell is the final product of a complex mixture of genetic, epigenetic and epitranscriptomic alterations, whose final interplay contribute to cancer onset and progression. This is specifically true for colorectal cancer, a tumor with a strong epigenetic component, which acts earlier than any other genetic alteration in promoting cancer cell malignant transformation. The pattern of progressive, and usually subtype-specific, DNA and histone modifications that occur in colorectal cancer has been extensively studied in the last decade, providing plenty of data to explore. For this tumor, it became recently evident that also RNA modifications play a relevant role in the activation of oncogenes or repression of tumor suppressor genes. In this review we provide a brief overview of all epigenetic and epitranscriptomic changes that have been found associated to colorectal cancer till now. We explore the impact of these alterations in cancer prognosis and response to treatment and discuss their potential use as cancer biomarkers.
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Affiliation(s)
- Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Ingrid Garajova
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.
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Boeckx N, Janssens K, Van Camp G, Rasschaert M, Papadimitriou K, Peeters M, Op de Beeck K. The predictive value of primary tumor location in patients with metastatic colorectal cancer: A systematic review. Crit Rev Oncol Hematol 2017; 121:1-10. [PMID: 29279095 DOI: 10.1016/j.critrevonc.2017.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/22/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide. It has been reported that left- and right-sided CRC harbor varying disease characteristics, which leads to a difference in prognosis and response to therapy. Recently, there have been retrospective studies about tumor location in metastatic CRC (mCRC) and its potential to predict the effect of anti-vascular endothelial growth factor and anti-epidermal growth factor receptor (anti-EGFR) therapies. In this review, we provide a comprehensive overview of the latest trials studying the predictive value of primary tumor location in mCRC and discuss biomarkers that might be associated with the differences in treatment response. Although data need to be interpreted with caution due to the absence of randomized trials stratified based on tumor location, patients with left-sided CRC seem to benefit more from anti-EGFR therapy than patients with right-sided CRC. Further clinical trials, stratified for tumor location, are warranted.
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Affiliation(s)
- Nele Boeckx
- Center of Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, 2650 Edegem, Belgium.
| | - Katleen Janssens
- Center of Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Guy Van Camp
- Center of Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, 2650 Edegem, Belgium.
| | - Marika Rasschaert
- Department of Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
| | | | - Marc Peeters
- Center of Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; Department of Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
| | - Ken Op de Beeck
- Center of Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, 2650 Edegem, Belgium.
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18
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LINE-1 hypomethylation status of circulating cell-free DNA in plasma as a biomarker for colorectal cancer. Oncotarget 2017; 8:11906-11916. [PMID: 28060757 PMCID: PMC5355314 DOI: 10.18632/oncotarget.14439] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
Colorectal cancer (CRC) is a serious public health problem and non-invasive biomarkers improving diagnosis or therapy are strongly required. Circulating cell-free DNA (cfDNA) has been a promising target for this purpose. In this study, we evaluated the potential of long interspersed nuclear element-1 (LINE-1) hypomethylation as a blood biomarker for CRC. LINE-1 hypomethylation level in plasma cfDNA in 114 CRC patients was retrospectively examined by absolute quantitative analysis of methylated alleles real-time PCR, and was expressed using LINE-1 hypomethylation index (LHI) [unmethylated copy number/ (methylated copy number + unmethylated copy number)]. Greater LHI values indicated enhanced hypomethylation. In our clinicopathological analysis, CRC patients with large tumors (≥6.0 cm), advanced N stage (≥2), and distant metastasis (M1) had statistically significantly higher cfDNA LHI than other CRC patients, suggesting cfDNA LHI as a disease progression biomarker for CRC. Furthermore, early stage I/II (n = 57) as well as advanced stage III/IV (n =57) CRC patients had significantly higher cfDNA LHI than healthy donors (n=53) [stage I/II: median 0.369 (95% confidence interval, 0.360–0.380) vs. 0.332 (0.325–0.339), P < 0.0001; stage III/IV: 0.372 (0.365–0.388) vs. 0.332 (0.325–0.339), P < 0.0001]. The receiver operating characteristic analysis showed that cfDNA LHI had the detection capacity of CRC with area under the curve(AUC) of 0.79 and 0.83 in stage I/II and stage III/IV CRC patients, respectively. The present study demonstrated for the first time the potential of plasma cfDNA LHI as a novel biomarker for CRC, particularly for early stage detection.
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Danese E, Montagnana M. Epigenetics of colorectal cancer: emerging circulating diagnostic and prognostic biomarkers. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:279. [PMID: 28758105 DOI: 10.21037/atm.2017.04.45] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide and the second leading cause of cancer-related mortality in western countries. Despite the high incidence, treatment options for advanced CRC remain limited and unsuccessful, resulting in a poor prognosis. Therefore, novel accurate diagnostic, prognostic and predictive biomarkers are clearly and urgently needed to detect advanced colon polyps and early stage CRC and to identify the most effective treatments for specific CRC patients. CRC is known to develop from early premalignant lesions to full blown cancer via a multi-step process involving a series of genetic mutations that accumulate over time. Recent improvement of our understanding of CRC biology and advances in genomic technologies has led to the identification of a variety of epigenetic alterations strongly involved in cancer initiation and progression. Among the epigenetic marks implicated in CRC the most widely studied are the global DNA hypomethylation, the promoter hypermethylation and the miRNAs dysregulations. Many evidence exist that such tumour associated alterations may serve as new potential biomarkers. Moreover, due the non-invasive, objective, and potential reproducible assessment, circulating epigenetic biomarkers have reached increasing attentions in the last few years. In this review, we attempt to analyze the existing most recent literature on the role of circulating DNA methylations and miRNAs alterations in CRC diagnosis and prognosis.
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Affiliation(s)
- Elisa Danese
- Clinical Biochemistry Section, University Hospital of Verona, Verona, Italy
| | - Martina Montagnana
- Clinical Biochemistry Section, University Hospital of Verona, Verona, Italy
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20
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Ulivi P, Scarpi E, Chiadini E, Marisi G, Valgiusti M, Capelli L, Casadei Gardini A, Monti M, Ruscelli S, Frassineti GL, Calistri D, Amadori D, Passardi A. Right- vs. Left-Sided Metastatic Colorectal Cancer: Differences in Tumor Biology and Bevacizumab Efficacy. Int J Mol Sci 2017; 18:ijms18061240. [PMID: 28598398 PMCID: PMC5486063 DOI: 10.3390/ijms18061240] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 12/11/2022] Open
Abstract
There is evidence of a different response to treatment with regard to the primary tumor localization (right-sided or left-sided) in patients with metastatic colorectal cancer (mCRC). We analyzed the different outcomes and biomolecular characteristics in relation to tumor localization in 122 of the 370 patients with metastatic colorectal cancer enrolled onto the phase III prospective multicenter “Italian Trial in Advanced Colorectal Cancer (ITACa)”, randomized to receive first-line chemotherapy (CT) or CT plus bevacizumab (CT + B). RAS and BRAF mutations; baseline expression levels of circulating vascular endothelial growth factor (VEGF), endothelial nitric oxide synthase (eNOS), cyclooxygenase-2 (COX2), ephrin type-B receptor 4 (EPHB4), hypoxia-inducible factor 1-alpha (HIF-1α), lactate dehydrogenase (LDH), and high-sensitivity C reactive protein (hs-CRP); and inflammatory indexes such as the neutrophil-to-lymphocyte ratio, platelet-lymphocyte rate and systemic immune-inflammation index were evaluated. Patients with right-sided tumors showed a longer median progression-free survival in the CT + B arm than in the CT group (12.6 vs. 9.0 months, respectively, p = 0.017). Baseline inflammatory indexes were significantly higher in left-sided tumors, whereas eNOS and EPHB4 expression was significantly higher and BRAF mutation more frequent in right-sided tumors. Our data suggest a greater efficacy of the CT + B combination in right-sided mCRC, which might be attributable to the lower inflammatory status and higher expression of pro-angiogenic factors that appear to characterize these tumors.
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Affiliation(s)
- Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Emanuela Scarpi
- Unit of Biostatistics and Clinical Trials, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Elisa Chiadini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Giorgia Marisi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Martina Valgiusti
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Laura Capelli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Andrea Casadei Gardini
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Manlio Monti
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Silvia Ruscelli
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Giovanni Luca Frassineti
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Dino Amadori
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Alessandro Passardi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014 Meldola, Italy.
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21
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Paul S, Bhattacharjee P, Giri AK, Bhattacharjee P. Arsenic toxicity and epimutagenecity: the new LINEage. Biometals 2017; 30:505-515. [PMID: 28516305 DOI: 10.1007/s10534-017-0021-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/09/2017] [Indexed: 12/15/2022]
Abstract
Global methylation pattern regulates the normal functioning of a cell. Research have shown arsenic alter these methylation landscapes within the genome leading to aberrant gene expression and inducts various pathophysiological outcomes. Long interspersed nuclear elements (LINE-1) normally remains inert due to heavy methylation of it's promoters, time and various environmental insults, they lose these methylation signatures and begin retro-transposition that has been associated with genomic instability and cancerous outcomes. Of the various high throughput technologies available to detect global methylation profile, development of LINE-1 methylation index shall provide a cost effect-screening tool to detect epimutagenic events in the wake of toxic exposure in a large number of individuals. In the present review, we tried to discuss the state of research and whether LINE-1 methylation can be considered as a potent epigenetic signature for arsenic toxicity.
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Affiliation(s)
- Somnath Paul
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. .,Department of Epigenetics & Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Center, The University of Texas, M.D. Anderson Cancer Center, Science Park, 1808 Park Road 1C, Smithville, TX, 78957, USA.
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India.
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India.
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22
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Ye D, Jiang D, Li Y, Jin M, Chen K. The role of LINE-1 methylation in predicting survival among colorectal cancer patients: a meta-analysis. Int J Clin Oncol 2017; 22:749-757. [PMID: 28343299 DOI: 10.1007/s10147-017-1106-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/23/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND The prognostic value of long interspersed nucleotide element-1 (LINE-1) methylation in patients with colorectal cancer (CRC) remains uncertain. We have therefore performed a meta-analysis to elucidate this issue. METHODS The PubMed and Web of Science databases were searched for studies published up to 30 June 2016 which reported on an association between LINE-1 methylation and overall survival (OS), disease-free survival (DFS), or cancer-specific survival (CSS) among CRC patients. The reference lists of the identified studies were also analyzed to identify additional eligible studies. Hazard ratios (HRs) with 95% confidence intervals (CIs) were pooled using the fixed-effects or the random-effects model. Stratification analysis and meta-regression analysis were performed to detect the source of heterogeneity. Analyses of sensitivity and publication bias were also carried out. RESULTS Thirteen independent studies involving 3620 CRC patients were recruited to the meta-analysis. LINE-1 hypomethylation was found to be significantly associated with shorter OS (HR 2.92, 95% CI 2.20-3.88, p < 0.001) and DFS (HR 2.18, 95% CI 1.46-3.27, p < 0.001), as well as unfavorable CSS (HR 1.96, 95% CI 1.35-2.85, p < 0.001). No heterogeneity was found among the studies evaluating the associations between LINE-1 hypomethylation and OS or DFS, with the exception being CSS. Moreover, meta-regression analysis suggested that one of the contributors to between-study heterogeneity on the association between LINE-1 methylation and CSS was statistical methodology. The subgroup analysis suggested that the association in studies using the Cox model statistical method (HR 2.76, 95% CI 1.90-4.01, p < 0.001) was stronger than that in studies using the Log-rank test (HR 1.41, 95% CI 1.07-1.87, p = 0.015). CONCLUSIONS The results of this meta-analysis suggest that LINE-1 methylation is significantly associated with the survival of CRC patients and that it could be a predictive factor for CRC prognosis.
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Affiliation(s)
- Ding Ye
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Danjie Jiang
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yingjun Li
- Department of Public Health, Hangzhou Medical School, Hangzhou, China
| | - Mingjuan Jin
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kun Chen
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China.
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23
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Hamada T, Keum N, Nishihara R, Ogino S. Molecular pathological epidemiology: new developing frontiers of big data science to study etiologies and pathogenesis. J Gastroenterol 2017; 52:265-275. [PMID: 27738762 PMCID: PMC5325774 DOI: 10.1007/s00535-016-1272-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 02/07/2023]
Abstract
Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality. This MPE approach can provide etiologic and pathogenic insights, potentially contributing to precision medicine for personalized prevention and treatment. Although breast, prostate, lung, and colorectal cancers have been among the most commonly studied diseases, the MPE approach can be used to study any disease. In addition to molecular features, host immune status and microbiome profile likely affect a disease process, and thus serve as informative biomarkers. As such, further integration of several disciplines into MPE has been achieved (e.g., pharmaco-MPE, immuno-MPE, and microbial MPE), to provide novel insights into underlying etiologic mechanisms. With the advent of high-throughput sequencing technologies, available genomic and epigenomic data have expanded dramatically. The MPE approach can also provide a specific risk estimate for each disease subgroup, thereby enhancing the impact of genome-wide association studies on public health. In this article, we present recent progress of MPE, and discuss the importance of accounting for the disease heterogeneity in the era of big-data health science and precision medicine.
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Affiliation(s)
- Tsuyoshi Hamada
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA
| | - NaNa Keum
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Reiko Nishihara
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Division of MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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Ardeljan D, Taylor MS, Ting DT, Burns KH. The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. Clin Chem 2017; 63:816-822. [PMID: 28188229 DOI: 10.1373/clinchem.2016.257444] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND A large portion of intronic and intergenic space in our genome consists of repeated sequences. One of the most prevalent is the long interspersed element-1 (LINE-1, L1) mobile DNA. LINE-1 is rightly receiving increasing interest as a cancer biomarker. CONTENT Intact LINE-1 elements are self-propagating. They code for RNA and proteins that function to make more copies of the genomic element. Our current understanding is that this process is repressed in most normal cells, but that LINE-1 expression is a hallmark of many types of malignancy. Here, we will consider features of cancer cells when cellular defense mechanisms repressing LINE-1 go awry. We will review evidence that genomic LINE-1 methylation, LINE-1-encoded RNAs, and LINE-1 ORF1p (open reading frame 1 protein) may be useful in cancer diagnosis. SUMMARY The repetitive and variable nature of LINE-1 DNA sequences poses unique challenges to studying them, but recent advances in reagents and next generation sequencing present opportunities to characterize LINE-1 expression and activity in cancers and to identify clinical applications.
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Affiliation(s)
- Daniel Ardeljan
- McKusick-Nathans Institute of Genetic Medicine (IGM) and.,Medical Scientist Training Program (MSTP), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - David T Ting
- Department of Medicine and the Massachusetts General Hospital Cancer Center, Boston, MA
| | - Kathleen H Burns
- McKusick-Nathans Institute of Genetic Medicine (IGM) and .,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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25
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Tumor LINE-1 Methylation Level in Association with Survival of Patients with Stage II Colon Cancer. Int J Mol Sci 2016; 18:ijms18010036. [PMID: 28035987 PMCID: PMC5297671 DOI: 10.3390/ijms18010036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022] Open
Abstract
Genome-wide DNA hypomethylation is associated with a worse prognosis in early-stage colorectal cancer. To measure genome-wide DNA methylation levels, long interspersed nucleotide element (LINE-1) repeats are used as a surrogate marker. Cohort studies on the clinical impact of genome-wide DNA methylation level in patients with only early-stage colon cancer, are currently lacking. This study aimed to investigate the prognostic value of LINE-1 methylation in a stage II colon cancer cohort (n = 164). Manual needle microdissection of tumor areas was performed on formalin-fixed paraffin-embedded tumor tissue sections followed by DNA extraction. Bisulfite converted DNA was used to assess tumor LINE-1 methylation level by qPCR. Patients with LINE-1 hypomethylated tumors had a significantly worse overall survival compared to patients with a higher level of LINE-1 tumor DNA methylation (HR 1.68, 95% CI 1.03–2.75; p = 0.04). This effect was more prominent in patients aged over 65 years (HR 2.00, 95% CI 1.13–3.52; p = 0.02), although the test for age interaction was not significant. No significant effect on recurrence-free survival was observed. Based on these results, tumor LINE-1 hypomethylation is associated with a worse overall survival in stage II colon cancer. Whether the origin of this causation is cancer-specific or age-related can be debated.
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26
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Kaneko M, Kotake M, Bando H, Yamada T, Takemura H, Minamoto T. Prognostic and predictive significance of long interspersed nucleotide element-1 methylation in advanced-stage colorectal cancer. BMC Cancer 2016; 16:945. [PMID: 27955637 PMCID: PMC5154037 DOI: 10.1186/s12885-016-2984-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 11/29/2016] [Indexed: 12/23/2022] Open
Abstract
Background Hypomethylation of Long Interspersed Nucleotide Element-1 (LINE-1) is associated with worse prognosis in colorectal cancer (CRC). However, little is known about the relevance of this marker for the prognosis and response to chemotherapy of metastatic and recurrent (advanced-stage) CRC. Our aim was therefore to investigate whether tumor LINE-1 hypomethylation correlates with patient survival and with response to 5-fluorouracil (5-FU)/ oxaliplatin (FOLFOX) chemotherapy in advanced-stage CRC. Methods The study included 40 CRC patients who developed metastasis or local recurrence after surgery and subsequently underwent FOLFOX therapy. Progression-free and overall survival were estimated using the Kaplan-Meier method. LINE-1 methylation levels in formalin-fixed and paraffin-embedded primary tumor tissues were measured by MethyLight assay and correlated with patient survival. In vitro analyses were also conducted with human colon cancer cell lines having different LINE-1 methylation levels to examine the effects of 5-FU and oxaliplatin on LINE-1 activity and DNA double-strand-breaks. Results Patients with LINE-1 hypomethylation showed significantly worse progression-free (median: 6.6 vs 9.4 months; P = 0.02) and overall (median: 16.6 vs 23.2 months; P = 0.01) survival following chemotherapy compared to patients with high methylation. LINE-1 hypomethylation was an independent factor for poor prognosis (P = 0.018) and was associated with a trend for non-response to FOLFOX chemotherapy. In vitro analysis showed that oxaliplatin increased the LINE-1 score in LINE-1-expressing (hypomethylated) cancer cells, thereby enhancing and prolonging the effect of 5-FU against these cells. This finding supports the observed correlation between tumor LINE-1 methylation and response to chemotherapy in CRC patients. Conclusions Tumor LINE-1 hypomethylation is an independent marker of poor prognosis in advanced-stage CRC and may also predict non-response to combination FOLFOX chemotherapy. Prospective studies are needed to optimize the measurement of tumor LINE-1 methylation and to confirm its clinical impact, particularly as a predictive marker. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2984-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mami Kaneko
- Department of General and Cardiothoracic Surgery, Graduate School of Medical Science, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8641, Japan. .,Department of Gastrointestinal Surgery, Ishikawa Prefectural Central Hospital, Kanazawa, Japan. .,Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
| | - Masanori Kotake
- Department of General and Cardiothoracic Surgery, Graduate School of Medical Science, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8641, Japan
| | - Hiroyuki Bando
- Department of Gastrointestinal Surgery, Ishikawa Prefectural Central Hospital, Kanazawa, Japan
| | - Tetsuji Yamada
- Department of Gastrointestinal Surgery, Ishikawa Prefectural Central Hospital, Kanazawa, Japan
| | - Hirofumi Takemura
- Department of General and Cardiothoracic Surgery, Graduate School of Medical Science, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8641, Japan
| | - Toshinari Minamoto
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
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