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Xia B, Lu Y, Liang J, Li F, Peng J, Wang J, Wan C, Ding J, Le C, Dai J, Guo B, Shen Z. Association of GAL-8 promoter methylation levels with coronary plaque inflammation. Int J Cardiol 2024; 401:131782. [PMID: 38246423 DOI: 10.1016/j.ijcard.2024.131782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/12/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
BACKGROUND AND AIMS Coronary heart disease (CHD) is a condition that carries a high risk of mortality and is associated with aging. CHD is characterized by the chronic inflammatory response of the coronary intima. Recent studies have shown that the methylation level of blood mononuclear cell DNA is closely associated with adverse events in CHD, but the roles and mechanisms of DNA methylation in CHD remain elusive. METHODS AND RESULTS In this study, the DNA methylation status within the epigenome of human coronary tissue in the sudden coronary death (SCD) group and control (CON) group of coronary heart disease was analyzed using the Illumina® Infinium Methylation EPIC BeadChip (850 K chip), resulting in the identification of a total of 2553 differentially methylated genes (DMGs). The differentially methylated genes were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and significant differential DNA methylation was found. Among the differentially hypomethylated genes were GAL-8, LTF, and RFPL3, while the highly methylated genes were TMEM9B, ANK3, and C6orF48. These genes were mainly enriched in 10 significantly enriched pathways, such as cell adhesion junctions, among which the differentially methylated gene GAL-8 was involved in inflammatory pathway signaling. For functional analysis of GAL-8, we first examined the differences in GAL-8 promoter methylation levels among different subgroups of human coronary tissue in the CON, CHD, and SCD groups using pyrophosphate sequencing. The results revealed reduced GAL-8 promoter methylation levels in the SCD group, while the difference between the CHD and CON groups was not statistically significant (P > 0.05). The reduced GAL-8 promoter methylation level was associated with upregulated GAL-8 expression, which led to increased expression of the inflammatory markers TNF-α, IL-1β, MCP-1, MIP-2, MMP-2, and MMP-9. This enhanced inflammatory response contributed to the accumulation of foam cells, thickening of the intima of human coronary arteries, and increased luminal stenosis, which promoted the occurrence of sudden coronary death. Next, we found that GAL-8 promoter methylation levels in PBMC were consistent with human coronary tissue. The unstable angina group (UAP) had significantly lower GAL-8 promoter methylation levels than stable angina (SAP) and healthy controls (CON) (P < 0.05), and there was a significant correlation between reduced GAL-8 promoter methylation levels and risk factors for coronary heart disease. These findings highlight the association between decreased GAL-8 promoter methylation and the presence of coronary heart disease risk factors. ROC curve analysis suggests that methylation of the GAL 8 promoter region is an independent risk factor for CHD. In conclusion, our study confirmed differential expression of GAL-8, LTF, MUC4D, TMEM9B, MYOM2, and ANK3 genes due to DNA methylation in the SCD group. We also established the consistency of GAL-8 promoter methylation alterations between human coronary tissue and patient peripheral blood monocytes. The decreased methylation level of the GAL-8 promoter may be related to the increased expression of GAL-8 and the coronary risk factors. CONCLUSIONS Accordingly, we hypothesized that reduced levels of GAL-8 promoter methylation may be an independent risk factor for adverse events in coronary heart disease.
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Affiliation(s)
- Bing Xia
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Yanlin Lu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China; School of Medicine and Science and Technology, Zunyi Medical University, Zunyi 563000, China
| | - Jingwei Liang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Fangqin Li
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Jin Peng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Changwu Wan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Jiuyang Ding
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Jialin Dai
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China
| | - Bing Guo
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China; Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China.
| | - Zheng Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, China; Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China.
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Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB. Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling. SCIENCE ADVANCES 2024; 10:eadk4423. [PMID: 38536911 PMCID: PMC10971413 DOI: 10.1126/sciadv.adk4423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
DNA methyltransferase inhibitor (DNMTi) efficacy in solid tumors is limited. Colon cancer cells exposed to DNMTi accumulate lysine-27 trimethylation on histone H3 (H3K27me3). We propose this Enhancer of Zeste Homolog 2 (EZH2)-dependent repressive modification limits DNMTi efficacy. Here, we show that low-dose DNMTi treatment sensitizes colon cancer cells to select EZH2 inhibitors (EZH2is). Integrative epigenomic analysis reveals that DNMTi-induced H3K27me3 accumulates at genomic regions poised with EZH2. Notably, combined EZH2i and DNMTi alters the epigenomic landscape to transcriptionally up-regulate the calcium-induced nuclear factor of activated T cells (NFAT):activating protein 1 (AP-1) signaling pathway. Blocking this pathway limits transcriptional activating effects of these drugs, including transposable element and innate immune response gene expression involved in viral defense. Analysis of primary human colon cancer specimens reveals positive correlations between DNMTi-, innate immune response-, and calcium signaling-associated transcription profiles. Collectively, we show that compensatory EZH2 activity limits DNMTi efficacy in colon cancer and link NFAT:AP-1 signaling to epigenetic therapy-induced viral mimicry.
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Affiliation(s)
- Alison A. Chomiak
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xiangqian Kong
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ying Cui
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kate E. Thurlow
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Evan M. Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Michael J. Topper
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen B. Baylin
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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3
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Sun A, Park P, Cole L, Vaidya H, Maegawa S, Keith K, Calendo G, Madzo J, Jelinek J, Jobin C, Issa JPJ. Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa. Epigenetics 2023; 18:2160568. [PMID: 36572998 PMCID: PMC9980687 DOI: 10.1080/15592294.2022.2160568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/11/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
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Affiliation(s)
- Ang Sun
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Pyounghwa Park
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Lauren Cole
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Himani Vaidya
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Shinji Maegawa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Research Department of Pediatrics, University of Texas, MD Anderson Cancer Center Department of Pediatrics, University of Texas, MD Anderson Cancer CenterHouston, TX, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Christian Jobin
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
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Meier HCS, Mitchell C, Karadimas T, Faul JD. Systemic inflammation and biological aging in the Health and Retirement Study. GeroScience 2023; 45:3257-3265. [PMID: 37501048 PMCID: PMC10643484 DOI: 10.1007/s11357-023-00880-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023] Open
Abstract
Chronic, low-level systemic inflammation associated with aging, or inflammaging, is a risk factor for several chronic diseases and mortality. Using data from the Health and Retirement Study, we generated a continuous latent variable for systemic inflammation from seven measured indicators of inflammation and examined associations with another biomarker of biological aging, DNA methylation age acceleration measured by epigenetic clocks, and 4-year mortality (N = 3,113). We found that greater systemic inflammation was positively associated with DNA methylation age acceleration for 10 of the 13 epigenetic clocks, after adjustment for sociodemographics and chronic disease risk factors. The latent variable for systemic inflammation was associated with 4-year mortality independent of DNA methylation age acceleration and was a better predictor of 4-year mortality than any of the epigenetic clocks examined, as well as mortality risk factors, including obesity and multimorbidity. Inflammaging and DNA methylation age acceleration may represent different biological processes contributing to mortality risk. Leveraging multiple measured inflammation markers to capture inflammaging is important for biology of aging research.
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Affiliation(s)
- Helen C S Meier
- Survey Research Center, Institute for Social Research, University of Michigan, 426 Thompson Street, Ann Arbor, MI, 48106-1248, USA.
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, 426 Thompson Street, Ann Arbor, MI, 48106-1248, USA
| | - Thomas Karadimas
- Survey Research Center, Institute for Social Research, University of Michigan, 426 Thompson Street, Ann Arbor, MI, 48106-1248, USA
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, 426 Thompson Street, Ann Arbor, MI, 48106-1248, USA
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5
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Badia-Ramentol J, Gimeno-Valiente F, Duréndez E, Martínez-Ciarpaglini C, Linares J, Iglesias M, Cervantes A, Calon A, Tarazona N. The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice. Cancer Treat Rev 2023; 121:102643. [PMID: 37871463 DOI: 10.1016/j.ctrv.2023.102643] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Adjuvant chemotherapy following surgical intervention remains the primary treatment option for patients with localized colorectal cancer (CRC). However, a significant proportion of patients will have an unfavorable outcome after current forms of chemotherapy. While reflecting the increasing complexity of CRC, the clinical application of molecular biomarkers provides information that can be utilized to guide therapeutic strategies. Among these, caudal-related homeobox transcription factor 2 (CDX2) emerges as a biomarker of both prognosis and relapse after therapy. CDX2 is a key transcription factor that controls intestinal fate. Although rarely mutated in CRC, loss of CDX2 expression has been reported mostly in right-sided, microsatellite-unstable tumors and is associated with aggressive carcinomas. The pathological assessment of CDX2 by immunohistochemistry can thus identify patients with high-risk CRC, but the evaluation of CDX2 expression remains challenging in a substantial proportion of patients. In this review, we discuss the roles of CDX2 in homeostasis and CRC and the alterations that lead to protein expression loss. Furthermore, we review the clinical significance of CDX2 assessment, with a particular focus on its current use as a biomarker for pathological evaluation and clinical decision-making. Finally, we attempt to clarify the molecular implications of CDX2 deficiency, ultimately providing insights for a more precise evaluation of CDX2 protein expression.
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Affiliation(s)
- Jordi Badia-Ramentol
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - Elena Duréndez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | | | - Jenniffer Linares
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Iglesias
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain; Department of Pathology, Hospital del Mar, Barcelona, CIBERONC, Spain
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | - Alexandre Calon
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain.
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6
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Tejedor JR, Peñarroya A, Gancedo-Verdejo J, Santamarina-Ojeda P, Pérez RF, López-Tamargo S, Díez-Borge A, Alba-Linares JJ, González-Del-Rey N, Urdinguio RG, Mangas C, Roberti A, López V, Morales-Ruiz T, Ariza RR, Roldán-Arjona T, Meijón M, Valledor L, Cañal MJ, Fernández-Martínez D, Fernández-Hevia M, Jiménez-Fonseca P, García-Flórez LJ, Fernández AF, Fraga MF. CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer. Clin Epigenetics 2023; 15:133. [PMID: 37612734 PMCID: PMC10464368 DOI: 10.1186/s13148-023-01546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated. RESULTS In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53-/- cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence. CONCLUSIONS These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes.
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Affiliation(s)
- Juan Ramón Tejedor
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Alfonso Peñarroya
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
| | - Javier Gancedo-Verdejo
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Pablo Santamarina-Ojeda
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Raúl F Pérez
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Sara López-Tamargo
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Ana Díez-Borge
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Viralgen Vector Core, 20009, San Sebastián, Gipuzkoa, Spain
| | - Juan J Alba-Linares
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Nerea González-Del-Rey
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Rocío G Urdinguio
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Cristina Mangas
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Annalisa Roberti
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
| | - Virginia López
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Mónica Meijón
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - Luis Valledor
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - Daniel Fernández-Martínez
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - María Fernández-Hevia
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Paula Jiménez-Fonseca
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Division of Oncology, Department of Medical Oncology, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Luis J García-Flórez
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
- Department of Surgery and Medical Surgical Specialties, University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Agustín F Fernández
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain.
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain.
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain.
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain.
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain.
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain.
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7
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Cui W, Huang Z, Jin SG, Johnson J, Lau KH, Hostetter G, Pfeifer GP. Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation. Cancer Res 2023; 83:2480-2495. [PMID: 37272752 PMCID: PMC10391329 DOI: 10.1158/0008-5472.can-23-0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023]
Abstract
Hypermethylation of CpG islands (CGI) is a common feature of cancer cells and predominantly affects Polycomb-associated genomic regions. Elucidating the underlying mechanisms leading to DNA hypermethylation in human cancer could help identify chemoprevention strategies. Here, we evaluated the role of Polycomb complexes and 5-methylcytosine (5mC) oxidases in protecting CGIs from DNA methylation and observed that four genes coding for components of Polycomb repressive complex 1 (PRC1) are downregulated in tumors. Inactivation of RYBP, a key activator of variant PRC1 complexes, in combination with all three 5mC oxidases (TET proteins) in nontumorigenic bronchial epithelial cells led to widespread hypermethylation of Polycomb-marked CGIs affecting almost 4,000 target genes, which closely resembled the DNA hypermethylation landscape observed in human squamous cell lung tumors. The RYBP- and TET-deficient cells showed methylation-associated aberrant regulation of cancer-relevant pathways, including defects in the Hippo tumor suppressor network. Notably, the quadruple knockout cells acquired a transformed phenotype, including anchorage-independent growth and formation of squamous cell carcinomas in mice. This work provides a mechanism promoting hypermethylation of CGIs and shows that such hypermethylation can lead to cell transformation. The breakdown of a two-pronged protection mechanism can be a route towards genome-wide hypermethylation of CGIs in tumors. SIGNIFICANCE Dysfunction of the Polycomb component RYBP in combination with loss of 5-methylcytosine oxidases promotes widespread hypermethylation of CpG islands in bronchial cells and induces tumorigenesis, resembling changes seen in human lung tumors.
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Affiliation(s)
- Wei Cui
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Zhijun Huang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Gerd P. Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
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8
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Chatila WK, Walch H, Hechtman JF, Moyer SM, Sgambati V, Faleck DM, Srivastava A, Tang L, Benhamida J, Ismailgeci D, Campos C, Wu F, Chang Q, Vakiani E, de Stanchina E, Weiser MR, Widmar M, Yantiss RK, Shah MA, Bass AJ, Stadler ZK, Katz LH, Mellinghoff IK, Sethi NS, Schultz N, Ganesh K, Kelsen D, Yaeger R. Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers. Nat Commun 2023; 14:110. [PMID: 36611031 PMCID: PMC9825391 DOI: 10.1038/s41467-022-35592-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 01/08/2023] Open
Abstract
Inflammation has long been recognized to contribute to cancer development, particularly across the gastrointestinal tract. Patients with inflammatory bowel disease have an increased risk for bowel cancers, and it has been posited that a field of genetic changes may underlie this risk. Here, we define the clinical features, genomic landscape, and germline alterations in 174 patients with colitis-associated cancers and sequenced 29 synchronous or isolated dysplasia. TP53 alterations, an early and highly recurrent event in colitis-associated cancers, occur in half of dysplasia, largely as convergent evolution of independent events. Wnt pathway alterations are infrequent, and our data suggest transcriptional rewiring away from Wnt. Sequencing of multiple dysplasia/cancer lesions from mouse models and patients demonstrates rare shared alterations between lesions. These findings suggest neoplastic bowel lesions developing in a background of inflammation experience lineage plasticity away from Wnt activation early during tumorigenesis and largely occur as genetically independent events.
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Affiliation(s)
- Walid K Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sydney M Moyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Valeria Sgambati
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amitabh Srivastava
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dorina Ismailgeci
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carl Campos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fan Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qing Chang
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Widmar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rhonda K Yantiss
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Manish A Shah
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adam J Bass
- Herbert Irving Comprehensive Cancer Research Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lior H Katz
- Gastroenterology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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9
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Alimohammadi M, Makaremi S, Rahimi A, Asghariazar V, Taghadosi M, Safarzadeh E. DNA methylation changes and inflammaging in aging-associated diseases. Epigenomics 2022; 14:965-986. [PMID: 36043685 DOI: 10.2217/epi-2022-0143] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aging as an inevitable phenomenon is associated with pervasive changes in physiological functions. There is a relationship between aging and the increase of several chronic diseases. Most age-related disorders are accompanied by an underlying chronic inflammatory state, as demonstrated by local infiltration of inflammatory cells and greater levels of proinflammatory cytokines in the bloodstream. Within inflammaging, many epigenetic events, especially DNA methylation, change. During the aging process, due to aberrations of DNA methylation, biological processes are disrupted, leading to the emergence or progression of a variety of human diseases, including cancer, neurodegenerative disorders, cardiovascular disease and diabetes. The focus of this review is on DNA methylation, which is involved in inflammaging-related activities, and how its dysregulation leads to human disorders.
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Affiliation(s)
- Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1983969411, Iran
| | - Shima Makaremi
- School of Medicine & Allied Medical Sciences, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
| | - Ali Rahimi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, 5618985991, Iran
| | - Vahid Asghariazar
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
| | - Mahdi Taghadosi
- Department of Immunology, Kermanshah University of Medical Sciences, Kermanshah, 6714869914, Iran
| | - Elham Safarzadeh
- Department of Microbiology, Parasitology, & Immunology, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
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10
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Ganduri V, Rajasekaran K, Duraiyarasan S, Adefuye MA, Manjunatha N. Colorectal Carcinoma, Cyclooxygenases, and COX Inhibitors. Cureus 2022; 14:e28579. [PMID: 36185863 PMCID: PMC9521169 DOI: 10.7759/cureus.28579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal carcinoma (CRC) is the most common of gastrointestinal cancers, the majority presenting with sporadic occurrence compared to the less frequently inherited syndromes. The increasing incidence, decreasing gender and age disparities, and the prevalent risk factors are concerning. The malignancy arising from benign precursor polyps transforms slowly over time. The adenoma variant polyps reported a marked upregulation of cyclooxygenases (COX), significantly COX-2 isoform, influenced by various determinants such as genetics, pathology, histology, and site of the carcinoma. These COX enzymes are responsible for prostaglandin synthesis and the consequent cascade of cell inflammation and proliferation. Therefore, COX inhibition by non-steroidal anti-inflammatory drugs (NSAIDs) targeted against both the isoforms COX-1 and COX-2 have been studied for decades in anticipation of preventing the occurrence of colorectal carcinoma in high-risk populations. This article has collated and highlighted the overexpression of COX enzymes by the adenomatous polyps and provides corroborating evidence from multiple studies in favor of COX inhibition by NSAIDs. Aspirin and Sulindac were two drugs to be initially proven to halt the progression and cause regression of the polyps. Celecoxib, a selective COX-2 inhibitor besides NSAIDs, was also used in experimental studies.
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11
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Second Cancer Onset in Myeloproliferative Neoplasms: What, When, Why? Int J Mol Sci 2022; 23:ijms23063177. [PMID: 35328597 PMCID: PMC8954627 DOI: 10.3390/ijms23063177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
The risk of developing a solid cancer is a major issue arising in the disease course of a myeloproliferative neoplasm (MPN). Although the connection between the two diseases has been widely described, the backstage of this complex scenario has still to be explored. Several cellular and molecular mechanisms have been suggested to link the two tumors. Sometimes the MPN is considered to trigger a second cancer but at other times both diseases seem to depend on the same source. Increasing knowledge in recent years has revealed emerging pathways, supporting older, more consolidated theories, but there are still many unresolved issues. Our work aims to present the biological face of the complex clinical scenario in MPN patients developing a second cancer, focusing on the main cellular and molecular pathways linking the two diseases.
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12
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Cheng E, Ou FS, Ma C, Spiegelman D, Zhang S, Zhou X, Bainter TM, Saltz LB, Niedzwiecki D, Mayer RJ, Whittom R, Hantel A, Benson A, Atienza D, Messino M, Kindler H, Giovannucci EL, Van Blarigan EL, Brown JC, Ng K, Gross CP, Meyerhardt JA, Fuchs CS. Diet- and Lifestyle-Based Prediction Models to Estimate Cancer Recurrence and Death in Patients With Stage III Colon Cancer (CALGB 89803/Alliance). J Clin Oncol 2022; 40:740-751. [PMID: 34995084 PMCID: PMC8887946 DOI: 10.1200/jco.21.01784] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Current tools in predicting survival outcomes for patients with colon cancer predominantly rely on clinical and pathologic characteristics, but increasing evidence suggests that diet and lifestyle habits are associated with patient outcomes and should be considered to enhance model accuracy. METHODS Using an adjuvant chemotherapy trial for stage III colon cancer (CALGB 89803), we developed prediction models of disease-free survival (DFS) and overall survival by additionally incorporating self-reported nine diet and lifestyle factors. Both models were assessed by multivariable Cox proportional hazards regression and externally validated using another trial for stage III colon cancer (CALGB/SWOG 80702), and visual nomograms of prediction models were constructed accordingly. We also proposed three hypothetical scenarios for patients with (1) good-risk, (2) average-risk, and (3) poor-risk clinical and pathologic features, and estimated their predictive survival by considering clinical and pathologic features with or without adding self-reported diet and lifestyle factors. RESULTS Among 1,024 patients (median age 60.0 years, 43.8% female), we observed 394 DFS events and 311 deaths after median follow-up of 7.3 years. Adding self-reported diet and lifestyle factors to clinical and pathologic characteristics meaningfully improved performance of prediction models (c-index from 0.64 [95% CI, 0.62 to 0.67] to 0.69 [95% CI, 0.67 to 0.72] for DFS, and from 0.67 [95% CI, 0.64 to 0.70] to 0.71 [95% CI, 0.69 to 0.75] for overall survival). External validation also indicated good performance of discrimination and calibration. Adding most self-reported favorable diet and lifestyle exposures to multivariate modeling improved 5-year DFS of all patients and by 6.3% for good-risk, 21.4% for average-risk, and 42.6% for poor-risk clinical and pathologic features. CONCLUSION Diet and lifestyle factors further inform current recurrence and survival prediction models for patients with stage III colon cancer.
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Affiliation(s)
- En Cheng
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Chao Ma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Donna Spiegelman
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
- Center on Methods for Implementation and Prevention Science, Yale School of Public Health, New Haven, CT
| | - Sui Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Xin Zhou
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
- Center on Methods for Implementation and Prevention Science, Yale School of Public Health, New Haven, CT
| | - Tiffany M. Bainter
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | | | - Donna Niedzwiecki
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC
| | - Robert J. Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Renaud Whittom
- Hôpital du Sacré-Coeur de Montréal, Montreal, Quebec, Canada
| | | | - Al Benson
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | | | | | | | - Edward L. Giovannucci
- Department of Epidemiology, and Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Erin L. Van Blarigan
- Department of Epidemiology and Biostatistics, and Urology, University of California, San Francisco, CA
| | - Justin C. Brown
- Cancer Metabolism Program, Pennington Biomedical Research Center, Baton Rouge, LA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Cary P. Gross
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
- Section of General Internal Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
- Cancer Outcomes, Public Policy, and Effectiveness Research Center, Yale Cancer Center, New Haven, CT
| | | | - Charles S. Fuchs
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
- Yale Cancer Center, Smilow Cancer Hospital, New Haven, CT
- Hematology and Oncology Product Development, Genentech & Roche, South San Francisco, CA
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13
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Nguyen K, Dobrowolski C, Shukla M, Cho WK, Luttge B, Karn J. Inhibition of the H3K27 demethylase UTX enhances the epigenetic silencing of HIV proviruses and induces HIV-1 DNA hypermethylation but fails to permanently block HIV reactivation. PLoS Pathog 2021; 17:e1010014. [PMID: 34673825 PMCID: PMC8562785 DOI: 10.1371/journal.ppat.1010014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/02/2021] [Accepted: 10/07/2021] [Indexed: 01/09/2023] Open
Abstract
One strategy for a functional cure of HIV-1 is "block and lock", which seeks to permanently suppress the rebound of quiescent HIV-1 by epigenetic silencing. For the bivalent promoter in the HIV LTR, both histone 3 lysine 27 tri-methylation (H3K27me3) and DNA methylation are associated with viral suppression, while H3K4 tri-methylation (H3K4me3) is correlated with viral expression. However, H3K27me3 is readily reversed upon activation of T-cells through the T-cell receptor. In an attempt to suppress latent HIV-1 in a stable fashion, we knocked down the expression or inhibited the activity of UTX/KDM6A, the major H3K27 demethylase, and investigated its impact on latent HIV-1 reactivation in T cells. Inhibition of UTX dramatically enhanced H3K27me3 levels at the HIV LTR and was associated with increased DNA methylation. In latently infected cells from patients, GSK-J4, which is a potent dual inhibitor of the H3K27me3/me2-demethylases JMJD3/KDM6B and UTX/KDM6A, effectively suppressed the reactivation of latent HIV-1 and also induced DNA methylation at specific sites in the 5'LTR of latent HIV-1 by the enhanced recruitment of DNMT3A to HIV-1. Nonetheless, suppression of HIV-1 through epigenetic silencing required the continued treatment with GSK-J4 and was rapidly reversed after removal of the drug. DNA methylation was also rapidly lost after removal of drug, suggesting active and rapid DNA-demethylation of the HIV LTR. Thus, induction of epigenetic silencing by histone and DNA methylation appears to be insufficient to permanently silence HIV-1 proviral transcription.
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Affiliation(s)
- Kien Nguyen
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Curtis Dobrowolski
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia, United States of America
| | - Meenakshi Shukla
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Won-Kyung Cho
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine (KIOM), Dong-gu, Daegu, Republic of Korea
| | - Benjamin Luttge
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
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14
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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15
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Abstract
OBJECTIVES Cannabis is a known teratogen. Data availability addressing both major congenital anomalies and cannabis use allowed us to explore their geospatial relationships. METHODS Data for the years 1998 to 2009 from Canada Health and Statistics Canada was analyzed in R. Maps have been drawn and odds ratios, principal component analysis, correlation matrices, least squares regression and geospatial regression analyses have been conducted using the R packages base, dplyr, epiR, psych, ggplot2, colorplaner and the spml and spreml functions from package splm. RESULTS Mapping showed cannabis use was more common in the northern Territories of Canada in the Second National Survey of Cannabis Use 2018. Total congenital anomalies, all cardiovascular defects, orofacial clefts, Downs syndrome and gastroschisis were all found to be more common in these same regions and rose as a function of cannabis exposure. When Canada was dichotomized into high and low cannabis use zones by Provinces v Territories the Territories had a higher rate of total congenital anomalies 450.026 v 390.413 (O.R. = 1.16 95%C.I. 1.08-1.25, P = 0.000058; attributable fraction in exposed 13.25%, 95%C.I. 7.04-19.04%). In geospatial analysis in a spreml spatial error model cannabis was significant both alone as a main effect (P < 2.0 × 10) and in all its first and second order interactions with both tobacco and opioids from P < 2.0 × 10. CONCLUSION These results show that the northern Territories of Canada share a higher rate of cannabis use together with elevated rates of total congenital anomalies, all cardiovascular defects, Down's syndrome and gastroschisis. This is the second report of a significant association between cannabis use and both total defects and all cardiovascular anomalies and the fourth published report of a link with Downs syndrome and thereby direct major genotoxicity. The correlative relationships described in this paper are confounded by many features of social disadvantage in Canada's northern territories. However, in the context of a similar broad spectrum of defects described both in animals and in epidemiological reports from Hawaii, Colorado, USA and Australia they are cause for particular concern and indicate further research.
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16
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Saleh HA, Yousef MH, Abdelnaser A. The Anti-Inflammatory Properties of Phytochemicals and Their Effects on Epigenetic Mechanisms Involved in TLR4/NF-κB-Mediated Inflammation. Front Immunol 2021; 12:606069. [PMID: 33868227 PMCID: PMC8044831 DOI: 10.3389/fimmu.2021.606069] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
Innate immune response induces positive inflammatory transducers and regulators in order to attack pathogens, while simultaneously negative signaling regulators are transcribed to maintain innate immune homeostasis and to avoid persistent inflammatory immune responses. The gene expression of many of these regulators is controlled by different epigenetic modifications. The remarkable impact of epigenetic changes in inducing or suppressing inflammatory signaling is being increasingly recognized. Several studies have highlighted the interplay of histone modification, DNA methylation, and post-transcriptional miRNA-mediated modifications in inflammatory diseases, and inflammation-mediated tumorigenesis. Targeting these epigenetic alterations affords the opportunity of attenuating different inflammatory dysregulations. In this regard, many studies have identified the significant anti-inflammatory properties of distinct naturally-derived phytochemicals, and revealed their regulatory capacity. In the current review, we demonstrate the signaling cascade during the immune response and the epigenetic modifications that take place during inflammation. Moreover, we also provide an updated overview of phytochemicals that target these mechanisms in macrophages and other experimental models, and go on to illustrate the effects of these phytochemicals in regulating epigenetic mechanisms and attenuating aberrant inflammation.
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Affiliation(s)
- Haidy A. Saleh
- Department of Chemistry, School of Sciences and Engineering, The American University in Cairo, Cairo, Egypt
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Mohamed H. Yousef
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, Cairo, Egypt
| | - Anwar Abdelnaser
- Institute of Global Public Health, School of Sciences and Engineering, The American University in Cairo, Cairo, Egypt
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17
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Scherer M, Nazarov PV, Toth R, Sahay S, Kaoma T, Maurer V, Vedeneev N, Plass C, Lengauer T, Walter J, Lutsik P. Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz. Nat Protoc 2020; 15:3240-3263. [PMID: 32978601 DOI: 10.1038/s41596-020-0369-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
DNA methylation profiling offers unique insights into human development and diseases. Often the analysis of complex tissues and cell mixtures is the only feasible option to study methylation changes across large patient cohorts. Since DNA methylomes are highly cell type specific, deconvolution methods can be used to recover cell type-specific information in the form of latent methylation components (LMCs) from such 'bulk' samples. Reference-free deconvolution methods retrieve these components without the need for DNA methylation profiles of purified cell types. Currently no integrated and guided procedure is available for data preparation and subsequent interpretation of deconvolution results. Here, we describe a three-stage protocol for reference-free deconvolution of DNA methylation data comprising: (i) data preprocessing, confounder adjustment using independent component analysis (ICA) and feature selection using DecompPipeline, (ii) deconvolution with multiple parameters using MeDeCom, RefFreeCellMix or EDec and (iii) guided biological inference and validation of deconvolution results with the R/Shiny graphical user interface FactorViz. Our protocol simplifies the analysis and guides the initial interpretation of DNA methylation data derived from complex samples. The harmonized approach is particularly useful to dissect and evaluate cell heterogeneity in complex systems such as tumors. We apply the protocol to lung cancer methylomes from The Cancer Genome Atlas (TCGA) and show that our approach identifies the proportions of stromal cells and tumor-infiltrating immune cells, as well as associations of the detected components with clinical parameters. The protocol takes slightly >3 d to complete and requires basic R skills.
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Affiliation(s)
- Michael Scherer
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shashwat Sahay
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tony Kaoma
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Valentin Maurer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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18
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Grape pomace inhibits colon carcinogenesis by suppressing cell proliferation and inducing epigenetic modifications. J Nutr Biochem 2020; 84:108443. [PMID: 32629240 DOI: 10.1016/j.jnutbio.2020.108443] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/23/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
Grape pomace (GP), a by-product of the wine and juice industry, is rich in bioflavonoids and dietary fibers. We hypothesized that GP has protective effects against colitis-associated colorectal cancer (CRC). Nine-week-old female mice were fed a control diet (CON) or CON with 5% grape pomace (GP) for 2 weeks, when mice were subjected to azoxymethane (AOM)/dextran sulfate sodium (DSS) induced-CRC induction. GP supplementation ameliorated the disease activity index (DAI) score, reduced tumor number, tumor size and pathological scores in AOM/DSS treated mice. Furthermore, dietary GP suppressed colonic expression of inflammatory cytokines, IL-1β and TNF-α, and inhibited NF-κB inflammatory signaling, while increased anti-inflammatory cytokine TGF-β mRNA expression. Colorectal inflammation is known to enhance Wnt signaling and cell proliferation. In agreement, the content of β-catenin, a key downstream mediator of Wnt signaling, was reduced as was the expression of Cyclin D1, phosphorylation and content of p53 and PCNA level in GP-fed mice. In addition, GP reduced the expression of ALDH1, a marker of cell stemness, and increased the expression of Cdx2, a key transcription factor initiating epithelial cell differentiation, DNA methylation of the promoter region of Cdx2 gene and hypermethylation of CpG island methylator phenotype (CIMP), which commonly occurs during CRC carcinogenesis, was alleviated in the GP group. In conclusion, GP supplementation suppressed colitis-associated CRC carcinogenesis, which was associated with the suppression of inflammation and cell proliferation and the enhancement of DNA demethylation in Cdx2 and CIMP genes in the colon. These data suggest that dietary GP supplementation has preventive effects against colorectal carcinogenesis.
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19
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Agliata I, Fernandez-Jimenez N, Goldsmith C, Marie JC, Bilbao JR, Dante R, Hernandez-Vargas H. The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells. Epigenetics 2020; 15:1068-1082. [PMID: 32281463 PMCID: PMC7518701 DOI: 10.1080/15592294.2020.1748916] [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] [Indexed: 02/07/2023] Open
Abstract
Abnormal DNA methylation has been described in human inflammatory conditions of the gastrointestinal tract, such as inflammatory bowel disease (IBD). As other complex diseases, IBD results from the balance between genetic predisposition and environmental exposures. As such, DNA methylation may be the consequence (and potential effector) of both, genetic susceptibility variants and/or environmental signals such as cytokine exposure. We attempted to discern between these two non-excluding possibilities by performing a combined analysis of published DNA methylation data in intestinal mucosal cells of IBD and control samples. We identified abnormal DNA methylation at different levels: deviation from mean methylation signals at site and region levels, and differential variability. A fraction of such changes is associated with genetic polymorphisms linked to IBD susceptibility. In addition, by comparing with another intestinal inflammatory condition (i.e., coeliac disease) we propose that aberrant DNA methylation can also be the result of unspecific processes such as chronic inflammation. Our characterization suggests that IBD methylomes combine intrinsic and extrinsic responses in intestinal mucosal cells, and could point to knowledge-based biomarkers of IBD detection and progression.
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Affiliation(s)
- Iolanda Agliata
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa, Spain
| | - Chloe Goldsmith
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France
| | - Julien C Marie
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France
| | - Jose R Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa, Spain.,Ciber de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) , Madrid, Spain
| | - Robert Dante
- Department of Signaling of Tumoral Escape, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon , Lyon, France
| | - Hector Hernandez-Vargas
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France.,Department of Translational Research and Innovation, Centre Léon Bérard , Lyon, France
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20
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Guarner-Lans V, Ramírez-Higuera A, Rubio-Ruiz ME, Castrejón-Téllez V, Soto ME, Pérez-Torres I. Early Programming of Adult Systemic Essential Hypertension. Int J Mol Sci 2020; 21:E1203. [PMID: 32054074 PMCID: PMC7072742 DOI: 10.3390/ijms21041203] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cardiovascular diseases are being included in the study of developmental origins of health and disease (DOHaD) and essential systemic hypertension has also been added to this field. Epigenetic modifications are one of the main mechanisms leading to early programming of disease. Different environmental factors occurring during critical windows in the early stages of life may leave epigenetic cues, which may be involved in the programming of hypertension when individuals reach adulthood. Such environmental factors include pre-term birth, low weight at birth, altered programming of different organs such as the blood vessels and the kidney, and living in disadvantageous conditions in the programming of hypertension. Mechanisms behind these factors that impact on the programming include undernutrition, oxidative stress, inflammation, emotional stress, and changes in the microbiota. These factors and their underlying causes acting at the vascular level will be discussed in this paper. We also explore the establishment of epigenetic cues that may lead to hypertension at the vascular level such as DNA methylation, histone modifications (methylation and acetylation), and the role of microRNAs in the endothelial cells and blood vessel smooth muscle which participate in hypertension. Since epigenetic changes are reversible, the knowledge of this type of markers could be useful in the field of prevention, diagnosis or epigenetic drugs as a therapeutic approach to hypertension.
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Affiliation(s)
- Verónica Guarner-Lans
- Department of Physiology, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico; (M.E.R.-R.); (V.C.-T.)
| | - Abril Ramírez-Higuera
- Nutrition Biochemistry Laboratory, Research and Food Development Unit. Veracruz Technological Institute, National Technological of Mexico, Veracruz 91897, Mexico;
| | - María Esther Rubio-Ruiz
- Department of Physiology, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico; (M.E.R.-R.); (V.C.-T.)
| | - Vicente Castrejón-Téllez
- Department of Physiology, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico; (M.E.R.-R.); (V.C.-T.)
| | - María Elena Soto
- Department of Immunology, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico 14080, Mexico;
| | - Israel Pérez-Torres
- Department of Cardiovascular Biomedicine, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico 14080, Mexico;
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21
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Alpoim-Moreira J, Fernandes C, Rebordão MR, Amaral A, Pinto-Bravo P, Bliebernicht M, Skarzynski DJ, Ferreira-Dias G. Collagens and DNA methyltransferases in mare endometrosis. Reprod Domest Anim 2020; 54 Suppl 3:46-52. [PMID: 31512314 DOI: 10.1111/rda.13515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 01/19/2023]
Abstract
Inflammation and fibroproliferative diseases may be modulated by epigenetic changes. Therefore, we suggest that epigenetic mechanisms could be involved in equine endometrosis pathogenesis. DNA methylation is one of the methods to evaluate epigenetics, through the transcription of methyltransferases (DNMT1, DNMT3A, DNMT3B). The correlation between DNMTs and collagen (COL) transcripts was assessed for the different Kenney and Doig's (Current Therapy in Theriogenology. Philadelphia: WB Saunders; 1986) endometrium categories. Endometrial biopsies were randomly collected from cyclic mares. Histological classification (category I, n = 13; II A, n = 17; II B, n = 12; and III, n = 7) and evaluation of COL1A2, COL3A1 and DNMTs transcripts by qPCR, were performed. Data were analysed by one-way analysis of variance (ANOVA), Kruskal-Wallis test and Pearson correlation. As mares aged, there was an increase in endometrium fibrosis (p < .01), and in DNMT1 mRNA (p < .001). Considering DNMT3B transcripts for each category, there was an increase with fibrosis (p < .05). No changes were observed for DNMT1 and DNMT3A transcripts. However, DNMT3A mRNA levels were the highest in all categories (p < .01). In category I endometrium, a positive correlation was observed for transcripts of all DNMTs in both COLs (p < .01). In category IIA, this correlation was also maintained for all DNMTs transcripts in COL1A2 (p < .05), but only for DNMT3B in COL3A1 (p < .05). In category IIB, there was a positive correlation between DNMT3B and COL3A1 (p < .05). In category III, a positive correlation was only observed between DNMT3B and COL3A1 (p < .05). Our results suggest that there is a disturbance in COLs and DNMTs correlation during fibrosis.
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Affiliation(s)
- Joana Alpoim-Moreira
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Carina Fernandes
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Maria Rosa Rebordão
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal.,Coimbra College of Agriculture, Polytechnic Institute of Coimbra, Coimbra, Portugal
| | - Ana Amaral
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Pedro Pinto-Bravo
- Coimbra College of Agriculture, Polytechnic Institute of Coimbra, Coimbra, Portugal
| | | | | | - Graça Ferreira-Dias
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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22
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Yamashita S, Nanjo S, Rehnberg E, Iida N, Takeshima H, Ando T, Maekita T, Sugiyama T, Ushijima T. Distinct DNA methylation targets by aging and chronic inflammation: a pilot study using gastric mucosa infected with Helicobacter pylori. Clin Epigenetics 2019; 11:191. [PMID: 31829249 PMCID: PMC6907118 DOI: 10.1186/s13148-019-0789-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background Aberrant DNA methylation is induced by aging and chronic inflammation in normal tissues. The induction by inflammation is widely recognized as acceleration of age-related methylation. However, few studies addressed target genomic regions and the responsible factors in a genome-wide manner. Here, we analyzed methylation targets by aging and inflammation, taking advantage of the potent methylation induction in human gastric mucosa by Helicobacter pylori infection-triggered inflammation. Results DNA methylation microarray analysis of 482,421 CpG probes, grouped into 270,249 genomic blocks, revealed that high levels of methylation were induced in 44,461 (16.5%) genomic blocks by inflammation, even after correction of the influence of leukocyte infiltration. A total of 61.8% of the hypermethylation was acceleration of age-related methylation while 21.6% was specific to inflammation. Regions with H3K27me3 were frequently hypermethylated both by aging and inflammation. Basal methylation levels were essential for age-related hypermethylation while even regions with little basal methylation were hypermethylated by inflammation. When limited to promoter CpG islands, being a microRNA gene and high basal methylation levels strongly enhanced hypermethylation while H3K27me3 strongly enhanced inflammation-induced hypermethylation. Inflammation was capable of overriding active transcription. In young gastric mucosae, genes with high expression and frequent mutations in gastric cancers were more frequently methylated than in old ones. Conclusions Methylation by inflammation was not simple acceleration of age-related methylation. Targets of aberrant DNA methylation were different between young and old gastric mucosae, and driver genes were preferentially methylated in young gastric mucosa.
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Affiliation(s)
- Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Sohachi Nanjo
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Emil Rehnberg
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Takao Maekita
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Toshiro Sugiyama
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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23
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Jones P, Lucock M, Scarlett CJ, Veysey M, Beckett EL. Folate and Inflammation – links between folate and features of inflammatory conditions. JOURNAL OF NUTRITION & INTERMEDIARY METABOLISM 2019. [DOI: 10.1016/j.jnim.2019.100104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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24
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Grazioso TP, Brandt M, Djouder N. Diet, Microbiota, and Colorectal Cancer. iScience 2019; 21:168-187. [PMID: 31669832 PMCID: PMC6889474 DOI: 10.1016/j.isci.2019.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/03/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023] Open
Abstract
The intestinal epithelium is a very dynamic tissue under a high regenerative pressure, which makes it susceptible to malignant transformation. Proper integration of various cell signaling pathways and a balanced cross talk between different cell types composing the organ are required to maintain intestinal homeostasis. Dysregulation of this balance can lead to colorectal cancer (CRC). Here, we review important insights into molecular and cellular mechanisms of CRC. We discuss how perturbation in complex regulatory networks, including the Wnt, Notch, BMP, and Hedgehog pathways; and how variations in inflammatory signaling, nutrients, and microbiota can affect intestinal homeostasis contributing to the malignant transformation of intestinal cells.
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Affiliation(s)
- Tatiana P Grazioso
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Marta Brandt
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas, CNIO, Madrid 28029, Spain.
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25
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Lin A, Wei T, Meng H, Luo P, Zhang J. Role of the dynamic tumor microenvironment in controversies regarding immune checkpoint inhibitors for the treatment of non-small cell lung cancer (NSCLC) with EGFR mutations. Mol Cancer 2019; 18:139. [PMID: 31526368 PMCID: PMC6745797 DOI: 10.1186/s12943-019-1062-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
Immunotherapy has been incorporated into the first- and second-line treatment strategies for non-small cell lung cancer (NSCLC), profoundly ushering in a new treatment landscape. However, both adaptive signaling and oncogenic (epidermal growth factor receptor (EGFR)-driven) signaling may induce PD-L1 upregulation in NSCLC. Nevertheless, the superiority of immune checkpoint inhibitors (ICIs) in advanced EGFR-mutant NSCLC is only moderate. ICIs appear to be well tolerated, but clinical activity for some advanced EGFR-mutant NSCLC patients has only been observed in a small proportion of trials. Hence, there are still several open questions about PD-L1 axis inhibitors in patients with NSCLC whose tumors harbor EGFR mutations, such as the effect of EGFR tyrosine kinase inhibitors (TKIs) or EGFR mutations in the tumor microenvironment (TME). Finding the answers to these questions requires ongoing trials and preclinical studies to identify the mechanisms explaining this possible increased susceptibility and to identify prognostic molecular and clinical markers that may predict benefits with PD-1 axis inhibition in this specific NSCLC subpopulation. The presence of multiple mechanisms, including dynamic immune TME profiles, changes in PD-L1 expression and low tumor mutational burdens, may explain the conflicting data regarding the correlation between PD-L1 axis inhibitors and EGFR mutation status. We conducted a review of this currently controversial topic in an attempt to aid in the decision-making process.
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Affiliation(s)
- Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Hui Meng
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
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26
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Amini M, Foroughi K, Talebi F, Aghagolzade Haji H, Kamali F, Jandaghi P, Hoheisel JD, Manoochehri M. GHSR DNA hypermethylation is a new epigenetic biomarker for gastric adenocarcinoma and beyond. J Cell Physiol 2019; 234:15320-15329. [PMID: 30677130 DOI: 10.1002/jcp.28179] [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: 09/18/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Aberrations of DNA methylation are early events in the development of tumors. In this study, we investigated the DNA methylation status of growth hormone secretagogue receptor (GHSR), a promising pan-cancer biomarker, in gastric cancer (GC). Initially, data sets from DNA methylation and gene expression studies available at Gene Expression Omnibus (GEO) were analyzed. Confirmation was done on primary tumor specimens and adjacent normal stomach tissue samples. Both analyses showed significant hypermethylation of GHSR. For further validation, The Cancer Genome Atlas data on stomach cancer was used. A receiver operating characteristic curve analysis yielded an area under the curve value of 0.85, corroborating its usefulness as a diagnostic marker. A genome-wide comethylation analysis revealed several correlated genes. CREB1 was found to act as an upstream regulator of this gene network. Furthermore, GHSR methylation was found to be a biomarker in several other tumor entities, namely cancers of the bladder, endometrium, esophagus, head and neck, liver, thyroid, kidney, and ovary. Our findings along with previous reports on other types of cancer suggest a high potential of GHSR gene methylation as a pan-cancer biomarker, which could be considered for liquid biopsy applications.
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Affiliation(s)
- Mohammad Amini
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Kobra Foroughi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Fatemeh Talebi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Hemat Aghagolzade Haji
- Department of Biochemistry, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Kamali
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran, Iran
| | - Pouria Jandaghi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mehdi Manoochehri
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran.,Molecular Genetics of Breast Cancer (B072), German Cancer Research Center (DKFZ), Heidelberg, Germany
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27
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Ermolaeva M, Neri F, Ori A, Rudolph KL. Cellular and epigenetic drivers of stem cell ageing. Nat Rev Mol Cell Biol 2019; 19:594-610. [PMID: 29858605 DOI: 10.1038/s41580-018-0020-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tissue stem cells have a pivotal role in tissue maintenance and regeneration throughout the lifespan of multicellular organisms. Loss of tissue homeostasis during post-reproductive lifespan is caused, at least in part, by a decline in stem cell function and is associated with an increased incidence of diseases. Hallmarks of ageing include the accumulation of molecular damage, failure of quality control systems, metabolic changes and alterations in epigenome stability. In this Review, we discuss recent evidence in support of a novel concept whereby cell-intrinsic damage that accumulates during ageing and cell-extrinsic changes in ageing stem cell niches and the blood result in modifications of the stem cell epigenome. These cumulative epigenetic alterations in stem cells might be the cause of the deregulation of developmental pathways seen during ageing. In turn, they could confer a selective advantage to mutant and epigenetically drifted stem cells with altered self-renewal and functions, which contribute to the development of ageing-associated organ dysfunction and disease.
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Affiliation(s)
- Maria Ermolaeva
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - K Lenhard Rudolph
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany. .,Medical Faculty Jena, University Hospital Jena (UKJ), Jena, Germany.
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28
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Jorgensen BG, Ro S. Role of DNA Methylation in the Development and Differentiation of Intestinal Epithelial Cells and Smooth Muscle Cells. J Neurogastroenterol Motil 2019; 25:377-386. [PMID: 31327220 PMCID: PMC6657918 DOI: 10.5056/jnm19077] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
The mammalian intestine contains many different cell types but is comprised of 2 main cell types: epithelial cells and smooth muscle cells. Recent in vivo and in vitro evidence has revealed that various alterations to the DNA methylation apparatus within both of these cell types can result in a variety of cellular phenotypes including modified differentiation status, apoptosis, and uncontrolled growth. Methyl groups added to cytosines in regulatory genomic regions typically act to repress associated gene transcription. Aberrant DNA methylation patterns are often found in cells with abnormal growth/differentiation patterns, including those cells involved in burdensome intestinal pathologies including inflammatory bowel diseases and intestinal pseudo-obstructions. The altered methylation patterns being observed in various cell cultures and DNA methyltransferase knockout models indicate an influential connection between DNA methylation and gastrointestinal cells’ development and their response to environmental signaling. As these modified DNA methylation levels are found in a number of pathological gastrointestinal conditions, further investigations into uncovering the causative nature, and controlled regulation, of this epigenetic modification is of great interest.
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Affiliation(s)
- Brian G Jorgensen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, USA
| | - Seungil Ro
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, USA
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29
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Yang ZH, Dang YQ, Ji G. Role of epigenetics in transformation of inflammation into colorectal cancer. World J Gastroenterol 2019; 25:2863-2877. [PMID: 31249445 PMCID: PMC6589733 DOI: 10.3748/wjg.v25.i23.2863] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/24/2019] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
Molecular mechanisms associated with inflammation-promoted tumorigenesis have become an important topic in cancer research. Various abnormal epigenetic changes, including DNA methylation, histone modification, chromatin remodeling, and noncoding RNA regulation, occur during the transformation of chronic inflammation into colorectal cancer (CRC). These changes not only accelerate transformation but also lead to cancer progression and metastasis by activating carcinogenic signaling pathways. The NF-κB and STAT3 signaling pathways play a particularly important role in the transformation of inflammation into CRC, and both are critical to cellular signal transduction and constantly activated in cancer by various abnormal changes including epigenetics. The NF-κB and STAT3 signals contribute to the microenvironment for tumorigenesis through secretion of a large number of pro-inflammatory cytokines and their crosstalk in the nucleus makes it even more difficult to treat CRC. Compared with gene mutation that is irreversible, epigenetic inheritance is reversible or can be altered by the intervention. Therefore, understanding the role of epigenetic inheritance in the inflammation-cancer transformation may elucidate the pathogenesis of CRC and promote the development of innovative drugs targeting transformation to prevent and treat this malignancy. This review summarizes the literature on the roles of epigenetic mechanisms in the occurrence and development of inflammation-induced CRC. Exploring the role of epigenetics in the transformation of inflammation into CRC may help stimulate futures studies on the role of molecular therapy in CRC.
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Affiliation(s)
- Zhen-Hua Yang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
- Digestive Endoscopy Department, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yan-Qi Dang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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30
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Bogen KT. Inflammation as a Cancer Co-Initiator: New Mechanistic Model Predicts Low/Negligible Risk at Noninflammatory Carcinogen Doses. Dose Response 2019; 17:1559325819847834. [PMID: 31205456 PMCID: PMC6537503 DOI: 10.1177/1559325819847834] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 01/10/2023] Open
Abstract
Linear-no-threshold (LNT) risk extrapolation has long been applied to estimate risks posed by low-level environmental carcinogen exposures, based on the 60-year-old multistage somatic mutation/clonal expansion (MSM) cancer theory. Recent evidence supports an alternative theory: Malignant tumors arise most efficiently from a stem cell that incurs requisite mutations and also is activated by inflammation to an epigenetically mediated and maintained state of adaptive hyperplasia (AH). This new inflammation-MSM (ISM) theory posits that inflammation-activated stem cells normally restricted to sites of injury-induced inflammation and tissue repair become uniquely susceptible to efficient carcinogenesis if normal post-inflammation AH termination is blocked by mutation. This theory posits that inflammation generally thus co-initiates cancer and transiently amplifies activated stem cells, implying that MSM theory (eg, the 2-stage stochastic "Moolgavkar, Venzon, Knudson [MVK]" model) is incomplete. Because inflammation dose-response typically is not LNT, the ISM theory predicts this is also true for most (perhaps all) carcinogens. The ISM (but not the MVK) model is shown to be consistent with recent data showing ∼100% carcinoma incidence (but not DNA adducts) in livers of rats exposed to aflatoxin B1 and was eliminated when that dose was co-administered with a highly potent anti-inflammatory agent. Experimental approaches to test ISM theory more robustly are discussed.
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31
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Thankam FG, Boosani CS, Dilisio MF, Agrawal DK. Epigenetic mechanisms and implications in tendon inflammation (Review). Int J Mol Med 2019; 43:3-14. [PMID: 30387824 PMCID: PMC6257858 DOI: 10.3892/ijmm.2018.3961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022] Open
Abstract
Cellular inflammation is not just an immediate response following pathogenic infections or resulting from damage due to injury, it is also associated with normal physiological functions, including wound healing and tissue repair. The existence of such a definitive role in normal physiology and in disease pathology indicates the presence of a regulatory mechanism that is tightly controlled in normal cells. A tight control over gene expression is associated with regulatory mechanisms in the cells, which can be either inducible or epigenetic. Among other intracellular mechanisms that contribute to epigenetic gene regulation, DNA methylation has been shown to maintain a tight control over gene expression through the actions of DNA methyltransferases (DNMTs). With a clear role in developmental and tissue‑specific temporal gene regulation, the involvement of DNMTs is evident in normal and pathological conditions. In this review article, inflammation in tendons associated with disease pathology and tissue repair or regeneration at the musculoskeletal joints is critically reviewed. More specifically, the review focuses on known epigenetic mechanisms and their role in the clinical presentation of the disease in human joint disorders associated with tendon inflammation, with an emphasis on the gene regulatory mechanisms that are controlled through DNA methylation, histone deacetylation, and microRNAs.
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Affiliation(s)
| | | | - Matthew F. Dilisio
- Department of Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE 68178, USA
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32
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Easwaran H, Baylin SB. Origin and Mechanisms of DNA Methylation Dynamics in Cancers. RNA TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-14792-1_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Kang PM, Kim YJ, Seo WT, Kang SH, Kim TS, Chun BK, Seo WI, Jeong JY, Chung JI. Correlation between 5-α reductase type 2 protein expression and methylation of 5-α reductase type 2 promotor gene of benign prostatic hyperplasia. World J Urol 2018; 37:709-718. [PMID: 30069579 DOI: 10.1007/s00345-018-2422-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/25/2018] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The enzyme 5-α reductase type 2 (5-AR 2) plays a key role in the development and maintenance of the prostate gland. We evaluated the level 5-AR 2 protein expression and the relationship between methylation of the 5-AR 2 gene-promoter and 5-AR 2 protein expression of benign prostatic hyperplasia (BPH). MATERIALS AND METHODS A total of 37 prostate samples were evaluated. These included 22 samples from men undergoing transurethral prostate resections and 15 non-cancerous transition-zone human prostate tissue samples taken following radical prostatectomy. We quantified 5-AR 2 protein expression and gene-promoter methylation status using common assay procedures. Clinical variables included age, body mass index (BMI), prostate-specific antigen (PSA) levels, lipid profiles, and prostate volumes. Univariate and multivariate statistical analyses were performed followed by stepwise logistic regression modeling. RESULTS We were able to extract DNA from 36 of the 37 tissue samples and 10 of these (28%) did not express the 5-AR 2 protein. In total, 26 patients (72%) had methylated 5-AR 2 promoter-regions. There was a strong correlation between methylation of the 5-AR 2 promoter-regions and low-absent 5-AR 2 protein expression (p = 0.0003). Increasing age significantly predicted methylation status and protein expression level (p = 0.013). CONCLUSIONS The level of 5-AR 2 protein expression varies among prostate tissue samples. Methylation of the 5-AR 2 gene-promoter may account for low or absent expression of 5-AR 2 in adult human prostate tissues. Increased age correlates with increased 5-AR 2 gene-promoter methylation and decreased protein expression in men with BPH.
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Affiliation(s)
- Pil Moon Kang
- Department of Urology, Kosin Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Young Jin Kim
- Department of Biochemistry, Kosin University College of Medicine, 262 Gamcheon-ro, Seo-gu, Busan, 49267, Korea.,Cancer Research Institute, Kosin University College of Medicine, Busan, Korea
| | - Won Tae Seo
- Department of Urology, Kosin Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Su Hwan Kang
- Department of Urology, Kosin Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Taek Sang Kim
- Department of Urology, Kosin Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Bong Kwon Chun
- Department of Pathology, Kosin University College of Medicine, Busan, Korea
| | - Won Ik Seo
- Department of Urology, Busan Paik Hospital, Inje University College of Medicine, Gaegeum-dong, Busanjin-gu, Busan, 614-735, Korea
| | - Jee-Yeong Jeong
- Department of Biochemistry, Kosin University College of Medicine, 262 Gamcheon-ro, Seo-gu, Busan, 49267, Korea. .,Cancer Research Institute, Kosin University College of Medicine, Busan, Korea.
| | - Jae Il Chung
- Department of Urology, Busan Paik Hospital, Inje University College of Medicine, Gaegeum-dong, Busanjin-gu, Busan, 614-735, Korea.
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Abstract
Chronic inflammation is an aberrantly prolonged form of a protective response to a loss of tissue homeostasis and it is involved in several steps of the carcinogenesis process. As a result, many cancers are inflammation-related. The systemic inflammatory response is associated with survival in advanced and localized cancers. Two categories of scores have been proposed to monitor the systemic inflammatory response, those derived from protein measurement and those based on counting inflammatory cells. This review aims to provide a critical appraisal of these 2 categories of surrogate markers. The 3 scale modified Glasgow prognostic score (mGPS) is based on the combination of C-reactive protein and albumin and is graded 0 to 2. It has been validated worldwide showing an independent prognostic value in patients with cancer in a variety of tumour types and tumour stages. Leukocytes-based scores are mainly neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) and lymphocyte-to-monocyte ratio (LMR). Elevated NLR and/or PLR and lower LMR seem to be associated with decreased survival, but the studies about these markers are very heterogeneous. The main limit is the variety of thresholds used to dichotomize patients, so that reproducibility and reliability of leukocytes-based scores can be questioned. Hence, there is no sufficient evidence to support their use in clinical practice. Comprehensive management of patients with operable and advanced cancer should integrate the host systemic inflammatory response by calculating the mGPS. It could be a helpful tool to tailor patients' management.
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Affiliation(s)
- Aurélien Dupré
- Liverpool Hepatobiliary Centre, Aintree University Hospital, Longmoor Lane, Liverpool L9 7AL, UK; Centre Léon Bérard, Department of Surgical Oncology, Lyon, F-69008, France.
| | - Hassan Z Malik
- Liverpool Hepatobiliary Centre, Aintree University Hospital, Longmoor Lane, Liverpool L9 7AL, UK
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35
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Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N. Epigenome-based cancer risk prediction: rationale, opportunities and challenges. Nat Rev Clin Oncol 2018; 15:292-309. [PMID: 29485132 DOI: 10.1038/nrclinonc.2018.30] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Allison Jones
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ewout W Steyerberg
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands.,Department of Biomedical Data Sciences, LUMC, Leiden, Netherlands
| | - Yvonne Vergouwe
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands
| | - Odette Wegwarth
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany.,Max Planck Institute for Human Development, Center for Adaptive Rationality, Berlin, Germany
| | - Felix G Rebitschek
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany
| | - Uwe Siebert
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria.,Harvard T. C. Chan School of Public Health, Center for Health Decision Science, Department of Health Policy and Management, Boston, MA, USA.,Oncotyrol: Center for Personalized Medicine, Innsbruck, Austria
| | - Gaby Sroczynski
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | - Inez D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ineke Bolt
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - David Cibula
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Michal Zikan
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, and Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nicoletta Colombo
- European Institute of Oncology and University Milan-Bicocca, Milan, Italy
| | - Nadia Harbeck
- Breast Center, Department of Gynaecology and Obstetrics, University of Munich (LMU), Munich, Germany
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, UK
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36
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Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice. Proc Natl Acad Sci U S A 2018; 115:E2348-E2357. [PMID: 29467291 PMCID: PMC5877957 DOI: 10.1073/pnas.1707337115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Advanced age is not only a major risk factor for a range of disorders within an aging individual but may also enhance susceptibility for disease in the next generation. In humans, advanced paternal age has been associated with increased risk for a number of diseases. Experiments in rodent models have provided initial evidence that paternal age can influence behavioral traits in offspring animals, but the overall scope and extent of paternal age effects on health and disease across the life span remain underexplored. Here, we report that old father offspring mice showed a reduced life span and an exacerbated development of aging traits compared with young father offspring mice. Genome-wide epigenetic analyses of sperm from aging males and old father offspring tissue identified differentially methylated promoters, enriched for genes involved in the regulation of evolutionarily conserved longevity pathways. Gene expression analyses, biochemical experiments, and functional studies revealed evidence for an overactive mTORC1 signaling pathway in old father offspring mice. Pharmacological mTOR inhibition during the course of normal aging ameliorated many of the aging traits that were exacerbated in old father offspring mice. These findings raise the possibility that inherited alterations in longevity pathways contribute to intergenerational effects of aging in old father offspring mice.
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37
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Abstract
In this issue of Cancer Cell, Huang et al. describe comprehensive genetic and epigenetic profiling of gastric intestinal metaplasia lesions from a longitudinal cohort in which outcome data allowed for identification of potential markers of gastric neoplastic progression.
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Affiliation(s)
- Paul Lochhead
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Emad M El-Omar
- St George and Sutherland Clinical School, University of New South Wales, Sydney NSW 2052, Australia.
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38
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Bontha SV, Maluf DG, Archer KJ, Dumur CI, Dozmorov M, King A, Akalin E, Mueller TF, Gallon L, Mas VR. Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach. Am J Transplant 2017; 17:3060-3075. [PMID: 28556588 PMCID: PMC5734859 DOI: 10.1111/ajt.14372] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/01/2017] [Accepted: 05/20/2017] [Indexed: 01/25/2023]
Abstract
Progressive fibrosis of the interstitium is the dominant final pathway in renal destruction in native and transplanted kidneys. Over time, the continuum of molecular events following immunological and nonimmunological insults lead to interstitial fibrosis and tubular atrophy and culminate in kidney failure. We hypothesize that these insults trigger changes in DNA methylation (DNAm) patterns, which in turn could exacerbate injury and slow down the regeneration processes, leading to fibrosis development and graft dysfunction. Herein, we analyzed biopsy samples from kidney allografts collected 24 months posttransplantation and used an integrative multi-omics approach to understand the underlying molecular mechanisms. The role of DNAm and microRNAs on the graft gene expression was evaluated. Enrichment analyses of differentially methylated CpG sites were performed using GenomeRunner. CpGs were strongly enriched in regions that were variably methylated among tissues, implying high tissue specificity in their regulatory impact. Corresponding to this methylation pattern, gene expression data were related to immune response (activated state) and nephrogenesis (inhibited state). Preimplantation biopsies showed similar DNAm patterns to normal allograft biopsies at 2 years posttransplantation. Our findings demonstrate for the first time a relationship among epigenetic modifications and development of interstitial fibrosis, graft function, and inter-individual variation on long-term outcomes.
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Affiliation(s)
- Sai Vineela Bontha
- Translational Genomics Transplant Laboratory, Transplant Division, University of Virginia, Department of Surgery, PO Box 800625. 409 Lane Rd, Charlottesville, VA, 22908- 0625, USA
| | - Daniel G. Maluf
- Translational Genomics Transplant Laboratory, Transplant Division, University of Virginia, Department of Surgery, PO Box 800625. 409 Lane Rd, Charlottesville, VA, 22908- 0625, USA
| | - Kellie J. Archer
- Division of Biostatistics, The Ohio State University, 1841 Neil Avenue, 240 Cunz Hall, Columbus, OH 43210
| | - Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, PO Box 980662, 1101 E. Marshall Street, Richmond, VA 23298-0662
| | - Mikhail Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, One Capitol Square, room 730, 830 East Main Street, Richmond, Virginia 23298
| | - Anne King
- Division of Nephrology, Internal Medicine. Virginia commonwealth University, VA, 1101 E. Marshall Street, Richmond, VA 23298-0662
| | - Enver Akalin
- Departments of Clinical Medicine and Surgery, Albert Einstein College of Medicine Montefiore Medical Center, 11 E 210th St, Bronx, NY 10467
| | - Thomas F. Mueller
- Division of Nephorology, Internal Medicine, University Hospital Zurich, Ramistrasse 100, Zurich-8091
| | - Lorenzo Gallon
- Department of Medicine-Nephrology, Northwestern University676 N St Clair St # 100, Chicago, IL 60611
| | - Valeria R. Mas
- Translational Genomics Transplant Laboratory, Transplant Division, University of Virginia, Department of Surgery, PO Box 800625. 409 Lane Rd, Charlottesville, VA, 22908- 0625, USA
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39
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The role of enteric neurons in the development and progression of colorectal cancer. Biochim Biophys Acta Rev Cancer 2017; 1868:420-434. [PMID: 28847715 DOI: 10.1016/j.bbcan.2017.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023]
Abstract
The enteric nervous system (ENS) is the intrinsic neural network of the gastrointestinal tract, which is essential for regulating gut functions and intestinal homeostasis. The importance of the ENS is underscored by the existence of severe gastrointestinal diseases, such as Hirschsprung's disease and intestinal pseudo-obstruction, which arise when the ENS fails to develop normally or becomes dysregulated. Moreover, it is known that enteric neurons are involved in intestinal inflammation. However, the role of the ENS in colorectal cancer (CRC) carcinogenesis remains poorly understood, even though processes like perineural invasion and neoneurogenesis are important factors in CRC. Here we summarize how enteric neurons are affected during CRC and discuss the influence of enteric neurons, either direct or indirect, on the development and/or progression of CRC. Finally, we illustrate how the ENS could be targeted as a potential anti-cancer therapy, establishing the ENS as an integral part of the tumor microenvironment.
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40
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Wang HC, Chen CW, Yang CL, Tsai IM, Hou YC, Chen CJ, Shan YS. Tumor-Associated Macrophages Promote Epigenetic Silencing of Gelsolin through DNA Methyltransferase 1 in Gastric Cancer Cells. Cancer Immunol Res 2017; 5:885-897. [DOI: 10.1158/2326-6066.cir-16-0295] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/07/2017] [Accepted: 08/15/2017] [Indexed: 11/16/2022]
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41
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Zhou W, Tian D, He J, Zhang L, Tang X, Zhang L, Wang Y, Li L, Zhao J, Yuan X, Peng S. Exposure scenario: Another important factor determining the toxic effects of PM2.5 and possible mechanisms involved. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 226:412-425. [PMID: 28449967 DOI: 10.1016/j.envpol.2017.04.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Worsening air pollution is a serious threat to public health in many urban and heavily industrialized areas. Particle size and chemical composition are well known determinants of the pathological response to air pollution. In addition, pathological responses may depend on the exposure profile (or scenario) of air pollution. For instance, we previously demonstrated that repeated exposure to low levels of fine airborne particulate matter (PM2.5) induced distinct epigenetic changes compared to acute high-doses exposure. In the present study, we evaluated the differential pathological responses of BEAS-2B human bronchial epithelial cells to two distinct PM2.5 exposure scenarios: 24-h exposure to high-doses PM2.5 (0, 6, 12, 24, 48, 96 μg/cm2) and 10 days' repeated exposure to low levels of PM2.5 (0, 1.5, 3, 6 μg/cm2). Acute exposure to high concentrations of PM2.5 caused ROS burst, marked DNA damage, dysfunction of the endoplasmic reticulum (ER) stress response, autophagy and necrotic cell death. In contrast, repeated low levels of PM2.5 led to sustained low-grade ROS accumulation, milder DNA damage, ER stress/unfolded protein response (UPR), S-phase arrest, apoptosis, and autophagy. Notably, most cells surviving repeated low-level exposure showed a series of abnormal adaptive responses, such as inhibition of mitochondria biogenesis and epigenetic dysregulation. These results indicate that different PM2.5 exposure scenarios induce distinct forms cytotoxicity and adaptive response. In addition to particle size and chemical composition, exposure scenario may be a critical factor determining the toxic health effects of PM2.5.
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Affiliation(s)
- Wei Zhou
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Dongdong Tian
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Jun He
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Li Zhang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Xiuli Tang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Lijun Zhang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Yimei Wang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Lizhong Li
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Jun Zhao
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Xiaoyan Yuan
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China.
| | - Shuangqing Peng
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China.
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Seidel DV, Azcárate-Peril MA, Chapkin RS, Turner ND. Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk. Semin Cancer Biol 2017; 46:191-204. [PMID: 28676459 DOI: 10.1016/j.semcancer.2017.06.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 12/18/2022]
Abstract
Colon cancer is a multifactorial disease associated with a variety of lifestyle factors. Alterations in the gut microbiota and the intestinal metabolome are noted during colon carcinogenesis, implicating them as critical contributors or results of the disease process. Diet is a known determinant of health, and as a modifier of the gut microbiota and its metabolism, a critical element in maintenance of intestinal health. This review summarizes recent evidence demonstrating the role and responses of the intestinal microbiota during colon tumorigenesis and the ability of dietary bioactive compounds and probiotics to impact colon health from the intestinal lumen to the epithelium and systemically. We first describe changes to the intestinal microbiome, metabolome, and epithelium associated with colon carcinogenesis. This is followed by a discussion of recent evidence indicating how specific classes of dietary bioactives, prebiotics, or probiotics affect colon carcinogenesis. Lastly, we briefly address the prospects of using multiple 'omics' techniques to integrate the effects of diet, host, and microbiota on colon tumorigenesis with the goal of more fully appreciating the interconnectedness of these systems and thus, how these approaches can be used to advance personalized nutrition strategies and nutrition research.
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Affiliation(s)
- Derek V Seidel
- Nutrition and Food Science Department, and Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA.
| | - M Andrea Azcárate-Peril
- Department of Medicine GI Division, University of North Carolina, Chapel Hill, NC 27599-7555, USA.
| | - Robert S Chapkin
- Nutrition and Food Science Department, and Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA.
| | - Nancy D Turner
- Nutrition and Food Science Department, and Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA.
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43
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Targeting polyamine metabolism for cancer therapy and prevention. Biochem J 2017; 473:2937-53. [PMID: 27679855 DOI: 10.1042/bcj20160383] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/10/2016] [Indexed: 12/22/2022]
Abstract
The chemically simple, biologically complex eukaryotic polyamines, spermidine and spermine, are positively charged alkylamines involved in many crucial cellular processes. Along with their diamine precursor putrescine, their normally high intracellular concentrations require fine attenuation by multiple regulatory mechanisms to keep these essential molecules within strict physiologic ranges. Since the metabolism of and requirement for polyamines are frequently dysregulated in neoplastic disease, the metabolic pathway and functions of polyamines provide rational drug targets; however, these targets have been difficult to exploit for chemotherapy. It is the goal of this article to review the latest findings in the field that demonstrate the potential utility of targeting the metabolism and function of polyamines as strategies for both chemotherapy and, possibly more importantly, chemoprevention.
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44
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Zhang J, Wu W, Xu S, Zhang J, Zhang J, Yu Q, Jiao Y, Wang Y, Lu A, You Y, Zhang J, Lu X. MicroRNA-105 inhibits human glioma cell malignancy by directly targeting SUZ12. Tumour Biol 2017; 39:1010428317705766. [PMID: 28618952 DOI: 10.1177/1010428317705766] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Glioma accounts for the majority of primary malignant brain tumors in adults and is highly aggressive. Although various therapeutic approaches have been applied, outcomes of glioma treatment remain poor. MicroRNAs are a class of small noncoding RNAs that function as regulators of gene expression. Accumulating evidence shows that microRNAs are associated with tumorigenesis and tumor progression. In this study, we found that miR-105 is significantly downregulated in glioma tissues and glioma cell lines. We identified suppressor of Zeste 12 homolog as a novel direct target of miR-105 and showed that suppressor of Zeste 12 homolog protein levels were inversely correlated with the levels of miR-105 expression in clinical specimens. Overexpression of miR-105 inhibited cell proliferation, tumorigenesis, migration, invasion, and drug sensitivity, whereas overexpression of suppressor of Zeste 12 homolog antagonized the tumor-suppressive functions of miR-105. Taken together, our results indicate that miR-105 plays a significant role in tumor behavior and malignant progression, which may provide a novel therapeutic strategy for the treatment of glioma and other cancers.
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Affiliation(s)
- Jie Zhang
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Weining Wu
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Shuo Xu
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jian Zhang
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jiale Zhang
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Qun Yu
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yuanyuan Jiao
- 2 Department of Hematology, Shengjing Hospital Affiliated to China Medical University, Shenyang, People's Republic of China
| | - Yingyi Wang
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Ailin Lu
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yongping You
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Junxia Zhang
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiaoming Lu
- 1 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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Maiuri AR, Peng M, Podicheti R, Sriramkumar S, Kamplain CM, Rusch DB, DeStefano Shields CE, Sears CL, O'Hagan HM. Mismatch Repair Proteins Initiate Epigenetic Alterations during Inflammation-Driven Tumorigenesis. Cancer Res 2017; 77:3467-3478. [PMID: 28522752 DOI: 10.1158/0008-5472.can-17-0056] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/30/2017] [Accepted: 05/04/2017] [Indexed: 01/05/2023]
Abstract
Aberrant silencing of genes by DNA methylation contributes to cancer, yet how this process is initiated remains unclear. Using a murine model of inflammation-induced tumorigenesis, we tested the hypothesis that inflammation promotes recruitment of epigenetic proteins to chromatin, initiating methylation and gene silencing in tumors. Compared with normal epithelium and noninflammation-induced tumors, inflammation-induced tumors gained DNA methylation at CpG islands, some of which are associated with putative tumor suppressor genes. Hypermethylated genes exhibited enrichment of repressive chromatin marks and reduced expression prior to tumorigenesis, at a time point coinciding with peak levels of inflammation-associated DNA damage. Loss of MutS homolog 2 (MSH2), a mismatch repair (MMR) protein, abrogated early inflammation-induced epigenetic alterations and DNA hypermethylation alterations observed in inflammation-induced tumors. These results indicate that early epigenetic alterations initiated by inflammation and MMR proteins lead to gene silencing during tumorigenesis, revealing a novel mechanism of epigenetic alterations in inflammation-driven cancer. Understanding such mechanisms will inform development of pharmacotherapies to reduce carcinogenesis. Cancer Res; 77(13); 3467-78. ©2017 AACR.
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Affiliation(s)
- Ashley R Maiuri
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Michael Peng
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | | | - Shruthi Sriramkumar
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Caitlin M Kamplain
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | | | | | - Cynthia L Sears
- Departments of Medicine and Oncology, Johns Hopkins University, Baltimore, Maryland.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Heather M O'Hagan
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana. .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
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Increased transforming growth factor β and interleukin 10 transcripts in peripheral blood mononuclear cells of colorectal cancer patients. Contemp Oncol (Pozn) 2017; 20:458-462. [PMID: 28239283 PMCID: PMC5320458 DOI: 10.5114/wo.2016.65605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
Aim of the study The ability of immune cells in peripheral blood to produce certain cytokines affects tumour-elicited inflammation. The aim of this study was to investigate the gene expression of interleukin 12A (IL-12A), IL-12B, IL-23A, IL-10, IL-6, transforming growth factor β (TGF-β), HDAC3, and iNOS in peripheral blood mononuclear cells (PBMC) from colorectal cancer (CRC) patients. Material and methods The venous blood for PBMC isolation was collected preoperatively and 10 days after surgery, from CRC patients. After isolation of total RNA and synthesis of cDNA, quantitative real-time PCR assays were performed. Results Our results demonstrated that among investigated cytokine genes IL-10 and TGF-β were significantly upregulated in patients with CRC compared to the control group, while the expression of IL-23 mRNA was significantly decreased in CRC patients. We observed significantly increased mRNA levels in CRC patients’ PBMC before surgery for IL-10 and TGF-β compared to both postoperative and control groups. We also found a significant upregulation of iNOS in early compared to advanced CRC. Conclusions Based on the results we can assume that PBMC gene expression programming in CRC patients drives local differentiation of Th cells towards Treg instead of the Th1 anti-tumour subpopulation.
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Progesterone Alleviates Endometriosis via Inhibition of Uterine Cell Proliferation, Inflammation and Angiogenesis in an Immunocompetent Mouse Model. PLoS One 2016; 11:e0165347. [PMID: 27776183 PMCID: PMC5077092 DOI: 10.1371/journal.pone.0165347] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/10/2016] [Indexed: 01/08/2023] Open
Abstract
Endometriosis, defined as growth of the endometrial cells outside the uterus, is an inflammatory disorder that is associated with chronic pelvic pain and infertility in women of childbearing age. Although the estrogen-dependence of endometriosis is well known, the role of progesterone in development of this disease remains poorly understood. In this study, we developed a disease model in which endometriosis was induced in the peritoneal cavities of immunocompetent female mice, and maintained with exogenous estrogen. The endometriosis-like lesions that were identified at a variety of ectopic locations exhibited abundant blood supply and extensive adhesions. Histological examination revealed that these lesions had a well-organized endometrial architecture and fibrotic response, resembling those recovered from clinical patients. In addition, an extensive proliferation, inflammatory response, and loss of estrogen receptor alpha (ERα) and progesterone receptor (PR) expression were also observed in these lesions. Interestingly, administration of progesterone before, but not after, lesion induction suppressed lesion expansion and maintained ERα and PR expressions. These progesterone-pretreated lesions exhibited attenuation in KI67, CD31, and pro-inflammatory cytokine expression as well as macrophage infiltration, indicating that progesterone ameliorates endometriosis progression by inhibiting cell proliferation, inflammation and neovascularization. Our studies further showed that suppression of global DNA methylation by application of DNA methyltransferase inhibitor to female mice bearing ectopic lesions restrained lesion expansion and restored ERα and PR expression in eutopic endometrium and ectopic lesions. These results indicate that epigenetic regulation of target gene expression via DNA methylation contributes, at least in part, to progesterone resistance in endometriosis.
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Maiuri AR, O'Hagan HM. Interplay Between Inflammation and Epigenetic Changes in Cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 144:69-117. [PMID: 27865469 DOI: 10.1016/bs.pmbts.2016.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immune responses can suppress tumorigenesis, but also contribute to cancer initiation and progression suggesting a complex interaction between the immune system and cancer. Epigenetic alterations, which are heritable changes in gene expression without changes to the DNA sequence, also play a role in carcinogenesis through silencing expression of tumor suppressor genes and activating oncogenic signaling. Interestingly, epithelial cells at sites of chronic inflammation undergo DNA methylation alterations that are similar to those present in cancer cells, suggesting that inflammation may initiate cancer-specific epigenetic changes in epithelial cells. Furthermore, epigenetic changes occur during immune cell differentiation and participate in regulating the immune response, including the regulation of inflammatory cytokines. Cancer cells utilize epigenetic silencing of immune-related genes to evade the immune response. This chapter will detail the interactions between inflammation and epigenetics in tumor initiation, promotion, and immune evasion and how these connections are being leveraged in cancer prevention and treatment.
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Affiliation(s)
- A R Maiuri
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN, United States
| | - H M O'Hagan
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN, United States; Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States.
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49
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Yang Z, Wong A, Kuh D, Paul DS, Rakyan VK, Leslie RD, Zheng SC, Widschwendter M, Beck S, Teschendorff AE. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biol 2016; 17:205. [PMID: 27716309 PMCID: PMC5046977 DOI: 10.1186/s13059-016-1064-3] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk. Results Here, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue. By focusing on promoter CpG sites that localize to Polycomb group target genes that are unmethylated in 11 different fetal tissue types, we show that increases in DNA methylation at these sites defines a tick rate which correlates with the estimated rate of stem cell division in normal tissues. Using matched DNA methylation and RNA-seq data, we further show that it correlates with an expression-based mitotic index in cancer tissue. We demonstrate that this mitotic-like clock is universally accelerated in cancer, including pre-cancerous lesions, and that it is also accelerated in normal epithelial cells exposed to a major carcinogen. Conclusions Unlike other epigenetic and mutational clocks or the telomere clock, the epigenetic clock proposed here provides a concrete example of a mitotic-like clock which is universally accelerated in cancer and precancerous lesions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1064-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhen Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Dirk S Paul
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - R David Leslie
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China. .,Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK. .,Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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50
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Abstract
SUMMARYEpigenetic changes are present in all human cancers and are now known to cooperate with genetic alterations to drive the cancer phenotype. These changes involve DNA methylation, histone modifiers and readers, chromatin remodelers, microRNAs, and other components of chromatin. Cancer genetics and epigenetics are inextricably linked in generating the malignant phenotype; epigenetic changes can cause mutations in genes, and, conversely, mutations are frequently observed in genes that modify the epigenome. Epigenetic therapies, in which the goal is to reverse these changes, are now one standard of care for a preleukemic disorder and form of lymphoma. The application of epigenetic therapies in the treatment of solid tumors is also emerging as a viable therapeutic route.
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Affiliation(s)
- Stephen B Baylin
- Cancer Biology Program, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21287
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan 49503
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