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Nam AR, Heo M, Lee KH, Kim JY, Won SH, Cho JY. The landscape of PBMC methylome in canine mammary tumors reveals the epigenetic regulation of immune marker genes and its potential application in predicting tumor malignancy. BMC Genomics 2023; 24:403. [PMID: 37460953 DOI: 10.1186/s12864-023-09471-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Genome-wide dysregulation of CpG methylation accompanies tumor progression and characteristic states of cancer cells, prompting a rationale for biomarker development. Understanding how the archetypic epigenetic modification determines systemic contributions of immune cell types is the key to further clinical benefits. RESULTS In this study, we characterized the differential DNA methylome landscapes of peripheral blood mononuclear cells (PBMCs) from 76 canines using methylated CpG-binding domain sequencing (MBD-seq). Through gene set enrichment analysis, we discovered that genes involved in the growth and differentiation of T- and B-cells are highly methylated in tumor PBMCs. We also revealed the increased methylation at single CpG resolution and reversed expression in representative marker genes regulating immune cell proliferation (BACH2, SH2D1A, TXK, UHRF1). Furthermore, we utilized the PBMC methylome to effectively differentiate between benign and malignant tumors and the presence of mammary gland tumors through a machine-learning approach. CONCLUSIONS This research contributes to a better knowledge of the comprehensive epigenetic regulation of circulating immune cells responding to tumors and suggests a new framework for identifying benign and malignant cancers using genome-wide methylome.
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Affiliation(s)
- A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Heo
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji-Yoon Kim
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Ho Won
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Luo HY, Shen HY, Perkins RS, Wang YX. Adenosine Kinase on Deoxyribonucleic Acid Methylation: Adenosine Receptor-Independent Pathway in Cancer Therapy. Front Pharmacol 2022; 13:908882. [PMID: 35721189 PMCID: PMC9200284 DOI: 10.3389/fphar.2022.908882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Methylation is an important mechanism contributing to cancer pathology. Methylation of tumor suppressor genes and oncogenes has been closely associated with tumor occurrence and development. New insights regarding the potential role of the adenosine receptor-independent pathway in the epigenetic modulation of DNA methylation offer the possibility of new interventional strategies for cancer therapy. Targeting DNA methylation of cancer-related genes is a promising therapeutic strategy; drugs like 5-Aza-2′-deoxycytidine (5-AZA-CdR, decitabine) effectively reverse DNA methylation and cancer cell growth. However, current anti-methylation (or methylation modifiers) are associated with severe side effects; thus, there is an urgent need for safer and more specific inhibitors of DNA methylation (or DNA methylation modifiers). The adenosine signaling pathway is reported to be involved in cancer pathology and participates in the development of tumors by altering DNA methylation. Most recently, an adenosine metabolic clearance enzyme, adenosine kinase (ADK), has been shown to influence methylation on tumor suppressor genes and tumor development and progression. This review article focuses on recent updates on ADK and its two isoforms, and its actions in adenosine receptor-independent pathways, including methylation modification and epigenetic changes in cancer pathology.
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Affiliation(s)
- Hao-Yun Luo
- Chongqing Medical University, Chongqing, China.,Department of Gastrointestinal and Anorectal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Hai-Ying Shen
- Department of Neuroscience, Legacy Research Institute, Portland, OR, United States.,Integrative Physiology and Neuroscience, Washington State University, Vancouver, WA, United States
| | - R Serene Perkins
- Legacy Tumor Bank, Legacy Research Institute, Portland, OR, United States.,Mid-Columbia Medical Center, The Dalles, OR, United States
| | - Ya-Xu Wang
- Chongqing Medical University, Chongqing, China.,Department of Gastrointestinal and Anorectal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
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3
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Mekonnen N, Yang H, Shin YK. Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front Oncol 2022; 12:880643. [PMID: 35785170 PMCID: PMC9247200 DOI: 10.3389/fonc.2022.880643] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination (HR) is a highly conserved DNA repair mechanism that protects cells from exogenous and endogenous DNA damage. Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) play an important role in the HR repair pathway by interacting with other DNA repair proteins such as Fanconi anemia (FA) proteins, ATM, RAD51, PALB2, MRE11A, RAD50, and NBN. These pathways are frequently aberrant in cancer, leading to the accumulation of DNA damage and genomic instability known as homologous recombination deficiency (HRD). HRD can be caused by chromosomal and subchromosomal aberrations, as well as by epigenetic inactivation of tumor suppressor gene promoters. Deficiency in one or more HR genes increases the risk of many malignancies. Another conserved mechanism involved in the repair of DNA single-strand breaks (SSBs) is base excision repair, in which poly (ADP-ribose) polymerase (PARP) enzymes play an important role. PARP inhibitors (PARPIs) convert SSBs to more cytotoxic double-strand breaks, which are repaired in HR-proficient cells, but remain unrepaired in HRD. The blockade of both HR and base excision repair pathways is the basis of PARPI therapy. The use of PARPIs can be expanded to sporadic cancers displaying the “BRCAness” phenotype. Although PARPIs are effective in many cancers, their efficacy is limited by the development of resistance. In this review, we summarize the prevalence of HRD due to mutation, loss of heterozygosity, and promoter hypermethylation of 35 DNA repair genes in ovarian, breast, colorectal, pancreatic, non-small cell lung cancer, and prostate cancer. The underlying mechanisms and strategies to overcome PARPI resistance are also discussed.
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Affiliation(s)
- Negesse Mekonnen
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Department of Veterinary Science, School of Animal Science and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hobin Yang
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
| | - Young Kee Shin
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Graduate School of Convergence Science and Technology, Seoul, South Korea
- LOGONE Bio Convergence Research Foundation, Center for Companion Diagnostics, Seoul, South Korea
- *Correspondence: Young Kee Shin,
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4
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Cao YN, Li QZ, Liu YX, Jin W, Hou R. Discovering the key genes and important DNA methylation regions in breast cancer. Hereditas 2022; 159:7. [PMID: 35063044 PMCID: PMC8781361 DOI: 10.1186/s41065-022-00220-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Breast cancer is the malignant tumor with the highest incidence in women. DNA methylation has an important effect on breast cancer, but the effect of abnormal DNA methylation on gene expression in breast cancer is still unclear. Therefore, it is very important to find therapeutic targets related to DNA methylation. RESULTS In this work, we calculated the DNA methylation distribution and gene expression level in cancer and para-cancerous tissues for breast cancer samples. We found that DNA methylation in key regions is closely related to gene expression by analyzing the relationship between the distribution characteristics of DNA methylation in different regions and the change of gene expression level. Finally, the 18 key genes (17 tumor suppressor genes and 1 oncogene) related to prognosis were confirmed by the survival analysis of clinical data. Some important DNA methylation regions in these genes that result in breast cancer were found. CONCLUSIONS We believe that 17 TSGs and 1 oncogene may be breast cancer biomarkers regulated by DNA methylation in key regions. These results will help to explore DNA methylation biomarkers as potential therapeutic targets for breast cancer.
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Affiliation(s)
- Yan-Ni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, No.235 West Daxue Street, Saihan District, Hohhot, 010021, P.R. China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, No.235 West Daxue Street, Saihan District, Hohhot, 010021, P.R. China.
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
| | - Yu-Xian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, No.235 West Daxue Street, Saihan District, Hohhot, 010021, P.R. China
| | - Wen Jin
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, No.235 West Daxue Street, Saihan District, Hohhot, 010021, P.R. China
| | - Rui Hou
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, No.235 West Daxue Street, Saihan District, Hohhot, 010021, P.R. China
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5
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Ray SK, Mukherjee S. Epigenetic Reprogramming and Landscape of Transcriptomic Interactions: Impending Therapeutic Interference of Triple-Negative Breast Cancer in Molecular Medicine. Curr Mol Med 2021; 22:835-850. [PMID: 34872474 DOI: 10.2174/1566524021666211206092437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
The mechanisms governing the development and progression of cancers are believed to be the consequence of hereditary deformities and epigenetic modifications. Accordingly, epigenetics has become an incredible and progressively explored field of research to discover better prevention and therapy for neoplasia, especially triple-negative breast cancer (TNBC). It represents 15-20% of all invasive breast cancers and will, in general, have bellicose histological highlights and poor clinical outcomes. In the early phases of triple-negative breast carcinogenesis, epigenetic deregulation modifies chromatin structure and influences the plasticity of cells. It up-keeps the oncogenic reprogramming of malignant progenitor cells with the acquisition of unrestrained selfrenewal capacities. Genomic impulsiveness in TNBC prompts mutations, copy number variations, as well as genetic rearrangements, while epigenetic remodeling includes an amendment by DNA methylation, histone modification, and noncoding RNAs of gene expression profiles. It is currently evident that epigenetic mechanisms assume a significant part in the pathogenesis, maintenance, and therapeutic resistance of TNBC. Although TNBC is a heterogeneous malaise that is perplexing to describe and treat, the ongoing explosion of genetic and epigenetic research will help to expand these endeavors. Latest developments in transcriptome analysis have reformed our understanding of human diseases, including TNBC at the molecular medicine level. It is appealing to envision transcriptomic biomarkers to comprehend tumor behavior more readily regarding its cellular microenvironment. Understanding these essential biomarkers and molecular changes will propel our capability to treat TNBC adequately. This review will depict the different aspects of epigenetics and the landscape of transcriptomics in triple-negative breast carcinogenesis and their impending application for diagnosis, prognosis, and treatment decision with the view of molecular medicine.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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6
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Seale KN, Tkaczuk KHR. Circulating Biomarkers in Breast Cancer. Clin Breast Cancer 2021; 22:e319-e331. [PMID: 34756687 DOI: 10.1016/j.clbc.2021.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/22/2021] [Accepted: 09/19/2021] [Indexed: 12/11/2022]
Abstract
Breast cancer management has progressed immensely over the decades, but the disease is still a major source of morbidity and mortality worldwide. Even with enhanced imaging detection and tissue biopsy capabilities, disease can progress on an ineffective treatment before additional information is obtained through standard methods of response evaluation, including the RECIST 1.1 criteria, widely used for assessment of treatment response and benefit from therapy.6 Circulating biomarkers have the potential to provide valuable insight into disease progression and response to therapy, and they can serve to identify actionable mutations and tumor characteristics that can direct therapy. These biomarkers can be collected at higher frequencies than imaging or tissue sampling, potentially allowing for more informed management. This review will evaluate the roles of circulating biomarkers in breast cancer, including the serum markers Carcinoembryonic antigen CA15-3, CA27-29, HER2 ECD, and investigatory markers such as GP88; and the components of the liquid biopsy, including circulating tumor cells, cell free DNA/DNA methylation, circulating tumor DNA, and circulating microRNA.
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Affiliation(s)
- Katelyn N Seale
- University of Maryland, School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, 22 South Greene Street, S9D12, Baltimore, MD 21201
| | - Katherine H R Tkaczuk
- University of Maryland, School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, 22 South Greene Street, S9D12, Baltimore, MD 21201.
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7
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Nomair AM, Ahmed SS, Mohammed AF, El Mansy H, Nomeir HM. SCGB3A1 gene DNA methylation status is associated with breast cancer in Egyptian female patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
In recent years, hypermethylation of gene promoters has emerged as one of the fundamental mechanisms for the inactivation of tumor suppressor genes and has a potential role in the early detection of breast cancer. The present study is a case-control study aimed to quantify the methylation levels in the promoters of secretoglobin 3A1 (SCGB3A1), and ataxia-telangiectasia mutated (ATM) genes and evaluate their relation to clinicopathological features of the tumor in a cohort of Egyptian female patients with breast cancer.
Methods
Genomic deoxyribonucleic acid (DNA) was extracted from 100 tissue samples, 50 breast cancer tissues and 50 adjacent non-cancerous breast tissues, then, it was subjected to bisulfite conversion. The converted DNA was amplified by real-time PCR; then, pyrosequencing was performed to quantify DNA methylation levels in four CpG sites in ATM and SCGB3A1 gene promoters. The methylation data were presented as the percentage of average methylation of all the observed CpG sites and were calculated for each sample and each gene.
Results
The percentage of DNA methylation of the SCGB3A1 promoter was significantly higher in the tumor group than in the normal group (P= 0.001). However, a non-statistical significance difference was found in the DNA methylation percentage of the ATM promoter in the tumor group compared to the normal group (P = 0.315). The SCGB3A1 promoter methylation frequency was significantly associated with estrogen receptors (ER) and progesterone receptors (PR) positive tumors, lymph node metastasis, and lymphovascular invasion. However, no association was found between ATM methylation status and the different clinicopathological features of the tumor.
Conclusions
The findings of this work showed that the SCGB3A1 promoter methylation was significantly higher in the tumor group and was significantly associated with different clinicopathologic features in breast cancer. It may be considered as a suitable biomarker for diagnosis and prognosis. However, the promoter methylation levels of the ATM gene in breast cancer cases were unable to distinguish between breast cancer tissues and adjacent normal tissues, and there is no evidence that epigenetic silencing by ATM methylation has a role in breast cancer pathogenesis.
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8
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Nassar FJ, Chamandi G, Tfaily MA, Zgheib NK, Nasr R. Peripheral Blood-Based Biopsy for Breast Cancer Risk Prediction and Early Detection. Front Med (Lausanne) 2020; 7:28. [PMID: 32118013 PMCID: PMC7026666 DOI: 10.3389/fmed.2020.00028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Among women, breast cancer (BC) is not only the most common cancer worldwide but also the leading cause of cancer death. Only 5–10% of breast cancer cases are attributed to inherited mutations (BRCA1, BRCA2, and other breast cancer susceptibility genes). Breast cancer incidence has been rising particularly in young women who are not eligible for mammography, and it has been acting as a burden especially in developing countries that lack screening and awareness programs. For this reason, research has shifted to use minimally invasive liquid biopsies especially blood-based biomarkers with potential value for breast cancer risk prediction and early detection. This mini-review will tackle the different blood-based biomarkers focusing mainly on circulating miRNA, circulating proteins, cell-free nucleic acids, methylation patterns, and exosomes. It also introduces the potential opportunities for the clinical use of these blood-based biomarkers for breast cancer risk prediction.
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Affiliation(s)
- Farah J Nassar
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghada Chamandi
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Mohamad Ali Tfaily
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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9
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Delmonico L, Silva Magalhães Costa MA, Gomes RJ, De Oliveira Vieira P, Da Silva ABP, Fournier MV, Scherrer LR, De Azevedo CM, Ornellas MHF, Alves G. Methylation profiling in promoter sequences of ATM and CDKN2A ( p14ARF/p16INK4a ) genes in blood and cfDNA from women with impalpable breast lesions. Oncol Lett 2020; 19:3003-3010. [PMID: 32218857 DOI: 10.3892/ol.2020.11382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The objective of the present study was to evaluate the epigenetic changes occurring in early stages of breast cancer. The present study investigated the methylation profile of the ATM, p14ARF and p16INK4a promoters in total blood and plasma cell-free DNA (cfDNA) from women with impalpable breast lesions compared with in total blood of a control cohort of women without breast lesions. The samples were evaluated using the methylation-specific PCR method. The Fisher's exact test was used to evaluate statistical significance between the methylation and clinical variables. A total of 111 women were evaluated, including 56 women with impalpable breast cancer (39/56 also had paired plasma cfDNA) and 55 women in the control cohort (55 blood DNA). For blood DNA from women with malignant impalpable breast lesions, p16INK4a exhibited the greatest percentage of methylation (48%), followed by ATM (37.5%) and p14ARF (27%) promoters, regardless of age variation. For plasma cfDNA, the methylation rates for ATM, p14ARF and p16INK4a were 26, 26 and 10%, respectively. The methylation rates for the blood DNA of controls were the lowest for ATM (9%), p14ARF (7%) and p16INK4a (7%). The women with impalpable breast lesions (benign and malignant lesions) exhibited the highest methylation rate, regardless of age, compared with the paired plasma cfDNA and controls. This epigenetic change was statistically significant for the promoters of ATM (P=0.009) and p16INK4a (P=0.001) (impalpable breast lesions vs. control). The present study demonstrated that epigenetic changes occurring in the ATM and CDKN2A genes detectable in liquid biopsy were associated with the development of impalpable breast lesions.
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Affiliation(s)
- Lucas Delmonico
- LaRBio-Radiation Laboratory in Biology, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | | | - Romario José Gomes
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Pâmella De Oliveira Vieira
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Ana Beatriz Passos Da Silva
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | | | | | | | - Maria Helena Faria Ornellas
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.,Postgraduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Gilda Alves
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.,Postgraduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
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10
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Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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11
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Sun J. RASSF-1A modulates proliferation-mediated oral squamous cell carcinoma progression. Cancer Cell Int 2019; 19:213. [PMID: 31423110 PMCID: PMC6693157 DOI: 10.1186/s12935-019-0932-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
Background To investigate the expression of RASSF-1A in oral squamous cell carcinoma (OSCC) and adjacent tissues, and to explore its mechanism of action in the development of OSCC. Methods RASSF-1A and proliferation-related protein expression in clinical and OSCC mouse models were detected by qPCR and western blot. In vitro experiments were used siRNA knockdown of RASSF-1A gene in SCC9 cells to detect cell proliferation, migration and apoptosis. In vivo experiments were performed using adenovirus overexpressing RASSF-1A gene in mice and observing tumor growth. Results The results of qPCR and western blot showed that the expression of RASSF-1A gene was decreased in OSCC, and the expression of CyclinD1 protein was increased. The results of co-immunoprecipitation showed that the two proteins were significantly combined in the oral cancer cell line. Knocking down the RASSF-1A gene in SCC9 cells promotes cell migration and proliferation, while reducing apoptosis and increasing CyclinD1 protein expression. Overexpression of RASSF-1A gene in mice reduces tumor volume and inhibits CyclinD1 protein expression. Conclusions Low expression of RASSF-1A gene in OSCC promotes the expression of CyclinD1 protein and tumor growth.
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Affiliation(s)
- Jianli Sun
- Department of Oral and Maxillofacial Surgery, Henan Provincial Hospital of Stomatology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450000 Henan China
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12
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Bodelon C, Ambatipudi S, Dugué PA, Johansson A, Sampson JN, Hicks B, Karlins E, Hutchinson A, Cuenin C, Chajès V, Southey MC, Romieu I, Giles GG, English D, Polidoro S, Assumma M, Baglietto L, Vineis P, Severi G, Herceg Z, Flanagan JM, Milne RL, Garcia-Closas M. Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies. Breast Cancer Res 2019; 21:62. [PMID: 31101124 PMCID: PMC6525390 DOI: 10.1186/s13058-019-1145-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental and genetic factors play an important role in the etiology of breast cancer. Several small blood-based DNA methylation studies have reported risk associations with methylation at individual CpGs and average methylation levels; however, these findings require validation in larger prospective cohort studies. To investigate the role of blood DNA methylation on breast cancer risk, we conducted a meta-analysis of four prospective cohort studies, including a total of 1663 incident cases and 1885 controls, the largest study of blood DNA methylation and breast cancer risk to date. METHODS We assessed associations with methylation at 365,145 CpGs present in the HumanMethylation450 (HM450K) Beadchip, after excluding CpGs that did not pass quality controls in all studies. Each of the four cohorts estimated odds ratios (ORs) and 95% confidence intervals (CI) for the association between each individual CpG and breast cancer risk. In addition, each study assessed the association between average methylation measures and breast cancer risk, adjusted and unadjusted for cell-type composition. Study-specific ORs were combined using fixed-effect meta-analysis with inverse variance weights. Stratified analyses were conducted by age at diagnosis (< 50, ≥ 50), estrogen receptor (ER) status (+/-), and time since blood collection (< 5, 5-10, > 10 years). The false discovery rate (q value) was used to account for multiple testing. RESULTS The average age at blood draw ranged from 52.2 to 62.2 years across the four cohorts. Median follow-up time ranged from 6.6 to 8.4 years. The methylation measured at individual CpGs was not associated with breast cancer risk (q value > 0.59). In addition, higher average methylation level was not associated with risk of breast cancer (OR = 0.94, 95% CI = 0.85, 1.05; P = 0.26; P for study heterogeneity = 0.86). We found no evidence of modification of this association by age at diagnosis (P = 0.17), ER status (P = 0.88), time since blood collection (P = 0.98), or CpG location (P = 0.98). CONCLUSIONS Our data indicate that DNA methylation measured in the blood prior to breast cancer diagnosis in predominantly postmenopausal women is unlikely to be associated with substantial breast cancer risk on the HM450K array. Larger studies or with greater methylation coverage are needed to determine if associations exist between blood DNA methylation and breast cancer risk.
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Affiliation(s)
- Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | | | - Joshua N. Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Belynda Hicks
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Eric Karlins
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Amy Hutchinson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham G. Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Dallas English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Silvia Polidoro
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manuela Assumma
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Gianluca Severi
- CESP (U1018 INSERM, Équipe Générations et Santé), Facultés de médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Roger L. Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
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Salama RH, Sayed ZEAA, Ashmawy AM, Elsewify WA, Ezzat GM, Mahmoud MA, Alsanory AA, Alsanory TA. Interrelations of Apoptotic and Cellular Senescence Genes Methylation in Inflammatory Bowel Disease Subtypes and Colorectal Carcinoma in Egyptians Patients. Appl Biochem Biotechnol 2019; 189:330-343. [PMID: 30989570 DOI: 10.1007/s12010-019-03017-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/27/2019] [Indexed: 12/24/2022]
Abstract
Ras-related domain family member 1 transcript variant A (RASSF1A) controls apoptosis and cell proliferation while p14/ARF gene has a regulatory role in cellular senescence. Failure of apoptosis and cellular senescence occurs during inflammatory bowel disease (IBD) and colorectal cancer (CRC). To reveal the role of peripheral leukocyte promoter methylation of RASSF1A and p14/ARF in the pathogenesis of IBD subtypes and CRC we investigated the methylation state of the two genes by methylation-specific polymerase chain reaction (MSP-PCR) in 60 CRC patients, 60 patients with IBD; 27 with ulcerative colitis and 33 had Crohn's disease and also in 30 healthy subjects. Methylated RASSF1A and p14/ARF genes were detected in 55% and 60% of CRC, while the frequency of the methylated RASSF1A and p14/ARF genes was 23.3% and 43.3% in IBD patients and 3.3% and 13.3% in the control group (P = 0.000 each). Also, the frequency of methylated RASSF1A gene was significantly higher in ulcerative colitis than in Crohn's disease, while a non-significant frequency of methylated p14/ARF was detected between ulcerative colitis and Crohn's disease. Furthermore, methylated RASSF1A and p14/ARF were associated with the grade of CRC but not associated with the age of patients, family history, or tumor location. Results suggest that methylated RASSF1A and p14/ARF are related to CRC and IBD pathogenesis and may be used as molecular biomarkers for early detection of CRC and IBD.
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Affiliation(s)
- Ragaa H Salama
- Department of Medical Biochemistry, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Ahmed M Ashmawy
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Wael A Elsewify
- Department of Internal Medicine, Faculty of Medicine, Aswan University, Aswan, Egypt
| | - Ghada M Ezzat
- Department of Medical Biochemistry, Faculty of Medicine, Assiut University, Assiut, Egypt.
| | - Mahmoud A Mahmoud
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Aya A Alsanory
- Students at Faculty of Medicine, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Tasneem A Alsanory
- Students at Faculty of Medicine, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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14
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Zhou C, Li J, Li Q, Liu H, Ye D, Wu Z, Shen Z, Deng H. The clinical significance of HOXA9 promoter hypermethylation in head and neck squamous cell carcinoma. J Clin Lab Anal 2019; 33:e22873. [PMID: 30843252 PMCID: PMC6595302 DOI: 10.1002/jcla.22873] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/13/2019] [Accepted: 02/10/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The purpose of the current study was to assess the association between HOXA9 (homeobox A9) promoter methylation and head and neck squamous cell carcinoma (HNSCC) and its diagnostic value. METHODS Quantitative methylation-specific PCR (qMSP) was applied to measure HOXA9 promoter methylation levels in 145 paired HNSCC and corresponding normal tissue samples. Data from the Cancer Genome Atlas (TCGA) database (n = 578; 528 HNSCC and 50 normal) were also analyzed. RESULTS Significantly higher levels of HOXA9 promoter methylation were detected in HNSCC, compared with normal, tissues (our cohort: P = 1.06E-35; TCGA cohort: P = 3.06E-39). Moreover, HOXA9 methylation was significantly increased in patients with advanced tumor (T) stage, lymph node metastasis, and advanced clinical stage. Areas under the receiver characteristic curves (AUCs) based on our cohort and TCGA data were 0.930 and 0.967, respectively. CONCLUSION In summary, our study reveals that HOXA9 promoter hypermethylation contributes to the risk of HNSCC and its progression and metastasis. Additionally, HOXA9 hypermethylation is a potential biomarker for the early diagnosis and screening of patients with HNSCC.
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Affiliation(s)
- Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Jinyun Li
- Department of Oncology and Hematology, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Qun Li
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Huigao Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Zhenhai Longsai Hospital, Ningbo, China
| | - Dong Ye
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Zhenhua Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center, Lihuili Eastern Hospital, Ningbo, China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Hongxia Deng
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
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15
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Guan Z, Yu H, Cuk K, Zhang Y, Brenner H. Whole-Blood DNA Methylation Markers in Early Detection of Breast Cancer: A Systematic Literature Review. Cancer Epidemiol Biomarkers Prev 2018; 28:496-505. [DOI: 10.1158/1055-9965.epi-18-0378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/09/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
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