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Raitoharju E, Rajić S, Marttila S. Non-coding 886 ( nc886/ vtRNA2-1), the epigenetic odd duck - implications for future studies. Epigenetics 2024; 19:2332819. [PMID: 38525792 DOI: 10.1080/15592294.2024.2332819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
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Affiliation(s)
- Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
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2
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Slowly M, Domingo-Relloso A, Santella RM, Haack K, Fallin DM, Terry MB, Rhoades DA, Herreros-Martinez M, Garcia-Esquinas E, Cole SA, Tellez-Plaza M, Navas-Acien A, Wu HC. Blood DNA methylation and liver cancer in American Indians: evidence from the Strong Heart Study. Cancer Causes Control 2024; 35:661-669. [PMID: 38010586 PMCID: PMC10960679 DOI: 10.1007/s10552-023-01822-8] [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: 04/29/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE Liver cancer incidence among American Indians/Alaska Natives has risen over the past 20 years. Peripheral blood DNA methylation may be associated with liver cancer and could be used as a biomarker for cancer risk. We evaluated the association of blood DNA methylation with risk of liver cancer. METHODS We conducted a prospective cohort study in 2324 American Indians, between age 45 and 75 years, from Arizona, Oklahoma, North Dakota and South Dakota who participated in the Strong Heart Study between 1989 and 1991. Liver cancer deaths (n = 21) were ascertained using death certificates obtained through 2017. The mean follow-up duration (SD) for non-cases was 25.1 (5.6) years and for cases, 11.0 (8.8) years. DNA methylation was assessed from blood samples collected at baseline using MethylationEPIC BeadChip 850 K arrays. We used Cox regression models adjusted for age, sex, center, body mass index, low-density lipoprotein cholesterol, smoking, alcohol consumption, and immune cell proportions to examine the associations. RESULTS We identified 9 CpG sites associated with liver cancer. cg16057201 annotated to MRFAP1) was hypermethylated among cases vs. non-cases (hazard ratio (HR) for one standard deviation increase in methylation was 1.25 (95% CI 1.14, 1.37). The other eight CpGs were hypomethylated and the corresponding HRs (95% CI) ranged from 0.58 (0.44, 0.75) for cg04967787 (annotated to PPRC1) to 0.77 (0.67, 0.88) for cg08550308. We also assessed 7 differentially methylated CpG sites associated with liver cancer in previous studies. The adjusted HR for cg15079934 (annotated to LPS1) was 1.93 (95% CI 1.10, 3.39). CONCLUSIONS Blood DNA methylation may be associated with liver cancer mortality and may be altered during the development of liver cancer.
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Affiliation(s)
- Monique Slowly
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Daniele M Fallin
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Mary Beth Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Dorothy A Rhoades
- Department of Medicine, Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK, USA
| | | | - Esther Garcia-Esquinas
- Universidad Autónoma de Madrid, Madrid, Spain
- CIBERESP (CIBER of Epidemiology and Public Health), Madrid, Spain
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Hui-Chen Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
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Chatterjee K, Mal S, Ghosh M, Chattopadhyay NR, Roy SD, Chakraborty K, Mukherjee S, Aier M, Choudhuri T. Blood-based DNA methylation in advanced Nasopharyngeal Carcinoma exhibited distinct CpG methylation signature. Sci Rep 2023; 13:22086. [PMID: 38086861 PMCID: PMC10716134 DOI: 10.1038/s41598-023-45001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 10/14/2023] [Indexed: 12/18/2023] Open
Abstract
The TNM staging system is currently used to detect cancer stages. Regardless, a small proportion of cancer patients recur even after therapy, suggesting more specific molecular tools are required to justify the stage-specific detection and prompt cancer diagnosis. Thus, we aimed to explore the blood-based DNA methylation signature of metastatic nasopharyngeal carcinoma (NPC) to establish a holistic methylation biomarker panel. For the identification of methylation signature, the EPIC BeadChip-based array was performed. Comparative analysis for identifying unique probes, validation, and functional studies was investigated by analyzing GEO and TCGA datasets. We observed 4093 differentially methylated probes (DMPs), 1232 hydroxymethylated probes, and 25 CpG islands. Gene expression study revealed both upregulated and downregulated genes. Correlation analysis suggested a positive (with a positive r, p ≤ 0.05) and negative (with a negative r, p ≤ 0.05) association with different cancers. TFBS analysis exhibited the binding site for many TFs. Furthermore, gene enrichment analysis indicated the involvement of those identified genes in biological pathways. However, blood-based DNA methylation data uncovered a distinct DNA methylation pattern, which might have an additive role in NPC progression by altering the TFs binding. Moreover, based on tissue-specificity, a variation of correlation between methylation and gene expression was noted in different cancers.
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Affiliation(s)
- Koustav Chatterjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Sudipa Mal
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Monalisha Ghosh
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | | | - Sankar Deb Roy
- Department of Radiation Oncology, Eden Medical Center, Dimapur, Nagaland, India
| | - Koushik Chakraborty
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Syamantak Mukherjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Moatoshi Aier
- Department of Pathology, Eden Medical Center, Dimapur, Nagaland, India
| | - Tathagata Choudhuri
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235.
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Zhang Y, Wang JW, Su X, Li JE, Wei XF, Yang JR, Gao S, Fan YC, Wang K. F-box protein 43 promoter methylation as a novel biomarker for hepatitis B virus-associated hepatocellular carcinoma. Front Microbiol 2023; 14:1267844. [PMID: 38029156 PMCID: PMC10652413 DOI: 10.3389/fmicb.2023.1267844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) has a high prevalence and poor prognosis worldwide. Therefore, it is urgent to find effective and timely diagnostic markers. The objective of this study was to evaluate the diagnostic value of F-box protein 43 promoter methylation in peripheral blood mononuclear cells (PBMCs) for HCC. Method A total of 247 participants were included in this study, comprising individuals with 123 hepatitis B virus-associated HCC, 79 chronic hepatitis B, and 45 healthy controls. F-box protein 43 methylation and mRNA levels in PBMCs were detected by MethyLight and quantitative real-time PCR. Result F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than the chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Relative mRNA expression levels of F-box protein 43 in HCC PBMCs were significantly higher than those in chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Receiver operating characteristic analysis of F-box protein 43 promoter methylation levels yielded an area under curve (AUC) of 0.793 with 76.42% sensitivity and 68.35% specificity when differentiating HCC from chronic hepatitis. These values for the F-box protein 43 promoter methylation level were superior to those of the alpha-fetoprotein serum (AFP) level (AUC: 0.780, sensitivity: 47.97%, and specificity: 96.20%), with increments in values for the combination of F-box protein 43 promoter methylation AFP levels (AUC: 0.888, sensitivity: 76.42%, and specificity: 86.08%). Conclusion Hypomethylation of the F-box protein 43 promoter in PBMCs is a promising biochemical marker for HBV-associated HCC.
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Affiliation(s)
- Ying Zhang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Wei Wang
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xing Su
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jin-E Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Fei Wei
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie-Ru Yang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
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Ghufran SM, Sharma P, Roy B, Jaiswal S, Aftab M, Sengupta S, Ghose S, Biswas S. Transcriptome wide functional analysis of HBx expressing human hepatocytes stimulated with endothelial cell cross-talk. Genomics 2023; 115:110642. [PMID: 37209778 PMCID: PMC7615065 DOI: 10.1016/j.ygeno.2023.110642] [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: 01/26/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Identification of genes dysregulated during the hepatitis B virus (HBV)-host cell interaction adds to the understanding of underlying molecular mechanisms and aids in discovering effective therapies to improve prognosis in hepatitis B virus (HBV)-infected individuals. Through bioinformatics analyses of transcriptomics data, this study aimed to identify potential genes involved in the cross-talk of human hepatocytes expressing the HBV viral protein HBx with endothelial cells. Transient transfection of HBV viral gene X (HBx) was performed in THLE2 cells using pcDNA3 constructs. Through mRNA Sequencing (RNA Seq) analysis, differentially expressed genes (DEGs) were identified. THLE2 cells transfected with HBx (THLE2x) were further treated with conditioned medium from cultured human umbilical vein derived endothelial cells (HUVEC-CM). Gene Ontology (GO) enrichment analysis revealed that interferon and cytokine signaling pathways were primarily enriched for the downregulated DEGs in THLE2x cells treated with HUVEC-CM. One significant module was selected following protein-protein interaction (PPI) network generation, and thirteen hub genes were identified from the module. The prognostic values of the hub genes were evaluated using Kaplan-Meier (KM) plotter, and three genes (IRF7, IFIT1, and IFITM1) correlated with poor disease specific survival (DSS) in HCC patients with chronic hepatitis. A comparison of the DEGs identified in HUVEC-stimulated THLE2x cells with four publicly available HBV-related HCC microarray datasets revealed that PLAC8 was consistently downregulated in all four HCC datasets as well as in HUVEC-CM treated THLE2x cells. KM plots revealed that PLAC8 correlated with worse relapse free survival and progression free survival in HCC patients with hepatitis B virus infection. This study provided molecular insights which may help develop a deeper understanding of HBV-host stromal cell interaction and open avenues for future research.
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Affiliation(s)
| | - Prachi Sharma
- Amity Institute of Molecular Medicine & Stem Cell Research, AUUP, Noida, India
| | - Bornika Roy
- Amity Institute of Molecular Medicine & Stem Cell Research, AUUP, Noida, India
| | - Shivani Jaiswal
- Amity Institute of Molecular Medicine & Stem Cell Research, AUUP, Noida, India
| | - Mehreen Aftab
- Division of Cellular and Molecular Oncology, National Institute of Cancer Prevention and Research, Noida, India
| | - Shinjinee Sengupta
- Amity Institute of Molecular Medicine & Stem Cell Research, AUUP, Noida, India
| | - Sampa Ghose
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India.
| | - Subhrajit Biswas
- Amity Institute of Molecular Medicine & Stem Cell Research, AUUP, Noida, India.
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Zeng Y, Chen HQ, Zhang Z, Fan J, Li JZ, Zhou SM, Wang N, Yan SP, Cao J, Liu JY, Zhou ZY, Liu WB. IFI44L as a novel epigenetic silencing tumor suppressor promotes apoptosis through JAK/STAT1 pathway during lung carcinogenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120943. [PMID: 36584854 DOI: 10.1016/j.envpol.2022.120943] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Numerous evidence showed that the occurrence and development of lung cancer is closely related to environmental pollution. Therefore, new environmental response predictive markers are urgently needed for early diagnosis and screening of lung cancer. Interferon-induced protein 44-like (IFI44L) has been shown to be related in a variety of tumors, but its function and mechanism during lung carcinogenesis still have remained largely unknown. In this study, gene expression and methylation status were analyzed through online tools and malignant transformation models. Differentially expressed cell models and xenograft tumor models were established and used to clarify the gene function. RT-qPCR, western blotting, immunohistochemistry, and co-immunoprecipitation (Co-IP) were used to explore the mechanism. Results showed that IFI44L was dramatically downexpressed during lung carcinogenesis, and its low expression may be attributed to DNA methylation. Overexpression of IFI44L obviously inhibited cell growth and promoted apoptosis. After knockdown of IFI44L expression, the proliferation ability was remarkably increased and the apoptosis was significantly reduced. Functional enrichment showed that IFI44L was involved in apoptosis and JAK/STAT1 signaling pathway, and was highly correlated with downstream molecules. After overexpression of IFI44L, the expression of P-STAT1 and downstream molecules XAF1, OAS1, OAS2 and OAS3 were significantly increased. After knockdown of STAT1 expression, the pro-apoptotic effect of IFI44L was reduced. Co-IP results showed that IFI44L had protein interaction with STAT1. Results proved that IFI44L promoted STAT1 phosphorylation and activated the JAK/STAT1 signaling pathway by directly binding to STAT1 protein, thereby leading to cell apoptosis. Our study revealed that IFI44L promotes cell apoptosis and exerts tumor suppressors by activating the JAK/STAT1 signaling pathway. It further suggests that IFI44L has clinical therapeutic potential and may be a promising biomarker during lung carcinogenesis.
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Affiliation(s)
- Yong Zeng
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Hong-Qiang Chen
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Jun Fan
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Jing-Zhi Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, Xinxiang Medical University, Xinxiang, Henan, 453003, PR China
| | - Shi-Meng Zhou
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, China Medical University, Shenyang, Liaoning, 110122, PR China
| | - Na Wang
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, PR China
| | - Su-Peng Yan
- Department of Sanitary Equipment and Metrology, School of Biomedical Engineering and Medical Imaging, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Zi-Yuan Zhou
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Wen-Bin Liu
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
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7
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Zeng Y, Zhang Z, Chen H, Fan J, Yuan W, Li J, Zhou S, Liu W. Comprehensive Analysis of Immune Implication and Prognostic Value of IFI44L in Non-Small Cell Lung Cancer. Front Oncol 2022; 11:798425. [PMID: 35047409 PMCID: PMC8761744 DOI: 10.3389/fonc.2021.798425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Interferon-induced protein 44-like (IFI44L), a type I interferon-stimulated gene (ISG), has been reported to be involved in innate immune processes and to act as a tumor suppressor in several cancers. However, its immune implication on lung cancer remains unclear. Here, we systemically analyzed the immune association of IFI44L with multiple tumor-infiltrating immune cells (TIICs) and immunomodulators through bioinformatics methods in The Cancer Genome Atlas (TCGA) lung cancer cohorts. Then, the IFI44L-related immunomodulators were selected to construct the prognostic signatures in the lung adenocarcinoma (LUAD) cohort and the lung squamous cell carcinoma (LUSC) cohort, respectively. Concordance index and time-dependent receiver operating characteristics (ROC) curves were applied to evaluate the prognostic signatures. GSE72094 and GSE50081 were used to validate the TCGA-LUAD signature and TCGA-LUSC signature, respectively. A nomogram was established by risk score and clinical features in the LUAD cohort. Finally, the prognostic value and biological function of IFI44L were verified in a real-world cohort and in vitro experiments. The results indicated that IFI44L showed significant correlation with TIICs in LUAD and LUSC samples. Functional enrichment analysis showed that IFI44L may participate in various cancer/immune-related pathways, including JAK/STAT signaling pathway and NF-κB signaling pathway. A total of 44 immunomodulators presented obvious association with IFI44L in the TCGA-LUAD cohort and a robust 10-immunomodulator signature was constructed. Patients in the higher-risk group presented worse prognosis than those in the lower-risk group. Notably, the risk signature was successfully validated in GSE72094. Multivariate Cox regression suggested that the risk signature could act as independent prognostic factors in both TCGA-LUAD and GSE72094 cohorts. Besides, a 17-immunomodulator signature was established in the TCGA-LUSC cohort and similar results were presented through analysis. The nomogram exhibited good accuracy in predicting overall survival (OS) outcome among TCGA-LUAD patients than the risk signature and other clinical features, with the area under curve values being 0.782 at 1 year, 0.825 at 3 years, and 0.792 at 5 years. Finally, tissue microarray analysis indicated that higher expression of IFI44L presented opposite relationship with pathological stage (p = 0.016) and a better outcome among lung cancer patients (p = 0.024). Functional experiments found that IFI44L overexpression significantly inhibited the proliferation, migration, and invasion in LUAD and LUSC cells; RT-qPCR experiments verified the correlation between the expression level of IFI44L with multiple immunomodulators in SPC-A-1 and NCI-H520 cells. In conclusion, our research highlighted that IFI44L is associated with tumor immune infiltration and provided information on IFI44L's immune implication, which indicates that IFI44L has potential clinical immunotherapeutic value and the proposed nomogram is a promising biomarker for non-small cell lung cancer patients.
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Affiliation(s)
- Yong Zeng
- Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China.,Department of Environmental Health, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Hongqiang Chen
- Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China.,Department of Environmental Health, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jun Fan
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wenbo Yuan
- Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China.,School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Jingzhi Li
- Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China.,School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Shimeng Zhou
- Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China.,School of Public Health, China Medical University, Shenyang, China
| | - Wenbin Liu
- Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China.,Department of Environmental Health, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China
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8
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Cui D, Li W, Jiang D, Wu J, Xie J, Wu Y. Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma. Front Med (Lausanne) 2021; 8:754709. [PMID: 34660653 PMCID: PMC8514776 DOI: 10.3389/fmed.2021.754709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) specifically infects liver cells, leading to progressive liver cirrhosis and significantly increasing the risk of hepatocellular carcinoma (HCC). The maturity of sequencing technology, improvement in bioinformatics data analysis and progress of omics technologies had improved research efficiency. The occurrence and progression of HCC are affected by multisystem and multilevel pathological changes. With the application of single-omics technologies, including genomics, transcriptomics, metabolomics and proteomics in tissue and body fluid samples, and even the novel development of multi-omics analysis on a single-cell platform, HBV-associated HCC changes can be better analyzed. The review summarizes the application of single omics and combined analysis of multi-omics data in HBV-associated HCC and proposes the importance of multi-omics analysis in the type of HCC, which provide the possibility for the precise diagnosis and therapy of HBV-associated HCC.
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Affiliation(s)
- Dawei Cui
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Li
- Center of Research Laboratory, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Daixi Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianguo Wu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Jue Xie
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
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9
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Li Y, Wu Y, Hu Y. Metabolites in the Tumor Microenvironment Reprogram Functions of Immune Effector Cells Through Epigenetic Modifications. Front Immunol 2021; 12:641883. [PMID: 33927716 PMCID: PMC8078775 DOI: 10.3389/fimmu.2021.641883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/15/2021] [Indexed: 12/29/2022] Open
Abstract
Cellular metabolism of both cancer and immune cells in the acidic, hypoxic, and nutrient-depleted tumor microenvironment (TME) has attracted increasing attention in recent years. Accumulating evidence has shown that cancer cells in TME could outcompete immune cells for nutrients and at the same time, producing inhibitory products that suppress immune effector cell functions. Recent progress revealed that metabolites in the TME could dysregulate gene expression patterns in the differentiation, proliferation, and activation of immune effector cells by interfering with the epigenetic programs and signal transduction networks. Nevertheless, encouraging studies indicated that metabolic plasticity and heterogeneity between cancer and immune effector cells could provide us the opportunity to discover and target the metabolic vulnerabilities of cancer cells while potentiating the anti-tumor functions of immune effector cells. In this review, we will discuss the metabolic impacts on the immune effector cells in TME and explore the therapeutic opportunities for metabolically enhanced immunotherapy.
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Affiliation(s)
- Yijia Li
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China.,Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Yangzhe Wu
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China.,Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Yi Hu
- Microbiology and Immunology Department, School of Medicine, Jinan University, Guangzhou, China
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10
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Xu G, Zhou X, Xing J, Xiao Y, Jin B, Sun L, Yang H, Du S, Xu H, Mao Y. Identification of RASSF1A promoter hypermethylation as a biomarker for hepatocellular carcinoma. Cancer Cell Int 2020; 20:547. [PMID: 33292241 PMCID: PMC7653745 DOI: 10.1186/s12935-020-01638-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Background RAS association domain family protein 1A (RASSF1A) promoter hypermethylation is suggested to be linked to hepatocellular carcinoma (HCC), but the results remained controversial. Methods We evaluated how RASSF1A promoter hypermethylation affects HCC risk and its clinicopathological characteristics through meta-analysis. Data on DNA methylation in HCC and relevant clinical data were also collected based on The Cancer Genome Atlas (TCGA) database to investigate the prognostic role of RASSF1A promoter hypermethylation in HCC. Results Forty-four articles involving 4777 individuals were enrolled in the pooled analyses. The RASSF1A promoter methylation rate was notably higher in the HCC cases than the non-tumor cases and healthy individuals, and was significantly related to hepatitis B virus (HBV) infection-positivity and large tumor size. Kaplan–Meier survival analysis revealed that HCC cases with RASSF1A promoter hypermethylation had worse outcomes. Receiver operating characteristic curves confirmed that RASSF1A promoter methylation may be a marker of HCC-related prognoses. Conclusions RASSF1A promoter hypermethylation is a promising biomarker for the diagnosis of HCC from tissue and peripheral blood, and is an emerging therapeutic target against HCC.
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Affiliation(s)
- Gang Xu
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaoxiang Zhou
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jiali Xing
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yao Xiao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Bao Jin
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lejia Sun
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Huayu Yang
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haifeng Xu
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Yilei Mao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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11
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Mehdi A, Cheishvili D, Arakelian A, Bismar TA, Szyf M, Rabbani SA. DNA methylation signatures of Prostate Cancer in peripheral T-cells. BMC Cancer 2020; 20:588. [PMID: 32576165 PMCID: PMC7310561 DOI: 10.1186/s12885-020-07078-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/15/2020] [Indexed: 01/03/2023] Open
Abstract
Background Prostate Cancer (PCa) is the second most common cancer in men where advancements have been made for early detection using imaging techniques, however these are limited by lesion size. Immune surveillance has emerged as an effective approach for early detection and to monitor disease progression. In recent studies, we have shown that host peripheral blood immune cells undergo changes in DNA methylation in liver and breast cancer. Methods In the current study, we examined the DNA methylation status of peripheral blood T cells of men with positive biopsy for PCa versus men with negative biopsy having benign prostate tissue, defined as controls. T cells DNA was isolated and subjected to Illumina Infinium methylation EPIC array and validated using Illumina amplicon sequencing and pyrosequencing platforms. Results Differential methylation of 449 CG sites between control and PCa T cell DNA showed a correlation with Gleason score (p < 0.05). Two hundred twenty-three differentially methylated CGs between control and PCa (∆ß +/− 10%, p < 0.05), were enriched in pathways involved in immune surveillance system. Three CGs which were found differentially methylated following DMP (Differentially methylated probes) analysis of ChAMP remained significant after BH (Benjamini-Hochberg) correction, of which, 2 CGs were validated. Predictive ability of combination of these 3 CGs (polygenic methylation score, PMS) to detect PCa had high sensitivity, specificity and overall accuracy. PMS also showed strong positive correlation with Gleason score and tumor volume of PCa patients. Conclusions Results from the current study provide for the first-time a potential role of DNA methylation changes in peripheral T cells in PCa. This non-invasive methodology may allow for early intervention and stratification of patients into different prognostic groups to reduce PCa associated morbidity from repeat invasive prostate biopsies and design therapeutic strategy to reduce PCa associated mortality.
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Affiliation(s)
- Ali Mehdi
- Department of Medicine, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David Cheishvili
- HKG Epitherapeutics, Hong Kong, China.,Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Tarek A Bismar
- Departments of Pathology & Laboratory Medicine, Oncology, Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Moshe Szyf
- Department of Pharmacology, McGill University, Montreal, Quebec, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University, Montreal, Quebec, Canada. .,Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC, H4A3J1, Canada.
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12
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Zhang C, Huang C, Sui X, Zhong X, Yang W, Hu X, Li Y. Association between gene methylation and HBV infection in hepatocellular carcinoma: A meta-analysis. J Cancer 2019; 10:6457-6465. [PMID: 31772678 PMCID: PMC6856736 DOI: 10.7150/jca.33005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
Gene methylation is an epigenetic alteration in hepatocellular carcinoma (HCC), and hepatitis B virus (HBV) plays a crucial role in carcinogenesis of HCC. However, the association between gene methylation and HBV infection in HCC remains unclear. In our study, we conducted a comprehensive meta-analysis to evaluate the association. A total of 1,148 studies were initially retrieved from some literature database. After a four-step filtration, we obtained 69 case-control studies in this meta-analysis. Our results showed six genes (p16, RASSF1A, GSTP1, APC, p15 and SFRP1) in HBV-positive carcinoma tissues, one gene (GSTP1) in HBV-positive adjacent tissues and two gene (p16 and APC) in HBV-positive carcinoma serums, which were significantly hypermethylated. Subgroup meta-analysis by geographical populations revealed that GSTP1 methylation was significantly higher in HBV-positive carcinoma tissues in China and Japan. In addition, p16 and RASSF1A methylation was significantly higher in China but not in Japan. Our study indicated that HBV infection could induce DNA methylation in HCC and DNA methylation could lead to the development of HBV-related HCC.
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Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Changxin Huang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xinbing Sui
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xueqing Zhong
- Department of Gastroenterology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Wenjun Yang
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xiangrong Hu
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yongqiang Li
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang, China
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13
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Liu Z, Ye Q, Wu L, Gao F, Xie H, Zhou L, Zheng S, Xu X. Metallothionein 1 family profiling identifies MT1X as a tumor suppressor involved in the progression and metastastatic capacity of hepatocellular carcinoma. Mol Carcinog 2018; 57:1435-1444. [PMID: 29873415 DOI: 10.1002/mc.22846] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 05/14/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022]
Abstract
Metallothionein 1 (MT1s) is a family of cysteine-rich proteins with diverse functions such as metal homeostasis, oxidative stress, and carcinogenesis. However, its involvement in hepatocellular carcinoma (HCC) remains not fully understood. We aimed to explore the contribution of the individual member of MT1s to HCC. Its member mRNA levels were determined in cohort 1 of normal (n = 30), cirrhotic (n = 30), peritumoral (n = 135), and HCC (n = 135). In cohort 1, seven of eight members were down-regulated during the transition from normal liver to HCC, and only MT1G and MT1X were correlated with tumor features and outcomes. The MT1X was selected to be further stained in cohort 2 consisting of a series of liver nodules (15 normal livers, 33 cirrhotic livers, 12 dysplastic nodules, 31 HCC, and 9 HCC metastasis), and in cohort 3 (HCC, n = 85). In cohort 2, MT1X immunoreactivity was reduced in HCC and lost in metastatic HCC and showed good diagnostic performance for HCC (AUC = 0.754, 95%IC = 0.659-0.849). In cohort 3, MT1X expression in peritumoral tissues was independent predictor for HCC (recurrence free survival: HR = 0.34, 95%CI = 0.17-0.66; overall survival: HR = 0.32, 95%CI = 0.16-0.60). Moreover, we found that ectopic overexpression of MT1X delayed G1/S progression of cell cycle and promoted apoptosis in HCC cells in vitro, and suppressed tumor growth and lung metastasis in nude mice in vivo. We further demonstrated that MT1X induces cell cycle arrest and apoptosis by inactivating NF-κB signaling in HCC. In conclusion, MT1X may serve as a candidate of prognostic indicator and inhibits the progression and metastasis of HCC.
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Affiliation(s)
- Zhikun Liu
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Qianwei Ye
- Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Lingjiao Wu
- Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Feng Gao
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Haiyang Xie
- Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Lin Zhou
- Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
| | - Xiao Xu
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Ministry of Public Health, Hangzhou, China
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14
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Lubecka K, Flower K, Beetch M, Qiu J, Kurzava L, Buvala H, Ruhayel A, Gawrieh S, Liangpunsakul S, Gonzalez T, McCabe G, Chalasani N, Flanagan JM, Stefanska B. Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development. Epigenetics 2018; 13:605-626. [PMID: 29927686 PMCID: PMC6140905 DOI: 10.1080/15592294.2018.1481706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/15/2018] [Indexed: 12/31/2022] Open
Abstract
Late onset of clinical symptoms in hepatocellular carcinoma (HCC) results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable tools that would distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed. We used the Illumina HumanMethylation450 BeadChip microarray to test whether white blood cell DNA, an easily accessible source of DNA, exhibits site-specific changes in DNA methylation in blood of diagnosed HCC patients (post-diagnostic, 24 cases, 24 controls) and in prospectively collected blood specimens of HCC patients who were cancer-free at blood collection (pre-diagnostic, 21 cases, 21 controls). Out of 22 differentially methylated loci selected for validation by pyrosequencing, 19 loci with neighbouring CpG sites (probes) were confirmed in the pre-diagnostic study group and subjected to verification in a prospective cirrhotic cohort (13 cases, 23 controls). We established for the first time 9 probes that could distinguish HBV-negative cirrhotic patients who subsequently developed HCC from those who stayed cancer-free. These probes were identified within regulatory regions of BARD1, MAGEB3, BRUNOL5, FXYD6, TET1, TSPAN5, DPPA5, KIAA1210, and LSP1. Methylation levels within DPPA5, KIAA1210, and LSP1 were higher in prospective samples from HCC cases vs. cirrhotic controls. The remaining probes were hypomethylated in cases compared with controls. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established probes have potential to be developed into a routine clinical test after validation in larger cohorts.
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Affiliation(s)
- Katarzyna Lubecka
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Kirsty Flower
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Megan Beetch
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Jay Qiu
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Lucinda Kurzava
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Hannah Buvala
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Adam Ruhayel
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Samer Gawrieh
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tracy Gonzalez
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - George McCabe
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Naga Chalasani
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James M Flanagan
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Barbara Stefanska
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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15
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Beetch M, Lubecka K, Kristofzski H, Suderman M, Stefanska B. Subtle Alterations in DNA Methylation Patterns in Normal Cells in Response to Dietary Stilbenoids. Mol Nutr Food Res 2018; 62:e1800193. [PMID: 29797699 DOI: 10.1002/mnfr.201800193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/18/2018] [Indexed: 01/24/2023]
Abstract
SCOPE Searching for correlations between dietary polyphenols and risk of chronic diseases has been a challenge due to the lack of quantitative evaluation methods of long-term exposure. We previously observed substantial DNA methylation changes in human cancer cells upon treatment with polyphenols of the stilbenoid class. When induced in normal cells, such molecular changes may persist and reflect chronic exposure. METHODS AND RESULTS Illumina 450K microarray is used to delineate a genome wide DNA methylation landscape in MCF10A human immortalized mammary epithelial cells exposed to resveratrol (RSV) at noncytotoxic 15 μM dose for 9 days. Subtle alterations are observed suggesting remodeling of DNA methylation patterns rather than switch on/off changes. Using pyrosequencing, DNA methylation is quantitatively measured at eight CpG sites located within KCNJ4, RNF169, BCHE, DAOA, HOXA9, RUNX3, KRTAP2-1, and TAGAP, upon exposure to RSV or pterostilbene and shows similar differences induced by both stilbenoids. Two of the probes, Runx3 and Kcnj4, are successfully verified in whole blood DNA from healthy rats on diets supplemented with stilbenoids. CONCLUSIONS The study provides strong support for testing the utility of polyphenol-mediated changes in DNA methylation as quantitative measures of long-term dietary exposures in nutritional epidemiology and clinical trials.
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Affiliation(s)
- Megan Beetch
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Katarzyna Lubecka
- Department of Biomedical Chemistry, Medical University of Lodz, Lodz, 92-215, Poland
| | - Heather Kristofzski
- Department of Nutrition Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Matthew Suderman
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Barbara Stefanska
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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16
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Parashar S, Cheishvili D, Mahmood N, Arakelian A, Tanvir I, Khan HA, Kremer R, Mihalcioiu C, Szyf M, Rabbani SA. DNA methylation signatures of breast cancer in peripheral T-cells. BMC Cancer 2018; 18:574. [PMID: 29776342 PMCID: PMC5960123 DOI: 10.1186/s12885-018-4482-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Immune surveillance acts as a defense mechanism in cancer, and its disruption is involved in cancer progression. DNA methylation reflects the phenotypic identity of cells and recent data suggested that DNA methylation profiles of T cells and peripheral blood mononuclear cells (PBMC) are altered in cancer progression. METHODS We enrolled 19 females with stage 1 and 2, nine with stage 3 and 4 and 9 age matched healthy women. T cells were isolated from peripheral blood and extracted DNA was subjected to Illumina 450 K DNA methylation array analysis. Raw data was analyzed by BMIQ, ChAMP and ComBat followed by validation of identified genes by pyrosequencing. RESULTS Analysis of data revealed ~ 10,000 sites that correlated with breast cancer progression and established a list of 89 CG sites that were highly correlated (p < 0.01, r > 0.7, r < - 0.7) with breast cancer progression. The vast majority of these sites were hypomethylated and enriched in genes with functions in the immune system. CONCLUSIONS The study points to the possibility of using DNA methylation signatures as a noninvasive method for early detection of breast cancer and its progression which need to be tested in clinical studies.
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Affiliation(s)
- Surabhi Parashar
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - David Cheishvili
- Department of Pharmacology and Therapeutics, McGill University Health Center, Montreal, QC, Canada.,Present address: Montreal EpiTerapia Inc., Montreal, QC, Canada
| | - Niaz Mahmood
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | | | | | - Richard Kremer
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Catalin Mihalcioiu
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University Health Center, Montreal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada.
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17
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Li Y, Ge C, Feng G, Xiao H, Dong J, Zhu C, Jiang M, Cui M, Fan S. Low dose irradiation facilitates hepatocellular carcinoma genesis involving HULC. Mol Carcinog 2018; 57:926-935. [PMID: 29573465 DOI: 10.1002/mc.22813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 12/27/2022]
Abstract
Irradiation exposure positive correlates with tumor formation, such as breast cancer and lung cancer. However, whether low dose irradiation induces hepatocarcinogenesis and the underlying mechanism remain poorly defined. In the present study, we reported that low dose irradiation facilitated the proliferation of hepatocyte through up-regulating HULC in vitro and in vivo. Low dose irradiation exposure elevated HULC expression level in hepatocyte. Deletion of heightened HULC erased the cells growth accelerated following low dose irradiation exposure. CDKN1, the neighbor gene of HULC, was down-regulated by overexpression of HULC following low dose irradiation exposure via complementary base pairing, resulting in promoting cell cycle process. Thus, our findings provide new insights into the mechanism of low dose irradiation-induced hepatocarcinogenesis through HULC/CDKN1 signaling, and shed light on the potential risk of low dose irradiation for the development of hepatocellular carcinoma in pre-clinical settings.
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Affiliation(s)
- Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Chang Ge
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Guoxing Feng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huiwen Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Changchun Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Mian Jiang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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18
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Cheng Q, Zhao B, Huang Z, Su Y, Chen B, Yang S, Peng X, Ma Q, Yu X, Zhao B, Ke X. Epigenome-wide study for the offspring exposed to maternal HBV infection during pregnancy, a pilot study. Gene 2018. [PMID: 29526602 DOI: 10.1016/j.gene.2018.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIM Hepatitis B virus (HBV) can be transmitted to infants, and is related to infants' later disease risk. Epigenetic change (such as DNA methylation) may be mechanism underlying the relationship. In this study, we aimed to investigate whether prenatal HBV infection could alter DNA methylation status in newborns. METHOD We selected 12 neonates with intrauterine HBV infection whose mothers were HBsAg-positive during pregnancy, relative to 12 HBV-free neonates with HBsAg-negative mothers. The pattern of genome-wide DNA methylation in the umbilical cord blood was investigated by Illumina Infinium Human Methylation 450K BeadChip. RESULT The average level of global methylation in infected neonates exposed to maternal HBV infection was not significantly different from controls. However, after adjusting for multiple comparisons, we found differential significance in the cases group compared to the controls for 663 CpG sites, associated with 534 genes. Among these sites, 53.85% (357/663) had decreased methylation (ΔM < 0) and 46.15% (306/663) had increased methylation (ΔM > 0). The average percentage change (Δβ) in methylation ranged from -46% to 36%. Validated by pyrosequencing, we identified 4 significantly differentially methylated CpG sites in the KLHL35 gene and additional CpGs for the CPT1B gene. These genes play a role in the development of hepatocellular and colorectal carcinoma and fatty acid oxidation, suggesting the candidature of these genes in HBV related disease. CONCLUSION Prenatal HBV exposure, even without malformation or preterm birth, may alter the epigenome profile in newborns. We identified a set of genes with differentially methylated CpG sites presented in the cord blood of HBV-infected newborns with HBsAg-positive mothers, demonstrating that DNA methylation status at birth can be used as a biomarker of prenatal exposure. These DNA methylation differences suggest a possible role for epigenetic processes in neonatal development in response to prenatal HBV exposure.
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Affiliation(s)
- Qijun Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Bin Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Zhenxiang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Yanhua Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Biqin Chen
- Women and Children's medical center, Siming District, Xiamen, Fujian, China
| | - Songjing Yang
- Women and Children's medical center, Siming District, Xiamen, Fujian, China
| | - Xueqi Peng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Qilin Ma
- Neurology Department, the First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Xiaoshan Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Benhua Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China.
| | - Xiayi Ke
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China.
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Zhang Y, Petropoulos S, Liu J, Cheishvili D, Zhou R, Dymov S, Li K, Li N, Szyf M. The signature of liver cancer in immune cells DNA methylation. Clin Epigenetics 2018; 10:8. [PMID: 29375724 PMCID: PMC5774119 DOI: 10.1186/s13148-017-0436-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background The idea that changes to the host immune system are critical for cancer progression was proposed a century ago and recently regained experimental support. Results Herein, the hypothesis that hepatocellular carcinoma (HCC) leaves a molecular signature in the host peripheral immune system was tested by profiling DNA methylation in peripheral blood mononuclear cells (PBMC) and T cells from a discovery cohort (n = 69) of healthy controls, chronic hepatitis, and HCC using Illumina 450K platform and was validated in two validation sets (n = 80 and n = 48) using pyrosequencing. Conclusions The study reveals a broad signature of hepatocellular carcinoma in PBMC and T cells DNA methylation which discriminates early HCC stage from chronic hepatitis B and C and healthy controls, intensifies with progression of HCC, and is highly enriched in immune function-related genes such as PD-1, a current cancer immunotherapy target. These data also support the feasibility of using these profiles for early detection of HCC.
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Affiliation(s)
- Yonghong Zhang
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - Sophie Petropoulos
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada.,3Deparment of Clinical Science, Karolinska Institutet, Alfred Nobels Allé 8, 141 52 Huddinge, Sweden
| | - Jinhua Liu
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - David Cheishvili
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada.,Montreal EpiTerapia Inc., 4567 Cecile, H9K1N2, Montreal, QC Canada
| | - Rudy Zhou
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada
| | - Sergiy Dymov
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada
| | - Kang Li
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - Ning Li
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - Moshe Szyf
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada
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G2/M checkpoint plays a vital role at the early stage of HCC by analysis of key pathways and genes. Oncotarget 2017; 8:76305-76317. [PMID: 29100313 PMCID: PMC5652707 DOI: 10.18632/oncotarget.19351] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/29/2017] [Indexed: 01/14/2023] Open
Abstract
The present study was designed to explore the molecular mechanism at the early stage of hepatocarcinoma (HCC) and identify the candidate genes and pathways changed significantly. We downloaded the gene expression file dataset GSE6764 from GEO, adopted the Robust Multi-array Average (RMA) algorithm to preprocess the raw file. 797 differentially expressed genes (DEGs) were screened out based on the SAM method using R language. Ingenuity Pathway Analysis (IPA) was used to perform canonical pathway analysis in order to calculate the most significantly changed pathways and predict the upstream regulators. In order to confirm the results from the DEGs which based on the individual gene level, the gene set enrichment analysis (GSEA) was done from the gene set level and the leading edge analysis was performed to find out the most appeared genes in several gene sets. The PPI network was built using GeneMANIA and the key genes were calculated using cytoHubba plugin based on cytoscape 3.4.0. We found that the Cell Cycle: G2/M DNA damage checkpoint regulation is the top-ranked pathways at the early stage of HCC by IPA. The high expression of several genes including CCNB1, CDC25B, XPO1, GMPS, KPNA2 and MELK is correlated with high risk, poor prognosis and shorter overall survival time in HCC patients by use of Kaplan-Meier Survival analysis. Taken together, our study showed that the G2/M checkpoint plays a vital role at the early HCC and the genes participate in the process may serve as biomarkers for the diagnosis and prognosis.
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Lin YY, Yu MW, Lin SM, Lee SD, Chen CL, Chen DS, Chen PJ. Genome-wide association analysis identifies a GLUL haplotype for familial hepatitis B virus-related hepatocellular carcinoma. Cancer 2017; 123:3966-3976. [PMID: 28662289 DOI: 10.1002/cncr.30851] [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: 03/22/2017] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND A family history of liver cancer increases the risk of developing hepatocellular carcinoma (HCC) by 2-fold to 10-fold among patients with chronic hepatitis B virus (HBV). Previous genome-wide association studies have identified many possible susceptible loci associated with sporadic HBV-related HCC. However, despite family history being a well-known risk factor for HBV-related HCC, to the authors' knowledge its genetic mechanisms and associating loci remain largely unknown or unexplored, most likely due to the relative rarity of familial HCC and the difficulty of sample collection. METHODS The authors conducted a genome-wide association study with 139 male cases with familial HBV-related HCC and 139 non-HCC male controls with chronic HBV. The results were corroborated further with an independent cohort of 101 patients with familial HBV-related HCC and comparison with both the 1000 Genomes Project and the Taiwan Biobank. RESULTS A total of 51 risk single-nucleotide polymorphisms (P≤1E-04) were identified in the association analyses, which included 2 clusters of associated single-nucleotide polymorphisms and haplotypes at 1q25.3 (glutamate-ammonia ligase [GLUL]/transmembrane epididymal protein 1 [TEDDM1]/long intergenic non-protein-coding RNA 272 [LINC00272]/regulator of G-protein signaling-like 1 [RGSL1]) and 17q11.2 (solute carrier family 13 member 2 [SLC13A2]/forkhead box N1 [FOXN1]). Both the GLUL and SLC13A2/FOXN1 haplotypes have large effect sizes and were found to be different from those found from genome-wide association studies of sporadic HCCs. CONCLUSIONS To the authors' knowledge, the current study is the first genome-wide association study to identify genetic factors for familial HBV-related HCC. The results identified 2 large effect susceptible haplotypes located at GLUL and SLC13A2/FOXN1. The current study findings also suggest different genetic susceptibility between familial and sporadic HBV-related HCC. Cancer 2017;123:3966-76. © 2017 American Cancer Society.
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Affiliation(s)
- You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Whei Yu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Shi-Ming Lin
- Liver Research Unit, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taipei, Taiwan
| | - Shou-Dong Lee
- Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei, Taiwan.,Division of Gastroenterology, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Chih-Ling Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Ding-Shinn Chen
- Hepatitis Research Center, National Taiwan University, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
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