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Hsieh MJ, Lo YS, Ho HY, Lin CC, Chuang YC, Chen MK. The Interaction between CLSPN Gene Polymorphisms and Alcohol Consumption Contributes to Oral Cancer Progression. Int J Mol Sci 2024; 25:1098. [PMID: 38256171 PMCID: PMC10816373 DOI: 10.3390/ijms25021098] [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: 11/03/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Most disease single nucleotide polymorphisms (SNPs) are regulatory and approximately half of heritability is occupied by the top 1% of genes, with the gene-level structure varying with the number of variants associated with the most common alleles. Cancer occurrence and progression are significantly affected by Claspin (CLSPN) gene polymorphism present in the population, which alters the expression, function, and regulation of the gene. CLSPN genotypes are associated with oral cancer, but the literature on this association is limited. As a result, the goal of this study is to investigate the correlation between CLSPN genotypes and oral cancers' development. This study will explore the presence of four CLSPN SNPs including rs12058760, rs16822339, rs535638 and rs7520495 gene polymorphisms, and analyze the expression of these genes in 304 cancer-free controls and 402 oral squamous cell carcinoma (OSCC) cases. Attempts have been made to obtain insight into the role of CLSPN gene polymorphisms in oral cancer through the analysis of this study. We demonstrated that the OSCC risk of individuals with four CLSPN SNPs relative to the wild type did not differ significantly from that of the wild type when the polymorphisms are analyzed according to individual habits. We further studied the mechanism by which CLSPN polymorphisms affect the progression of clinicopathological features in OSCC patients. The results of the degree of cell differentiation showed that compared with patients of rs7520495 SNP carrying the CC genotype, the incidence of poor cell differentiation in patients carrying the CC + GG genotype was higher (AOR: 1.998-fold; 95% CI, 1.127-3.545; p = 0.018). In particular, patients with the G genotype of rs7520495 had increased poor cell differentiation compared with patients with the C genotype (AOR: 4.736-fold; 95% CI, 1.306-17.178; p = 0.018), especially in the drinking group. On the basis of our analysis of the Cancer Genome Atlas dataset, we found that higher CLSPN levels were associated with poorer cell differentiation in oral cancers. In this study, we provide the first evidence showing that CLSPN SNPs contribute to oral cancer. Whether or not rs7520495 can be used as a confirmatory factor in the future is uncertain, but it seems likely that it can be used as an important factor in predicting recurrence, response to treatment and medication toxicity to patients with oral cancer.
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Affiliation(s)
- Ming-Ju Hsieh
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
- Doctoral Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Yu-Sheng Lo
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Hsin-Yu Ho
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Chia-Chieh Lin
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Yi-Ching Chuang
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Mu-Kuan Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
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2
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Flores SV, Roco-Videla Á, Maureira-Carsalade N, Olguín-Barraza M. [Statistical association between genetic markers and food addiction: methodological considerations]. NUTR HOSP 2023; 40:1306-1307. [PMID: 37929828 DOI: 10.20960/nh.04871] [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] [Indexed: 11/07/2023] Open
Abstract
Introduction
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Affiliation(s)
- Sergio V Flores
- Facultad de Ciencias de la Salud. Universidad Autónoma de Chile. Chile. Departamento de Ingeniería Industrial. Facultad de Ingeniería y Tecnología. Universidad San Sebastián
| | - Ángel Roco-Videla
- Facultad de Medicina. Universidad Católica de la Santísima Concepción
| | - Nelson Maureira-Carsalade
- Departamento de Ingeniería Civil. Facultad de Ingeniería. Universidad Católica de la Santísima Concepción
| | - Mariela Olguín-Barraza
- Facultad de Ciencias de Salud. Programa de Magister en Ciencias Químico-Biológicas. Universidad Bernardo O'Higgins
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3
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Seo H, Park JH, Hwang JT, Choi HK, Park SH, Lee J. Epigenetic Profiling of Type 2 Diabetes Mellitus: An Epigenome-Wide Association Study of DNA Methylation in the Korean Genome and Epidemiology Study. Genes (Basel) 2023; 14:2207. [PMID: 38137029 PMCID: PMC10743302 DOI: 10.3390/genes14122207] [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: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Diabetes is characterized by persistently high blood glucose levels and severe complications and affects millions of people worldwide. In this study, we explored the epigenetic landscape of diabetes using data from the Korean Genome and Epidemiology Study (KoGES), specifically the Ansung-Ansan (AS-AS) cohort. Using epigenome-wide association studies, we investigated DNA methylation patterns in patients with type 2 diabetes mellitus (T2DM) and those with normal glucose regulation. Differential methylation analysis revealed 106 differentially methylated probes (DMPs), with the 10 top DMPs prominently associated with TXNIP, PDK4, NBPF20, ARRDC4, UFM1, PFKFB2, C7orf50, and ABCG1, indicating significant changes in methylation. Correlation analysis highlighted the association between the leading DMPs (e.g., cg19693031 and cg26974062 for TXNIP and cg26823705 for NBPF20) and key glycemic markers (fasting plasma glucose and hemoglobin A1c), confirming their relevance in T2DM. Moreover, we identified 62 significantly differentially methylated regions (DMRs) spanning 61 genes. A DMR associated with PDE1C showed hypermethylation, whereas DMRs associated with DIP2C, FLJ90757, PRSS50, and TDRD9 showed hypomethylation. PDE1C and TDRD9 showed a strong positive correlation between the CpG sites included in each DMR, which have previously been implicated in T2DM-related processes. This study contributes to the understanding of epigenetic modifications in T2DM. These valuable insights can be utilized in identifying potential biomarkers and therapeutic targets for effective management and prevention of diabetes.
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Affiliation(s)
| | | | | | | | | | - Jangho Lee
- Korea Food Research Institute, Wanju-gun 55365, Jeollabuk-do, Republic of Korea; (H.S.); (J.-H.P.); (J.-T.H.); (H.-K.C.); (S.-H.P.)
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4
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Michalczyk K, Kapczuk P, Witczak G, Tousty P, Bosiacki M, Kurzawski M, Chlubek D, Cymbaluk-Płoska A. An Assessment of MT1A (rs11076161), MT2A (rs28366003) and MT1L (rs10636) Gene Polymorphisms and MT2 Concentration in Women with Endometrial Pathologies. Genes (Basel) 2023; 14:genes14030773. [PMID: 36981043 PMCID: PMC10048541 DOI: 10.3390/genes14030773] [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: 02/15/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Several studies have indicated a relationship between metallothionein (MT) polymorphisms and the development of different pathologies, including neoplastic diseases. However, no studies thus far have been conducted on the influence of MT polymorphisms and the development of endometrial lesions, including endometrial cancer. This study included 140 patients with normal endometrial tissue, endometrial polyps, uterine myomas and endometrial cancer. The tissue MT2 concentration was determined using the ELISA method. MT1A, MT2A and MT1L polymorphisms were analyzed using TaqMan real-time PCR genotyping assays. We found no statistical difference between the tissue MT2 concentration in patients with EC vs. benign endometrium (p = 0.579). However, tissue MT2 concentration was significantly different between uterine fibromas and normal endometrial tissue samples (p = 0.019). Menopause status did not influence the tissue MT2 concentration (p = 0.282). There were no significant associations between the prevalence of MT1A, MT2A and MT1L polymorphisms and MT2 concentration. The age, menopausal status, and diabetes status of patients were identified as EC risk factors.
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Affiliation(s)
- Kaja Michalczyk
- Department of Gynecological Surgery and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Patrycja Kapczuk
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Grzegorz Witczak
- Department of Gynecological Surgery and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Piotr Tousty
- Department of Obstetrics and Gynecology, Pomeranian Medical University, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
| | - Mateusz Bosiacki
- Department of Functional Diagnostics and Physical Medicine, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Mateusz Kurzawski
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Aneta Cymbaluk-Płoska
- Department of Reconstructive Surgery and Gynecological Oncology, Pomeranian Medical University in Szczecin, Al. Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
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Worthington M, Aurelus C, Banerjee N, Krauss C, Kahan W, Banerjee S, Gavin S, Bartlett V, Payne G, Rousch J, Verma M, Sarkar F, Banerjee HN. A Study to Investigate the Role of Noncoding RNA miR146 Alpha as a Potential Biomarker in Prostate Cancer. JOURNAL OF ANALYTICAL ONCOLOGY 2022; 11:21-23. [PMID: 36540895 PMCID: PMC9762859 DOI: 10.30683/1927-7229.2022.11.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
There is a need for additional biomarkers for the diagnosis and prognosis of prostate cancer. MicroRNAs are a class of non-protein coding RNA molecules that are frequently dysregulated in different cancers including prostate cancer and show promise as diagnostic biomarkers and targets for therapy. Here we describe the role of micro RNA 146 a (miR-146a) which may serve as a diagnostic marker for prostate cancer, as indicated from the data presented in this report. Also, a pilot study indicated differential expression of miR-146a in prostate cancer cell lines and tissues from different racial groups. This report provides a novel insight into understanding the prostate carcinogenesis.
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Affiliation(s)
- Myla Worthington
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Chelsey Aurelus
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Narendra Banerjee
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Christopher Krauss
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - William Kahan
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Satyendra Banerjee
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Sherita Gavin
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Victoria Bartlett
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Gloria Payne
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Jeffrey Rousch
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
| | - Mukesh Verma
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Suite 4E102, 9609 Medical Center Drive, Bethesda, USA
| | - Fazlul Sarkar
- Department of Pathology, Wayne State University and Barbara Karmanos Cancer Center, Detroit, USA
| | - Hirendra Nath Banerjee
- Department of Natural Sciences, Elizabeth City State University, University of North Carolina, NC 27909, USA
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Wang YW, Hu N, Li XH. Genetic and Epigenetic Regulation of Brain Organoids. Front Cell Dev Biol 2022; 10:948818. [PMID: 35846370 PMCID: PMC9283755 DOI: 10.3389/fcell.2022.948818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 12/05/2022] Open
Abstract
Revealing the mechanisms of neural development and the pathogenesis of neural diseases are one of the most challenging missions in life science. Pluripotent stem cells derived brain organoids mimic the development, maturation, signal generation, and function of human brains, providing unique advantage for neurology. Single-cell RNA sequencing (scRNA-Seq) and multielectrode array independently revealed the similarity between brain organoids and immature human brain at early developmental stages, in the context of gene transcription and dynamic network of neuronal signals. Brain organoids provided the unique opportunity to investigate the underlying mechanism of neural differentiation, senescence, and pathogenesis. In this review, we summarized the latest knowledge and technology in the brain organoid field, the current and potential applications in disease models and pre-clinic studies, with emphasizing the importance of transcriptional and epigenetic analysis.
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Zhang Z, Ji J, Liu H. Drug Repurposing in Oncology: Current Evidence and Future Direction. Curr Med Chem 2021; 28:2175-2194. [PMID: 33109032 DOI: 10.2174/0929867327999200820124111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/17/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Drug repurposing, the application of known drugs and compounds with a primary non-oncology purpose, might be an attractive strategy to offer more effective treatment options to cancer patients at a low cost and reduced time. METHODS This review described a total of 10 kinds of non-oncological drugs from more than 100 mechanical studies as well as evidence from population-based studies. The future direction of repurposed drug screening is discussed by using patient-derived tumor organoids. RESULTS Many old drugs showed previously unknown effects or off-target effects and can be intelligently applied for cancer chemoprevention and therapy. The identification of repurposed drugs needs to combine evidence from mechanical studies and population-based studies. Due to the heterogeneity of cancer, patient-derived tumor organoids can be used to screen the non-oncological drugs in vitro. CONCLUSION These identified old drugs could be repurposed in oncology and might be added as adjuvants and finally benefit patients with cancers.
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Affiliation(s)
- Zhenzhan Zhang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianguang Ji
- Center for Primary Health Care Research, Lund University/Region Skåne, Sweden
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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8
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The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. EPIGENOMES 2021; 5:epigenomes5020012. [PMID: 34968299 PMCID: PMC8594691 DOI: 10.3390/epigenomes5020012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022] Open
Abstract
Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.
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9
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Rosa RR, Garcia MA, Alves PT, Sousa EM, Pimentel LS, Barbosa LD, Loyola AM, Goulart LR, Faria PC, Cardoso SV. Revisiting the metallothionein genes polymorphisms and the risk of oral squamous cell carcinoma in a Brazilian population. Med Oral Patol Oral Cir Bucal 2021; 26:e334-e340. [PMID: 33340085 PMCID: PMC8141308 DOI: 10.4317/medoral.24215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/23/2020] [Indexed: 11/15/2022] Open
Abstract
Background Metallothioneins (MTs) gene polymorphisms have been associated with the ability of free radical scavenging and detoxification of heavy metals leading to cancer development. Our aim was to revisit, in a Brazilian population, single-nucleotide polymorphisms (SNPs) of the MT gene family previously associated with oral squamous cell carcinoma (OSCC).
Material and Methods A case-control investigation with 28 OSCC patients and 45 controls was conducted, using conventional risk factors (tobacco use and alcohol consumption) as covariates. SNPs genotyping for rs8052334 (MT1B), rs964372 (MT1B), and rs1610216 (MT2A) was performed by PCR-RFLP, and SNPs for rs11076161 (MT1A) were analyzed by TaqMan assay.
Results The only SNP associated with increased risk for OSCC was the MT-1A AA genotype (OR = 4.7; p = 0.01). We have also evidenced for the first time a significant linkage disequilibrium between the SNPs of MT-2A and MT-1A in this population with the highest frequency (30%) of the unfavorable haplotype G/A/C/T (rs1610216 / rs11076161 / rs964372 / rs8052334) of MT gene polymorphisms (OR = 6.2; p = 0.04). Interestingly, after removing the effects of conventional risk factors, we have uncovered the significance of the AA genotype of the rs11076161 with increased odds of 19-fold higher towards OSCC development.
Conclusions This is the first demonstration that a significant linkage disequilibrium among gene polymorphisms of the MT family may affect susceptibility to oral cancer, which is conditioned by the G/A/C/T haplotype (rs1610216/rs11076161/rs964372/ rs8052334) and the MT-1A gene polymorphism has a potential clinical utility for the OSCC risk assessment. Key words:Oral squamous cell carcinoma, polymorphism, metallothionein, oral cancer.
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Affiliation(s)
- R-R Rosa
- Federal University of Uberlândia School of Dentistry, Area of Pathology Av. Pará, nº 1.720, CEP: 38.405-320 Uberlândia - MG, Brazil
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10
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Zhang YH, Li H, Zeng T, Chen L, Li Z, Huang T, Cai YD. Identifying Transcriptomic Signatures and Rules for SARS-CoV-2 Infection. Front Cell Dev Biol 2021; 8:627302. [PMID: 33505977 PMCID: PMC7829664 DOI: 10.3389/fcell.2020.627302] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
The world-wide Coronavirus Disease 2019 (COVID-19) pandemic was triggered by the widespread of a new strain of coronavirus named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Multiple studies on the pathogenesis of SARS-CoV-2 have been conducted immediately after the spread of the disease. However, the molecular pathogenesis of the virus and related diseases has still not been fully revealed. In this study, we attempted to identify new transcriptomic signatures as candidate diagnostic models for clinical testing or as therapeutic targets for vaccine design. Using the recently reported transcriptomics data of upper airway tissue with acute respiratory illnesses, we integrated multiple machine learning methods to identify effective qualitative biomarkers and quantitative rules for the distinction of SARS-CoV-2 infection from other infectious diseases. The transcriptomics data was first analyzed by Boruta so that important features were selected, which were further evaluated by the minimum redundancy maximum relevance method. A feature list was produced. This list was fed into the incremental feature selection, incorporating some classification algorithms, to extract qualitative biomarker genes and construct quantitative rules. Also, an efficient classifier was built to identify patients infected with SARS-COV-2. The findings reported in this study may help in revealing the potential pathogenic mechanisms of COVID-19 and finding new targets for vaccine design.
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Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, China
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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Piña-Sánchez P, Chávez-González A, Ruiz-Tachiquín M, Vadillo E, Monroy-García A, Montesinos JJ, Grajales R, Gutiérrez de la Barrera M, Mayani H. Cancer Biology, Epidemiology, and Treatment in the 21st Century: Current Status and Future Challenges From a Biomedical Perspective. Cancer Control 2021; 28:10732748211038735. [PMID: 34565215 PMCID: PMC8481752 DOI: 10.1177/10732748211038735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Since the second half of the 20th century, our knowledge about the biology of cancer has made extraordinary progress. Today, we understand cancer at the genomic and epigenomic levels, and we have identified the cell that starts neoplastic transformation and characterized the mechanisms for the invasion of other tissues. This knowledge has allowed novel drugs to be designed that act on specific molecular targets, the immune system to be trained and manipulated to increase its efficiency, and ever more effective therapeutic strategies to be developed. Nevertheless, we are still far from winning the war against cancer, and thus biomedical research in oncology must continue to be a global priority. Likewise, there is a need to reduce unequal access to medical services and improve prevention programs, especially in countries with a low human development index.
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Affiliation(s)
- Patricia Piña-Sánchez
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | | | - Martha Ruiz-Tachiquín
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Eduardo Vadillo
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Alberto Monroy-García
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Juan José Montesinos
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Rocío Grajales
- Department of Medical Oncology, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Marcos Gutiérrez de la Barrera
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
- Clinical Research Division, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Hector Mayani
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
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12
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Rehman S, Aatif M, Rafi Z, Khan MY, Shahab U, Ahmad S, Farhan M. Effect of non-enzymatic glycosylation in the epigenetics of cancer. Semin Cancer Biol 2020; 83:543-555. [DOI: 10.1016/j.semcancer.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/09/2023]
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13
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Stevenson M, Nath Banerjee H, Banerjee N, Rawat K, Chen L, Worthington M, Hodge S, Walker R, Verma M, Sarkar F, Mandal S. A health disparities study of MicroRNA-146a expression in prostate cancer samples derived from African American and European American patients. ACTA ACUST UNITED AC 2020; 10. [PMID: 32968471 DOI: 10.5430/jst.v10n2p1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Considering the prevalence of prostate cancer all over the world, it is desired to have tools, technologies, and biomarkers which help in early detection of the disease and discriminate different races and ethnic groups. Genetic information from the single gene analysis and genome-wide association studies have identified few biomarkers, however, the drivers of prostate cancer remain unknown in the majority of prostate cancer patients. In those cases where genetic association has been identified, the genes confer only a modest risk of this cancer, hence, making them less relevant for risk counseling and disease management. There is a need for additional biomarkers for diagnosis and prognosis of prostate cancer. MicroRNAs are a class of non-protein coding RNA molecules that are frequently dysregulated in different cancers including prostate cancer and show promise as diagnostic biomarkers and targets for therapy. Here we describe the role of micro RNA 146a (miR-146a) which may serve as a diagnostic and prognostic marker for prostate cancer, as indicated from the data presented in this report. Also, a pilot study indicated differential expression of miR-146a in prostate cancer cell lines and tissues from different racial groups. Reduced expression of miR-146a was observed in African American tumor tissues compared to those from European Whites This report provides a novel insight into understanding the prostate carcinogenesis.
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Affiliation(s)
- Monet Stevenson
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Hirendra Nath Banerjee
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Narendra Banerjee
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Kuldeep Rawat
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Lin Chen
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Myla Worthington
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Sasha Hodge
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Rayshawn Walker
- Department of Natural,Pharmacy and Health, Elizabeth City State University/University of North Carolina, Elizabeth, United States
| | - Mukesh Verma
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Suite 4E102, 9609 Medical Center Drive, Bethesda, United States
| | - Fazlul Sarkar
- Department of Pathology, Wayne State University and Barbara Karmanos Cancer Center, Detroit, United States
| | - Santosh Mandal
- Department of Chemistry, Morgan State University, Baltimore, United States
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Murat K, Grüning B, Poterlowicz PW, Westgate G, Tobin DJ, Poterlowicz K. Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy. Gigascience 2020; 9:5836679. [PMID: 32401319 PMCID: PMC7219210 DOI: 10.1093/gigascience/giaa049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 02/24/2020] [Accepted: 04/21/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Infinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG locus in the human genome based on Illumina's bead technology and is one of the most common techniques used in epigenome-wide association studies. Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850,000 CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured >450,000 and 27,000 loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable. RESULTS We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy (http://galaxyproject.org), a web-based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way. CONCLUSIONS The pipeline provides a group of integrated analytical methods wrapped into an easy-to-use interface. Our tool is available from the Galaxy ToolShed, GitHub repository, and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.
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Affiliation(s)
- Katarzyna Murat
- Center for Skin Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Björn Grüning
- Freiburg Galaxy Team, University of Freiburg, Fahnenbergplatz, 79085 Freiburg im Breisgau, Germany
| | | | - Gillian Westgate
- Center for Skin Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Desmond J Tobin
- The Charles Institute for Dermatology, Belfield, School of Medicine, University College Dublin, Ireland
| | - Krzysztof Poterlowicz
- Center for Skin Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, UK
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Verma M, Agarwal N, Verma M, Kumar V. Epigenetics and animal models: applications in cancer control and treatment. Anim Biotechnol 2020. [DOI: 10.1016/b978-0-12-811710-1.00004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mishra A, Verma M. Prognostic value of epigenomic profiling in lung cancer. Transl Cancer Res 2019; 8:350-353. [PMID: 35116766 PMCID: PMC8798437 DOI: 10.21037/tcr.2019.03.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 03/27/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Alok Mishra
- Johns Hopkins University, Baltimore, MD, USA
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Ji J, Sundquist J, Sundquist K. Use of terbinafine and risk of death in patients with prostate cancer: A population‐based cohort study. Int J Cancer 2018; 144:1888-1895. [DOI: 10.1002/ijc.31901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Jianguang Ji
- Center for Primary Health Care ResearchLund University/Region Skåne Lund Sweden
| | - Jan Sundquist
- Center for Primary Health Care ResearchLund University/Region Skåne Lund Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and PolicyIcahn School of Medicine at Mount Sinai New York NY
| | - Kristina Sundquist
- Center for Primary Health Care ResearchLund University/Region Skåne Lund Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and PolicyIcahn School of Medicine at Mount Sinai New York NY
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Bae JM. Researches of Epigenetic Epidemiology for Infections and Radiation as Carcinogen. J Prev Med Public Health 2018; 51:169-172. [PMID: 30071703 PMCID: PMC6078917 DOI: 10.3961/jpmph.18.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
In recent years, a number of studies have been reported on the various types of cancer arising from epigenetic alterations, including reports that these epigenetic alterations occur as a result of radiation exposure or infection. Thyroid cancer and breast cancer, in particular, have high cancer burden, and it has been confirmed that radiation exposure or onco-viral infection are linked to increased risk of development of these two types of cancer, respectively. Thus, the environment-epigenetic alteration-cancer occurrence (EEC) hypothesis has been suggested. This paper reviews the trends in research supporting this hypothesis for radiation exposure and onco-viral infection. If more evidences accumulate for the EEC hypothesis from future research, those findings may greatly aid in the prevention, early diagnosis, treatment, and prognosis of the thyroid cancer and breast cancer.
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Affiliation(s)
- Jong-Myon Bae
- Department of Preventive Medicine, Jeju National University School of Medicine, Jeju, Korea
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Singh G, Singh V, Sobolewski M, Cory-Slechta DA, Schneider JS. Sex-Dependent Effects of Developmental Lead Exposure on the Brain. Front Genet 2018; 9:89. [PMID: 29662502 PMCID: PMC5890196 DOI: 10.3389/fgene.2018.00089] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/02/2018] [Indexed: 11/23/2022] Open
Abstract
The role of sex as an effect modifier of developmental lead (Pb) exposure has until recently received little attention. Lead exposure in early life can affect brain development with persisting influences on cognitive and behavioral functioning, as well as, elevated risks for developing a variety of diseases and disorders in later life. Although both sexes are affected by Pb exposure, the incidence, manifestation, and severity of outcomes appears to differ in males and females. Results from epidemiologic and animal studies indicate significant effect modification by sex, however, the results are not consistent across studies. Unfortunately, only a limited number of human epidemiological studies have included both sexes in independent outcome analyses limiting our ability to draw definitive conclusions regarding sex-differentiated outcomes. Additionally, due to various methodological differences across studies, there is still not a good mechanistic understanding of the molecular effects of lead on the brain and the factors that influence differential responses to Pb based on sex. In this review, focused on prenatal and postnatal Pb exposures in humans and animal models, we discuss current literature supporting sex differences in outcomes in response to Pb exposure and explore some of the ideas regarding potential molecular mechanisms that may contribute to sex-related differences in outcomes from developmental Pb exposure. The sex-dependent variability in outcomes from developmental Pb exposure may arise from a combination of complex factors, including, but not limited to, intrinsic sex-specific molecular/genetic mechanisms and external risk factors including sex-specific responses to environmental stressors which may act through shared epigenetic pathways to influence the genome and behavioral output.
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Affiliation(s)
- Garima Singh
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Vikrant Singh
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Marissa Sobolewski
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Deborah A Cory-Slechta
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Jay S Schneider
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
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