1
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Okuka N, Schuh V, Krammer U, Polovina S, Sumarac-Dumanovic M, Milinkovic N, Velickovic K, Djordjevic B, Haslberger A, Ivanovic ND. Epigenetic Aspects of a New Probiotic Concept-A Pilot Study. Life (Basel) 2023; 13:1912. [PMID: 37763315 PMCID: PMC10533075 DOI: 10.3390/life13091912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/02/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Several studies report the important role of an altered gut microbiota in the development of obesity, highlighting the potential use of probiotics in the treatment of obesity. The aim of this study is to investigate the effect of a novel probiotic approach on the expression of specific miRNAs and mRNAs associated with obesity in combination with the hypocholesterolemic octacosanol. Twenty overweight/obese women participated in a randomized, placebo-controlled, double-blind study and were randomly divided into two groups: the intervention group (daily one capsule containing Lactobacillus plantarum 299v (DSM9843), Saccharomyces cerevisiae var. boulardii, and 40 mg octacosanol; N = 12) and the placebo group (N = 8). Changes in lipid parameters and expression of miRNAs and mRNAs were assessed before (T0) and after the 12-week intervention (T1). After the intervention, the expression of miR-155-5p (9.38 ± 0.85 vs. 8.38 ± 1.06, p = 0.05) and miR-24-3p (3.42 ± 0.38 vs. 2.71 ± 0.97, p = 0.031) showed significant decreases in the intervention group when compared to the control group. At T1, the expression of miR-155-5p (8.69 ± 1.31 vs. 9.3 ± 0.85, p = 0.04), miR-125b-5p (5.41 ± 1.18 vs. 5.99 ± 1.36, p = 0.049), and TNF-α (10.24 ± 1.66 vs. 11.36 ± 1.12, p = 0.009) were significantly decreased in the intervention group. No changes in lipids and anthropometric parameters were observed. The novel probiotic approach had a positive effect on regulating the expression of certain miRNAs and mRNAs important for regulating inflammation and adipogenesis, which are essential for obesity onset and control.
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Affiliation(s)
- Nina Okuka
- Department of Bromatology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Bosnia and Herzegovina;
| | | | | | - Snezana Polovina
- Clinic for Endocrinology, Diabetes and Diseases of Metabolism, Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Mirjana Sumarac-Dumanovic
- School of Medicine, University of Belgrade, Clinic for Endocrinology, Diabetes and Diseases of Metabolism, 11000 Belgrade, Serbia
| | - Neda Milinkovic
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, 11000 Belgrade, Serbia
| | - Ksenija Velickovic
- Department of Cell and Tissue Biology, Faculty of Biology, University of Belgrade; 11000 Belgrade, Serbia
| | - Brizita Djordjevic
- Department of Bromatology, Faculty of Pharmacy, University of Belgrade, 11000 Belgrade, Serbia
| | | | - Nevena Dj. Ivanovic
- Department of Bromatology, Faculty of Pharmacy, University of Belgrade, 11000 Belgrade, Serbia
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2
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Zare A, Salehpour A, Khoradmehr A, Bakhshalizadeh S, Najafzadeh V, Almasi-Turk S, Mahdipour M, Shirazi R, Tamadon A. Epigenetic Modification Factors and microRNAs Network Associated with Differentiation of Embryonic Stem Cells and Induced Pluripotent Stem Cells toward Cardiomyocytes: A Review. Life (Basel) 2023; 13:life13020569. [PMID: 36836926 PMCID: PMC9965891 DOI: 10.3390/life13020569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 02/22/2023] Open
Abstract
More research is being conducted on myocardial cell treatments utilizing stem cell lines that can develop into cardiomyocytes. All of the forms of cardiac illnesses have shown to be quite amenable to treatments using embryonic (ESCs) and induced pluripotent stem cells (iPSCs). In the present study, we reviewed the differentiation of these cell types into cardiomyocytes from an epigenetic standpoint. We also provided a miRNA network that is devoted to the epigenetic commitment of stem cells toward cardiomyocyte cells and related diseases, such as congenital heart defects, comprehensively. Histone acetylation, methylation, DNA alterations, N6-methyladenosine (m6a) RNA methylation, and cardiac mitochondrial mutations are explored as potential tools for precise stem cell differentiation.
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Affiliation(s)
- Afshin Zare
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Aria Salehpour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Shabnam Bakhshalizadeh
- Reproductive Development, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vahid Najafzadeh
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Sahar Almasi-Turk
- Department of Basic Sciences, School of Medicine, Bushehr University of Medical Sciences, Bushehr 7514633341, Iran
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 5166653431, Iran
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 5166653431, Iran
- Correspondence: (M.M.); (R.S.); (A.T.)
| | - Reza Shirazi
- Department of Anatomy, School of Medical Sciences, Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (M.M.); (R.S.); (A.T.)
| | - Amin Tamadon
- PerciaVista R&D Co., Shiraz 7135644144, Iran
- Correspondence: (M.M.); (R.S.); (A.T.)
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3
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Fabrizio FP, Sparaneo A, Muscarella LA. Monitoring EGFR-lung cancer evolution: a possible beginning of a "methylation era" in TKI resistance prediction. Front Oncol 2023; 13:1137384. [PMID: 37152062 PMCID: PMC10157092 DOI: 10.3389/fonc.2023.1137384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
The advances in scientific knowledge on biological therapies of the last two decades have impressively oriented the clinical management of non-small-cell lung cancer (NSCLC) patients. The treatment with tyrosine kinase inhibitors (TKIs) in patients harboring Epidermal Growth Factor Receptor (EGFR)-activating mutations is dramatically associated with an improvement in disease control. Anyhow, the prognosis for this selected group of patients remains unfavorable, due to the innate and/or acquired resistance to biological therapies. The methylome analysis of many tumors revealed multiple patterns of methylation at single/multiple cytosine-phosphate-guanine (CpG) sites that are linked to the modulation of several cellular pathways involved in cancer onset and progression. In lung cancer patients, ever increasing evidences also suggest that the association between DNA methylation changes at promoter/intergenic regions and the consequent alteration of gene-expression signatures could be related to the acquisition of resistance to biological therapies. Despite this intriguing hypothesis, large confirmatory studies are demanded to consolidate and finalize many preliminary observations made in this field. In this review, we will summarize the available knowledge about the dynamic role of DNA methylation in EGFR-mutated NSCLC patients.
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Cao-Lei L, Saumier D, Fortin J, Brunet A. A narrative review of the epigenetics of post-traumatic stress disorder and post-traumatic stress disorder treatment. Front Psychiatry 2022; 13:857087. [PMID: 36419982 PMCID: PMC9676221 DOI: 10.3389/fpsyt.2022.857087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Epigenetic research in post-traumatic stress disorder (PTSD) is essential, given that environmental stressors and fear play such a crucial role in its development. As such, it may provide a framework for understanding individual differences in the prevalence of the disorder and in treatment response. This paper reviews the epigenetic markers associated with PTSD and its treatment, including candidate genes and epigenome-wide studies. Because the etiopathogenesis of PTSD rests heavily on learning and memory, we also draw upon animal neuroepigenetic research on the acquisition, update and erasure of fear memory, focusing on the mechanisms associated with memory reconsolidation. Reconsolidation blockade (or impairment) treatment in PTSD has been studied in clinical trials and, from a neurological perspective, may hold promise for identifying epigenetic markers of successful therapy. We conclude this paper by discussing several key considerations and challenges in epigenetic research on PTSD in humans.
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Affiliation(s)
- Lei Cao-Lei
- Research Center of the Douglas Mental Health University Institute (CIUSSS-ODIM), Montreal, QC, Canada
| | - Daniel Saumier
- Research Center of the Douglas Mental Health University Institute (CIUSSS-ODIM), Montreal, QC, Canada
| | - Justine Fortin
- Research Center of the Douglas Mental Health University Institute (CIUSSS-ODIM), Montreal, QC, Canada
- Department of Psychology, Université du Québec à Montréal, Montreal, QC, Canada
| | - Alain Brunet
- Research Center of the Douglas Mental Health University Institute (CIUSSS-ODIM), Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
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5
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Sheel A, Addison S, Nuguru SP, Manne A. Is Cell-Free DNA Testing in Pancreatic Ductal Adenocarcinoma Ready for Prime Time? Cancers (Basel) 2022; 14:3453. [PMID: 35884515 DOI: 10.3390/cancers14143453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/03/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Pancreatic cancer is a deadly cancer with limited treatment options. It is often detected in most people at stages where cure is not possible. There is no good test to know if a person will respond to treatment or if there is any disease beyond what can be seen by available imaging tests. Genetic material from the tumor is expected to float in the blood. Studying the alterations in the genetic material could help detect the tumor early, give an idea about its aggressiveness and response to available treatments, and facilitate the discovery of newer therapies. The focus of the studies so far has been on only one kind of genetic aberration, mutations, which has not given us great results. There is a need to explore another type of change known as methylation that could hold answers for managing pancreatic cancers better. Abstract Cell-free DNA (cfDNA) testing currently does not have a significant role in PDA management: it is insufficient to diagnose PDA, and its use is primarily restricted to identifying targetable mutations (if tissue is insufficient or unavailable). cfDNA testing has the potential to address critical needs in PDA management, such as pre-operative risk stratification (POR), prognostication, and predicting (and monitoring) treatment response. Prior studies have focused primarily on somatic mutations, specifically KRAS variants, and have shown limited success in addressing prognosis and POR. Recent studies have demonstrated the importance of other less prevalent mutations (ERBB2 and TP53), but no studies have provided reliable mutation panels for clinical use. Methylation aberrations in cfDNA (epigenetic markers) in PDA have been relatively less explored. However, early evidence has suggested they offer diagnostic and, to some extent, prognostic value. The inclusion of epigenetic markers of cfDNA adds another dimension to genomic testing and may open new therapeutic avenues beyond addressing critical areas of need in PDA treatment. For cfDNA to substantially influence PDA management, concerted efforts are required to include less frequent mutations and epigenetic markers. Furthermore, relying on KRAS mutations for PDA management will always be inadequate.
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Noronha NY, Barato M, Sae-Lee C, Pinhel MADS, Watanabe LM, Pereira VAB, Rodrigues GDS, Morais DA, de Sousa WT, Souza VCDO, Plaça JR, Salgado W, Barbosa F, Plösch T, Nonino CB. Corrigendum: Novel Zinc-Related Differentially Methylated Regions in Leukocytes of Women With and Without Obesity. Front Nutr 2022; 9:911493. [PMID: 35571956 PMCID: PMC9097217 DOI: 10.3389/fnut.2022.911493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fnut.2022.785281.].
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Affiliation(s)
- Natália Yumi Noronha
- Department of Internal Medicine, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Mariana Barato
- Department of Molecular Biology, São José do Rio Preto Medical School, São Paulo, Brazil
| | - Chanachai Sae-Lee
- Research Division, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Marcela Augusta de Souza Pinhel
- Department of Internal Medicine, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil.,Department of Molecular Biology, São José do Rio Preto Medical School, São Paulo, Brazil
| | - Lígia Moriguchi Watanabe
- Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | | | - Déborah Araújo Morais
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Wellington Tavares de Sousa
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Vanessa Cristina de Oliveira Souza
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Jessica Rodrigues Plaça
- National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell-Based Therapy, São Paulo, Brazil
| | - Wilson Salgado
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, São Paulo, Brazil
| | - Fernando Barbosa
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Carla Barbosa Nonino
- Department of Internal Medicine, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil.,Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
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Bento L, Vögler O, Sas-Barbeito A, Muncunill J, Ros T, Martínez J, Quintero-Duarte A, Ramos R, Asensio VJ, Fernández-Rodríguez C, Salar A, Navarro A, del Campo R, Ibarra J, Alemany R, Gutiérrez A. Screening for Prognostic microRNAs Associated with Treatment Failure in Diffuse Large B Cell Lymphoma. Cancers (Basel) 2022; 14:cancers14041065. [PMID: 35205813 PMCID: PMC8870558 DOI: 10.3390/cancers14041065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Around 30–40% of patients with diffuse large B cell lymphoma suffer early relapse after standard chemotherapy, but today no prediction whether a patient belongs to this group is possible. MicroRNA are small nucleotide sequences that regulate cellular functions via post-transcriptional modification of gene expression and can serve as prognostic biomarkers. A novel two-step strategy first used a small patient discovery group to identify possible microRNA candidates by comparing their levels in chemosensitive and chemoresistant patients via microarray. Overexpression of these microRNA was then analyzed in a large patient cohort and, as a result, three new microRNA biomarkers with prognostic potential could be identified. Early identification of those patients being at risk of failure with standard therapy is a prerequisite to develop more efficient treatments and a step towards precision medicine. Abstract Diffuse large B cell lymphoma (DLBCL) treatment with R-CHOP regimen produces 5-year progression-free survival and overall survival of around 60–70%. Our objective was to discover prognostic biomarkers allowing early detection of the remaining 30–40% with poor long-term outcome. For this purpose, we applied a novel strategy: from a cohort of DLBCL patients, treated with standard therapy, a discovery group of 12 patients with poor prognosis (advanced stage III–IV, R-IPI > 2) was formed, consisting of six chemoresistant (refractory/early relapse < 12 months) and six chemosensitive (complete remission > 3 years) subjects. By using microarray assays, the most differentially expressed miRNAs were defined as an initial set of prognostic miRNA candidates. Their expression was then analyzed in a validation cohort of 68 patients and the three miRNAs with the most significant impact on event-free and overall survival were selected. In the DLBCL cell line U-2932 the transfection with miR-1244 and miR-193b-5p, but not miR-1231, blocked the effect of CHOP on cell viability. A subsequent gene set enrichment analysis in patients revealed the implication of the first two miRNAs in cell cycle control and chemoresistance-related pathways, whereas the last one was involved in immunological processes. In conclusion, this novel strategy identified three promising prognostic markers for DLBCL patients at high risk of failure with standard therapy.
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Affiliation(s)
- Leyre Bento
- Department of Hematology, Son Espases University Hospital, 07120 Palma, Spain; (L.B.); (T.R.); (J.M.)
- Group of Clinic and Biology of Hematological Neoplasms, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain; (A.S.-B.); (R.d.C.)
| | - Oliver Vögler
- Group of Advanced Therapies and Biomarkers in Clinical Oncology, Research Institute of Health Sciences (IdISBa-IUNICS), University of the Balearic Islands, 07122 Palma, Spain;
- Group of Clinical and Translational Research, Department of Biology, University of the Balearic Islands, 07122 Palma, Spain
| | - Adriana Sas-Barbeito
- Group of Clinic and Biology of Hematological Neoplasms, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain; (A.S.-B.); (R.d.C.)
- Group of Advanced Therapies and Biomarkers in Clinical Oncology, Research Institute of Health Sciences (IdISBa-IUNICS), University of the Balearic Islands, 07122 Palma, Spain;
| | - Josep Muncunill
- Group of Genomics-Bioinformatics Platform, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain;
| | - Teresa Ros
- Department of Hematology, Son Espases University Hospital, 07120 Palma, Spain; (L.B.); (T.R.); (J.M.)
- Group of Clinic and Biology of Hematological Neoplasms, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain; (A.S.-B.); (R.d.C.)
| | - Jordi Martínez
- Department of Hematology, Son Espases University Hospital, 07120 Palma, Spain; (L.B.); (T.R.); (J.M.)
- Group of Clinic and Biology of Hematological Neoplasms, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain; (A.S.-B.); (R.d.C.)
| | - Adriana Quintero-Duarte
- Department of Pathology, Son Espases University Hospital, 07120 Palma, Spain; (A.Q.-D.); (R.R.)
| | - Rafael Ramos
- Department of Pathology, Son Espases University Hospital, 07120 Palma, Spain; (A.Q.-D.); (R.R.)
| | - Víctor Jose Asensio
- Molecular Diagnosis and Clinical Genetics Unit (GENIB), Son Espases University Hospital, 07120 Palma, Spain;
- Group of Health Genomics, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain
| | - Concepción Fernández-Rodríguez
- Department of Pathology, Hospital del Mar-IMIM, 08003 Barcelona, Spain;
- Group of Applied Clinical Research in Hematology, Cancer Research Program-IMIM, Hospital del Mar Medical Research Institute, 08003 Barcelona, Spain;
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
| | - Antonio Salar
- Group of Applied Clinical Research in Hematology, Cancer Research Program-IMIM, Hospital del Mar Medical Research Institute, 08003 Barcelona, Spain;
- Department of Hematology, Hospital del Mar-IMIM, 08003 Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
| | - Raquel del Campo
- Group of Clinic and Biology of Hematological Neoplasms, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain; (A.S.-B.); (R.d.C.)
- Department of Hematology, Son Llàtzer University Hospital, 07198 Palma, Spain
| | - Javier Ibarra
- Department of Pathology, Son Llàtzer University Hospital, 07198 Palma, Spain;
| | - Regina Alemany
- Group of Advanced Therapies and Biomarkers in Clinical Oncology, Research Institute of Health Sciences (IdISBa-IUNICS), University of the Balearic Islands, 07122 Palma, Spain;
- Group of Clinical and Translational Research, Department of Biology, University of the Balearic Islands, 07122 Palma, Spain
- Correspondence: (R.A.); (A.G.)
| | - Antonio Gutiérrez
- Department of Hematology, Son Espases University Hospital, 07120 Palma, Spain; (L.B.); (T.R.); (J.M.)
- Group of Clinic and Biology of Hematological Neoplasms, Health Research Institute of the Balearic Islands (IdISBa), 07010 Palma, Spain; (A.S.-B.); (R.d.C.)
- Correspondence: (R.A.); (A.G.)
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8
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de Sousa MML, Ye J, Luna L, Hildrestrand G, Bjørås K, Scheffler K, Bjørås M. Impact of Oxidative DNA Damage and the Role of DNA Glycosylases in Neurological Dysfunction. Int J Mol Sci 2021; 22:12924. [PMID: 34884729 PMCID: PMC8657561 DOI: 10.3390/ijms222312924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
The human brain requires a high rate of oxygen consumption to perform intense metabolic activities, accounting for 20% of total body oxygen consumption. This high oxygen uptake results in the generation of free radicals, including reactive oxygen species (ROS), which, at physiological levels, are beneficial to the proper functioning of fundamental cellular processes. At supraphysiological levels, however, ROS and associated lesions cause detrimental effects in brain cells, commonly observed in several neurodegenerative disorders. In this review, we focus on the impact of oxidative DNA base lesions and the role of DNA glycosylase enzymes repairing these lesions on brain function and disease. Furthermore, we discuss the role of DNA base oxidation as an epigenetic mechanism involved in brain diseases, as well as potential roles of DNA glycosylases in different epigenetic contexts. We provide a detailed overview of the impact of DNA glycosylases on brain metabolism, cognition, inflammation, tissue loss and regeneration, and age-related neurodegenerative diseases based on evidence collected from animal and human models lacking these enzymes, as well as post-mortem studies on patients with neurological disorders.
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Affiliation(s)
- Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Jing Ye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
| | - Gunn Hildrestrand
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
| | - Karine Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Katja Scheffler
- Department of Neurology, St. Olavs Hospital, 7006 Trondheim, Norway;
- Department of Laboratory Medicine, St. Olavs Hospital, 7006 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
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9
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Abstract
Although PSA-based prostate cancer (PCa) screening had a positive impact in reducing PCa mortality, it also led to overdiagnosis, overtreatment and to a significant number of unnecessary biopsies. In the post-PSA era, new biomarkers have emerged that can complement the information given by PSA, towards a better cancer diagnostic specificity, and also allow a better estimate of the aggressiveness of the disease and its clinical outcome. That means those markers have the potential to assist the clinician in the decision-making processes, such as whether or not to perform a biopsy, and to make the best treatment choice among the new therapeutic options available, including active surveillance (AS) in lower risk disease. In this article, we will review several of those more recent diagnostic markers (4Kscore®, [-2]proPSA and Prostate Health Index (PHI), SelectMDx®, ConfirmMDx®, Progensa® Prostate Cancer Antigen 3, Mi-Prostate Score, ExoDx™ Prostate Test, the Stockholm-3 test and ERSPC risk calculators) and prognostic markers (OncotypeDX® Genomic Prostate Score, Prolaris®, Decipher® and ProMark®). We will also address some new liquid biopsy approaches - circulating tumour cells and cell-free DNA (cfDNA) - with a potential role in metastatic castration-resistant PCa and will briefly give some future perspectives, mostly outlooking epigenetic markers.
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Affiliation(s)
- Manuel M Garrido
- Department of Clinical Pathology, 90463Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal.,Department of Laboratory Medicine, 37811Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Rui M Bernardino
- Department of Urology, 90463Centro Hospitalar Universitário de Lisboa central, Lisbon, Portugal
| | - José C Marta
- Department of Clinical Pathology, 90463Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, 14924Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - João T Guimarães
- Department of Clinical Pathology, Centro Hospitalar Universitário de São João, Porto, Portugal.,Department of Biomedicine, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,EPIUnit, Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
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10
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Kim YJ, Tamadon A, Kim YY, Kang BC, Ku SY. Epigenetic Regulation of Cardiomyocyte Differentiation from Embryonic and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:8599. [PMID: 34445302 PMCID: PMC8395249 DOI: 10.3390/ijms22168599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022] Open
Abstract
With the intent to achieve the best modalities for myocardial cell therapy, different cell types are being evaluated as potent sources for differentiation into cardiomyocytes. Embryonic stem cells and induced pluripotent stem cells have great potential for future progress in the treatment of myocardial diseases. We reviewed aspects of epigenetic mechanisms that play a role in the differentiation of these cells into cardiomyocytes. Cardiomyocytes proliferate during fetal life, and after birth, they undergo permanent terminal differentiation. Upregulation of cardiac-specific genes in adults induces hypertrophy due to terminal differentiation. The repression or expression of these genes is controlled by chromatin structural and epigenetic changes. However, few studies have reviewed and analyzed the epigenetic aspects of the differentiation of embryonic stem cells and induced pluripotent stem cells into cardiac lineage cells. In this review, we focus on the current knowledge of epigenetic regulation of cardiomyocyte proliferation and differentiation from embryonic and induced pluripotent stem cells through histone modification and microRNAs, the maintenance of pluripotency, and its alteration during cardiac lineage differentiation.
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Affiliation(s)
- Yong-Jin Kim
- Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul 08308, Korea;
| | - Amin Tamadon
- Department of Marine Stem Cell and Tissue Engineering, Bushehr University of Medical Sciences, Bushehr 14174, Iran;
| | - Yoon-Young Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea;
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Byeong-Cheol Kang
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
| | - Seung-Yup Ku
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea;
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul 03080, Korea
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Abstract
Introduction Chronic neurological diseases are a major cause of mortality and morbidity in the world. With increasing life expectancy in the developing world, the incidence and prevalence of these diseases are predicted to rise even further. This has also contributed to an increase in disability-adjusted life years (DALYs) for noncommunicable diseases. Treatment for such diseases also poses a challenge with multiple genetic and epigenetic factors leading to a varied outcome. Personalization of treatment is one way that treatment outcome/prognosis of disease can be improved, and pharmacogenomics plays a significant role in this context. Methodology This article reviewed the evidence pertaining to the association of genetic and epigenetic markers with major neurological disorders like multiple sclerosis (MS), Alzheimer's disease (AD), and Parkinson's disease (PD), which are a major source of burden among neurological disorders. Types of studies included are peer-reviewed original research articles from the PubMed database (1999-2018). Results This study compiled data regarding specific genetic and epigenetic markers with a significant correlation between the clinical diagnosis of the disease and prognosis of therapy from 65 studies. In a single platform, this review highlights the clues to some vital questions, such as why interferon beta (IFN-β) therapy fails to improve symptoms in all MS patients? why cholinesterase inhibitors fail to improve cognitive impairment in a subset of people suffering from AD? or why some individuals on levodopa (L-DOPA) for PD suffer from side-effects ranging from dyskinesia to hallucination while others do not? Conclusion This article summarizes the genetic and epigenetic factors that may either require monitoring or help in deciding future pharmacotherapy in a patient suffering from MS, AD, and PD. As the health care system develops and reaches newer heights, we expect more and more of these biomarkers to be used as pharmacotherapeutic outcome indicators.
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Affiliation(s)
| | - Pranav Sopory
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, India
| | - K H Reeta
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, India
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12
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Gomes Assenço RA, Alves Mota E, De Oliveira VF, De Castro Borges W, Guerra-Sá R. Epigenetic Markers Associated with Schistosomiasis. Helminthologia 2021; 58:28-40. [PMID: 33664616 DOI: 10.2478/helm-2021-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
It is important to consider the use of the epigenome as source of complementary data for genome knowledge, which is suitable for the diagnosis of schistosomiasis. Usually, a laboratory diagnosis of schistosomiasis is performed by means of 1. Egg detection in the stool or urine by microscopy remains with limited sensitivity; 2. Immunological screening, in which positivity persists after treatment, and 3. Molecular appraisals prevail over the disadvantages of the currently used methods. In this sense, molecular methodologies are being developed based on epigenetic biomarkers, aiming to improve the diagnosis of the disease and clinical treatment as early as possible to prevent the occurrence of serious liver damage.
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Misawa K, Imai A, Kanazawa T, Mima M, Yamada S, Mochizuki D, Yamada T, Shinmura D, Ishikawa R, Kita J, Yamaguchi Y, Misawa Y, Mineta H. G Protein-Coupled Receptor Genes, PTGDR1, PTGDR2, and PTGIR, Are Candidate Epigenetic Biomarkers and Predictors for Treated Patients with HPV-Associated Oropharyngeal Cancer. Microorganisms 2020; 8:microorganisms8101504. [PMID: 33003642 PMCID: PMC7601742 DOI: 10.3390/microorganisms8101504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Differences in the biology of human papillomavirus (HPV)-associated oropharyngeal cancers (OPCs) and HPV-negative OPCs may have implications in patient management. Early detection is imperative to reduce HPV-associated OPC mortality. Circulating tumor DNA (ctDNA) can potentially serve as a biomarker for monitoring clinically relevant cancer-related genetic and epigenetic modifications. We analyzed the methylation status of 24 G protein-coupled receptor (GPCR) genes in verification (85 OPC primary samples) and validation (8 OPC ctDNA samples) studies using quantitative methylation-specific polymerase chain reaction (Q-MSP). The Q-MSP-based verification study with 85 OPC primary samples revealed the GPCR genes that were significantly associated with recurrence in high methylation groups (≥14 methylated genes) with OPC and HPV-associated OPC (p < 0.001). In the Kaplan–Meier estimate and multivariate Cox proportional hazard analyses, 13 GPCR genes were significantly related to increased recurrence in the methylation group. Furthermore, the validation study on ctDNA showed that three of these genes (Prostaglandin D2 receptor 1: PTGDR1, Prostaglandin D2 receptor 2: PTGDR2, and Prostaglandin I2 Receptor: PTGIR) had a prediction performance as emerging biomarkers. We characterized the relationship between the methylation status of GPCR genes and outcomes in HPV-associated OPC. Our results highlight the potential utility of ctDNA methylation-based detection for the clinical management of HPV-associated OPC.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
- Correspondence: ; Tel.: 81-53-435-2252; Fax: 81-53-435-2253
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Takeharu Kanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan;
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Satoshi Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Taiki Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Daichi Shinmura
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Jyunya Kita
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Yuki Yamaguchi
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
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Lossow K, Kopp JF, Schwarz M, Finke H, Winkelbeiner N, Renko K, Meçi X, Ott C, Alker W, Hackler J, Grune T, Schomburg L, Haase H, Schwerdtle T, Kipp AP. Aging affects sex- and organ-specific trace element profiles in mice. Aging (Albany NY) 2020; 12:13762-13790. [PMID: 32620712 PMCID: PMC7377894 DOI: 10.18632/aging.103572] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/13/2020] [Indexed: 12/18/2022]
Abstract
A decline of immune responses and dynamic modulation of the redox status are observed during aging and are influenced by trace elements such as copper, iodine, iron, manganese, selenium, and zinc. So far, analytical studies have focused mainly on single trace elements. Therefore, we aimed to characterize age-specific profiles of several trace elements simultaneously in serum and organs of adult and old mice. This allows for correlating multiple trace element levels and to identify potential patterns of age-dependent alterations. In serum, copper and iodine concentrations were increased and zinc concentration was decreased in old as compared to adult mice. In parallel, decreased copper and elevated iron concentrations were observed in liver. The age-related reduction of hepatic copper levels was associated with reduced expression of copper transporters, whereas the increased hepatic iron concentrations correlated positively with proinflammatory mediators and Nrf2-induced ferritin H levels. Interestingly, the age-dependent inverse regulation of copper and iron was unique for the liver and not observed in any other organ. The physiological importance of alterations in the iron/copper ratio for liver function and the aging process needs to be addressed in further studies.
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Affiliation(s)
- Kristina Lossow
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,German Institute of Human Nutrition, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Johannes F Kopp
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Maria Schwarz
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Hannah Finke
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Nicola Winkelbeiner
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Kostja Renko
- Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany.,German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Xheni Meçi
- Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany
| | - Christiane Ott
- German Institute of Human Nutrition, Nuthetal, Germany.,DZHK German Centre for Cardiovascular Research, Berlin, Germany
| | - Wiebke Alker
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Department of Food Chemistry and Toxicology, Technische Universität Berlin, Berlin, Germany
| | - Julian Hackler
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany
| | - Tilman Grune
- German Institute of Human Nutrition, Nuthetal, Germany
| | - Lutz Schomburg
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany
| | - Hajo Haase
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Department of Food Chemistry and Toxicology, Technische Universität Berlin, Berlin, Germany
| | - Tanja Schwerdtle
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Anna P Kipp
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
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Wadowska K, Bil-Lula I, Trembecki Ł, Śliwińska-Mossoń M. Genetic Markers in Lung Cancer Diagnosis: A Review. Int J Mol Sci 2020; 21:E4569. [PMID: 32604993 PMCID: PMC7369725 DOI: 10.3390/ijms21134569] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most often diagnosed cancer in the world and the most frequent cause of cancer death. The prognosis for lung cancer is relatively poor and 75% of patients are diagnosed at its advanced stage. The currently used diagnostic tools are not sensitive enough and do not enable diagnosis at the early stage of the disease. Therefore, searching for new methods of early and accurate diagnosis of lung cancer is crucial for its effective treatment. Lung cancer is the result of multistage carcinogenesis with gradually increasing genetic and epigenetic changes. Screening for the characteristic genetic markers could enable the diagnosis of lung cancer at its early stage. The aim of this review was the summarization of both the preclinical and clinical approaches in the genetic diagnostics of lung cancer. The advancement of molecular strategies and analytic platforms makes it possible to analyze the genome changes leading to cancer development-i.e., the potential biomarkers of lung cancer. In the reviewed studies, the diagnostic values of microsatellite changes, DNA hypermethylation, and p53 and KRAS gene mutations, as well as microRNAs expression, have been analyzed as potential genetic markers. It seems that microRNAs and their expression profiles have the greatest diagnostic potential value in lung cancer diagnosis, but their quantification requires standardization.
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Affiliation(s)
- Katarzyna Wadowska
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (K.W.); (I.B.-L.)
| | - Iwona Bil-Lula
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (K.W.); (I.B.-L.)
| | - Łukasz Trembecki
- Department of Radiation Oncology, Lower Silesian Oncology Center, 53-413 Wroclaw, Poland;
- Department of Oncology, Faculty of Medicine, Wroclaw Medical University, 53-413 Wroclaw, Poland
| | - Mariola Śliwińska-Mossoń
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (K.W.); (I.B.-L.)
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Pamidimukkala NV, Leonard MK, Snyder D, McCorkle JR, Kaetzel DM. Metastasis Suppressor NME1 Directly Activates Transcription of the ALDOC Gene in Melanoma Cells. Anticancer Res 2018; 38:6059-6068. [PMID: 30396920 DOI: 10.21873/anticanres.12956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/05/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND/AIM NME/NM23 nucleoside diphosphate kinase 1 (NME1) is a metastasis suppressor gene, exhibiting reduced expression in metastatic cancers and the ability to suppress metastatic activity of cancer cells. We previously identified NME1-regulated genes with prognostic value in human melanoma. This study was conducted in melanoma cell lines aiming to elucidate the mechanism through which NME regulates one of these genes, aldolase C (ALDOC). MATERIALS AND METHODS ALDOC mRNA and protein expression was measured using qRT-PCR and immunoblot analyses. Promoter-luciferase constructs and chromatin immunoprecipitation were employed to measure the impact of NME1 on ALDOC transcription. RESULTS NME1 enhanced ALDOC transcription, evidenced by increased expression of ALDOC pre-mRNA and activity of an ALDOC promoter-luciferase module. NME1 was detected at the ALDOC promoter, and forced NME1 expression resulted in enhanced occupancy of the promoter by NME1, increased presence of epigenetic activation markers (H3K4me3 and H3K27ac), and recruitment of RNA polymerase II. CONCLUSION This is the first study to indicate that NME1 induces transcription through its direct binding to the promoter region of a target gene.
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Affiliation(s)
- Nidhi V Pamidimukkala
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| | - Mary Kathryn Leonard
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| | - Devin Snyder
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| | | | - David M Kaetzel
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A. .,Markey Cancer Center, University of Kentucky, Lexington, KY, U.S.A.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland-Baltimore, Baltimore, MD, U.S.A
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Misawa K, Imai A, Mochizuki D, Misawa Y, Endo S, Hosokawa S, Ishikawa R, Mima M, Shinmura K, Kanazawa T, Mineta H. Genes encoding neuropeptide receptors are epigenetic markers in patients with head and neck cancer: a site-specific analysis. Oncotarget 2017; 8:76318-28. [PMID: 29100314 DOI: 10.18632/oncotarget.19356] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/29/2017] [Indexed: 02/07/2023] Open
Abstract
Staging and pathological grading systems are useful but imperfect predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). To identify potential prognostic markers, we examined the methylation status of eight neuropeptide receptor gene promoters in 231 head and neck squamous cell carcinomas. The NPFFR1, NPFFR2, HCRTR1, HCRTR2, NPY1R, NPY2R, NPY4R, and NPY5R promoters were methylated in 80.5%, 79.2%, 67.1%, 73.2%, 35.1%, 36.4%, 38.5%, and 35.9% of the samples, respectively. In a multivariate Cox proportional hazards analysis, the odds ratio for recurrence was 2.044 (95% confidence interval [CI], 1.323–3.156; P = 0.001) when the NPY2R promoter was methylated. In patients without lymph node metastasis (n = 100), methylation of NPY2R (compared with methylation of the other seven genes) best correlated with poor disease-free survival (DFS) (odds ratio, 2.492; 95% CI, 1.190–5.215; P = 0.015). In patients with oral cancer (n = 69), methylated NPY1R and NPY2R were independent prognostic factors for poor DFS, both individually and, even more so, in combination (odds ratio, 3.90; 95% CI, 1.523–9.991; P = 0.005). Similar findings were observed for NPY2R and NPY4R in patients with oropharyngeal cancer (n = 162) (odds ratio, 5.663; 95% CI, 1.507–21.28; P = 0.010).
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Ahmed AU, Williams BR, Hannigan GE. Transcriptional Activation of Inflammatory Genes: Mechanistic Insight into Selectivity and Diversity. Biomolecules 2015; 5:3087-111. [PMID: 26569329 DOI: 10.3390/biom5043087] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/11/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022] Open
Abstract
Acute inflammation, an integral part of host defence and immunity, is a highly conserved cellular response to pathogens and other harmful stimuli. An inflammatory stimulation triggers transcriptional activation of selective pro-inflammatory genes that carry out specific functions such as anti-microbial activity or tissue healing. Based on the nature of inflammatory stimuli, an extensive exploitation of selective transcriptional activations of pro-inflammatory genes is performed by the host to ensure a defined inflammatory response. Inflammatory signal transductions are initiated by the recognition of inflammatory stimuli by transmembrane receptors, followed by the transmission of the signals to the nucleus for differential gene activations. The differential transcriptional activation of pro-inflammatory genes is precisely controlled by the selective binding of transcription factors to the promoters of these genes. Among a number of transcription factors identified to date, NF-κB still remains the most prominent and studied factor for its diverse range of selective transcriptional activities. Differential transcriptional activities of NF-κB are dictated by post-translational modifications, specificities in dimer formation, and variability in activation kinetics. Apart from the differential functions of transcription factors, the transcriptional activation of selective pro-inflammatory genes is also governed by chromatin structures, epigenetic markers, and other regulators as the field is continuously expanding.
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Abstract
Objective Methods Results Conclusions
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Tetievsky A, Assayag M, Ben-Hamo R, Efroni S, Cohen G, Abbas A, Horowitz M. Heat acclimation memory: do the kinetics of the deacclimated transcriptome predispose to rapid reacclimation and cytoprotection? J Appl Physiol (1985) 2014; 117:1262-77. [PMID: 25237184 DOI: 10.1152/japplphysiol.00422.2014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Faster reinduction of heat acclimation (AC) after its decline indicates "AC memory." Our previous results revealed involvement of epigenetic mechanisms of transcriptional regulation. We hypothesized that the decline of AC (DeAC) is a period of "dormant memory" during which many processes are alerted to enable rapid reacclimation (ReAC). Using a genomewide approach we studied the AC, DeAC, and ReAC transcriptomes, to uncover hallmark pathways linked to "molecular memory" in the cardioacclimatome. Fifty rats subjected to heat acclimation [34°C for 2d (AC2d) or 30d (AC30)], DeAC (24°C, 30 days), ReAC (34°C, 2 days), and untreated controls were used. The GeneChip Rat Gene 1.0 ST Array was employed for left ventricular (cardiac) mRNA hybridization. Three independent bioinformatic analyses showed that 1) during AC2d enrichment of DNA impair/repair-linked genes is seen, and this is the molecular on-switch of acclimation; 2) genes activated in AC30 underlie the qualitative physiological adaptations of cardiac performance; 3) particular molecular programs encompassing constitutive upregulation of p38 MAPK, Jak/Stat, and Akt pathways and targets are specifically activated during DeAC and ReAC; and 4) epigenetic markers such as linker histones (histones H1 cluster), associated with nucleosome spacing, transcriptional chromatin modifiers, poly-(ADP-ribose) polymerase-1 (PARP1) linked to chromatin compaction, and microRNAs are only altered during DeAC/ReAC. The latter are newcomers to the AC/DeAC puzzle. We suggest that these transcriptional responses maintain euchromatin and proteostasis and enable faster physiological recovery upon ReAC by rapidly reestablishing the protected acclimated cardiophenotype. We propose that the cardiac AC model can be applied to acclimation processes in general.
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Affiliation(s)
- Anna Tetievsky
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University, Jerusalem, Israel; and
| | - Miri Assayag
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University, Jerusalem, Israel; and
| | - Rotem Ben-Hamo
- The Mina and Everard Goodman Faculty of Life Science Bar Ilan University, Ramat Gan, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science Bar Ilan University, Ramat Gan, Israel
| | - Gal Cohen
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University, Jerusalem, Israel; and
| | - Atallah Abbas
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University, Jerusalem, Israel; and
| | - Michal Horowitz
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University, Jerusalem, Israel; and
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Schütte B, El Hajj N, Kuhtz J, Nanda I, Gromoll J, Hahn T, Dittrich M, Schorsch M, Müller T, Haaf T. Broad DNA methylation changes of spermatogenesis, inflammation and immune response-related genes in a subgroup of sperm samples for assisted reproduction. Andrology 2013; 1:822-9. [PMID: 23996961 PMCID: PMC4033565 DOI: 10.1111/j.2047-2927.2013.00122.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 01/08/2023]
Abstract
Aberrant sperm DNA methylation patterns, mainly in imprinted genes, have been associated with male subfertility and oligospermia. Here, we performed a genome-wide methylation analysis in sperm samples representing a wide range of semen parameters. Sperm DNA samples of 38 males attending a fertility centre were analysed with Illumina HumanMethylation27 BeadChips, which quantify methylation of >27 000 CpG sites in cis-regulatory regions of almost 15 000 genes. In an unsupervised analysis of methylation of all analysed sites, the patient samples clustered into a major and a minor group. The major group clustered with samples from normozoospermic healthy volunteers and, thus, may more closely resemble the normal situation. When correlating the clusters with semen and clinical parameters, the sperm counts were significantly different between groups with the minor group exhibiting sperm counts in the low normal range. A linear model identified almost 3000 CpGs with significant methylation differences between groups. Functional analysis revealed a broad gain of methylation in spermatogenesis-related genes and a loss of methylation in inflammation- and immune response-related genes. Quantitative bisulfite pyrosequencing validated differential methylation in three of five significant candidate genes on the array. Collectively, we identified a subgroup of sperm samples for assisted reproduction with sperm counts in the low normal range and broad methylation changes (affecting approximately 10% of analysed CpG sites) in specific pathways, most importantly spermatogenesis-related genes. We propose that epigenetic analysis can supplement traditional semen parameters and has the potential to provide new insights into the aetiology of male subfertility.
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Affiliation(s)
- B Schütte
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany; Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
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Abstract
A decade since the first evidence implicating the cell cycle transcription factor Forkhead Box M1 (FOXM1) in human tumorigenesis, a slew of subsequent studies revealed an oncogenic role of FOXM1 in the majority of human cancers including oral, nasopharynx, oropharynx, esophagus, breast, ovary, prostate, lung, liver, pancreas, kidney, colon, brain, cervix, thyroid, bladder, uterus, testis, stomach, skin, and blood. Its aberrant upregulation in almost all different cancer types suggests a fundamental role for FOXM1 in tumorigenesis. Its dose-dependent expression pattern correlated well with tumor progression starting from cancer predisposition and initiation, early premalignancy and progression, to metastatic invasion. In addition, emerging studies have demonstrated a causal link between FOXM1 and chemotherapeutic drug resistance. Despite the well-established multifaceted roles for FOXM1 in all stages of oncogenesis, its translation into clinical benefit is yet to materialize. In this contribution, I reviewed and discussed how our current knowledge on the oncogenic mechanisms of FOXM1 could be exploited for clinical use as biomarker for risk prediction, early cancer screening, molecular diagnostics/prognostics, and/or companion diagnostics for personalized cancer therapy.
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Affiliation(s)
- Muy-Teck Teh
- Centre for Clinical and Diagnostic Oral Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London London, UK
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