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Kavaklioglu G, Podhornik A, Vcelkova T, Marjanovic J, Beck MA, Phan-Canh T, Mair T, Miccolo C, Drino A, Doni M, Egger G, Chiocca S, Modic M, Seiser C. The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition. eLife 2025; 13:RP96850. [PMID: 40112032 PMCID: PMC11925450 DOI: 10.7554/elife.96850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2025] Open
Abstract
Repression of retrotransposition is crucial for the successful fitness of a mammalian organism. The domesticated transposon protein L1TD1, derived from LINE-1 (L1) ORF1p, is an RNA-binding protein that is expressed only in some cancers and early embryogenesis. In human embryonic stem cells, it is found to be essential for maintaining pluripotency. In cancer, L1TD1 expression is highly correlative with malignancy progression and as such considered a potential prognostic factor for tumors. However, its molecular role in cancer remains largely unknown. Our findings reveal that DNA hypomethylation induces the expression of L1TD1 in HAP1 human tumor cells. L1TD1 depletion significantly modulates both the proteome and transcriptome and thereby reduces cell viability. Notably, L1TD1 associates with L1 transcripts and interacts with L1 ORF1p protein, thereby facilitating L1 retrotransposition. Our data suggest that L1TD1 collaborates with its ancestral L1 ORF1p as an RNA chaperone, ensuring the efficient retrotransposition of L1 retrotransposons, rather than directly impacting the abundance of L1TD1 targets. In this way, L1TD1 might have an important role not only during early development but also in tumorigenesis.
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Affiliation(s)
- Gülnihal Kavaklioglu
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
| | - Alexandra Podhornik
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
| | - Terezia Vcelkova
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
| | - Jelena Marjanovic
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
| | - Mirjam A Beck
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
| | - Trinh Phan-Canh
- Medical University of Vienna, Max Perutz Labs Vienna, Campus Vienna BiocenterViennaAustria
| | - Theresia Mair
- Department of Pathology, Medical University of ViennaViennaAustria
| | - Claudia Miccolo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCSMilanItaly
| | - Aleksej Drino
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
| | - Mirko Doni
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCSMilanItaly
| | - Gerda Egger
- Department of Pathology, Medical University of ViennaViennaAustria
| | - Susanna Chiocca
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCSMilanItaly
| | - Miha Modic
- National Institute of ChemistryLjubljanaSlovenia
- Dementia Research Institute at King’s College London and The Francis Crick instituteLondonUnited Kingdom
| | - Christian Seiser
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of ViennaViennaAustria
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Mateo-Fernández M, Alves-Martínez P, Del Río-Celestino M, Font R, Merinas-Amo T, Alonso-Moraga Á. Nutraceutical Potential and Food Safety of Fructose in Soda and Diet Beverages. Foods 2025; 14:648. [PMID: 40002094 PMCID: PMC11854732 DOI: 10.3390/foods14040648] [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: 12/28/2024] [Revised: 02/04/2025] [Accepted: 02/12/2025] [Indexed: 02/27/2025] Open
Abstract
Fructose has been considered as an additive from soda beverages. For the approval of new additives or to extend the usage of an approved one, it is necessary to conduct toxicological studies in order to evaluate the DNA damage induced by these compounds. Our study is based on evaluating the safety and the nutraceutical potential of Fructose (FRU), a soda cola beverage (Pepsi-cola, PEP), and a diet soda cola (Diet Coke, DCC), characterizing the DNA changes induced in the Drosophila melanogaster organism model and in the human leukemia HL-60 cells performing different assays. Our results showed neither the toxicity nor mutagenic activity of FRU, PEP, and DCC in Drosophila melanogaster, while only PEP exhibited protective effects in the antitoxity assay, showing an 80% survival rate in combined treatments. FRU, but not PEP, enhanced lifespan parameters by up to 23 more days at the 5 mg/mL concentration. All three substances exhibited chemopreventive properties in some of the checkpoints carried out related to clastogenicity and methylation patterns in HL-60 cells. In conclusion, the tested compounds were safe at tested concentrations in Drosophila and showed moderate chemopreventive activity.
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Affiliation(s)
- Marcos Mateo-Fernández
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (M.M.-F.); (P.A.-M.); (T.M.-A.); (Á.A.-M.)
| | - Pilar Alves-Martínez
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (M.M.-F.); (P.A.-M.); (T.M.-A.); (Á.A.-M.)
| | | | - Rafael Font
- Agri-Food Laboratory, CAGPDS, Avd. Menéndez Pidal, s/n, 14080 Córdoba, Spain;
| | - Tania Merinas-Amo
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (M.M.-F.); (P.A.-M.); (T.M.-A.); (Á.A.-M.)
| | - Ángeles Alonso-Moraga
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (M.M.-F.); (P.A.-M.); (T.M.-A.); (Á.A.-M.)
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Dević Pavlić S, Šverko R, Barišić A, Mladenić T, Vraneković J, Stanković A, Peterlin A, Peterlin B, Ostojić S, Pereza N. MTHFR Gene Polymorphisms and DNA Methylation in Idiopathic Spontaneous Preterm Birth. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:2028. [PMID: 39768908 PMCID: PMC11728409 DOI: 10.3390/medicina60122028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 11/26/2024] [Accepted: 12/06/2024] [Indexed: 01/16/2025]
Abstract
Background and Objectives: Preterm birth (PTB) is a complex condition with various contributing factors, including genetic and epigenetic influences such as DNA methylation. Methylenetetrahydrofolate reductase (MTHFR) plays a critical role in DNA methylation and the remethylation of homocysteine. This study aimed to investigate the association between maternal MTHFR C677T and A1298C polymorphisms, LINE-1 DNA methylation levels, and the risk of idiopathic spontaneous preterm birth (SPTB) in Caucasian women from Croatia and Slovenia. Materials and Methods: A total of 50 women with SPTB (<34 weeks of gestation) and 50 control women were included in the study. MTHFR polymorphisms were analyzed using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and LINE-1 DNA methylation levels were quantified using the MethyLight method. Results: The study found no significant differences in MTHFR C677T and A1298C polymorphisms' genotype or allele frequencies between women with SPTB and controls. Additionally, no statistical significance of LINE-1 DNA methylation was found between the genotypes of the MTHFR polymorphisms analyzed. Conclusions: The study suggests no conclusive association between MTHFR C677T and A1298C polymorphisms, LINE-1 DNA methylation, and SPTB in Croatian and Slovenian women. Considering prior evidence connecting MTHFR polymorphisms, hyperhomocysteinemia, and PTB, the lack of homocysteine measurements and unassessed impact of folate or vitamin B supplementation limit the conclusions.
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Affiliation(s)
- Sanja Dević Pavlić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (T.M.); (J.V.); (S.O.); (N.P.)
| | - Roberta Šverko
- Department of Internal medicine, University Hospital Rijeka, 51000 Rijeka, Croatia;
| | - Anita Barišić
- Department of Gynecology and Obstetrics, University Hospital Rijeka, 51000 Rijeka, Croatia;
| | - Tea Mladenić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (T.M.); (J.V.); (S.O.); (N.P.)
| | - Jadranka Vraneković
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (T.M.); (J.V.); (S.O.); (N.P.)
| | - Aleksandra Stanković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11351 Belgrade, Serbia;
| | - Ana Peterlin
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia;
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (T.M.); (J.V.); (S.O.); (N.P.)
| | - Nina Pereza
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (T.M.); (J.V.); (S.O.); (N.P.)
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Merinas-Amo T, Merinas-Amo R, Alonso-Moraga Á, Font R, Del Río Celestino M. In Vivo and In Vitro Studies Assessing the Safety of Monosodium Glutamate. Foods 2024; 13:3981. [PMID: 39683053 DOI: 10.3390/foods13233981] [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: 11/05/2024] [Revised: 12/05/2024] [Accepted: 12/07/2024] [Indexed: 12/18/2024] Open
Abstract
The controversial results of research on monosodium glutamate demand a new data corpus for the overall safety evaluation. Both animal and cellular model systems have been used to add a multilevel scope on its biological effects. The Drosophila melanogaster animal model has been used to test a wide range of concentrations for safety purposes: toxicity, genotoxicity, longevity and health span. Medium concentrations corresponding to the human acceptable daily intake (ADI) (0.06 mg/mL) were not toxic nor genotoxic for Drosophila and safe for the lifespan parameters. Once safety was determined, the possible nutraceutical effects of monosodium glutamate was monitored in terms of antitoxicity, antigenotoxicity assays and health span. The results for protective activity against hydrogen peroxide were positive in terms of the medium concentration, antitoxic and antigenotoxic in terms of inhibiting the genotoxicity induced by the oxidative toxin up to 43.7% and increasing the health span expectancy by 32% in terms of days. Monosodium glutamate has been demonstrated to be cytotoxic against the model tumour cell line HL-60, not only in a necrotic way but through internucleosomal DNA fragmentation antitumour activity. The significant LINE1 DNA sequence methylation of HL-60 tumour cells induced by monosodium glutamate is a molecular marker for chemoprevention. Conclusions: the slight or non-significant positive nutraceutical and chemo preventive potential showed by monosodium glutamate at its ADI concentration can be considered as a safe dose for a moderate consumption.
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Affiliation(s)
| | | | | | - Rafael Font
- Agri-Food Laboratory, CAGPDS, Av. Menéndez Pidal, s/n, 14080 Córdoba, Spain
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Nakasone ES, Zemla TJ, Yu M, Lin SY, Ou FS, Carter K, Innocenti F, Saltz L, Grady WM, Cohen SA. Evaluating the utility of ZNF331 promoter methylation as a prognostic and predictive marker in stage III colon cancer: results from CALGB 89803 (Alliance). Epigenetics 2024; 19:2349980. [PMID: 38716804 PMCID: PMC11085945 DOI: 10.1080/15592294.2024.2349980] [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: 09/20/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
While epigenomic alterations are common in colorectal cancers (CRC), few epigenomic biomarkers that risk-stratify patients have been identified. We thus sought to determine the potential of ZNF331 promoter hypermethylation (mZNF331) as a prognostic and predictive marker in colon cancer. We examined the association of mZNF331 with clinicopathologic features, relapse, survival, and treatment efficacy in patients with stage III colon cancer treated within a randomized adjuvant chemotherapy trial (CALGB/Alliance89803). Residual tumour tissue was available for genomic DNA extraction and methylation analysis for 385 patients. ZNF331 promoter methylation status was determined by bisulphite conversion and fluorescence-based real-time polymerase chain reaction. Kaplan-Meier estimator and Cox proportional hazard models were used to assess the prognostic and predictive role of mZNF331 in this well-annotated dataset, adjusting for clinicopathologic features and standard molecular markers. mZNF331 was observed in 267/385 (69.4%) evaluable cases. Histopathologic features were largely similar between patients with mZNF331 compared to unmethylated ZNF331 (unmZNFF31). There was no significant difference in disease-free or overall survival between patients with mZNF331 versus unmZNF331 colon cancers, even when adjusting for clinicopathologic features and molecular marker status. Similarly, there was no difference in disease-free or overall survival across treatment arms when stratified by ZNF331 methylation status. While ZNF331 promoter hypermethylation is frequently observed in CRC, our current study of a small subset of patients with stage III colon cancer suggests limited applicability as a prognostic marker. Larger studies may provide more insight and clarity into the applicability of mZNF331 as a prognostic and predictive marker.
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Affiliation(s)
- Elizabeth S. Nakasone
- Division of Oncology, University of Washington, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tyler J. Zemla
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - She Yu Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- School of Life Sciences, Nantong University, Nantong, P.R. China
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Kelly Carter
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leonard Saltz
- Department of Gastrointestinal Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William M. Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Gastroenterology, University of Washington, Seattle, WA, USA
| | - Stacey A. Cohen
- Division of Oncology, University of Washington, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Du J, Liu H, Wang P, Wu W, Zheng F, Wang Y, Meng B. Identification and analysis of inflammation-related biomarkers in tetralogy of Fallot. Transl Pediatr 2024; 13:1033-1050. [PMID: 39144431 PMCID: PMC11320004 DOI: 10.21037/tp-24-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 05/31/2024] [Indexed: 08/16/2024] Open
Abstract
Background Studies have revealed that inflammatory response is relevant to the tetralogy of Fallot (TOF). However, there are no studies to systematically explore the role of the inflammation-related genes (IRGs) in TOF. Therefore, based on bioinformatics, we explored the biomarkers related to inflammation in TOF, laying a theoretical foundation for its in-depth study. Methods TOF-related datasets (GSE36761 and GSE35776) were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between TOF and control groups were identified in GSE36761. And DEGs between TOF and control groups were intersected with IRGs to obtain differentially expressed IRGs (DE-IRGs). Afterwards, the least absolute shrinkage and selection operator (LASSO) and random forest (RF) were utilized to identify the biomarkers. Next, immune analysis was carried out. The transcription factor (TF)-mRNA, lncRNA-miRNA-mRNA, and miRNA-single nucleotide polymorphism (SNP)-mRNA networks were created. Finally, the potential drugs targeting the biomarkers were predicted. Results There were 971 DEGs between TOF and control groups, and 29 DE-IRGs were gained through the intersection between DEGs and IRGs. Next, a total of five biomarkers (MARCO, CXCL6, F3, SLC7A2, and SLC7A1) were acquired via two machine learning algorithms. Infiltrating abundance of 18 immune cells was significantly different between TOF and control groups, such as activated B cells, neutrophil, CD56dim natural killer cells, etc. The TF-mRNA network contained 4 mRNAs, 31 TFs, and 33 edges, for instance, ELF1-CXCL6, CBX8-SLC7A2, ZNF423-SLC7A1, ZNF71-F3. The lncRNA-miRNA-mRNA network was created, containing 4 mRNAs, 4 miRNAs, and 228 lncRNAs. Afterwards, nine SNPs locations were identified in the miRNA-SNP-mRNA network. A total of 21 drugs were predicted, such as ornithine, lysine, arginine, etc. Conclusions Our findings detected five inflammation-related biomarkers (MARCO, CXCL6, F3, SLC7A2, and SLC7A1) for TOF, providing a scientific reference for further studies of TOF.
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Affiliation(s)
- Junzhe Du
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Huaipu Liu
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Pengcheng Wang
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Wenzhi Wu
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Fengnan Zheng
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Yuanxiang Wang
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Baoying Meng
- Department of Cardiothoracic Surgery, Shenzhen Children's Hospital, Shenzhen, China
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Ozcivit Erkan IB, Seyisoglu HH, Benbir Senel G, Karadeniz D, Ozdemir F, Kalayci A, Seven M, Gokmen Inan N. An Evaluation of DNA Methylation Levels and Sleep in Relation to Hot Flashes: A Cross-Sectional Study. J Clin Med 2024; 13:3502. [PMID: 38930031 PMCID: PMC11204679 DOI: 10.3390/jcm13123502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/26/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Objectives: We aimed to evaluate the DNA methylation levels in perimenopausal and postmenopausal women, measured through Long Interspersed Element-1 (LINE-1) and Alu, and the sleep parameters in relation to the presence of hot flashes (HFs). Methods: This cross-sectional study included 30 peri- or postmenopausal women aged between 45 and 55. The menopausal status was determined according to STRAW + 10 criteria and all participants had a low cardiovascular disease (CVD) risk profile determined by Framingham risk score. The sample was divided into two groups based on the presence or absence of HFs documented in their medical history during their initial visit: Group 1 (n = 15) with HFs present and Group 2 (n = 15) with HFs absent. The patients had polysomnography test and HFs were recorded both by sternal skin conductance and self-report overnight. Genomic DNA was extracted from the women's blood and methylation status was analyzed by fluorescence-based real-time quantitative PCR. The quantified value of DNA methylation of a target gene was normalized by β-actin. The primary outcome was the variation in methylation levels of LINE-1 and Alu and sleep parameters according to the presence of HFs. Results: LINE-1 and Alu methylation levels were higher in Group 1 (HFs present), although statistically non-significant. LINE-1 methylation levels were negatively correlated with age. Sleep efficiency was statistically significantly lower for women in Group 1 (HFs present) (74.66% ± 11.16% vs. 82.63% ± 7.31%; p = 0.03). The ratio of duration of awakening to total sleep time was statistically significantly higher in Group 1 (HFs present) (22.38% ± 9.99% vs. 15.07% ± 6.93, p = 0.03). Objectively recorded hot flashes were significantly higher in Group 1 (4.00 ± 3.21 vs. 1.47 ± 1.46, p = 0.03). None of the cases in Group 2 self-reported HF despite objectively recorded HFs during the polysomnography. The rate of hot flash associated with awakening was 41.4% in the whole sample. Conclusions: Women with a history of hot flashes exhibited lower sleep efficiency and higher awakening rates. Although a history of experiencing hot flashes was associated with higher LINE-1 and Alu methylation levels, no statistical significance was found. Further studies are needed to clarify this association. This study was funded by the Scientific Research Projects Coordination Unit of Istanbul University-Cerrahpasa. Project number: TTU-2021-35629.
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Affiliation(s)
- Ipek Betul Ozcivit Erkan
- Department of Obstetrics and Gynaecology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpaşa Mah. Kocamustafapaşa Cad. No:34/E Fatih/İSTANBUL, Istanbul 34098, Turkey;
| | - Hasan Hakan Seyisoglu
- Department of Obstetrics and Gynaecology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpaşa Mah. Kocamustafapaşa Cad. No:34/E Fatih/İSTANBUL, Istanbul 34098, Turkey;
| | - Gulcin Benbir Senel
- Sleep Disorders Units, Department of Neurology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (G.B.S.); (D.K.)
| | - Derya Karadeniz
- Sleep Disorders Units, Department of Neurology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (G.B.S.); (D.K.)
| | - Filiz Ozdemir
- Department of Medical Genetics, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (F.O.); (A.K.); (M.S.)
| | - Aysel Kalayci
- Department of Medical Genetics, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (F.O.); (A.K.); (M.S.)
| | - Mehmet Seven
- Department of Medical Genetics, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (F.O.); (A.K.); (M.S.)
| | - Neslihan Gokmen Inan
- Department of Computer Engineering, College of Engineering, Koc University, Istanbul 34450, Turkey;
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Carlund O, Thörn E, Osterman P, Fors M, Dernstedt A, Forsell MNE, Erlanson M, Landfors M, Degerman S, Hultdin M. Semimethylation is a feature of diffuse large B-cell lymphoma, and subgroups with poor prognosis are characterized by global hypomethylation and short telomere length. Clin Epigenetics 2024; 16:68. [PMID: 38773655 PMCID: PMC11110316 DOI: 10.1186/s13148-024-01680-4] [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: 02/16/2024] [Accepted: 05/13/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Large B-cell lymphoma (LBCL) is the most common lymphoma and is known to be a biologically heterogeneous disease regarding genetic, phenotypic, and clinical features. Although the prognosis is good, one-third has a primary refractory or relapsing disease which underscores the importance of developing predictive biological markers capable of identifying high- and low-risk patients. DNA methylation (DNAm) and telomere maintenance alterations are hallmarks of cancer and aging. Both these alterations may contribute to the heterogeneity of the disease, and potentially influence the prognosis of LBCL. RESULTS We studied the DNAm profiles (Infinium MethylationEPIC BeadChip) and relative telomere lengths (RTL) with qPCR of 93 LBCL cases: Diffuse large B-cell lymphoma not otherwise specified (DLBCL, n = 66), High-grade B-cell lymphoma (n = 7), Primary CNS lymphoma (n = 8), and transformation of indolent B-cell lymphoma (n = 12). There was a substantial methylation heterogeneity in DLBCL and other LBCL entities compared to normal cells and other B-cell neoplasms. LBCL cases had a particularly aberrant semimethylated pattern (0.15 ≤ β ≤ 0.8) with large intertumor variation and overall low hypermethylation (β > 0.8). DNAm patterns could not be used to distinguish between germinal center B-cell-like (GC) and non-GC DLBCL cases. In cases treated with R-CHOP-like regimens, a high percentage of global hypomethylation (β < 0.15) was in multivariable analysis associated with worse disease-specific survival (DSS) (HR 6.920, 95% CI 1.499-31.943) and progression-free survival (PFS) (HR 4.923, 95% CI 1.286-18.849) in DLBCL and with worse DSS (HR 5.147, 95% CI 1.239-21.388) in LBCL. These cases with a high percentage of global hypomethylation also had a higher degree of CpG island methylation, including islands in promoter-associated regions, than the cases with less hypomethylation. Additionally, telomere length was heterogenous in LBCL, with a subset of the DLBCL-GC cases accounting for the longest RTL. Short RTL was independently associated with worse DSS (HR 6.011, 95% CI 1.319-27.397) and PFS (HR 4.689, 95% CI 1.102-19.963) in LBCL treated with R-CHOP-like regimens. CONCLUSION We hypothesize that subclones with high global hypomethylation and hypermethylated CpG islands could have advantages in tumor progression, e.g. by inactivating tumor suppressor genes or promoting treatment resistance. Our findings suggest that cases with high global hypomethylation and thus poor prognosis could be candidates for alternative treatment regimens including hypomethylating drugs.
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Affiliation(s)
- Olivia Carlund
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Elina Thörn
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
| | - Pia Osterman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Maja Fors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Andy Dernstedt
- Department of Clinical Microbiology, Infection and Immunology, Umeå University, Umeå, Sweden
| | - Mattias N E Forsell
- Department of Clinical Microbiology, Infection and Immunology, Umeå University, Umeå, Sweden
| | - Martin Erlanson
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Infection and Immunology, Umeå University, Umeå, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden.
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Harachi M, Masui K, Shimizu E, Murakami K, Onizuka H, Muragaki Y, Kawamata T, Nakayama H, Miyata M, Komori T, Cavenee WK, Mischel PS, Kurata A, Shibata N. DNA hypomethylator phenotype reprograms glutamatergic network in receptor tyrosine kinase gene-mutated glioblastoma. Acta Neuropathol Commun 2024; 12:40. [PMID: 38481314 PMCID: PMC10935831 DOI: 10.1186/s40478-024-01750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
DNA methylation is crucial for chromatin structure and gene expression and its aberrancies, including the global "hypomethylator phenotype", are associated with cancer. Here we show that an underlying mechanism for this phenotype in the large proportion of the highly lethal brain tumor glioblastoma (GBM) carrying receptor tyrosine kinase gene mutations, involves the mechanistic target of rapamycin complex 2 (mTORC2), that is critical for growth factor signaling. In this scenario, mTORC2 suppresses the expression of the de novo DNA methyltransferase (DNMT3A) thereby inducing genome-wide DNA hypomethylation. Mechanistically, mTORC2 facilitates a redistribution of EZH2 histone methyltransferase into the promoter region of DNMT3A, and epigenetically represses the expression of DNA methyltransferase. Integrated analyses in both orthotopic mouse models and clinical GBM samples indicate that the DNA hypomethylator phenotype consistently reprograms a glutamate metabolism network, eventually driving GBM cell invasion and survival. These results nominate mTORC2 as a novel regulator of DNA hypomethylation in cancer and an exploitable target against cancer-promoting epigenetics.
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Affiliation(s)
- Mio Harachi
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan.
| | - Erika Shimizu
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Kumiko Murakami
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Hiromi Onizuka
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
- Center for Advanced Medical Engineering Research and Development, Kobe University, Kobe, Hyogo, 650-0047, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Hisako Nakayama
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Mariko Miyata
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Takashi Komori
- Department of Neuropathology, Tokyo Metropolitan Neurological Hospital, Musashinodai, Tokyo, 156-8506, Japan
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Atsushi Kurata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Noriyuki Shibata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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10
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Inciuraite R, Steponaitiene R, Raudze O, Kulokiene U, Kiudelis V, Lukosevicius R, Ugenskiene R, Adamonis K, Kiudelis G, Jonaitis LV, Kupcinskas J, Skieceviciene J. Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level. Sci Rep 2024; 14:4456. [PMID: 38396014 PMCID: PMC10891043 DOI: 10.1038/s41598-024-55076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
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Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ruta Steponaitiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Odeta Raudze
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ugne Kulokiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Kestutis Adamonis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania.
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11
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Zhang L, Zhang W, Mu Y, Hu H, Dong K, Wen X, Ye Z, Sun Q, Yan B, Mao Z, Xiao X. Ultrasensitive and Quantitative DNA Methylation Detection Method Based on the MutS Protein. Anal Chem 2023; 95:18828-18835. [PMID: 38078896 DOI: 10.1021/acs.analchem.3c04013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
DNA methylation is closely related to cancer. It is generally accepted that DNA methylation detection is crucial in cancer diagnosis, prognosis, and treatment monitoring. Therefore, there is an urgent demand for developing a simple, rapid, highly sensitive, and highly specific methylation detection method to detect DNA methylation at specific sites quantitatively. In this work, we introduce a DNA methylation detection method based on MutS and methylation-specific PCR, named MutS-based methylation-specific PCR (MB-MSP), which has the advantages of simplicity, speed, high specificity, sensitivity, and broad applicability. Utilizing the MutS's ability to bind mismatched base pairs, we inhibit not only the amplification of unmethylated DNA but also nonspecific primer amplification. We achieved a detection sensitivity of 0.5% for the methylated genes of ACP1, CLEC11A, and SEPT9 by MB-MSP. It has a good linear relationship and a detection time of only 1.5 h. To validate the feasibility of the MB-MSP method in clinical application, we conducted methylation detection on plasma-circulating tumor DNA samples from 10 liver cancer patients and 5 healthy people, achieving a 100% accuracy rate. In conclusion, MB-MSP, as a novel and reliable DNA methylation detection tool, holds significant application value and potential for advancing early cancer diagnosis.
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Affiliation(s)
- Lei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Yaoqin Mu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Xu Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Zhengxin Ye
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Qiangqiang Sun
- Wuhan Yujian Biotechnology, Co. Ltd., Wuhan 430000, P.R. China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
- Ningxia Human Sperm Bank, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, P.R. China
| | - Zenghui Mao
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha 410007, P.R. China
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha 410007, P.R. China
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12
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Faraj Tabrizi P, Peters I, Schimansky I, Dubrowinskaja N, Reese C, Tezval H, Kuczyk MA, Serth J. Alteration of Cadherin 3 Expression and DNA Methylation in Association with Aggressive Renal Cell Carcinoma. Int J Mol Sci 2023; 24:16476. [PMID: 38003666 PMCID: PMC10670999 DOI: 10.3390/ijms242216476] [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: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Cadherins (calcium-dependent adhesion proteins) are important in cellular adhesion and may play a role in the development and progression of renal cell carcinoma (RCC). This study investigated changes in cadherin 3 (CDH3; P-cadherin) mRNA expression, DNA methylation, and protein expression in RCC and compared the results with the histopathological and clinical characteristics of patients. The possible contribution of CDH3 to tumor cell invasiveness was tested in a functional assay using siRNA-based suppression of CDH3 expression and subsequent real-time impedance analysis using a Matrigel invasion model. Our analyses revealed a tumor-specific loss of CDH3 mRNA expression, CDH3 DNA hypermethylation, and loss of distal tubular and collecting duct CDH3 protein expression in RCC. A relatively higher methylation level in tumors was associated with a loss of cell differentiation and higher clinical stage. siRNA-induced suppression of CDH3 expression modulated the invasion characteristics of tumor cells in the impedance-based real-time cellular analysis. Our results indicate that loss of CDH3 expression is common in RCC and may contribute to the pathogenesis of a subset of RCC. Further studies to reveal the mechanisms of loss of expression and its effects on the invasive behavior of renal tumor cells are required.
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Affiliation(s)
- Pouriya Faraj Tabrizi
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Inga Peters
- Department of Urology, Krankenhaus Nordwest, 60488 Frankfurt, Germany
| | - Inga Schimansky
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Natalia Dubrowinskaja
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Christel Reese
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Hossein Tezval
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Antonius Kuczyk
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
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13
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Shao Z, Han Y, Zhou D. Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA. BMC Genomics 2023; 24:439. [PMID: 37542258 PMCID: PMC10403921 DOI: 10.1186/s12864-023-09541-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND DNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a significant role in various biological processes. Nonetheless, the presence of 5-methylcytosine (5mC) in mitochondrial DNA remains controversial, as data ranging from the lack of 5mC to very extensive 5mC have been reported. RESULTS By conducting comprehensive bioinformatic analyses of both published and our own data, we reveal that previous observations of extensive and strand-biased mtDNA-5mC are likely artifacts due to a combination of factors including inefficient bisulfite conversion, extremely low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). To reduce false positive mtDNA-5mC signals, we establish an optimized procedure for library preparation and data analysis of bisulfite sequencing. Leveraging our modified workflow, we demonstrate an even distribution of 5mC signals across the mtDNA and an average methylation level ranging from 0.19% to 0.67% in both cell lines and primary cells, which is indistinguishable from the background noise. CONCLUSIONS We have developed a framework for analyzing mtDNA-5mC through bisulfite sequencing, which enables us to present multiple lines of evidence for the lack of extensive 5mC in mammalian mtDNA. We assert that the data available to date do not support the reported presence of mtDNA-5mC.
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Affiliation(s)
- Zhenyu Shao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yang Han
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University & Chinese Academy of Medical Sciences (RU069), Shanghai, 200032, China
| | - Dan Zhou
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University & Chinese Academy of Medical Sciences (RU069), Shanghai, 201399, China.
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14
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Carlund O, Norberg A, Osterman P, Landfors M, Degerman S, Hultdin M. DNA methylation variations and epigenetic aging in telomere biology disorders. Sci Rep 2023; 13:7955. [PMID: 37193737 DOI: 10.1038/s41598-023-34922-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.
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Affiliation(s)
- Olivia Carlund
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Anna Norberg
- Department of Medical Biosciences, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Pia Osterman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden.
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15
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DNA methylation changes and increased mRNA expression of coagulation proteins, factor V and thrombomodulin in Fuchs endothelial corneal dystrophy. Cell Mol Life Sci 2023; 80:62. [PMID: 36773096 PMCID: PMC9922242 DOI: 10.1007/s00018-023-04714-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Late-onset Fuchs endothelial corneal dystrophy (FECD) is a disease affecting the corneal endothelium (CE), associated with a cytosine-thymine-guanine repeat expansion at the CTG18.1 locus in the transcription factor 4 (TCF4) gene. It is unknown whether CTG18.1 expansions affect global methylation including TCF4 gene in CE or whether global CE methylation changes at advanced age. Using genome-wide DNA methylation array, we investigated methylation in CE from FECD patients with CTG18.1 expansions and studied the methylation in healthy CE at different ages. The most revealing DNA methylation findings were analyzed by gene expression and protein analysis. 3488 CpGs had significantly altered methylation pattern in FECD though no substantial changes were found in TCF4. The most hypermethylated site was in a predicted promoter of aquaporin 1 (AQP1) gene, and the most hypomethylated site was in a predicted promoter of coagulation factor V (F5 for gene, FV for protein). In FECD, AQP1 mRNA expression was variable, while F5 gene expression showed a ~ 23-fold increase. FV protein was present in both healthy and affected CE. Further gene expression analysis of coagulation factors interacting with FV revealed a ~ 34-fold increase of thrombomodulin (THBD). THBD protein was detected only in CE from FECD patients. Additionally, we observed an age-dependent hypomethylation in elderly healthy CE.Thus, tissue-specific genome-wide and gene-specific methylation changes associated with altered gene expression were discovered in FECD. TCF4 pathological methylation in FECD because of CTG18.1 expansion was ruled out.
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Alves VRG, Micali D, Ota VK, Bugiga AVG, Muniz Carvalho C, Belangero SI. A Systematic Review of LINE-1 Methylation Profile in Psychiatric Disorders. Complex Psychiatry 2023; 9:119-129. [PMID: 37404869 PMCID: PMC10315007 DOI: 10.1159/000530641] [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: 10/05/2022] [Accepted: 04/03/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction Long interspersed nuclear elements (LINEs) are endogenous retrotransposable elements. A few studies have linked the methylation pattern of LINE-1 to different mental disorders (e.g., post-traumatic stress disorder [PTSD], autism spectrum disorder [ASD], panic disorder [PD]). We sought to unify the existing knowledge in the field and provide a better understanding of the association between mental disorders and LINE-1 methylation. Methods A systematic review was executed with 12 eligible articles according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results For psychotic disorders, PTSD, ASD, and PD, lower LINE-1 methylation levels were detected, whereas for mood disorders, the findings are controversial. The studies were conducted with subjects aged 18-80 years. Peripheral blood samples were utilized in 7/12 articles. Conclusion Although most studies have shown that LINE-1 hypomethylation was associated with mental disorders, there were still some divergences (i.e., hypermethylation associated with mental disorders). These studies suggest that LINE-1 methylation may be an important factor related to the development of mental disorders and highlight the need to better comprehend the biological mechanisms underlying the role of LINE-1 in mental disorders pathophysiology.
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Affiliation(s)
- Vitória Rodrigues Guimarães Alves
- Department of Psychiatry and Medical Psychology, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC, Laboratory of Integrative Neuroscience, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Danilo Micali
- LiNC, Laboratory of Integrative Neuroscience, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Vanessa Kiyomi Ota
- LiNC, Laboratory of Integrative Neuroscience, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Amanda Victória Gomes Bugiga
- LiNC, Laboratory of Integrative Neuroscience, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Carolina Muniz Carvalho
- Department of Psychiatry and Medical Psychology, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC, Laboratory of Integrative Neuroscience, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Sintia Iole Belangero
- Department of Psychiatry and Medical Psychology, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC, Laboratory of Integrative Neuroscience, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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17
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Carvalho CM, Coimbra BM, Bugiga A, Marques DF, Kiyomi Ota V, Mello AF, Mello MF, Belangero SI. Hyperarousal Symptom Severity in Women with Posttraumatic Stress Disorder Might Be Associated with LINE-1 Hypomethylation in Childhood Sexual Abuse Victims. Complex Psychiatry 2023; 9:44-56. [PMID: 37034826 PMCID: PMC10080193 DOI: 10.1159/000529698] [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: 11/04/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction Sexual assault and a history of childhood sexual abuse (CSA) are related to posttraumatic stress disorder (PTSD) development. Long interspersed nuclear elements (LINE-1) are transposable elements, and their methylation is used to infer DNA global methylation. DNA methylation can be affected by trauma exposition which in turn would be associated with PTSD. Thus, we investigated if the LINE-1 methylation pattern is related to PTSD symptoms in females with a history of CSA. Methods This is a case-control study that examined, at baseline (W1), 64 women victims of sexual assault diagnosed with PTSD and 31 patients with PTSD who completed the 1-year follow-up (W2). Participants were categorized into two groups according to the presence of CSA (PTSDCSA+: NW1 = 19, NW2 = 10; PTSDCSA-: NW1 = 45, NW2 = 21). PTSD symptoms (re-experiencing, avoidance, hyperarousal, alterations in cognition/mood) were assessed using the Clinician-Administered PTSD Scale, and the history of CSA was assessed by the Childhood Trauma Questionnaire. LINE-1 methylation was measured in three sites (CpG1, CpG2, CpG3) located in the 5'UTR region using bisulfite conversion followed by pyrosequencing. Linear regression models were performed to test the relation between LINE-1 CpG sites methylation and PTSD symptoms. Results We found a negative association between CpG2 methylation and hyperarousal symptoms among those in the PTSDCSA+ group in W1 (adjusted p = 0.003) compared to the PTSDCSA- group (p > 0.05). Still, no association was observed between other PTSD symptoms and other CpG sites. Further, in the longitudinal analysis, LINE-1 hypomethylation was no longer observed in PTSD participants exposed to CSA. Conclusion Our findings suggest that LINE-1 methylation may help understand the relationship between trauma and PTSD. However, more studies are needed to investigate LINE-1 as an epigenetic marker of psychiatric disorders.
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Affiliation(s)
- Carolina Muniz Carvalho
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Bruno Messina Coimbra
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Psychiatry, Amsterdam Public Health Research Institute and Amsterdam Neuroscience Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Amanda Bugiga
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division of Department of Morphology and Genetics of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Diogo Ferri Marques
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Vanessa Kiyomi Ota
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division of Department of Morphology and Genetics of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Andrea Feijó Mello
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Marcelo Feijó Mello
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Sintia Iole Belangero
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division of Department of Morphology and Genetics of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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18
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Song X, Song X, Lai W, Wang H. Hyperactive DNA Cutting for Unbiased UHPLC-MS/MS Quantification of Epigenetic DNA Marks by Engineering DNase I Mutants. Anal Chem 2022; 94:17670-17676. [PMID: 36490323 DOI: 10.1021/acs.analchem.2c04485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic DNA modifications, such as 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine, are associated with a variety of diseases and potential biomarkers for cancer diagnosis and therapy. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays are considered to be the gold standard for qualitative and quantitative detection of DNA modifications. DNA digestion for converting long DNA polymer into 2'-deoxynucleosides is an important preprocessing step to achieve sensitive and accurate LC-MS/MS quantification. Here, we showed that, as stimulated by divalent metal ions, Mg2+ and Mn2+, the engineered human DNase I Q9R:E13R:N74K mutant can efficiently digest DNA in the presence of monovalent metal ions at a high concentration (e.g., 1 M NaCl), showing hyperactivity on DNA cutting. We also found that the engineered DNase I mutants display exceptional DNA-cutting activity over a wider pH range (5.5-9.5). Due to their hyperactivity and high salt tolerance, the engineered DNase I mutants cut DNA 5mC and dC efficiently. Benefitting from this DNA-cutting hyperactivity, we demonstrated an LC-MS/MS assay for unbiased and accurate quantification of DNA 5mC.
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Affiliation(s)
- Xingrui Song
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinyue Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Abe I, Suzuki K, Kimura Y, Tamaki S, Endo Y, Ichida K, Muto Y, Watanabe F, Saito M, Konishi F, Rikiyama T. Enhancement of DNA hypomethylation alterations by gastric and bile acids promotes chromosomal instability in Barrett's epithelial cell line. Sci Rep 2022; 12:20710. [PMID: 36456615 PMCID: PMC9715700 DOI: 10.1038/s41598-022-25279-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Gastric and bile acid reflux leads to chronic inflammation, resulting in methylation alterations in Barrett's esophagus (BE) together with chromosomal instability (CIN). We investigated DNA hypomethylation following acid exposure and confirmed its significance in BE-related carcinogenesis by inducing CIN in vitro. OACP4C, an esophageal cancer cell line, and CP-A, a non-dysplastic cell line originating from BE, were exposed to acidic conditions using deoxycholic acid. CP-A exhibited substantially increased DNA hypomethylation of alpha satellite sequences in the centromere region, as well as increased levels of alpha satellite transcripts, but no changes were observed in the long interspersed nucleotide element-1 sequences distributed throughout the entire genome. These changes were not clearly found in OACP4C. Copy number changes at specific chromosomes were identified in CP-A, along with an increased number of cells exhibiting abnormal segregations, whereas these changes were rarely observed in OACP4C. The changes were maintained after several cell divisions. These findings suggest that alpha satellites are likely targets of DNA hypomethylation induced by acid exposure. CP-A was more sensitive to acid exposure than OACP4C, indicating that acid-induced DNA hypomethylation is involved in cancer development rather than progression, which could be involved in the underlying mechanism of esophagogastric junction carcinoma development.
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Affiliation(s)
- Iku Abe
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Koichi Suzuki
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Yasuaki Kimura
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Sawako Tamaki
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Yuhei Endo
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Kosuke Ichida
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Yuta Muto
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Fumiaki Watanabe
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Masaaki Saito
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
| | - Fumio Konishi
- Department of Surgery, Nerima-Hikarigaoka Hospital, 2-5-1, Hikarigaoka, Nerima-ku, Tokyo, 179-0072 Japan
| | - Toshiki Rikiyama
- grid.410804.90000000123090000Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-Cho, Omiya-Ku, Saitama, 330-8503 Japan
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20
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Symonds L, Yu M, Zhang Y, Ou FS, Zemla TJ, Carter K, Bertagnolli M, Innocenti F, Bosch LJW, Meijer GA, Carvalho B, Grady WM, Cohen SA. Evaluation of methylated DCR1 as a biomarker for response to adjuvant irinotecan-based therapy in stage III colon cancer: cancer and leukaemia Group B 89803 (Alliance). Epigenetics 2022; 17:1715-1725. [PMID: 35412430 PMCID: PMC9621073 DOI: 10.1080/15592294.2022.2058225] [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: 07/21/2021] [Revised: 03/01/2022] [Accepted: 03/22/2022] [Indexed: 11/03/2022] Open
Abstract
Aberrantly methylated genes contribute to the landscape of epigenetic alterations in colorectal adenocarcinoma. The global CpG Island methylator phenotype (CIMP) and individually methylated genes are potential prognostic/predictive biomarkers. Research suggests an association between methylated DCR1 (mDCR1) and lack of benefit with irinotecan (IFL) treatment. We assessed the association between DCR1 methylation status and survival in patients receiving adjuvant fluorouracil/ leucovorin (5-FU/LV) or IFL. We analysed data from patients with stage III colon adenocarcinoma randomly assigned to adjuvant 5-FU/LV or IFL in CALGB 89803 (Alliance). The primary endpoint was overall survival (OS), and the secondary endpoint was disease-free survival (DFS). Using tumour sample DNA, we evaluated the association between survival, DCR1 methylation status, and molecular subgroups (BRAF, KRAS, mismatch repair status, CIMP status) using Kaplan-Meier estimator and Cox proportional hazard model. mDCR1 was observed in 221/400 (55%) colon cancers. Histopathologic features were similar between mDCR1 and unmethylated DCR1 (unDCR1) colon cancers. There was no difference in OS (p = 0.83) or DFS (p = 0.85) based on DCR1 methylation status. There was no association between methylation status and response to IFL . In patients with unDCR1 and KRAS-wildtype tumours, those who received IFL had a nearly two-fold worse DFS compared to patients who received 5-FU/LV (HR = 1.85, 95% CI (0.97-3.53, p = 0.06). This relationship was not notable among other subgroups. In stage III colon cancer patients, mDCR1 status did not associate with response to irinotecan. Larger studies may suggest an association between the iridocene response and molecular subgroups.
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Affiliation(s)
- Lynn Symonds
- Division of Oncology, University of Washington, Seattle, WA, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - YuHong Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Fang-Shu Ou
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - Tyler J. Zemla
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - Kelly Carter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Monica Bertagnolli
- Office of the Alliance Group Chair, Boston, MA, USA
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Linda JW Bosch
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Gastroenterology, University of Washington, Seattle, Washington, USA
| | - Stacey A. Cohen
- Division of Oncology, University of Washington, Seattle, WA, USA
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21
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El-Ahwany E, Hassan M, Elzallat M, Abdelsalam L, El-Sawy MAH, Seyam M. Association of Sat-a and Alu methylation status with HCV-induced chronic liver disease and hepatocellular carcinoma. Virus Res 2022; 321:198928. [PMID: 36100006 DOI: 10.1016/j.virusres.2022.198928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The combination of epigenetic and genetic abnormalities contributes together to the development of liver cancer. The methylation status of the repetitive elements (REs) in DNA has been investigated in a variety of human illnesses. However, the methylation patterns of Sat-α and Alu REs in chronic liver disease (CLD) and hepatocellular carcinoma (HCC) caused by hepatitis C virus (HCV) have never been studied before. METHODOLOGY In this study, 3 groups of participants including 50 patients having HCV-induced CLD, 50 patients having HCV-induced HCC, and 46 healthy subjects were subjected to measurement of Sat-α and Alu methylation using the quantitative MethyLight assay. RESULTS Sat-α and Alu methylation percentages decreased significantly in both CLD and HCC, compared to control. Also, a significant Sat-α hypomethylation was detected in HCC, compared to CLD. In addition, Sat-α and Alu methylation showed a significant decline as lesion size grew. However, only Sat-α hypomethylation was significantly increased in association with portal vein thrombosis and the MELD score. Sat-α methylation percentage had the highest sensitivity and specificity for diagnosing HCC (100% and 84.4%) followed by α-fetoprotein (80% and 84.4%) and Alu methylation (66% and 61.5%). Furthermore, there was a strong positive correlation between Sat-α and Alu methylation. CONCLUSIONS Measuring Sat-α and Alu methylation provides us with a new tool for early detecting HCV-induced CLD and hepatocarcinogenesis. Sat-α has the potential to be utilized as an independent predictive parameter for HCC development and progression because of its ability to distinguish between CLD and HCC with their different MELD scores.
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Affiliation(s)
- Eman El-Ahwany
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Marwa Hassan
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt.
| | - Mohamed Elzallat
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Lobna Abdelsalam
- Human Genetics Department, Faculty of Medicine, Cairo University, Cairo, Egypt; Human Genetics Department, Faculty of Medicine, University of North Carolina, USA
| | | | - Moataz Seyam
- Hepato-Gastroenterology Department, Theodor Bilharz Research Institute, Giza, Egypt
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22
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Serhii K, Anastasiia H, Oksana M, Kyrylo L, Liubov S, Nataliia V, Iryna I, Rostyslav S, Alla R. Tristetraprolin expression levels and methylation status in breast cancer. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Tajbakhsh J, Mortazavi F, Gupta NK. DNA methylation topology differentiates between normal and malignant in cell models, resected human tissues, and exfoliated sputum cells of lung epithelium. Front Oncol 2022; 12:991120. [DOI: 10.3389/fonc.2022.991120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundGlobal DNA hypomethylation is a prominent feature of cancer cells including lung cancer, that has not been widely explored towards cancer diagnosis. In this study we assess the comparative distribution of global DNA methylation in normal cells versus cancer cells in various specimen models.MethodsWe used in situ immunofluorescence labeling of overall 5-methylcytosine (5mC) and covisualization of global DNA (gDNA) by 4’,6-diamidino-2-phenylindole (DAPI), confocal microscopy and 3D image analysis to derive 5mC/DAPI colocalization patterns in human cell lines (BEAS-2B, A549, H157) and upper respiratory epithelial cells derived from various sources (i.e., sputum from healthy and cancer patients, and resected tissues from normal parenchyma and lung tumors).ResultsBy introducing 5mC/DAPI colocalization index as a metric we could distinguish between normal epithelial cells and aberrantly hypomethylated cancer cells. Cultured lung cancer cells (H157 and A549) had significantly lower indices compared to normal cells (BEAS-2B). Furthermore, we were able to identify such extensively hypomethylated low-index cells in tumor tissues and the matching sputum from cancer patients. In contrast, the indices of cells derived from sputum of healthy individuals had more similarity to epithelial cells of normal parenchyma and the phenotypically normal BEAS-2B cells.ConclusionsThe results suggest that 5mC topology using high-resolution image cytometry shows potential for identifying hypomethylated cancerous cells in human tissues and amongst normal cells in matching sputum, which may render a valuable surrogate for biopsied tissues. This promising feature deserves further validation in more comprehensive studies.
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24
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George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf Y. Epigenomic reprogramming in iAs-mediated carcinogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 96:319-365. [PMID: 36858778 DOI: 10.1016/bs.apha.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Arsenic is a naturally occurring metal carcinogen found in the Earth's crust. Millions of people worldwide are chronically exposed to arsenic through drinking water and food. Exposure to inorganic arsenic has been implicated in many diseases ranging from acute toxicities to malignant transformations. Despite the well-known deleterious health effects of arsenic exposure, the molecular mechanisms in arsenic-mediated carcinogenesis are not fully understood. Since arsenic is non-mutagenic, the mechanism by which arsenic causes carcinogenesis is via alterations in epigenetic-regulated gene expression. There are two possible ways by which arsenic may modify the epigenome-indirectly through an arsenic-induced generation of reactive oxygen species which then impacts chromatin remodelers, or directly through interaction and modulation of chromatin remodelers. Whether directly or indirectly, arsenic modulates epigenetic gene regulation and our understanding of the direct effect of this modulation on chromatin structure is limited. In this chapter we will discuss the various ways by which inorganic arsenic affects the epigenome with consequences in health and disease.
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Affiliation(s)
- Smitha George
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Richard N Cassidy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Wesley N Saintilnord
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
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25
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Ogata A, Kondo M, Yoshikawa M, Okano M, Tsutsumi T, Aboshi H. Dental age estimation based on DNA methylation using real-time methylation-specific PCR. Forensic Sci Int 2022; 340:111445. [DOI: 10.1016/j.forsciint.2022.111445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/17/2022] [Accepted: 08/28/2022] [Indexed: 11/28/2022]
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26
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Chen S, Xie P, Cowan M, Huang H, Cardenas H, Keathley R, Tanner EJ, Fleming GF, Moroney JW, Pant A, Akasha AM, Davuluri RV, Kocherginsky M, Zhang B, Matei D. Epigenetic priming enhances antitumor immunity in platinum-resistant ovarian cancer. J Clin Invest 2022; 132:e158800. [PMID: 35671108 PMCID: PMC9282926 DOI: 10.1172/jci158800] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
BackgroundImmune checkpoint inhibitors (ICIs) have modest activity in ovarian cancer (OC). To augment their activity, we used priming with the hypomethylating agent guadecitabine in a phase II study.MethodsEligible patients had platinum-resistant OC, normal organ function, measurable disease, and received up to 5 prior regimens. The treatment included guadecitabine (30 mg/m2) on days 1-4, and pembrolizumab (200 mg i.v.) on day 5, every 21 days. The primary endpoint was the response rate. Tumor biopsies, plasma, and PBMCs were obtained at baseline and after treatment.ResultsAmong 35 evaluable patients, 3 patients had partial responses (8.6%), and 8 (22.9%) patients had stable disease, resulting in a clinical benefit rate of 31.4% (95% CI: 16.9%-49.3%). The median duration of clinical benefit was 6.8 months. Long-interspersed element 1 (LINE1) was hypomethylated in post-treatment PBMCs, and methylomic and transcriptomic analyses showed activation of antitumor immunity in post-treatment biopsies. High-dimensional immune profiling of PBMCs showed a higher frequency of naive and/or central memory CD4+ T cells and of classical monocytes in patients with a durable clinical benefit or response (CBR). A higher baseline density of CD8+ T cells and CD20+ B cells and the presence of tertiary lymphoid structures in tumors were associated with a durable CBR.ConclusionEpigenetic priming using a hypomethylating agent with an ICI was feasible and resulted in a durable clinical benefit associated with immune responses in selected patients with recurrent OC.Trial registrationClinicalTrials.gov NCT02901899.FundingUS Army Medical Research and Material Command/Congressionally Directed Medical Research Programs (USAMRMC/CDMRP) grant W81XWH-17-0141; the Diana Princess of Wales Endowed Professorship and LCCTRAC funds from the Robert H. Lurie Comprehensive Cancer Center; Walter S. and Lucienne Driskill Immunotherapy Research funds; Astex Pharmaceuticals; Merck & Co.; National Cancer Institute (NCI), NIH grants CCSG P30 CA060553, CCSG P30 CA060553, and CA060553.
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Affiliation(s)
- Siqi Chen
- Department of Medicine, Hematology/Oncology Division
| | - Ping Xie
- Department of Medicine, Hematology/Oncology Division
| | | | - Hao Huang
- Department of Obstetrics and Gynecology
| | | | - Russell Keathley
- Department of Obstetrics and Gynecology
- Driskill Graduate Training Program in Life Sciences, and
| | - Edward J. Tanner
- Department of Obstetrics and Gynecology
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Gini F. Fleming
- Department of Medicine, Hematology/Oncology Division, University of Chicago, Chicago, Illinois, USA
| | - John W. Moroney
- Department of Medicine, Hematology/Oncology Division, University of Chicago, Chicago, Illinois, USA
| | - Alok Pant
- Northwestern Medicine, Lake Forest Hospital, Lake Forest, Illinois, USA
| | - Azza M. Akasha
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ramana V. Davuluri
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA
| | - Masha Kocherginsky
- Department of Obstetrics and Gynecology
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Division of Biostatistics, Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Bin Zhang
- Department of Medicine, Hematology/Oncology Division
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Daniela Matei
- Department of Obstetrics and Gynecology
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Jesse Brown VA Medical Center, Chicago, Illinois, USA
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27
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Watcharanurak P, Mutirangura A. Human RNA-directed DNA methylation methylates high-mobility group box 1 protein-produced DNA gaps. Epigenomics 2022; 14:741-756. [PMID: 35762252 DOI: 10.2217/epi-2022-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: DNA sequences around HMGB1-produced DNA gaps are hypermethylates. DNA methylation of interspersed repetitive sequences (IRS) such as Alu elements can be established through AGO4-mediating, RNA-directed DNA methylation (RdDM). HMGB1 depletion, DNA gap reduction and global hypomethylation promote genomic instability. Methods: HMGB1, SIRT1, AGO4 and DNA gap colocalizations were evaluated. Then, Alu methylation was analyzed in HMGB1-deficient or HMGB1-overexpressing cells and Alu siRNA-transfected HMGB1-deficient cells. Results: HMGB1, SIRT1, AGO4 and DNA gap are colocalized in the nucleus. Moreover, HMGB1 or Alu siRNA increased Alu methylation, whereas Alu siRNA could not methylate HMGB1-deficient cells. Conclusion: AGO4 play a role in methylating DNA sequence around HMGB1-produced DNA gaps and localize DNA gap in IRS, and loss of intranuclear HMGB1 causes global hypomethylation.
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Affiliation(s)
- Papitchaya Watcharanurak
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.,Department of Anatomy, Center of Excellence in Molecular Genetics of Cancer & Human Disease, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Center of Excellence in Molecular Genetics of Cancer & Human Disease, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
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28
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Pinto R, Hauge T, Jeanmougin M, Pharo HD, Kresse SH, Honne H, Winge SB, Five MB, Kumar T, Mala T, Hauge T, Johnson E, Lind GE. Targeted genetic and epigenetic profiling of esophageal adenocarcinomas and non-dysplastic Barrett's esophagus. Clin Epigenetics 2022; 14:77. [PMID: 35701814 PMCID: PMC9195284 DOI: 10.1186/s13148-022-01287-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/10/2022] [Indexed: 11/22/2022] Open
Abstract
Background Despite the efforts to describe the molecular landscape of esophageal adenocarcinoma (EAC) and its precursor lesion Barrett’s esophagus (BE), discrepant findings are reported. Here, we investigated the prevalence of selected genetic (TP53 mutations and microsatellite instability (MSI) status) and epigenetic (DNA promoter hypermethylation of APC, CDKN2A, MGMT, TIMP3 and MLH1) modifications in a series of 19 non-dysplastic BE and 145 EAC samples. Additional biopsies from adjacent normal tissue were also evaluated. State-of-the-art methodologies and well-defined scoring criteria were applied in all molecular analyses. Results Overall, we confirmed frequent TP53 mutations among EAC (28%) in contrast to BE, which harbored no mutations. We demonstrated that MSI and MLH1 promoter hypermethylation are rare events, both in EAC and in BE. Our findings further support that APC, CDKN2A, MGMT and TIMP3 promoter hypermethylation is frequently seen in both lesions (21–89%), as well as in a subset of adjacent normal samples (up to 12%). Conclusions Our study further enlightens the molecular background of BE and EAC. To the best of our knowledge, this is one of the largest studies addressing a targeted analysis of genetic and epigenetic modifications simultaneously across a combined series of non-dysplastic BE and EAC samples. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01287-7.
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Affiliation(s)
- Rita Pinto
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Tobias Hauge
- Department of Pediatric and Gastrointestinal Surgery, Oslo University Hospital, Ullevål, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Heidi D Pharo
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Stine H Kresse
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Hilde Honne
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Sara B Winge
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - May-Britt Five
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Theresa Kumar
- Department of Pathology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Tom Mala
- Department of Pediatric and Gastrointestinal Surgery, Oslo University Hospital, Ullevål, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Truls Hauge
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Egil Johnson
- Department of Pediatric and Gastrointestinal Surgery, Oslo University Hospital, Ullevål, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway. .,Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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Endo Y, Suzuki K, Kimura Y, Tamaki S, Aizawa H, Abe I, Watanabe F, Kato T, Saito M, Futsuhara K, Noda H, Konishi F, Rikiyama T. Genome‑wide DNA hypomethylation drives a more invasive pancreatic cancer phenotype and has predictive occult distant metastasis and prognosis potential. Int J Oncol 2022; 60:61. [PMID: 35419613 PMCID: PMC9015190 DOI: 10.3892/ijo.2022.5351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/22/2022] [Indexed: 11/06/2022] Open
Abstract
Genome‑wide DNA hypomethylation is the most common molecular feature in human cancers associated with chromosomal instability (CIN), which is involved in the mechanisms that regulate pancreatic cancer (PC) metastasis. It was investigated whether genome‑wide DNA hypomethylation affects the phenotype in PC via CIN in vitro, and its significance on the biological behavior of PC was verified. The relative demethylation level (RDL) of long interspersed nucleotide element‑1 (LINE‑1) in human PC cell lines was used to characterize DNA hypomethylation using methylation‑specific quantitative (q)PCR. CIN was estimated by changes in chromosomal copy number using comparative genomic hybridization analysis. Abnormal segregation of chromosomes was assessed by immunocytochemistry, and the DNA damage response was evaluated using the number of anti‑γH2AX positive cells. Invasion ability was assessed using a Matrigel invasion assay. Clinical specimens from 49 patients with PC who underwent curative surgery were evaluated for a correlation of DNA hypomethylation with clinical outcome. Successful induction of genome‑wide DNA hypomethylation in PC cells led to copy number changes in specific chromosomal regions. The number of cells with abnormal segregation of chromosomes significantly increased with the number of anti‑γH2AX positive cells. The invasive potential of these cells also significantly increased. The occurrence of occult distant metastasis in the clinical specimens and receiver operating characteristic analysis clearly identified those who were and were not likely to have occult distant metastasis, with high LINE‑1 RDL significantly correlated with the presence of occult distant metastasis (P=0.035) and poor prognosis (P=0.048). The significance of genome‑wide DNA hypomethylation on the biological behavior of PC, which promotes a more invasive phenotype via CIN in vitro and predicts the susceptibility to occult distant metastasis and poor prognosis in patients with PC was revealed.
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Affiliation(s)
- Yuhei Endo
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Koichi Suzuki
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Yasuaki Kimura
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Sawako Tamaki
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Hidetoshi Aizawa
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Iku Abe
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Fumiaki Watanabe
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Takaharu Kato
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Masaaki Saito
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Kazushige Futsuhara
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | - Hiroshi Noda
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
| | | | - Toshiki Rikiyama
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama 330-8503, Japan
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30
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Zhang H, Zou Q, Ju Y, Song C, Chen D. Distance-based support vector machine to predict DNA N6-methyladenine modification. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220404145517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
DNA N6-methyladenine plays an important role in the restriction-modification system to isolate invasion from adventive DNA. The shortcomings of the high time-consumption and high costs of experimental methods have been exposed, and some computational methods have emerged. The support vector machine theory has received extensive attention in the bioinformatics field due to its solid theoretical foundation and many good characteristics.
Objective:
General machine learning methods include an important step of extracting features. The research has omitted this step and replaced with easy-to-obtain sequence distances matrix to obtain better results
Method:
First sequence alignment technology was used to achieve the similarity matrix. Then a novel transformation turned the similarity matrix into a distance matrix. Next, the similarity-distance matrix is made positive semi-definite so that it can be used in the kernel matrix. Finally, the LIBSVM software was applied to solve the support vector machine.
Results:
The five-fold cross-validation of this model on rice and mouse data has achieved excellent accuracy rates of 92.04% and 96.51%, respectively. This shows that the DB-SVM method has obvious advantages compared with traditional machine learning methods. Meanwhile this model achieved 0.943,0.982 and 0.818 accuracy,0.944, 0.982, and 0.838 Matthews correlation coefficient and 0.942, 0.982 and 0.840 F1 scores for the rice, M. musculus and cross-species genome datasets, respectively.
Conclusion:
These outcomes show that this model outperforms the iIM-CNN and csDMA in the prediction of DNA 6mA modification, which are the lastest research on DNA 6mA.
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Affiliation(s)
- Haoyu Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610051, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610051, China
| | - Ying Ju
- School of Informatics, Xiamen University, Xiamen 361005, China
| | - Chenggang Song
- Beidahuang Industry Group General Hospital, Harbin 150001, China
| | - Dong Chen
- College of Electrical and Information Engineering, Quzhou University, Quzhou 324000, China
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31
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Mrkonjic M, Turashvili G. EPM2AIP1 Immunohistochemistry Can Be Used as Surrogate Testing for MLH1 Promoter Methylation in Endometrial Cancer. Am J Surg Pathol 2022; 46:376-382. [PMID: 34772843 DOI: 10.1097/pas.0000000000001832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Immunohistochemical (IHC) evaluation of DNA mismatch repair proteins (MMR) has become routine practice for Lynch syndrome screening and/or part of diagnostic evaluation in endometrial cancer. Approximately 20% to 30% of endometrial carcinomas demonstrate microsatellite instability due to defective DNA MMR. Vast majority of MLH1/PMS2-deficient tumors are sporadic and show MLH1 promoter methylation. MLH1 methylation testing by quantitative polymerase chain reaction-based technique is time, labor, and tissue intensive with an average institutional turnaround time of 2 weeks. MLH1 and EPM2AIP1 genes share a common promoter whose methylation has been shown to affect both genes. We assessed whether IHC for EPM2AIP1 in combination with MMR proteins can serve as surrogate marker for MLH1 promoter methylation status. We performed a retrospective review of all MLH1/PMS2-deficient endometrial carcinomas that underwent MLH1 promoter methylation testing from January 1 to September 31, 2020, at our institution. Microscopic slides were reviewed and EMP2AIP1 IHC was performed. The results were correlated with MLH1 promoter methylation status (percent methylated rate). A total of 119 cases were identified and successfully tested. Nuclear EPM2AIP1 protein expression was observed in benign endometrial cells and myometrial smooth muscle cells. Loss of nuclear EPM2AIP1 staining was identified in 90/110 (81.8%) methylated tumors with additional 14/110 (12.7%) cases showing aberrant staining patterns. Only 6/110 (5.5%) tumors demonstrated intact EPM2AIP1 nuclear expression in presence of MLH1 promoter methylation. EMP2AIP1 IHC is concordant with MLH1 promoter methylation results in 95% of endometrial carcinomas (94.5% sensitivity, 98.1% positive predictive value) and shows promise as a surrogate marker for methylation testing.
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Affiliation(s)
- Miralem Mrkonjic
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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32
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Toxicological and Nutraceutical Screening Assays of Some Artificial Sweeteners. Processes (Basel) 2022. [DOI: 10.3390/pr10020410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Artificial sweeteners are food additives worldwide used instead of fructose or glucose in many diet beverages. Furthermore, diet beverages intake has been increasing every year. Thus, some food agencies should regulate it based on toxicological studies. Debates and controversial results are demonstrated, and authority can revise its decision on the basis of new data reporting toxicological effects since cyclamate has been forbidden in some countries. Therefore, the aim of this study was to report new data about the toxicity of acesulfame-k, aspartame, and cyclamate, which are useful for authority agencies, determining the toxic potential and nutraceutical capabilities of these compounds. The toxicity, antitoxicity, genotoxicity, antigenotoxicity, and life expectancy assays were carried out in Drosophila as an in vivo model. In addition, in vitro HL-60 line cell was used to evaluate the chemopreventive activity determining the cytotoxic effect and the capability of producing DNA damage due to internucleosomal fragmentation or DNA strand breaks. Furthermore, the methylated status of these cancer cells treated with the tested compounds was assayed as a cancer therapy. Our results demonstrated that all tested compounds were neither toxic nor genotoxic, whereas these compounds resulted in antigenotoxic and cytotoxic substances, except for cyclamate. Aspartame showed antitoxic effects in Drosophila. All tested compounds decreased the quality of life of this in vivo organism model. Acesulfame-k, aspartame, and cyclamate induced DNA damage in the HL-60 cell line in the comet assay, and acesulfame-k generally increased the methylation status. In conclusion, all tested artificial sweeteners were safe compounds at assayed concentrations since toxicity and genotoxicity were not significantly induced in flies. Moreover, Aspartame and Cyclamate showed protective activity against a genotoxin in Drosophila Regarding nutraceutical potential, acesulfame-k and aspartame could be demonstrated to be chemopreventive due to the cytotoxicity activity shown by these compounds. According to DNA fragmentation and comet assays, a necrotic way could be the main mechanism of death cells induced by acesulfame-k and aspartame. Finally, Acesulfame-K hypermethylated repetitive elements, which are hypomethylated in cancer cells resulting in a benefit to humans.
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Abstract
Nowadays, a general interest in improving health in order to achieve better conditions of life is increasing. Diet is a complex factor affecting health conditions. We analysed the biological activities of three types of alcohol-free lager beer (a blond, a pale-blond and a stout beer) as well as epicatechin gallate (ECG) as one of their most abundant phenols with the aim of revealing them as nutraceuticals. For that purpose, we carried out safety and protective assays of the tested substances in the well-known Drosophila melanogaster animal model. Moreover, chemoprevention studies on human leukaemia cells (HL-60) in an in vitro model were carried out to evaluate the viability and genomic damage potential of the studied compounds on the tumour cell line. Results suggest the safety properties of all compounds, although pale-blond and stout beer only showed genotoxic activity at the lowest concentrations assayed. Moreover, alcohol-free beers and phenols were able to protect against H2O2 oxidative damage as well as to induce an increase in longevity with an improvement of the quality of life in the in vivo animal model assayed. Promising results were obtained with the alcohol-free beers and ECG in the in vitro assays with human leukaemia cells as they inhibited the tumour cells’ growth, induced DNA damage and modified the methylation status of such a cancer cell line. To sum up, alcohol-free beers should be of interest not only because of their reduced calories and isotonic properties but because they can be recognised as nutraceutical substances.
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Kato D, Takegami Y, Seki T, Nakashima H, Osawa Y, Suzuki K, Yamada H, Hasegawa Y, Imagama S. DNA methylation is associated with muscle loss in community-dwelling older men -the Yakumo study- : a preliminary experimental study. NAGOYA JOURNAL OF MEDICAL SCIENCE 2022; 84:60-68. [PMID: 35392004 PMCID: PMC8971031 DOI: 10.18999/nagjms.84.1.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/17/2021] [Indexed: 12/04/2022]
Abstract
Frailty is a state of reduced muscle strength and activity in older people. DNA methylation is associated with osteoporosis and muscle loss in murine and other animal studies, but there are no epidemiological studies in humans. This study aimed to assess the association of osteoporosis and muscle loss with DNA methylation in community-dwelling older people. This cross-sectional study was performed in a rural part of Japan. We analyzed 204 subjects (98 men and 106 women). In univariate analysis, the two groups were compared according to the presence or absence of osteoporosis and of muscle loss. Logistic regression analysis was performed to determine predictors of frailty in the muscle loss group. We used age, sex, body mass index, smoking history, drinking history, serum albumin and C-reactive protein levels, diabetes, hypertension, hyperlipidemia, heart disease history, and LINE-1 DNA methylation as the factors. Probability values < 0.05 were considered to be statistically significant. The levels of LINE-1 DNA methylation in leukocytes were associated with muscle loss in men over the age of 60. LINE-1 DNA methylation levels were not associated with bone mineral density in either the men or women over the age of 60. LINE-1 DNA methylation levels in leukocytes correlated significantly with the risk of frailty in men over the age of 60. Promoting an understanding of DNA methylation may lead to a better understanding of the pathophysiology of muscle loss.
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Affiliation(s)
- Daisaku Kato
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiko Takegami
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taisuke Seki
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Nakashima
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Osawa
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yukiharu Hasegawa
- Department of Rehabilitation, Kansai University of Welfare Science, Kashiwabara, Japan
| | - Shiro Imagama
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Hernandez-Landero F, Sanchez-Garcia E, Gomez-Crisostomo N, Contreras-Paredes A, Eduardo MA, de la Cruz-Hernandez E. Anthropometric, biochemical, and haematological indicators associated with hyperhomocysteinemia and their relation to global DNA methylation in a young adult population. Epigenetics 2021; 17:1269-1280. [PMID: 34923898 DOI: 10.1080/15592294.2021.2013420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Increased homocysteine (Hcy) levels have been associated with a higher risk of cardiovascular and neurodegenerative diseases. Passive DNA demethylation has been suggested as one of the mechanisms implicated in the development of these conditions, and most studies have investigated this relationship in older adult populations. Therefore, this study aimed to evaluate the relationship between corporal composition and biochemical and haematological indicators with plasma homocysteine levels and genome-wide methylation (Alu, LINE-1, and SAT2) in a population of healthy young adults (median age, 18 years). We showed that the prevalence of hyperhomocysteinemia was significantly higher in men (18.5%) than in women (6.6%) (P = 0.034). Increased Hcy level was substantially associated with higher levels of body mass index and visceral fat in females, whereas in males, it was significantly associated with reduced red cell distribution width and high-density lipoprotein (HDL) cholesterol (HDL-C) levels and increased low-density lipoprotein/HDL ratio. Hypomethylation of Alu was significantly associated with reduced levels of HDL-C (<40.0 mg dL-1), whereas hypomethylation of LINE-1 and SAT2 was significantly associated with higher levels of skeletal muscle (<39.3%) in males. These results highlight the participation of hormonal factors in regulating Hcy metabolism, primarily in the female population, whereas changes in DNA methylation observed in males might be associated with the consumption of a protein diet with high levels of methionine, independent of increased Hcy levels.
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Affiliation(s)
- Fernanda Hernandez-Landero
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Erika Sanchez-Garcia
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Nancy Gomez-Crisostomo
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Adriana Contreras-Paredes
- Laboratory of Molecular Biology of Oncogenic Viruses, Unit of Biomedical Research in Cancer, National Cancer Institute - Biomedical Research Institute, National Autonomous University of Mexico, Mexico City, Mexico
| | - Martínez Abundis Eduardo
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Erick de la Cruz-Hernandez
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
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Barišić A, Stanković A, Stojković L, Pereza N, Ostojić S, Peterlin A, Peterlin B, Vraneković J. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth. Biol Res Nurs 2021; 24:85-93. [PMID: 34727781 DOI: 10.1177/10998004211043571] [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: 12/12/2022]
Abstract
Despite considerable effort aimed at decreasing the incidence of spontaneous preterm birth (SPTB), it remains the leading cause of infant mortality and morbidity. The aim of this study was to evaluate maternal LINE-1 DNA methylation (DNAm), along with DNMT polymorphisms and factors proposed to modulate DNAm, in patients who delivered early preterm. This case-control study included women who delivered spontaneously early preterm (23-336/7 weeks of gestation), and control women. DNAm was analyzed in peripheral blood lymphocytes by quantification of LINE-1 DNAm using the MethyLight method. There was no significant difference in LINE-1 DNAm between patients with early PTB and controls. Among the investigated predictors, only the history of previous PTB was significantly associated with LINE-1 DNAm in PTB patients (β = -0.407; R2 = 0.131; p = 0.011). The regression analysis showed the effect of DNMT3B rs1569686 TT+TG genotypes on LINE-1 DNAm in patients with familial PTB (β = -0.524; R2 = 0.275; p = 0.037). Our findings suggest novel associations of maternal LINE-1 DNA hypomethylation with DNMT3B rs1569686 T allele. These results also contribute to the understanding of a complex (epi)genetic and environmental relationship underlying the early PTB.
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Affiliation(s)
- Anita Barišić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Aleksandra Stanković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Ljiljana Stojković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Nina Pereza
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ana Peterlin
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Slovenia
| | - Jadranka Vraneković
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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Górska A, Jabłońska E, Reszka E, Niedoszytko M, Lange M, Gruchała‐Niedoszytko M, Jarczak J, Strapagiel D, Górska‐Ponikowska M, Bastian P, Pelikant‐Małecka I, Kalinowski L, Nedoszytko B. DNA methylation profile in patients with indolent systemic mastocytosis. Clin Transl Allergy 2021; 11:e12074. [PMID: 34754417 PMCID: PMC8561632 DOI: 10.1002/clt2.12074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mastocytosis is a clinically heterogeneous, usually acquired disease of the mast cells with a survival time that depends on the onset of the disease and ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The crucial element in pathogenesis is the presence of oncogenic KIT somatic mutation D816V. Further epigenetic alterations are responsible for regulating the expression of genes. It is essential to identify indicators of disease progression, and the specific clinical picture to establish an appropriate therapeutic strategy. OBJECTIVE The aim of this study was to analyze the relation of mastocytosis symptoms and epigenetic changes, and to identify epigenetic predictors of the disease. METHODS Global DNA methylation profile analysis was performed in peripheral blood collected from 73 patients with indolent systemic mastocytosis (ISM) and 43 healthy adult volunteers. Levels of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) were determined using an ELISA-based method, while the methylation of the Alu and LINE-1 repeats were assayed with the quantitative methylation-specific PCR technique. A questionnaire interview was conducted among the study participants to collect data on possible epigenetic modifiers. Additionally, the methylation profile was compared between three human mast cell lines: ROSA KIT D816V, ROSA KIT WT, and HMC-1.1 KIT V560G, in order to assess the association between KIT mutations and methylation profile. RESULTS A significantly lower level of DNA hydroxymethylation (5-hmC) in the blood was found in patients with ISM as compared to the controls (0.022% vs. 0.042%, p = 0.0001). Differences in the markers of global DNA methylation (5-mC, Alu, LINE-1) were not statistically significant, although they did indicate generally higher DNA methylation in patients with mastocytosis. The 5-hmC level was significantly associated with allergy (p = 0.011) in patients with ISM, showing a higher level of 5-hmC in patients with allergy as compared to patients without allergy. The in vitro study revealed significant differences between the studied cell lines at the level of 5-mC, Alu, and LINE-1. CONCLUSIONS This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. A possible association between KIT mutations and methylation status observed in human mast cell lines requires further investigation in human studies. CLINICAL IMPLICATIONS Epigenetic alterations are involved in mastocytosis pathology. The possible role of allergy as an important epigenetic modifier suggests the more impaired function of mast cells in ISM patients without allergy. CAPSULE SUMMARY Decreased DNA demethylation in the blood DNA of patients with ISM confirms that epigenetic alterations are involved in mastocytosis pathology. We observed a possible role of allergy as an important epigenetic modifier. There is a possible association between KIT mutations and the methylation status observed in human mast cell lines.
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Affiliation(s)
| | - Ewa Jabłońska
- Department of Translational ResearchNofer Institute of Occupational MedicineLodzPoland
| | - Edyta Reszka
- Department of Translational ResearchNofer Institute of Occupational MedicineLodzPoland
| | | | - Magdalena Lange
- Department of Dermatology, Venerology and AllergologyMedical University of GdanskGdanskPoland
| | | | - Justyna Jarczak
- Department of Molecular BiophysicsUniversity of LodzLodzPoland
| | | | | | - Paulina Bastian
- Department of Medical ChemistryMedical University of GdanskGdanskPoland
| | | | - Leszek Kalinowski
- Department of Clinical AnalyticsMedical University of GdanskGdanskPoland
| | - Bogusław Nedoszytko
- Department of Dermatology, Venerology and AllergologyMedical University of GdanskGdanskPoland
- Invicta Fertility and Reproductive CenterMolecular LaboratorySopotPoland
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Somatic Hypomethylation of Pericentromeric SST1 Repeats and Tetraploidization in Human Colorectal Cancer Cells. Cancers (Basel) 2021; 13:cancers13215353. [PMID: 34771515 PMCID: PMC8582499 DOI: 10.3390/cancers13215353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/06/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023] Open
Abstract
Somatic DNA hypomethylation and aneuploidy are hallmarks of cancer, and there is evidence for a causal relationship between them in knockout mice but not in human cancer. The non-mobile pericentromeric repetitive elements SST1 are hypomethylated in about 17% of human colorectal cancers (CRC) with some 5-7% exhibiting strong age-independent demethylation. We studied the frequency of genome doubling, a common event in solid tumors linked to aneuploidy, in randomly selected single cell clones of near-diploid LS174T human CRC cells differing in their level of SST1 demethylation. Near-diploid LS174T cells underwent frequent genome-doubling events generating near-tetraploid clones with lower levels of SST1 methylation. In primary CRC, strong SST1 hypomethylation was significantly associated with global genomic hypomethylation and mutations in TP53. This work uncovers the association of the naturally occurring demethylation of the SST1 pericentromeric repeat with the onset of spontaneous tetraploidization in human CRC cells in culture and with TP53 mutations in primary CRCs. Altogether, our findings provide further support for an oncogenic pathway linking somatic hypomethylation and genetic copy number alterations in a subset of human CRC.
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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An Epigenetic Perspective on Intra-Tumour Heterogeneity: Novel Insights and New Challenges from Multiple Fields. Cancers (Basel) 2021; 13:cancers13194969. [PMID: 34638453 PMCID: PMC8508087 DOI: 10.3390/cancers13194969] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Although research on cancer biology in recent decades has unveiled the main genetic perturbations driving the onset of tumorigenesis, we are still far from properly treating this disease without the occurrence of drug resistance and metastatic burden. This achievement is hampered by the onset of intra-tumour heterogeneity (ITH), which increases cancer cell fitness and plasticity, thereby fostering cell adaptation to foreign environments and stimuli. In this review, we discuss the contribution of the epigenetic factors in sustaining ITH and their interplay with the tumour microenvironment. We also highlight the recent technological advancements that are contributing to defining the epigenetic mechanisms governing tumour heterogeneity at the single-cell level. Abstract Cancer is a group of heterogeneous diseases that results from the occurrence of genetic alterations combined with epigenetic changes and environmental stimuli that increase cancer cell plasticity. Indeed, multiple cancer cell populations coexist within the same tumour, favouring cancer progression and metastatic dissemination as well as drug resistance, thereby representing a major obstacle for treatment. Epigenetic changes contribute to the onset of intra-tumour heterogeneity (ITH) as they facilitate cell adaptation to perturbation of the tumour microenvironment. Despite being its central role, the intrinsic multi-layered and reversible epigenetic pattern limits the possibility to uniquely determine its contribution to ITH. In this review, we first describe the major epigenetic mechanisms involved in tumourigenesis and then discuss how single-cell-based approaches contribute to dissecting the key role of epigenetic changes in tumour heterogeneity. Furthermore, we highlight the importance of dissecting the interplay between genetics, epigenetics, and tumour microenvironments to decipher the molecular mechanisms governing tumour progression and drug resistance.
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Copur S, Rossing P, Afsar B, Sag AA, Siriopol D, Kuwabara M, Ortiz A, Kanbay M. A primer on metabolic memory: why existing diabesity treatments fail. Clin Kidney J 2021; 14:756-767. [PMID: 34512957 PMCID: PMC8422888 DOI: 10.1093/ckj/sfaa143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 11/28/2022] Open
Abstract
Despite massive government and private sector investments into prevention of cardiovascular disease, diabetes mellitus and obesity, efforts have largely failed, and the burden of cost remains in the treatment of downstream morbidity and mortality, with overall stagnating outcomes. A new paradigm shift in the approach to these patients may explain why existing treatment strategies fail, and offer new treatment targets. This review aims to provide a clinician-centred primer on metabolic memory, defined as the sum of irreversible genetic, epigenetic, cellular and tissue-level alterations that occur with long-time exposure to metabolic derangements.
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Affiliation(s)
- Sidar Copur
- Department of Medicine, Koc University School of Medicine, Istanbul, Turkey
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Baris Afsar
- Department of Internal Medicine, Division of Nephrology, Suleyman Demirel University School of Medicine, Isparta, Turkey
| | - Alan A Sag
- Department of Radiology, Division of Vascular and Interventional Radiology, Duke University Medical Center, Durham, NC, USA
| | - Dimitrie Siriopol
- Nephrology Clinic, Dialysis and Renal Transplant Center, 'C.I. PARHON' University Hospital, 'Grigore T. Popa' University of Medicine, Iasi, Romania
| | | | - Alberto Ortiz
- School of Medicine, Dialysis Unit, IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Mehmet Kanbay
- Department of Medicine, Division of Nephrology, Koc University School of Medicine, Istanbul, Turkey
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Udomsinprasert W, Sakuntasri W, Jittikoon J, Chaikledkaew U, Honsawek S, Chantratita W, Wattanapokayakit S, Mahasirimongkol S. Global DNA hypomethylation of Alu and LINE-1 transposable elements as an epigenetic biomarker of anti-tuberculosis drug-induced liver injury. Emerg Microbes Infect 2021; 10:1862-1872. [PMID: 34467830 PMCID: PMC8451674 DOI: 10.1080/22221751.2021.1976079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite being highly effective, anti-tuberculosis (TB) drugs often induce adverse liver injury, anti-TB drug-induced liver injury (ATDILI), leading to treatment failure given no sensitive and selective ATDILI markers. Herein, we conducted a case–control association study to determine whether global DNA methylation of Alu and LINE-1 transposable elements responsible for genomic stability and transcriptional regulation was correlated with clinical parameters indicating ATDILI in TB patients and might serve as an ATDILI biomarker. Alu and LINE-1 methylation levels in blood leukocyte of 130 TB patients (80 ATDILI cases and 50 non-ATDILI cases) and 100 healthy controls were quantified using quantitative combined bisulfite restriction analysis. Both TB patients with and without ATDILI had significantly lower methylation levels of Alu and LINE-1 elements than healthy controls. Compared with non-ATDILI patients, Alu methylation levels were significantly decreased in ATDILI patients, commensurate with LINE-1 methylation analysis. Hypomethylation of Alu and LINE-1 measured within 1–7 days of TB treatment was independently associated with raised levels of serum aminotransferases assessed within 8–60 days of TB treatment. Receiver operating characteristic curve analysis uncovered that Alu and LINE-1 methylation levels were both more sensitive and specific for differentiating ATDILI cases from non-ATDILI cases than serum aminotransferases after starting TB treatment within 1–7 days. Kaplan-Meier analysis displayed a significant association between hypomethylation of Alu and LINE-1 elements and an increased rate of ATDILI occurrence in TB patients. Collectively, global DNA hypomethylation of Alu and LINE-1 elements would reflect ATDILI progression and might serve as novel sensitive and specific ATDILI biomarkers.
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Affiliation(s)
| | - Wanchaloem Sakuntasri
- Master of Science Program in Biopharmaceutical Sciences, Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Usa Chaikledkaew
- Social and Administrative Pharmacy Division, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.,Mahidol University Health Technology Assessment (MUHTA) Graduate Program, Mahidol University, Bangkok, Thailand
| | - Sittisak Honsawek
- Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sukanya Wattanapokayakit
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Genomic Medicine Centre, Nonthaburi, Thailand
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Genomic Medicine Centre, Nonthaburi, Thailand
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Zhou J, Xiong Y, Dong X, Wang H, Qian Y, Ma D, Li X. Genome-wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development-associated genes in fetuses with cardiac defects. Exp Ther Med 2021; 22:1032. [PMID: 34373718 PMCID: PMC8343574 DOI: 10.3892/etm.2021.10464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
DNA methylation, as an epigenetic mechanism, has a vital role in heart development. An increasing number of studies have investigated aberrant DNA methylation in pediatric or adult heart samples from patients with congenital heart defects (CHD). Placenta tissue, umbilical cord blood, or newborn blood have also been used to detect DNA methylation biomarkers for CHD. However, few studies have compared the methylation levels in fetal heart tissue with cardiac defects with that in normal controls. The present study conducted an integrative whole-genome and CpG site-specific DNA methylation analysis of fetal heart samples from 17 isolated cardiac defect cases, 14 non-isolated cardiac defect cases, and 22 controls with normal hearts, using methylated DNA immunoprecipitation microarray and MassARRAY EpiTYPER assays. Expression of genes adjacent to differentially methylated regions (DMRs) was measured by RT-qPCR and western blot analysis. The results revealed that fetuses with cardiac defects presented global hypomethylation. Genomic analysis of DMRs revealed that a proportion of DMRs were located in exons (12.4%), distal intergenic regions (11.14%), and introns (8.97%). Only 55.7% of DMRs were observed at promoter regions. Functional enrichment analysis for genes adjacent to these DMRs revealed that hypomethylated genes were involved in embryonic heart tube morphogenesis and immune-related regulation functions. Intergenic hypermethylation of EGFR and solute carrier family 19 member 1 (SLC19A1), and intragenic hypomethylation of NOTCH1 were validated in fetal heart tissues with cardiac defects. Only SLC19A1 expression was significantly decreased at the mRNA level, while EGFR, NOTCH1, and SLC19A1 expression were all significantly decreased at the protein level. In conclusion, the present study demonstrated that fetal cardiac defects may be associated with alterations in regional and single CpG site methylation outside of promoter regions, resulting in differentiated expression of corresponding genes associated with heart development. These results present new insights into the epigenetic mechanisms underlying abnormal heart development.
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Affiliation(s)
- Jizi Zhou
- Department of Prenatal Diagnosis and Fetal Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China
| | - Yu Xiong
- Department of Prenatal Diagnosis and Fetal Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China
| | - Xinran Dong
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Huijun Wang
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Yanyan Qian
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Xiaotian Li
- Department of Prenatal Diagnosis and Fetal Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China.,The Shanghai Key Laboratory of Birth Defects, Fudan University, Shanghai 200032, P.R. China
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In Silico identification of a common mobile element insertion in exon 4 of RP1. Sci Rep 2021; 11:13381. [PMID: 34183725 PMCID: PMC8238996 DOI: 10.1038/s41598-021-92834-4] [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: 01/22/2021] [Accepted: 06/14/2021] [Indexed: 11/18/2022] Open
Abstract
Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232–0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.
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Stojković L, Zec M, Zivkovic M, Bundalo M, Bošković M, Glibetić M, Stankovic A. Polyphenol-Rich Aronia melanocarpa Juice Consumption Affects LINE-1 DNA Methylation in Peripheral Blood Leukocytes in Dyslipidemic Women. Front Nutr 2021; 8:689055. [PMID: 34222308 PMCID: PMC8247759 DOI: 10.3389/fnut.2021.689055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/26/2021] [Indexed: 12/27/2022] Open
Abstract
Cardiovascular disease (CVD) is associated with alterations in DNA methylation and polyunsaturated fatty acid (PUFA) profile, both modulated by dietary polyphenols. The present parallel, placebo-controlled study (part of the original clinical study registered as NCT02800967 at www.clinicaltrials.gov) aimed to determine the impact of 4-week daily consumption of polyphenol-rich Aronia melanocarpa juice (AMJ) treatment on Long Interspersed Nucleotide Element-1 (LINE-1) methylation in peripheral blood leukocytes and on plasma PUFAs, in subjects (n = 54, age range of 40.2 ± 6.7 years) at moderate CVD risk, including an increased body mass index, central obesity, high normal blood pressure, and/or dyslipidemia. The goal was also to examine whether factors known to affect DNA methylation (folate intake levels, MTHFR C677T gene variant, anthropometric and metabolic parameters) modulated the LINE-1 methylation levels upon the consumption of polyphenol-rich aronia juice. Experimental analysis of LINE-1 methylation was done by MethyLight method. MTHFR C677T genotypes were determined by the polymerase chain reaction–restriction fragment length polymorphism method, and folate intake was assessed by processing the data from the food frequency questionnaire. PUFAs were measured by gas–liquid chromatography, and serum lipid profile was determined by using Roche Diagnostics kits. The statistical analyses were performed using Statistica software package. In the comparison after vs. before the treatment period, in dyslipidemic women (n = 22), we observed significant decreases in LINE-1 methylation levels (97.54 ± 1.50 vs. 98.39 ± 0.86%, respectively; P = 0.01) and arachidonic acid/eicosapentaenoic acid ratio [29.17 ± 15.21 vs. 38.42 (25.96–89.58), respectively; P = 0.02]. The change (after vs. before treatment) in LINE-1 methylation directly correlated with the presence of MTHFR 677T allele, average daily folate intake, and the change in serum low-density lipoprotein cholesterol but inversely correlated with the change in serum triacylglycerols (R = 0.72, R2 = 0.52, adjusted R2 = 0.36, P = 0.03). The current results imply potential cardioprotective effects of habitual polyphenol-rich aronia juice consumption achieved through the modifications of DNA methylation pattern and PUFAs in subjects at CVD risk, which should be further confirmed. Hence, the precision nutrition-driven modulations of both DNA methylation and PUFA profile may become targets for new approaches in the prevention of CVD.
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Affiliation(s)
- Ljiljana Stojković
- Laboratory for Radiobiology and Molecular Genetics, Department of Health and Environmental Research, "Vinča" Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Manja Zec
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.,Department of Nutritional Sciences, University of Arizona, Tucson, AZ, United States
| | - Maja Zivkovic
- Laboratory for Radiobiology and Molecular Genetics, Department of Health and Environmental Research, "Vinča" Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maja Bundalo
- Laboratory for Radiobiology and Molecular Genetics, Department of Health and Environmental Research, "Vinča" Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.,Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Maja Bošković
- Laboratory for Radiobiology and Molecular Genetics, Department of Health and Environmental Research, "Vinča" Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Glibetić
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Stankovic
- Laboratory for Radiobiology and Molecular Genetics, Department of Health and Environmental Research, "Vinča" Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nat Commun 2021; 12:2490. [PMID: 33941775 PMCID: PMC8093215 DOI: 10.1038/s41467-021-22665-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically ‘recognizes’ H4K20me3 via its first bromo-adjacent-homology domain (DNMT1BAH1). Engagement of DNMT1BAH1-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1’s activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability. How histone modifications crosstalk with DNA methylation to regulate epigenomic patterning and genome stability in mammals remains elusive. Here, the authors show that DNA methyltransferase DNMT1 is a reader for histone H4K20 trimethylation via its BAH1 domain, which leads to optimal maintenance of DNA methylation at repetitive LINE-1 elements.
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Reszka E, Jabłońska E, Lesicka M, Wieczorek E, Kapelski P, Szczepankiewicz A, Pawlak J, Dmitrzak-Węglarz M. An altered global DNA methylation status in women with depression. J Psychiatr Res 2021; 137:283-289. [PMID: 33730603 DOI: 10.1016/j.jpsychires.2021.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 12/23/2022]
Abstract
Sparse studies have shown that specific biomarkers of a global DNA methylation status may be related to various mental diseases and states, including: bipolar disorder (BD), anxiety and major depression disorder (MDD). The objective of this study was to analyze potential variation of the above mentioned global methylation status in women with depression. 38 women with a current and clinically confirmed depressive episode suffering from BD type I, type II or MDD and 71 women from the general population and at similar age were recruited for the study. Alu and LINE-1 methylation was assayed with the quantitative methylation-specific PCR technique with TaqMan probes, while the 5-mC and 5-hmC level was determined using the ELISA-based method. Significantly higher levels of 5-mC, Alu and LINE-1 methylation were observed in the women with depression as compared to the controls; while the 5-hmC level revealed to be significantly lower. The BD type I patients presented the highest level of 5-mC of all the women with a depressive episode. 5-mC level in the patients was positively and significantly correlated with the severity of the symptoms of depression. Relationships between Alu or LINE-1 methylation and 5-mC level were statistically significant only in the case of the control women. Alu and LINE-1 methylation do not constitute suitable biomarkers of global DNA methylation in the investigated patients. These findings require confirmation in case-control and prospective epidemiological studies.
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Affiliation(s)
- Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - Ewa Jabłońska
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Monika Lesicka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Edyta Wieczorek
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Aleksandra Szczepankiewicz
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Joanna Pawlak
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Monika Dmitrzak-Węglarz
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
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Katzendorn O, Peters I, Dubrowinskaja N, Tezval H, Tabrizi PF, von Klot CA, Hennenlotter J, Lafos M, Kuczyk MA, Serth J. DNA methylation of tumor associated calcium signal transducer 2 (TACSTD2) loci shows association with clinically aggressive renal cell cancers. BMC Cancer 2021; 21:444. [PMID: 33882870 PMCID: PMC8061065 DOI: 10.1186/s12885-021-08172-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/08/2021] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation is frequently observed in the development and progression of many human tumors as well as renal cell cancer (RCC). Tumor Associated Calcium Signal Transducer 2 (TACSTD2) participates in cell cycle progression through MAPK signalling pathway activation. Moreover, tumor-specific hypermethylation and association with aggressive cancer characteristics has been found for lung adenocarcinoma, hepatocellular carcinoma and cholangiocarcinoma. Whether TACSTD2 is tumor specifically hypermethylated in RCC or shows association of methylation with adverse clinicopathological parameters and survival of patients has not been investigated at yet. Methods Quantitative methylation-specific PCR (qMSP) analysis of a locus in the intron 1 region of TACSTD2 gene was carried out in a cross-sectional study of 127 paired RCC and normal samples. In silico analysis of TACSTD2 methylation in the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) dataset of 280 patients served as validation cohort. Statistical analyses were carried out using the two-sided paired t-test for matched tumor and normal sample comparisons, logistic regression for subgroup comparisons, Cox regression for analysis of recurrence free survival (RFS) and Pearson correlation analysis for correlation of TACSTD2 methylation and TACSTD2 mRNA in KIRC data. Results Higher methylation levels in RCC were significantly associated with advanced disease (p < 0.001), high tumor stage (p = 0.003), tumor differentiation (p = 0.033) and presence of lymph node (p = 0.021) or distant metastases (p = 0.008). TACSTD2 hypermethylation was associated with a shorter RFS of patients and demonstrate statistical independency from clinical parameters as state of metastasis, tumor stage, grade and state of advanced disease. In silico validation using TCGA KIRC data also demonstrated association of TACSTD2 loci with adverse clinicopathology and shortened RFS of patients. In addition, in silico analyses of TCGA KIRC data showed an inverse correlation between DNA methylation levels of TACSTD2 and mRNA expression. Conclusions Our results suggest an association between TACSTD2 methylation and disease progression and clinical course of RCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08172-1.
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Affiliation(s)
- Olga Katzendorn
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany.
| | - Natalia Dubrowinskaja
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Christoph A von Klot
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Jörg Hennenlotter
- Department of Urology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Markus A Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
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Mateo-Fernández M, Valenzuela-Gómez F, Font R, Del Río-Celestino M, Merinas-Amo T, Alonso-Moraga Á. In Vivo and In Vitro Assays Evaluating the Biological Activity of Taurine, Glucose and Energetic Beverages. Molecules 2021; 26:2198. [PMID: 33920365 PMCID: PMC8069289 DOI: 10.3390/molecules26082198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/05/2023] Open
Abstract
Taurine is one of the main ingredients used in energy drinks which are highly consumed in adolescents for their sugary taste and stimulating effect. With energy drinks becoming a worldwide phenomenon, the biological effects of these beverages must be evaluated in order to fully comprehend the potential impact of these products on the health due to the fact nutrition is closely related to science since the population consumes food to prevent certain diseases. Therefore, the aim of this study was to evaluate the biological effects of taurine, glucose, classic Red Bull® and sugar-free Red Bull® in order to check the food safety and the nutraceutical potential of these compounds, characterising different endpoints: (i) Toxicology, antitoxicology, genotoxicology and life expectancy assays were performed in the Drosophila melanogaster model organism; (ii) The in vitro chemopreventive activity of testing compounds was determined by assessing their cytotoxicity, the proapoptotic DNA-damage capability to induce internucleosomal fragmentation, the strand breaks activity and the modulator role on the methylation status of genomic repetitive sequences of HL-60 promyelocytic cells. Whereas none tested compounds showed toxic or genotoxic effect, all tested compounds exerted antitoxic and antigenotoxic activity in Drosophila. Glucose, classic Red Bull® and sugar-free Red Bull® were cytotoxic in HL-60 cell line. Classic Red Bull® induced DNA internucleosomal fragmentation although none of them exhibited DNA damage on human leukaemia cells. In conclusion, the tested compounds are safe on Drosophila melanogaster and classic Red Bull® could overall possess nutraceutical potential in the in vivo and in vitro model used in this study. Besides, taurine could holistically be one of the bioactive compounds responsible for the biological activity of classic Red Bull®.
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Affiliation(s)
- Marcos Mateo-Fernández
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (T.M.-A.); (Á.A.-M.)
| | | | - Rafael Font
- Agri-Food Laboratory, Avda. Menéndez Pidal, s/n, 14080 Córdoba, Spain; (R.F.); (M.D.R.-C.)
| | | | - Tania Merinas-Amo
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (T.M.-A.); (Á.A.-M.)
| | - Ángeles Alonso-Moraga
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain; (T.M.-A.); (Á.A.-M.)
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Tsuboi Y, Yamada H, Munetsuna E, Fujii R, Yamazaki M, Ando Y, Mizuno G, Ishikawa H, Ohashi K, Hashimoto S, Hamajima N, Suzuki K. Global DNA hypermethylation in peripheral blood mononuclear cells and cardiovascular disease risk: a population-based propensity score-matched cohort study. J Epidemiol Community Health 2021; 75:890-895. [PMID: 33766847 DOI: 10.1136/jech-2020-215382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/12/2021] [Accepted: 03/11/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND DNA methylation plays an important role in the pathogenesis and progression of cardiovascular disease (CVD) but the prospective association of DNA methylation with CVD has not been evaluated. Here, we conducted a prospective study to examine whether long interspersed nuclear element-1 (LINE-1) DNA methylation is associated with CVD mortality in a Japanese population. METHODS We targeted 822 Japanese who participated in a health check-up in 1990 and had no clinical history of cancer, stroke or ischaemic heart disease. DNA was extracted from peripheral blood mononuclear cells and LINE-1 DNA methylation at three CpG sites was measured using a pyrosequencing method. We used propensity score (PS) matching to reduce the effect of potential confounding. RESULTS During 18 118.7 persons-years of follow-up, there were 329 deaths from all-causes and 85 deaths from CVD. In PS-matched analysis, a significantly higher HR for CVD mortality was observed in the hypermethylation group than in the hypomethylation group for elderly participants (HR 2.77; 95% CI 1.55 to 4.93). No significant association between LINE-1 DNA methylation and CVD was observed for middle-aged participants. CONCLUSIONS Based on this prospective study, we suggest that LINE-1 DNA hypermethylation is associated with increased CVD mortality risk in an elderly population.
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Affiliation(s)
- Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Mirai Yamazaki
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Takamatsu, Kagawa, Japan
| | - Yoshitaka Ando
- Department of Clinical Biochemistry, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Genki Mizuno
- Department of Clinical Biochemistry, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Hiroaki Ishikawa
- Department of Clinical Biochemistry, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Koji Ohashi
- Department of Clinical Biochemistry, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
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