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Thongsroy J, Mutirangura A. The inverse association between DNA gaps and HbA1c levels in type 2 diabetes mellitus. Sci Rep 2023; 13:18987. [PMID: 37923892 PMCID: PMC10624909 DOI: 10.1038/s41598-023-46431-2] [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: 06/10/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
Naturally occurring DNA gaps have been observed in eukaryotic DNA, including DNA in nondividing cells. These DNA gaps are found less frequently in chronologically aging yeast, chemically induced senescence cells, naturally aged rats, D-galactose-induced aging model rats, and older people. These gaps function to protect DNA from damage, so we named them youth-associated genomic stabilization DNA gaps (youth-DNA-gaps). Type 2 diabetes mellitus (type 2 DM) is characterized by an early aging phenotype. Here, we explored the correlation between youth-DNA-gaps and the severity of type 2 DM. Here, we investigated youth-DNA-gaps in white blood cells from normal controls, pre-DM, and type 2 DM patients. We found significantly decreased youth-DNA-gap numbers in the type 2 DM patients compared to normal controls (P = 0.0377, P = 0.0018 adjusted age). In the type 2 DM group, youth-DNA-gaps correlate directly with HbA1c levels. (r = - 0.3027, P = 0.0023). Decreased youth-DNA-gap numbers were observed in patients with type 2 DM and associated with increased HbA1c levels. Therefore, the decrease in youth-DNA-gaps is associated with the molecular pathogenesis of high blood glucose levels. Furthermore, youth-DNA-gap number is another marker that could be used to determine the severity of type 2 DM.
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Affiliation(s)
- Jirapan Thongsroy
- School of Medicine, Walailak University, Nakhon Si Thammarat, 80160, Thailand.
- Research Center in Tropical Pathobiology, Walailak University, Nakhon Si Thammarat, 80160, Thailand.
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Enkhbaatar T, Skoneczny M, Stępień K, Mołoń M, Skoneczna A. Live while the DNA lasts. The role of autophagy in DNA loss and survival of diploid yeast cells during chronological aging. Aging (Albany NY) 2023; 15:9965-9983. [PMID: 37815879 PMCID: PMC10599738 DOI: 10.18632/aging.205102] [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: 06/13/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
Aging is inevitable and affects all cell types, thus yeast cells are often used as a model in aging studies. There are two approaches to studying aging in yeast: replicative aging, which describes the proliferative potential of cells, and chronological aging, which is used for studying post-mitotic cells. While analyzing the chronological lifespan (CLS) of diploid Saccharomyces cerevisiae cells, we discovered a remarkable phenomenon: ploidy reduction during aging progression. To uncover the mechanism behind this unusual process we used yeast strains undergoing a CLS assay, looking for various aging parameters. Cell mortality, regrowth ability, autophagy induction and cellular DNA content measurements indicated that during the CLS assay, dying cells lost their DNA, and only diploids survived. We demonstrated that autophagy was responsible for the gradual loss of DNA. The nucleophagy marker activation at the start of the CLS experiment correlated with the significant drop in cell viability. The activation of piecemeal microautophagy of nucleus (PMN) markers appeared to accompany the chronological aging process until the end. Our findings emphasize the significance of maintaining at least one intact copy of the genome for the survival of post-mitotic diploid cells. During chronological aging, cellular components, including DNA, are exposed to increasing stress, leading to DNA damage and fragmentation in aging cells. We propose that PMN-dependent clearance of damaged DNA from the nucleus helps prevent genome rearrangements. However, as long as one copy of the genome can be rebuilt, cells can still survive.
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Affiliation(s)
- Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Karolina Stępień
- Institute of Medical Sciences, Rzeszów University, Rzeszów 35-959, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, Rzeszów 35-601, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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Thongsroy J, Mutirangura A. Decreased Alu methylation in type 2 diabetes mellitus patients increases HbA1c levels. J Clin Lab Anal 2023; 37:e24966. [PMID: 37743692 PMCID: PMC10623537 DOI: 10.1002/jcla.24966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/20/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023] Open
Abstract
INTRODUCTION Alu hypomethylation is a common epigenetic process that promotes genomic instability with aging phenotypes, which leads to type 2 diabetes mellitus (type 2 DM). Previously, our results showed significantly decreased Alu methylation levels in type 2 DM patients. In this study, we aimed to investigate the longitudinal changes in Alu methylation levels in these patients. RESULTS We observed significantly decreased Alu methylation levels in type 2 DM patients compared with normal (p = 0.0462). Moreover, our findings demonstrated changes in Alu hypomethylation over a follow-up period within the same individuals (p < 0.0001). A reduction in Alu methylation was found in patients with increasing HbA1c levels (p = 0.0013) and directly correlated with increased HbA1c levels in type 2 DM patients (r = -0.2273, p = 0.0387). CONCLUSIONS Alu methylation in type 2 DM patients progressively decreases with increasing HbA1c levels. This observation suggests a potential association between Alu hypomethylation and the underlying molecular mechanisms of elevated blood glucose. Furthermore, monitoring Alu methylation levels may serve as a valuable biomarker for assessing the clinical outcomes of type 2 DM.
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Affiliation(s)
- Jirapan Thongsroy
- School of MedicineWalailak UniversityNakhon Si ThammaratThailand
- Research Center in Tropical PathobiologyWalailak UniversityNakhon Si ThammaratThailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human DiseasesChulalongkorn UniversityBangkokThailand
- Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
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Thongsroy J, Mutirangura A. The association between Alu hypomethylation and the severity of hypertension. PLoS One 2022; 17:e0270004. [PMID: 35802708 PMCID: PMC9269909 DOI: 10.1371/journal.pone.0270004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/02/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction Epigenetic changes that cause genomic instability may be the basis of pathogenic processes of age-associated noncommunicable diseases (NCDs). Essential hypertension is one of the most common NCDs. Alu hypomethylation is an epigenetic event that is commonly found in elderly individuals. Epigenomic alterations are also found in age-associated NCDs such as osteoporosis and diabetes mellitus. Alu methylation prevents DNA from being damaged. Therefore, Alu hypomethylated DNA accumulates DNA damage and, as a result, causes organ function deterioration. Here, we report that Alu hypomethylation is a biomarker for essential hypertension. Results We investigated Alu methylation levels in white blood cells from normal controls, patients with prehypertension, and patients with hypertension. The hypertension group possessed the lowest Alu methylation level when classified by systolic blood pressure and diastolic blood pressure (P = 0.0002 and P = 0.0088, respectively). In the hypertension group, a higher diastolic blood pressure and a lower Alu methylation level were observed (r = -0.6278). Moreover, we found that changes in Alu hypomethylation in the four years of follow-up in the same person were directly correlated with increased diastolic blood pressure. Conclusions Similar to other age-associated NCDs, Alu hypomethylation is found in essential hypertension and is directly correlated with severity, particularly with diastolic blood pressure. Therefore, Alu hypomethylation may be linked with the molecular pathogenesis of high blood pressure and can be used for monitoring the clinical outcome of this disease.
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Affiliation(s)
- Jirapan Thongsroy
- School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
- * E-mail:
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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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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Yasom S, Watcharanurak P, Bhummaphan N, Thongsroy J, Puttipanyalears C, Settayanon S, Chalertpet K, Khumsri W, Kongkaew A, Patchsung M, Siriwattanakankul C, Pongpanich M, Pin‐on P, Jindatip D, Wanotayan R, Odton M, Supasai S, Oo TT, Arunsak B, Pratchayasakul W, Chattipakorn N, Chattipakorn S, Mutirangura A. The roles of HMGB1-produced DNA gaps in DNA protection and aging biomarker reversal. FASEB Bioadv 2022; 4:408-434. [PMID: 35664831 PMCID: PMC9164245 DOI: 10.1096/fba.2021-00131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022] Open
Abstract
The endogenous DNA damage triggering an aging progression in the elderly is prevented in the youth, probably by naturally occurring DNA gaps. Decreased DNA gaps are found during chronological aging in yeast. So we named the gaps "Youth-DNA-GAPs." The gaps are hidden by histone deacetylation to prevent DNA break response and were also reduced in cells lacking either the high-mobility group box (HMGB) or the NAD-dependent histone deacetylase, SIR2. A reduction in DNA gaps results in shearing DNA strands and decreasing cell viability. Here, we show the roles of DNA gaps in genomic stability and aging prevention in mammals. The number of Youth-DNA-GAPs were low in senescent cells, two aging rat models, and the elderly. Box A domain of HMGB1 acts as molecular scissors in producing DNA gaps. Increased gaps consolidated DNA durability, leading to DNA protection and improved aging features in senescent cells and two aging rat models similar to those of young organisms. Like the naturally occurring Youth-DNA-GAPs, Box A-produced DNA gaps avoided DNA double-strand break response by histone deacetylation and SIRT1, a Sir2 homolog. In conclusion, Youth-DNA-GAPs are a biomarker determining the DNA aging stage (young/old). Box A-produced DNA gaps ultimately reverse aging features. Therefore, DNA gap formation is a potential strategy to monitor and treat aging-associated diseases.
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Affiliation(s)
- Sakawdaurn Yasom
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Papitchaya Watcharanurak
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Narumol Bhummaphan
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | | | - Charoenchai Puttipanyalears
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Sirapat Settayanon
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Kanwalat Chalertpet
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Wilunplus Khumsri
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Aphisek Kongkaew
- Research Administration Section, Faculty of MedicineChiang Mai UniversityChiang MaiThailand
| | - Maturada Patchsung
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Chutha Siriwattanakankul
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of ScienceChulalongkorn UniversityBangkokThailand,Omics Sciences and Bioinformatics Center, Faculty of ScienceChulalongkorn UniversityBangkokThailand
| | - Piyapat Pin‐on
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Depicha Jindatip
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Rujira Wanotayan
- Department of Radiological Technology, Faculty of Medical TechnologyMahidol UniversityNakhon PathomThailand
| | - Mingkwan Odton
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Suangsuda Supasai
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Thura Tun Oo
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Busarin Arunsak
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Wasana Pratchayasakul
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Nipon Chattipakorn
- Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand,Cardiac Electrophysiology Unit, Department of Physiology, Faculty of MedicineChiang Mai UniversityChiang MaiThailand
| | - Siriporn Chattipakorn
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
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Ruta LL, Farcasanu IC. Saccharomyces cerevisiae and Caffeine Implications on the Eukaryotic Cell. Nutrients 2020; 12:nu12082440. [PMID: 32823708 PMCID: PMC7468979 DOI: 10.3390/nu12082440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Caffeine-a methylxanthine analogue of the purine bases adenine and guanine-is by far the most consumed neuro-stimulant, being the active principle of widely consumed beverages such as coffee, tea, hot chocolate, and cola. While the best-known action of caffeine is to prevent sleepiness by blocking the adenosine receptors, caffeine exerts a pleiotropic effect on cells, which lead to the activation or inhibition of various cell integrity pathways. The aim of this review is to present the main studies set to investigate the effects of caffeine on cells using the model eukaryotic microorganism Saccharomyces cerevisiae, highlighting the caffeine synergy with external cell stressors, such as irradiation or exposure to various chemical hazards, including cigarette smoke or chemical carcinogens. The review also focuses on the importance of caffeine-related yeast phenotypes used to resolve molecular mechanisms involved in cell signaling through conserved pathways, such as target of rapamycin (TOR) signaling, Pkc1-Mpk1 mitogen activated protein kinase (MAPK) cascade, or Ras/cAMP protein kinase A (PKA) pathway.
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Mutirangura A. A Hypothesis to Explain How the DNA of Elderly People Is Prone to Damage: Genome-Wide Hypomethylation Drives Genomic Instability in the Elderly by Reducing Youth-Associated Gnome-Stabilizing DNA Gaps. Epigenetics 2019. [DOI: 10.5772/intechopen.83372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Mutirangura A. Is global hypomethylation a nidus for molecular pathogenesis of age-related noncommunicable diseases? Epigenomics 2019; 11:577-579. [PMID: 31070049 DOI: 10.2217/epi-2019-0064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer & Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Pongpanich M, Patchsung M, Mutirangura A. Pathologic Replication-Independent Endogenous DNA Double-Strand Breaks Repair Defect in Chronological Aging Yeast. Front Genet 2018; 9:501. [PMID: 30410502 PMCID: PMC6209823 DOI: 10.3389/fgene.2018.00501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/05/2018] [Indexed: 12/27/2022] Open
Abstract
Reduction of physiologic replication-independent endogenous DNA double strand breaks (Phy-RIND-EDSBs) in chronological aging yeast increases pathologic RIND-EDSBs (Path-RIND-EDSBs). Path-RIND-EDSBs can occur spontaneously in non-dividing cells without any inductive agents, and they must be repaired immediately otherwise their accumulation can lead to senescence. If yeasts have DSB repair defect, retention of Path-RIND-EDSBs can be found. Previously, we found that Path-RIND-EDSBs are not only produced but also retained in chronological aging yeast. Here, we evaluated if chronological aging yeasts have a DSB repair defect. We found a significant accumulation of Path-RIND-EDSBs around the same level in aging cells and caffeine treated cells and at a much higher level in the DSB repair mutant cells. Especially in the mutant, some unknown sequence was found inserted at the breaks. In addition, % difference of cell viability between HO induced and non-induced cells was significantly greater in aging cells. Our results suggested that RIND-EDSBs repair efficiency declines, but is not absent, in chronological aging yeast which might promote senescence phenotype. When a repair protein is deficient, an alternative pathway might be employed or an end modification process might occur as inserted sequences at the breaks were observed. Restoring repair defects might slow down the deterioration of cells from chronological aging.
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Affiliation(s)
- Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Maturada Patchsung
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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