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Patchsung M, Homchan A, Aphicho K, Suraritdechachai S, Wanitchanon T, Pattama A, Sappakhaw K, Meesawat P, Wongsatit T, Athipanyasilp A, Jantarug K, Athipanyasilp N, Buahom J, Visanpattanasin S, Niljianskul N, Chaiyen P, Tinikul R, Wichukchinda N, Mahasirimongkol S, Sirijatuphat R, Angkasekwinai N, Crone MA, Freemont PS, Joung J, Ladha A, Abudayyeh O, Gootenberg J, Zhang F, Chewapreecha C, Chanarat S, Horthongkham N, Pakotiprapha D, Uttamapinant C. A Multiplexed Cas13-Based Assay with Point-of-Care Attributes for Simultaneous COVID-19 Diagnosis and Variant Surveillance. CRISPR J 2022; 6:99-115. [PMID: 36367987 PMCID: PMC7614457 DOI: 10.1089/crispr.2022.0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection-such as multiplexed detection for viral variant surveillance-may limit their widespread adoption. Herein, we developed a robust multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)-including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)-all the while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool-CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance that can be locally manufactured-may enable sustainable use of CRISPR diagnostics technologies for COVID-19 and other diseases in POC settings.
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Affiliation(s)
- Maturada Patchsung
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Aimorn Homchan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Thanyapat Wanitchanon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom.,Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Hinxton, United Kingdom
| | - Archiraya Pattama
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Khomkrit Sappakhaw
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Artittaya Athipanyasilp
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Krittapas Jantarug
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Niracha Athipanyasilp
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Juthamas Buahom
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Supapat Visanpattanasin
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | | | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Nuanjun Wichukchinda
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Hinxton, United Kingdom
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Hinxton, United Kingdom
| | - Rujipas Sirijatuphat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Nasikarn Angkasekwinai
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Michael A Crone
- London Biofoundry, Imperial College Translation and Innovation Hub, London, United Kingdom; Hinxton, United Kingdom.,Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; Hinxton, United Kingdom.,UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom; Hinxton, United Kingdom
| | - Paul S Freemont
- London Biofoundry, Imperial College Translation and Innovation Hub, London, United Kingdom; Hinxton, United Kingdom.,Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; Hinxton, United Kingdom.,UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom; Hinxton, United Kingdom
| | - Julia Joung
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Alim Ladha
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Omar Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Jonathan Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; and Hinxton, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sittinan Chanarat
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
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2
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Inside Cover: Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET (Angew. Chem. Int. Ed. 37/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202210188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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3
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022; 61:e202203061. [PMID: 35656865 PMCID: PMC7613822 DOI: 10.1002/anie.202203061] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/24/2022]
Abstract
We report a bioinformatic workflow and subsequent discovery of a new polyethylene terephthalate (PET) hydrolase, which we named MG8, from the human saliva metagenome. MG8 has robust PET plastic degradation activities under different temperature and salinity conditions, outperforming several naturally occurring and engineered hydrolases in degrading PET. Moreover, we genetically encoded 2,3-diaminopropionic acid (DAP) in place of the catalytic serine residue of MG8, thereby converting a PET hydrolase into a covalent binder for bio-functionalization of PET. We show that MG8(DAP), in conjunction with a split green fluorescent protein system, can be used to attach protein cargos to PET as well as other polyester plastics. The discovery of a highly active PET hydrolase from the human metagenome—currently an underexplored resource for industrial enzyme discovery—as well as the repurposing of such an enzyme into a plastic functionalization tool, should facilitate ongoing efforts to degrade and maximize reusability of PET.
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Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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4
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Madan Babu M, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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5
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Piyachat Meesawat
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Thanakrit Wongsatit
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Jariya Jitdee
- Chulalongkorn University Faculty of Science Chemistry THAILAND
| | | | - Maturada Patchsung
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Kanokpol Aphicho
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Surased Suraritdechachai
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - Shan Tang
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | - Wipa Suginta
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - M. Madan Babu
- St Jude Children's Research Hospital Department of Structural Biology Structural Biology UNITED STATES
| | - Jason W Chin
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | | | | | - Chayasith Uttamapinant
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering 555 Moo 1 PayupnaiWangchan Valley 21210 Rayong THAILAND
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Patchsung M, Jantarug K, Pattama A, Aphicho K, Suraritdechachai S, Meesawat P, Sappakhaw K, Leelahakorn N, Ruenkam T, Wongsatit T, Athipanyasilp N, Eiamthong B, Lakkanasirorat B, Phoodokmai T, Niljianskul N, Pakotiprapha D, Chanarat S, Homchan A, Tinikul R, Kamutira P, Phiwkaow K, Soithongcharoen S, Kantiwiriyawanitch C, Pongsupasa V, Trisrivirat D, Jaroensuk J, Wongnate T, Maenpuen S, Chaiyen P, Kamnerdnakta S, Swangsri J, Chuthapisith S, Sirivatanauksorn Y, Chaimayo C, Sutthent R, Kantakamalakul W, Joung J, Ladha A, Jin X, Gootenberg JS, Abudayyeh OO, Zhang F, Horthongkham N, Uttamapinant C. Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA. Nat Biomed Eng 2020; 4:1140-1149. [PMID: 32848209 DOI: 10.1038/s41551-020-00603-x] [Citation(s) in RCA: 356] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
Abstract
Nucleic acid detection by isothermal amplification and the collateral cleavage of reporter molecules by CRISPR-associated enzymes is a promising alternative to quantitative PCR. Here, we report the clinical validation of the specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) assay using the enzyme Cas13a from Leptotrichia wadei for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the virus that causes coronavirus disease 2019 (COVID-19)-in 154 nasopharyngeal and throat swab samples collected at Siriraj Hospital, Thailand. Within a detection limit of 42 RNA copies per reaction, SHERLOCK was 100% specific and 100% sensitive with a fluorescence readout, and 100% specific and 97% sensitive with a lateral-flow readout. For the full range of viral load in the clinical samples, the fluorescence readout was 100% specific and 96% sensitive. For 380 SARS-CoV-2-negative pre-operative samples from patients undergoing surgery, SHERLOCK was in 100% agreement with quantitative PCR with reverse transcription. The assay, which we show is amenable to multiplexed detection in a single lateral-flow strip incorporating an internal control for ribonuclease contamination, should facilitate SARS-CoV-2 detection in settings with limited resources.
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Affiliation(s)
- Maturada Patchsung
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Krittapas Jantarug
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Archiraya Pattama
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Khomkrit Sappakhaw
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Nattawat Leelahakorn
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Theerawat Ruenkam
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Niracha Athipanyasilp
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Thitima Phoodokmai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | | | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sittinan Chanarat
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Aimorn Homchan
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Philaiwarong Kamutira
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kochakorn Phiwkaow
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Sahachat Soithongcharoen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chadaporn Kantiwiriyawanitch
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Vinutsada Pongsupasa
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Sirichai Kamnerdnakta
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jirawat Swangsri
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suebwong Chuthapisith
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yongyut Sirivatanauksorn
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutikarn Chaimayo
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ruengpung Sutthent
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wannee Kantakamalakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Julia Joung
- Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Alim Ladha
- Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Xin Jin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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Chalertpet K, Pin-On P, Aporntewan C, Patchsung M, Ingrungruanglert P, Israsena N, Mutirangura A. Argonaute 4 as an Effector Protein in RNA-Directed DNA Methylation in Human Cells. Front Genet 2019; 10:645. [PMID: 31333722 PMCID: PMC6620710 DOI: 10.3389/fgene.2019.00645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/18/2019] [Indexed: 01/06/2023] Open
Abstract
DNA methylation of specific genome locations contributes to the distinct functions of multicellular organisms. DNA methylation can be governed by RNA-dependent DNA methylation (RdDM). RdDM is carried out by endogenous small-RNA-guided epigenomic editing complexes that add a methyl group to a precise DNA location. In plants, the Argonaute 4 (AGO4) protein is one of the main catalytic components involved in RdDM. Although small interfering RNA or short hairpin RNA has been shown to be able to guide DNA methylation in human cells, AGO protein-regulated RdDM in humans has not yet been evaluated. This study aimed to identify a key regulatory AGO protein involved in human RdDM by bioinformatics and to explore its function in RdDM by a combination of AGO4 knockdown, Alu small interfering RNA transfection, AGO4-expressing plasmid transfection, chromatin immunoprecipitation, cell-penetrating peptide-tagged AGO4 combined Alu single-guide RNA transfection, and methylation analyses. We found that first, human AGO4 showed stronger genome-wide association with DNA methylation than AGO1–AGO3. Second, endogenous AGO4 depletion demethylated DNA of known AGO4 bound loci. Finally, exogenous AGO4 de novo methylated the bound DNA sequences. Therefore, we discovered that AGO4 plays a role in human RdDM.
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Affiliation(s)
- Kanwalat Chalertpet
- Interdisciplinary Program of Biomedical Sciences, Faculty of the Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Piyapat Pin-On
- Interdisciplinary Program of Biomedical Sciences, Faculty of the Graduate School, Chulalongkorn University, Bangkok, Thailand.,Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Chatchawit Aporntewan
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Maturada Patchsung
- Interdisciplinary Program of Biomedical Sciences, Faculty of the Graduate School, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Praewphan Ingrungruanglert
- Stem Cells and Cell Therapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nipan Israsena
- Stem Cells and Cell Therapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [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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10
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Thongsroy J, Patchsung M, Pongpanich M, Settayanon S, Mutirangura A. Reduction in replication-independent endogenous DNA double-strand breaks promotes genomic instability during chronological aging in yeast. FASEB J 2018; 32:fj201800218RR. [PMID: 29812972 DOI: 10.1096/fj.201800218rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism that causes genomic instability in nondividing aging cells is unknown. Our previous study of mutant yeast suggested that 2 types of replication-independent endogenous DNA double-strand breaks (RIND-EDSBs) exist and that they play opposing roles. The first type, known as physiologic RIND-EDSBs, were ubiquitous in the G0 phase of both yeast and human cells in certain genomic locations and may act as epigenetic markers. Low RIND-EDSB levels were found in mutants that lacked chromatin-condensing proteins, such as the high-mobility group box (HMGB) proteins and Sir2. The second type is referred to as pathologic RIND-EDSBs. High pathological RIND-EDSB levels were found in DSB repair mutants. Under normal physiologic conditions, these excess RIND-EDSBs are repaired in much the same way as DNA lesions. Here, chronological aging in yeast reduced physiological RIND-EDSBs and cell viability. A strong correlation was observed between the reduction in RIND-EDSBs and viability in aging yeast cells ( r = 0.94, P < 0.0001). We used galactose-inducible HO endonuclease (HO) and nhp6a∆, an HMGB protein mutant, to evaluate the consequences of reduced physiological RIND-EDSB levels. The HO-induced cells exhibited a sustained reduction in RIND-EDSBs at various levels for several days. Interestingly, we found that lower physiologic RIND-EDSB levels resulted in decreased cell viability ( r = 0.69, P < 0.0001). Treatment with caffeine, a DSB repair inhibitor, increased pathological RIND-EDSBs, which were distinguished from physiologic RIND-EDSBs by their lack of sequences prior to DSB in untreated cells [odds ratio (OR) ≤1]. Caffeine treatment in both the HO-induced and nhp6a∆ cells markedly increased OR ≤1 breaks. Therefore, physiological RIND-EDSBs play an epigenetic role in preventing pathological RIND-EDSBs, a type of DNA damage. In summary, the reduction of physiological RIND-EDSB level is a genomic instability mechanism in chronologically aging cells.-Thongsroy, J., Patchsung, M., Pongpanich, M., Settayanon, S., Mutirangura, A. Reduction in replication-independent endogenous DNA double-strand breaks promotes genomic instability during chronological aging in yeast.
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Affiliation(s)
- Jirapan Thongsroy
- School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
| | - Maturada Patchsung
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sirapat Settayanon
- 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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11
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Patchsung M, Settayanon S, Pongpanich M, Mutirangura D, Jintarith P, Mutirangura A. Alu siRNA to increase Alu element methylation and prevent DNA damage. Epigenomics 2018; 10:175-185. [PMID: 29336607 DOI: 10.2217/epi-2017-0096] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Global DNA hypomethylation promoting genomic instability leads to cancer and deterioration of human health with age. AIM To invent a biotechnology that can reprogram this process. METHODS We used Alu siRNA to direct Alu interspersed repetitive sequences methylation in human cells. We evaluated the correlation between DNA damage and Alu methylation levels. RESULTS We observed an inverse correlation between Alu element methylation and endogenous DNA damage in white blood cells. Cells transfected with Alu siRNA exhibited high Alu methylation levels, increased proliferation, reduced endogenous DNA damage and improved resistance to DNA damaging agents. CONCLUSION Alu methylation stabilizes the genome by preventing accumulation of DNA damage. Alu siRNA could be useful for evaluating reprograming of the global hypomethylation phenotype in cancer and aging cells.
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Affiliation(s)
- Maturada Patchsung
- Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Sirapat Settayanon
- Program of Medical Science, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics & Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Center for Excellence in Molecular Genetics of Cancer & Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Dharm Mutirangura
- Center for Excellence in Molecular Genetics of Cancer & Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Pornrutsami Jintarith
- Omics Sciences & Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer & Human Diseases, Chulalongkorn University, Bangkok, Thailand.,Department of Tropical Nutrition & Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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12
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Thongsroy J, Patchsung M, Mutirangura A. The association between Alu hypomethylation and severity of type 2 diabetes mellitus. Clin Epigenetics 2017; 9:93. [PMID: 28883893 PMCID: PMC5580285 DOI: 10.1186/s13148-017-0395-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/24/2017] [Indexed: 12/24/2022] Open
Abstract
Background Cellular senescence due to genomic instability is believed to be one of the mechanisms causing health problems in diabetes mellitus (DM). Low methylation levels of Alu elements or Alu hypomethylation, an epigenomic event causing genomic instability, were commonly found in aging people and patients with aging phenotypes, such as osteoporosis. Results We investigate Alu methylation levels of white blood cells of type 2 DM, pre-DM, and control. The DM group possess the lowest Alu methylation (P < 0.001, P < 0.0001 adjusted age). In the DM group, Alu hypomethylation is directly correlated with high fasting blood sugar, HbA1C, and blood pressure. Conclusion Genome-wide hypomethylation may be one of the underlining mechanisms causing genomic instability in type 2 DM. Moreover, Alu methylation levels may be a useful biomarker for monitoring cellular senescence in type 2 DM patients. Electronic supplementary material The online version of this article (10.1186/s13148-017-0395-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jirapan Thongsroy
- School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
| | - Maturada Patchsung
- Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, 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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13
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Pongpanich M, Patchsung M, Thongsroy J, Mutirangura A. Characteristics of replication-independent endogenous double-strand breaks in Saccharomyces cerevisiae. BMC Genomics 2014; 15:750. [PMID: 25179264 PMCID: PMC4158086 DOI: 10.1186/1471-2164-15-750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/29/2014] [Indexed: 11/25/2022] Open
Abstract
Background Replication-independent endogenous double-strand breaks (RIND-EDSBs) occur in both humans and yeast in the absence of inductive agents and DNA replication. In human cells, RIND-EDSBs are hypermethylated, preferentially retained in the heterochromatin and unbound by γ-H2AX. In single gene deletion yeast strains, the RIND-EDSB levels are altered; the number of RIND-EDSBs is higher in strains with deletions of histone deacetylase, endonucleases, topoisomerase, or DNA repair regulators, but lower in strains with deletions of the high-mobility group box proteins or Sir2. In summary, RIND-EDSBs are different from pathologic DSBs in terms of their causes and consequences. In this study, we identified the nucleotide sequences surrounding RIND-EDSBs and investigated the features of these sequences as well as their break locations. Results In recent work, we detected RIND-EDSBs using ligation mediated PCR. In this study, we sequenced RIND-EDSB PCR products of resting state Saccharomyces cerevisiae using next-generation sequencing to analyze RIND-EDSB sequences. We found that the break locations are scattered across a number of chromosomes. The number of breaks correlated with the size of the chromosomes. Most importantly, the break occurrences had sequence pattern specificity. Specifically, the majority of the breaks occurred immediately after the sequence “ACGT” (P = 2.2E-156). Because the “ACGT” sequence does not occur primarily in the yeast genome, this specificity of the “ACGT” sequence cannot be attributed to chance. Conclusions RIND-EDSBs occur non-randomly; that is, they are produced and retained by specific mechanisms. Because these particular mechanisms regulate their generation and they possess potentially specific functions, RIND-EDSBs could be epigenetic marks. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-750) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand.
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