1
|
Bellani MA, Huang J, Zhang J, Gali H, Thazhathveetil AK, Pokharel D, Majumdar I, Shaik A, Seidman MM. Imaging the cellular response to an antigen tagged interstrand crosslinking agent. DNA Repair (Amst) 2023; 128:103525. [PMID: 37320956 PMCID: PMC10413329 DOI: 10.1016/j.dnarep.2023.103525] [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: 04/02/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
Immunofluorescence imaging is a standard experimental tool for monitoring the response of cellular factors to DNA damage. Visualizing the recruitment of DNA Damage Response (DDR) components requires high affinity antibodies, which are generally available. In contrast, reagents for the display of the lesions that induce the response are far more limited. Consequently, DDR factor accumulation often serves as a surrogate for damage, without reporting the actual inducing structure. This limitation has practical implications given the importance of the response to DNA reactive drugs such as those used in cancer therapy. These include interstrand crosslink (ICL) forming compounds which are frequently employed clinically. Among them are the psoralens, natural products that form ICLs upon photoactivation and applied therapeutically since antiquity. However, despite multiple attempts, antibodies against psoralen ICLs have not been developed. To overcome this limitation, we developed a psoralen tagged with an antigen for which there are commercial antibodies. In this report we describe our application of the tagged psoralen in imaging experiments, and the unexpected discoveries they revealed.
Collapse
Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD 21703, USA
| | | | | | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Alagia A, Ketley RF, Gullerova M. Proximity Ligation Assay for Detection of R-Loop Complexes upon DNA Damage. Methods Mol Biol 2022; 2528:289-303. [PMID: 35704199 DOI: 10.1007/978-1-0716-2477-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In situ Proximity Ligation Assay (PLA ) can be used to detect the close proximity (less than ~40 nm) of two biological molecules of interest in cells. Here we report the application of this method for the specific detection of R-loop interacting proteins and RNA modifications in close proximity to R-loops in non-damage and ionizing radiation (IR) induced DNA damage conditions.
Collapse
Affiliation(s)
- Adele Alagia
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ruth F Ketley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
5
|
Lutze J, Warrington SE, Kron SJ. TdT-dUTP DSB End Labeling (TUDEL), for Specific, Direct In Situ Labeling of DNA Double Strand Breaks. Methods Mol Biol 2022; 2394:299-317. [PMID: 35094335 PMCID: PMC8820263 DOI: 10.1007/978-1-0716-1811-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The genome of a living cell is continuously damaged by various exogenous and endogenous factors yielding multiple types of DNA damage including base damage and damage to the sugar-phosphate backbone of DNA. Double Strand Breaks (DSBs) are the most severe form of DNA damage and if left unchecked, may precipitate genomic rearrangements, cell death or contribute to malignancy. In clinical contexts, radiation is often used to induce DSBs as a form of genotoxic therapy. Despite the importance of DSBs and their repair, as yet there is no facile assay to detect DSBs in situ or to quantify their location or proximity to other cellular constituents. Such an assay would help to disentangle DDR signaling pathways and identify new molecular players involved in DSB repair. These efforts, in turn, may facilitate drug screening and accelerate the discovery of novel, more effective genotoxic agents. We have developed such an assay, presented here, and term it TdT-dUTP DSB End Labeling (TUDEL).TUDEL makes use of Terminal Deoxynucleotidyl Transferase (TdT), a template-independent DNA polymerase. TdT is commonly used in TUNEL assays to yield a binary output of DNA damage. We have adapted this approach, using TdT and EdUTP to label individual DNA double strand breaks in irradiated cells and detecting the incorporated EdU with fluorescent probes via Click chemistry. This tool complements and is compatible with existing, indirect methods to track DSBs such as immunofluorescent detection of γH2AX. TUDEL is also sufficiently specific, sensitive, quantitative, and robust to replace the neutral Comet assay for routine measurement of DSB formation and repair. Here we present a protocol for TUDEL.
Collapse
Affiliation(s)
- Julian Lutze
- The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Sara E Warrington
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Stephen J Kron
- The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
6
|
Nikitaki Z, Pariset E, Sudar D, Costes SV, Georgakilas AG. In Situ Detection of Complex DNA Damage Using Microscopy: A Rough Road Ahead. Cancers (Basel) 2020; 12:E3288. [PMID: 33172046 PMCID: PMC7694657 DOI: 10.3390/cancers12113288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Complexity of DNA damage is considered currently one if not the primary instigator of biological responses and determinant of short and long-term effects in organisms and their offspring. In this review, we focus on the detection of complex (clustered) DNA damage (CDD) induced for example by ionizing radiation (IR) and in some cases by high oxidative stress. We perform a short historical perspective in the field, emphasizing the microscopy-based techniques and methodologies for the detection of CDD at the cellular level. We extend this analysis on the pertaining methodology of surrogate protein markers of CDD (foci) colocalization and provide a unique synthesis of imaging parameters, software, and different types of microscopy used. Last but not least, we critically discuss the main advances and necessary future direction for the better detection of CDD, with important outcomes in biological and clinical setups.
Collapse
Affiliation(s)
- Zacharenia Nikitaki
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
| | - Eloise Pariset
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
- Universities Space Research Association (USRA), Mountain View, CA 94043, USA
| | - Damir Sudar
- Life Sciences Department, Quantitative Imaging Systems LLC, Portland, OR 97209, USA;
| | - Sylvain V. Costes
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
| | - Alexandros G. Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
| |
Collapse
|
7
|
Mavragani IV, Nikitaki Z, Kalospyros SA, Georgakilas AG. Ionizing Radiation and Complex DNA Damage: From Prediction to Detection Challenges and Biological Significance. Cancers (Basel) 2019; 11:E1789. [PMID: 31739493 PMCID: PMC6895987 DOI: 10.3390/cancers11111789] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022] Open
Abstract
Biological responses to ionizing radiation (IR) have been studied for many years, generally showing the dependence of these responses on the quality of radiation, i.e., the radiation particle type and energy, types of DNA damage, dose and dose rate, type of cells, etc. There is accumulating evidence on the pivotal role of complex (clustered) DNA damage towards the determination of the final biological or even clinical outcome after exposure to IR. In this review, we provide literature evidence about the significant role of damage clustering and advancements that have been made through the years in its detection and prediction using Monte Carlo (MC) simulations. We conclude that in the future, emphasis should be given to a better understanding of the mechanistic links between the induction of complex DNA damage, its processing, and systemic effects at the organism level, like genomic instability and immune responses.
Collapse
Affiliation(s)
| | | | | | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780 Athens, Greece
| |
Collapse
|
8
|
Pessina F, Giavazzi F, Yin Y, Gioia U, Vitelli V, Galbiati A, Barozzi S, Garre M, Oldani A, Flaus A, Cerbino R, Parazzoli D, Rothenberg E, d'Adda di Fagagna F. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat Cell Biol 2019; 21:1286-1299. [PMID: 31570834 PMCID: PMC6859070 DOI: 10.1038/s41556-019-0392-4] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/16/2019] [Indexed: 12/31/2022]
Abstract
Damage-induced long non-coding RNAs (dilncRNA) synthesized at DNA double-strand breaks (DSBs) by RNA polymerase II are necessary for DNA-damage-response (DDR) focus formation. We demonstrate that induction of DSBs results in the assembly of functional promoters that include a complete RNA polymerase II preinitiation complex, MED1 and CDK9. Absence or inactivation of these factors causes a reduction in DDR foci both in vivo and in an in vitro system that reconstitutes DDR events on nucleosomes. We also show that dilncRNAs drive molecular crowding of DDR proteins, such as 53BP1, into foci that exhibit liquid-liquid phase-separation condensate properties. We propose that the assembly of DSB-induced transcriptional promoters drives RNA synthesis, which stimulates phase separation of DDR factors in the shape of foci.
Collapse
Affiliation(s)
- Fabio Pessina
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ubaldo Gioia
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Valerio Vitelli
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Sara Barozzi
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Amanda Oldani
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Andrew Flaus
- Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Roberto Cerbino
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Dario Parazzoli
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Fabrizio d'Adda di Fagagna
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
- Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia, Italy.
| |
Collapse
|