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Aguzzoli Heberle B, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nat Biotechnol 2024:10.1038/s41587-024-02245-9. [PMID: 38778214 DOI: 10.1038/s41587-024-02245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Determining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. We identified 1,917 medically relevant genes expressing multiple isoforms in the frontal cortex where 1,018 had multiple isoforms with different protein-coding sequences. Of these 1,018 genes, 57 are implicated in brain-related diseases including major depression, schizophrenia, Parkinson's disease and Alzheimer disease. Our study also uncovered 53 new RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. We also reported on five mitochondrially encoded, spliced RNA isoforms. We found 99 differentially expressed RNA isoforms between cases with Alzheimer disease and controls.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - J Anthony Brandon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Madeline L Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Kayla A Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ketsile I Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Brendan J White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Lacey A Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Grant A Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Mark E Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Patricia H Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Brittney A Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Edward J Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- UK Dementia Research Institute at The University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA.
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA.
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左 志, 孟 庆, 崔 家, 郭 克, 卞 华. [An artificial neural network diagnostic model for scleroderma and immune cell infiltration analysis based on mitochondria-associated genes]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2024; 44:920-929. [PMID: 38862450 PMCID: PMC11166723 DOI: 10.12122/j.issn.1673-4254.2024.05.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Indexed: 06/13/2024]
Abstract
OBJECTIVE To establish a diagnostic model for scleroderma by combining machine learning and artificial neural network based on mitochondria-related genes. METHODS The GSE95065 and GSE59785 datasets of scleroderma from GEO database were used for analyzing expressions of mitochondria-related genes, and the differential genes were identified by Random forest, LASSO regression and SVM algorithms. Based on these differential genes, an artificial neural network model was constructed, and its diagnostic accuracy was evaluated by 10-fold crossover verification and ROC curve analysis using the verification dataset GSE76807. The mRNA expressions of the key genes were verified by RT-qPCR in a mouse model of scleroderma. The CIBERSORT algorithm was used to estimate the bioinformatic association between scleroderma and the screened biomarkers. RESULTS A total of 24 differential genes were obtained, including 11 up-regulated and 13 down-regulated genes. Seven most relevant mitochondria-related genes (POLB, GSR, KRAS, NT5DC2, NOX4, IGF1, and TGM2) were screened using 3 machine learning algorithms, and the artificial neural network diagnostic model was constructed. The model showed an area under the ROC curves of 0.984 for scleroderma diagnosis (0.740 for the verification dataset and 0.980 for cross-over validation). RT-qPCR detected significant up-regulation of POLB, GSR, KRAS, NOX4, IGF1 and TGM2 mRNAs and significant down-regulation of NT5DC2 in the mouse models of scleroderma. Immune cell infiltration analysis showed that the differential genes in scleroderma were associated with follicular helper T cells, immature B cells, resting dendritic cells, memory activated CD4+T cells, M0 macrophages, monocytes, resting memory CD4+T cells and mast cell activation. CONCLUSION The artificial neural network diagnostic model for scleroderma established in this study provides a new perspective for exploring the pathogenesis of scleroderma.
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Sobol RW. Mouse models to explore the biological and organismic role of DNA polymerase beta. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:57-71. [PMID: 38619421 PMCID: PMC11027944 DOI: 10.1002/em.22593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Gene knock-out (KO) mouse models for DNA polymerase beta (Polβ) revealed that loss of Polβ leads to neonatal lethality, highlighting the critical organismic role for this DNA polymerase. While biochemical analysis and gene KO cell lines have confirmed its biochemical role in base excision repair and in TET-mediated demethylation, more long-lived mouse models continue to be developed to further define its organismic role. The Polb-KO mouse was the first of the Cre-mediated tissue-specific KO mouse models. This technology was exploited to investigate roles for Polβ in V(D)J recombination (variable-diversity-joining rearrangement), DNA demethylation, gene complementation, SPO11-induced DNA double-strand break repair, germ cell genome stability, as well as neuronal differentiation, susceptibility to genotoxin-induced DNA damage, and cancer onset. The revolution in knock-in (KI) mouse models was made possible by CRISPR/cas9-mediated gene editing directly in C57BL/6 zygotes. This technology has helped identify phenotypes associated with germline or somatic mutants of Polβ. Such KI mouse models have helped uncover the importance of key Polβ active site residues or specific Polβ enzyme activities, such as the PolbY265C mouse that develops lupus symptoms. More recently, we have used this KI technology to mutate the Polb gene with two codon changes, yielding the PolbL301R/V303R mouse. In this KI mouse model, the expressed Polβ protein cannot bind to its obligate heterodimer partner, Xrcc1. Although the expressed mutant Polβ protein is proteolytically unstable and defective in recruitment to sites of DNA damage, the homozygous PolbL301R/V303R mouse is viable and fertile, yet small in stature. We expect that this and additional targeted mouse models under development are poised to reveal new biological and organismic roles for Polβ.
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Affiliation(s)
- Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912
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Chen S, Zhang W, Li X, Cao Z, Liu C. DNA polymerase beta connects tumorigenicity with the circadian clock in liver cancer through the epigenetic demethylation of Per1. Cell Death Dis 2024; 15:78. [PMID: 38245510 PMCID: PMC10799862 DOI: 10.1038/s41419-024-06462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
The circadian-controlled DNA repair exhibits a strong diurnal rhythm. Disruption in circadian clock and DNA repair is closely linked with hepatocellular carcinoma (HCC) progression, but the mechanism remains unknown. Here, we show that polymerase beta (POLB), a critical enzyme in the DNA base excision repair pathway, is rhythmically expressed at the translational level in mouse livers. Hepatic POLB dysfunction dampens clock homeostasis, whereas retards HCC progression, by mediating the methylation of the 4th CpG island on the 5'UTR of clock gene Per1. Clinically, POLB is overexpressed in human HCC samples and positively associated with poor prognosis. Furthermore, the hepatic rhythmicity of POLB protein expression is orchestrated by Calreticulin (CALR). Our findings provide important insights into the molecular mechanism underlying the synergy between clock and food signals on the POLB-driven BER system and reveal new clock-dependent carcinogenetic effects of POLB. Therefore, chronobiological modulation of POLB may help to promote precise interventions for HCC.
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Affiliation(s)
- Siyu Chen
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Wenxiang Zhang
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiao Li
- Department of Pathology, First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zhengyu Cao
- Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China.
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Heberle BA, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552162. [PMID: 37609156 PMCID: PMC10441303 DOI: 10.1101/2023.08.06.552162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimer's disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinson's disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimer's disease genes such as APP (Aβ precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimer's cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | | | - Madeline L. Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Kayla A. Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Ketsile I. Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Brendan J. White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Lacey A. Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Grant A. Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Mark E. Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Patricia H. Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Brittney A. Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY
| | - Edward J. Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | - Justin B. Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, Arizona
| | - Mark T. W. Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
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Huang D, Zuo Y, Zhang C, Sun G, Jing Y, Lei J, Ma S, Sun S, Lu H, Cai Y, Zhang W, Gao F, Peng Xiang A, Belmonte JCI, Liu GH, Qu J, Wang S. A single-nucleus transcriptomic atlas of primate testicular aging reveals exhaustion of the spermatogonial stem cell reservoir and loss of Sertoli cell homeostasis. Protein Cell 2023; 14:888-907. [PMID: 36929025 PMCID: PMC10691849 DOI: 10.1093/procel/pwac057] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
The testis is pivotal for male reproduction, and its progressive functional decline in aging is associated with infertility. However, the regulatory mechanism underlying primate testicular aging remains largely elusive. Here, we resolve the aging-related cellular and molecular alterations of primate testicular aging by establishing a single-nucleus transcriptomic atlas. Gene-expression patterns along the spermatogenesis trajectory revealed molecular programs associated with attrition of spermatogonial stem cell reservoir, disturbed meiosis and impaired spermiogenesis along the sequential continuum. Remarkably, Sertoli cell was identified as the cell type most susceptible to aging, given its deeply perturbed age-associated transcriptional profiles. Concomitantly, downregulation of the transcription factor Wilms' Tumor 1 (WT1), essential for Sertoli cell homeostasis, was associated with accelerated cellular senescence, disrupted tight junctions, and a compromised cell identity signature, which altogether may help create a hostile microenvironment for spermatogenesis. Collectively, our study depicts in-depth transcriptomic traits of non-human primate (NHP) testicular aging at single-cell resolution, providing potential diagnostic biomarkers and targets for therapeutic interventions against testicular aging and age-related male reproductive diseases.
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Grants
- 2022M712216 National Key Research and Development Program of China
- 81921006, 82125011, 92149301, 92168201, 91949209, 92049304, 92049116, 32121001, 82192863, 82122024, 82071588, 32000500, 31900523, 82201714, 82271600, 82201727 National Natural Science Foundation of China
- 11000022T000000461062 Beijing-affiliated Medical Research
- CAS-WX2021SF-0301, CAS-WX2021SF-0101, CAS-WX2022SDC-XK14 Youth Innovation Promotion Association
- CAS-WX2021SF-0301 Youth Innovation Promotion Association
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Affiliation(s)
- Daoyuan Huang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yuesheng Zuo
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Chen Zhang
- The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
| | - Guoqiang Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Jing
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghui Lei
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Aging Biomarker Consortium, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
| | - Huifen Lu
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
- Sino-Danish Center for Education and Research, Beijing 101408, China
- Aging Biomarker Consortium, China
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510000, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510000, China
| | | | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Aging Biomarker Consortium, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Aging Biomarker Consortium, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
- Aging Biomarker Consortium, China
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Herrmann GK, Yin YW. The Role of Poly(ADP-ribose) Polymerase 1 in Nuclear and Mitochondrial Base Excision Repair. Biomolecules 2023; 13:1195. [PMID: 37627260 PMCID: PMC10452840 DOI: 10.3390/biom13081195] [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: 04/15/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Poly(ADP-ribose) (PAR) Polymerase 1 (PARP-1), also known as ADP-ribosyl transferase with diphtheria toxin homology 1 (ARTD-1), is a critical player in DNA damage repair, during which it catalyzes the ADP ribosylation of self and target enzymes. While the nuclear localization of PARP-1 has been well established, recent studies also suggest its mitochondrial localization. In this review, we summarize the differences between mitochondrial and nuclear Base Excision Repair (BER) pathways, the involvement of PARP-1 in mitochondrial and nuclear BER, and its functional interplay with other BER enzymes.
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Affiliation(s)
- Geoffrey K. Herrmann
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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8
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Ashraf S, Deshpande N, Vasanth S, Melangath G, Wong RJ, Zhao Y, Price MO, Price FW, Jurkunas UV. Dysregulation of DNA repair genes in Fuchs endothelial corneal dystrophy. Exp Eye Res 2023; 231:109499. [PMID: 37169279 PMCID: PMC10246500 DOI: 10.1016/j.exer.2023.109499] [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: 12/01/2022] [Revised: 03/27/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Fuchs Endothelial Corneal Dystrophy (FECD), a late-onset oxidative stress disorder, is the most common cause of corneal endothelial degeneration and is genetically associated with CTG repeat expansion in Transcription Factor 4 (TCF4). We previously reported accumulation of nuclear (nDNA) and mitochondrial (mtDNA) damage in FECD. Specifically, mtDNA damage was a prominent finding in development of disease in the ultraviolet-A (UVA) induced FECD mouse model. We hypothesize that an aberrant DNA repair may contribute to the increased DNA damage seen in FECD. We analyzed differential expression profiles of 84 DNA repair genes by real-time PCR arrays using Human DNA Repair RT-Profiler plates using cDNA extracted from Descemet's membrane-corneal endothelium (DM-CE) obtained from FECD patients with expanded (>40) or non-expanded (<40) intronic CTG repeats in TCF4 gene and from age-matched normal donors. Change in mRNA expression of <0.5- or >2.0-fold in FECD relative to normal was set as cutoff for down- or upregulation. Downregulated mitochondrial genes were further validated using the UVA-based mouse model of FECD. FECD specimens exhibited downregulation of 9 genes and upregulation of 8 genes belonging to the four major DNA repair pathways, namely, base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), and double strand break (DSB) repair, compared to normal donors. MMR gene MSH2 and BER gene POLB were preferentially upregulated in expanded FECD. BER genes LIG3 and NEIL2, DSB repair genes PARP3 and TOP3A, NER gene XPC, and unclassified pathway gene TREX1, were downregulated in both expanded and non-expanded FECD. MtDNA repair genes, Lig3, Neil2, and Top3a, were also downregulated in the UVA-based mouse model of FECD. Our findings identify impaired DNA repair pathways that may play an important role in DNA damage due to oxidative stress as well as genetic predisposition noted in FECD.
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Affiliation(s)
- Shazia Ashraf
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Neha Deshpande
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Shivakumar Vasanth
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Geetha Melangath
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Raymond J Wong
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Yan Zhao
- Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States
| | - Marianne O Price
- Price Vision Group and Cornea Research Foundation of America, Indianapolis, IN, 46260, United States
| | - Francis W Price
- Price Vision Group and Cornea Research Foundation of America, Indianapolis, IN, 46260, United States
| | - Ula V Jurkunas
- Schepens Eye Research Institute, Boston, MA, 02114, United States; Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, United States.
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9
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Szymanski MR, Karlowicz A, Herrmann GK, Cen Y, Yin YW. Human EXOG Possesses Strong AP Hydrolysis Activity: Implication on Mitochondrial DNA Base Excision Repair. J Am Chem Soc 2022; 144:23543-23550. [PMID: 36516439 PMCID: PMC10920074 DOI: 10.1021/jacs.2c10558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most oxidative damage on mitochondrial DNA is corrected by the base excision repair (BER) pathway. However, the enzyme that catalyzes the rate-limiting reaction─deoxyribose phosphate (dRP) removal─in the multienzymatic reaction pathway has not been completely determined in mitochondria. Also unclear is how a logical order of enzymatic reactions is ensured. Here, we present structural and enzymatic studies showing that human mitochondrial EXOG (hEXOG) exhibits strong 5'-dRP removal ability. We show that, unlike the canonical dRP lyases that act on a single substrate, hEXOG functions on a variety of abasic sites, including 5'-dRP, its oxidized product deoxyribonolactone (dL), and the stable synthetic analogue tetrahydrofuran (THF). We determined crystal structures of hEXOG complexed with a THF-containing DNA and with a partial gapped DNA to 2.9 and 2.1 Å resolutions, respectively. The structures illustrate that hEXOG uses a controlled 5'-exonuclease activity to cleave the third phosphodiester bond away from the 5'-abasic site. This study provides a structural basis for hEXOG's broad spectrum of substrates. Further, we show that hEXOG can set the order of BER reactions by generating an ideal substrate for the subsequent reaction in BER and inhibit off-pathway reactions.
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Affiliation(s)
- Michal R Szymanski
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Anna Karlowicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | | | - Yana Cen
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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10
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Romesberg A, Van Houten B. Targeting Mitochondrial Function with Chemoptogenetics. Biomedicines 2022; 10:2459. [PMID: 36289721 PMCID: PMC9599259 DOI: 10.3390/biomedicines10102459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Mitochondria are ATP-generating organelles in eukaryotic cells that produce reactive oxygen species (ROS) during oxidative phosphorylation (OXPHOS). Mitochondrial DNA (mtDNA) is packaged within nucleoids and, due to its close proximity to ROS production, endures oxidative base damage. This damage can be repaired by base excision repair (BER) within the mitochondria, or it can be degraded via exonucleases or mitophagy. Persistent mtDNA damage may drive the production of dysfunctional OXPHOS components that generate increased ROS, or OXPHOS components may be directly damaged by ROS, which then can cause more mtDNA damage and create a vicious cycle of ROS production and mitochondrial dysfunction. If mtDNA damage is left unrepaired, mtDNA mutations including deletions can result. The accumulation of mtDNA mutations has been associated with conditions ranging from the aging process to cancer and neurodegenerative conditions, but the sequence of events leading to mtDNA mutations and deletions is yet unknown. Researchers have utilized many systems and agents for generating ROS in mitochondria to observe the downstream effects on mtDNA, ROS, and mitochondrial function; yet, there are various drawbacks to these methodologies that limit their precision. Here, we describe a novel chemoptogenetic approach to target oxidative damage to mitochondria and mtDNA with a high spatial and temporal resolution so that the downstream effects of ROS-induced damage can be measured with a high precision in order to better understand the mechanism of mitochondrial dysfunction in aging, cancer, and neurodegenerative diseases.
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Affiliation(s)
- Amy Romesberg
- Department of Biological Sciences, College of Arts and Sciences, Carlow University, 3333 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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11
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Chatterjee D, Das P, Chakrabarti O. Mitochondrial Epigenetics Regulating Inflammation in Cancer and Aging. Front Cell Dev Biol 2022; 10:929708. [PMID: 35903542 PMCID: PMC9314556 DOI: 10.3389/fcell.2022.929708] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/09/2022] [Indexed: 12/14/2022] Open
Abstract
Inflammation is a defining factor in disease progression; epigenetic modifications of this first line of defence pathway can affect many physiological and pathological conditions, like aging and tumorigenesis. Inflammageing, one of the hallmarks of aging, represents a chronic, low key but a persistent inflammatory state. Oxidative stress, alterations in mitochondrial DNA (mtDNA) copy number and mis-localized extra-mitochondrial mtDNA are suggested to directly induce various immune response pathways. This could ultimately perturb cellular homeostasis and lead to pathological consequences. Epigenetic remodelling of mtDNA by DNA methylation, post-translational modifications of mtDNA binding proteins and regulation of mitochondrial gene expression by nuclear DNA or mtDNA encoded non-coding RNAs, are suggested to directly correlate with the onset and progression of various types of cancer. Mitochondria are also capable of regulating immune response to various infections and tissue damage by producing pro- or anti-inflammatory signals. This occurs by altering the levels of mitochondrial metabolites and reactive oxygen species (ROS) levels. Since mitochondria are known as the guardians of the inflammatory response, it is plausible that mitochondrial epigenetics might play a pivotal role in inflammation. Hence, this review focuses on the intricate dynamics of epigenetic alterations of inflammation, with emphasis on mitochondria in cancer and aging.
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Affiliation(s)
- Debmita Chatterjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- *Correspondence: Oishee Chakrabarti, ; Debmita Chatterjee, ; Palamou Das,
| | - Palamou Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhabha National Institute, Mumbai, India
- *Correspondence: Oishee Chakrabarti, ; Debmita Chatterjee, ; Palamou Das,
| | - Oishee Chakrabarti
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhabha National Institute, Mumbai, India
- *Correspondence: Oishee Chakrabarti, ; Debmita Chatterjee, ; Palamou Das,
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12
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Monitoring DNA polymerase β mitochondrial localization and dynamics. DNA Repair (Amst) 2022; 116:103357. [PMID: 35717762 PMCID: PMC9253048 DOI: 10.1016/j.dnarep.2022.103357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022]
Abstract
Mouse fibroblasts lacking (null) DNA polymerase β (pol β) were transfected with fluorescently tagged pol β and stained with biomarkers to allow visualization within living cells by confocal microscopy. Transient transfection resulted in varying pol β expression levels. Separating cells into three groups based on pol β fluorescence intensity and morphological distribution, permitted analysis of the concentration dependence and spatial distribution of cytoplasmic pol β. Colocalization between pol β and mitochondria was pol β concentration dependent. A decrease in overlap with nucleoids containing mitochondrial DNA (mtDNA) was observed at the highest pol β intensity where pol β exhibits a tubular appearance, suggesting the ability to load elevated levels of pol β into mitochondria readily available for relocation to damaged mtDNA. The dynamics of pol β and mitochondrial nucleoids were followed by confocal recording of time series images. Two populations of mitochondrial nucleoids were observed, with and without pol β. Micro-irradiation, known to form DNA single-strand breaks, in a line across nucleus and cytoplasm of pol β stably transfected cells enhanced apparent localization of pol β with mitochondria in the perinuclear region of the cytoplasm near the nuclear membrane. Exposure of pol β expressing cells to H2O2 resulted in a time-dependent increase in cytoplasmic pol β observed by immunofluorescence analysis of fixed cells. Further screening revealed increased levels of colocalization of pol β with a mitochondrial probe and an increase in oxidative DNA damage in the cytoplasm. ELISA quantification confirmed an increase of an oxidative mitochondrial base lesion, 7,8-dihydro-8-oxoguanine, after H2O2 treatment. Taken together, the results suggest that pol β is recruited to mitochondria in response to oxidatively-induced mtDNA damage to participate in mtDNA repair.
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13
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Schreier HK, Wiehe RS, Ricchetti M, Wiesmüller L. Polymerase ζ is Involved in Mitochondrial DNA Maintenance Processes in Concert with APE1 Activity. Genes (Basel) 2022; 13:genes13050879. [PMID: 35627264 PMCID: PMC9141751 DOI: 10.3390/genes13050879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial DNA (mtDNA) damaged by reactive oxygen species (ROS) triggers so far poorly understood processes of mtDNA maintenance that are coordinated by a complex interplay among DNA repair, DNA degradation, and DNA replication. This study was designed to identify the proteins involved in mtDNA maintenance by applying a special long-range PCR, reflecting mtDNA integrity in the minor arc. A siRNA screening of literature-based candidates was performed under conditions of enforced oxidative phosphorylation revealing the functional group of polymerases and therein polymerase ζ (POLZ) as top hits. Thus, POLZ knockdown caused mtDNA accumulation, which required the activity of the base excision repair (BER) nuclease APE1, and was followed by compensatory mtDNA replication determined by the single-cell mitochondrial in situ hybridization protocol (mTRIP). Quenching reactive oxygen species (ROS) in mitochondria unveiled an additional, ROS-independent involvement of POLZ in the formation of a typical deletion in the minor arc region. Together with data demonstrating the localization of POLZ in mitochondria, we suggest that POLZ plays a significant role in mtDNA turnover, particularly under conditions of oxidative stress.
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Affiliation(s)
- Heike Katrin Schreier
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Rahel Stefanie Wiehe
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, CEDEX 15, 75724 Paris, France;
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
- Correspondence:
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14
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Allkanjari K, Baldock RA. Beyond base excision repair: an evolving picture of mitochondrial DNA repair. Biosci Rep 2021; 41:BSR20211320. [PMID: 34608928 PMCID: PMC8527207 DOI: 10.1042/bsr20211320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are highly specialised organelles required for key cellular processes including ATP production through cellular respiration and controlling cell death via apoptosis. Unlike other organelles, mitochondria contain their own DNA genome which encodes both protein and RNA required for cellular respiration. Each cell may contain hundreds to thousands of copies of the mitochondrial genome, which is essential for normal cellular function - deviation of mitochondrial DNA (mtDNA) copy number is associated with cellular ageing and disease. Furthermore, mtDNA lesions can arise from both endogenous or exogenous sources and must either be tolerated or corrected to preserve mitochondrial function. Importantly, replication of damaged mtDNA can lead to stalling and introduction of mutations or genetic loss, mitochondria have adapted mechanisms to repair damaged DNA. These mechanisms rely on nuclear-encoded DNA repair proteins that are translocated into the mitochondria. Despite the presence of many known nuclear DNA repair proteins being found in the mitochondrial proteome, it remains to be established which DNA repair mechanisms are functional in mammalian mitochondria. Here, we summarise the existing and emerging research, alongside examining proteomic evidence, demonstrating that mtDNA damage can be repaired using Base Excision Repair (BER), Homologous Recombination (HR) and Microhomology-mediated End Joining (MMEJ). Critically, these repair mechanisms do not operate in isolation and evidence for interplay between pathways and repair associated with replication is discussed. Importantly, characterising non-canonical functions of key proteins and understanding the bespoke pathways used to tolerate, repair or bypass DNA damage will be fundamental in fully understanding the causes of mitochondrial genome mutations and mitochondrial dysfunction.
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Affiliation(s)
- Kathrin Allkanjari
- Formerly: Solent University Southampton, East Park Terrace, Southampton, SO14 0YN, UK
| | - Robert A. Baldock
- School of Natural and Social Sciences, University of Gloucestershire, Francis Close Hall, Swindon Road, Cheltenham GL50 4AZ, UK
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15
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Maldonado E, Morales-Pison S, Urbina F, Solari A. Molecular and Functional Characteristics of DNA Polymerase Beta-Like Enzymes From Trypanosomatids. Front Cell Infect Microbiol 2021; 11:670564. [PMID: 34422676 PMCID: PMC8375306 DOI: 10.3389/fcimb.2021.670564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
Trypanosomatids are a group of primitive unicellular eukaryotes that can cause diseases in plants, insects, animals, and humans. Kinetoplast genome integrity is key to trypanosomatid cell survival and viability. Kinetoplast DNA (kDNA) is usually under attack by reactive oxygen and nitric species (ROS and RNS), damaging the DNA, and the cells must remove and repair those oxidatively generated lesions in order to survive and proliferate. Base excision repair (BER) is a well-conserved pathway for DNA repair after base damage, single-base loss, and single-strand breaks, which can arise from ROS, RSN, environmental genotoxic agents, and UV irradiation. A powerful BER system has been described in the T. cruzi kinetoplast and it is mainly carried out by DNA polymerase β (pol β) and DNA polymerase β-PAK (pol β-PAK), which are kinetoplast-located in T. cruzi as well as in other trypanosomatids. Both pol β and pol β-PAK belong to the X-family of DNA polymerases (pol X family), perform BER in trypanosomatids, and display intrinsic 5-deoxyribose phosphate (dRP) lyase and DNA polymerase activities. However, only Pol β-PAK is able to carry out trans-lesion synthesis (TLS) across 8oxoG lesions. T. cruzi cells overexpressing pol β are more resistant to ROS and are also more efficient to repair 8oxoG compared to control cells. Pol β seems to play a role in kDNA replication, since it associates with kinetoplast antipodal sites in those development stages in trypanosomatids which are competent for cell replication. ROS treatment of cells induces the overexpression of pol β, indicating that plays a role in kDNA repair. In this review, we will summarize the main features of trypanosomatid minicircle kDNA replication and the biochemical characteristics of pol β-like enzymes and their involvement in BER and kDNA replication. We also summarize key structural features of trypanosomatid pol β compared to their mammalian (human) counterpart.
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Affiliation(s)
- Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sebastian Morales-Pison
- Laboratorio de Genética Molecular Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Fabiola Urbina
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Aldo Solari
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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16
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Baptiste BA, Baringer SL, Kulikowicz T, Sommers JA, Croteau DL, Brosh RM, Bohr VA. DNA polymerase β outperforms DNA polymerase γ in key mitochondrial base excision repair activities. DNA Repair (Amst) 2021; 99:103050. [PMID: 33540226 PMCID: PMC7887074 DOI: 10.1016/j.dnarep.2021.103050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/13/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022]
Abstract
DNA polymerase beta (POLβ), well known for its role in nuclear DNA base excision repair (BER), has been shown to be present in the mitochondria of several different cell types. Here we present a side-by-side comparison of BER activities of POLβ and POLγ, the mitochondrial replicative polymerase, previously thought to be the only mitochondrial polymerase. We find that POLβ is significantly more proficient at single-nucleotide gap filling, both in substrates with ends that require polymerase processing, and those that do not. We also show that POLβ has a helicase-independent functional interaction with the mitochondrial helicase, TWINKLE. This interaction stimulates strand-displacement synthesis, but not single-nucleotide gap filling. Importantly, we find that purified mitochondrial extracts from cells lacking POLβ are severely deficient in processing BER intermediates, suggesting that mitochondrially localized DNA POLβ may be critical for cells with high energetic demands that produce greater levels of oxidative stress and therefore depend upon efficient BER for mitochondrial health.
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Affiliation(s)
- Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Stephanie L Baringer
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA.
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17
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Do Y, Matsuda S, Inatomi T, Nakada K, Yasukawa T, Kang D. The accessory subunit of human DNA polymerase γ is required for mitochondrial DNA maintenance and is able to stabilize the catalytic subunit. Mitochondrion 2020; 53:133-139. [PMID: 32470614 DOI: 10.1016/j.mito.2020.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 01/10/2023]
Abstract
Human DNA polymerase γ (POLG) is a mitochondria-specific replicative DNA polymerase consisting of a single catalytic subunit, POLGα, and a dimeric accessory subunit, POLGβ. To gain a deeper understanding of the role of POLGβ, we knocked out this protein in cultured human cybrid cells and established numerous knockout clones. POLGβ-knockout clones presented a clear phenotype of mitochondrial DNA loss, indicating that POLGβ is necessary for mitochondrial DNA replication. Moreover, POLGβ-knockout cells showed a severe decrease in POLGα levels and acute suppression of POLGβ expression efficiently down-regulated POLGα levels. These results suggest that, in addition to its role as the processivity factor of POLG, POLGβ acts as a POLGα stabilizer, an important role for POLGβ in mitochondrial DNA maintenance.
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Affiliation(s)
- Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Teppei Inatomi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kazuto Nakada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, 305-8572, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan.
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
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18
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Beard WA, Horton JK, Prasad R, Wilson SH. Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism. Annu Rev Biochem 2020; 88:137-162. [PMID: 31220977 DOI: 10.1146/annurev-biochem-013118-111315] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair systems to deter changes to their genetic material. Base excision DNA repair involves a number of enzymes and protein cofactors that hasten repair of damaged DNA bases. Recent advances have identified macromolecular complexes that assemble at the DNA lesion and mediate repair. The repair of base lesions generally requires five enzymatic activities: glycosylase, endonuclease, lyase, polymerase, and ligase. The protein cofactors and mechanisms for coordinating the sequential enzymatic steps of repair are being revealed through a range of experimental approaches. We discuss the enzymes and protein cofactors involved in eukaryotic base excision repair, emphasizing the challenge of integrating findings from multiple methodologies. The results provide an opportunity to assimilate biochemical findings with cell-based assays to uncover new insights into this deceptively complex repair pathway.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
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19
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Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci 2020; 77:35-59. [PMID: 31722068 PMCID: PMC7050493 DOI: 10.1007/s00018-019-03368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Max S Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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20
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Kotrys AV, Szczesny RJ. Mitochondrial Gene Expression and Beyond-Novel Aspects of Cellular Physiology. Cells 2019; 9:cells9010017. [PMID: 31861673 PMCID: PMC7017415 DOI: 10.3390/cells9010017] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are peculiar organelles whose proper function depends on the crosstalk between two genomes, mitochondrial and nuclear. The human mitochondrial genome (mtDNA) encodes only 13 proteins; nevertheless, its proper expression is essential for cellular homeostasis, as mtDNA-encoded proteins are constituents of mitochondrial respiratory complexes. In addition, mtDNA expression results in the production of RNA molecules, which influence cell physiology once released from the mitochondria into the cytoplasm. As a result, dysfunctions of mtDNA expression may lead to pathologies in humans. Here, we review the mechanisms of mitochondrial gene expression with a focus on recent findings in the field. We summarize the complex turnover of mitochondrial transcripts and present an increasing body of evidence indicating new functions of mitochondrial transcripts. We discuss mitochondrial gene regulation in different cellular contexts, focusing on stress conditions. Finally, we highlight the importance of emerging aspects of mitochondrial gene regulation in human health and disease.
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21
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Ježek P, Dlasková A. Dynamic of mitochondrial network, cristae, and mitochondrial nucleoids in pancreatic β-cells. Mitochondrion 2019; 49:245-258. [DOI: 10.1016/j.mito.2019.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022]
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22
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Alteration of mitochondrial DNA homeostasis in drug-induced liver injury. Food Chem Toxicol 2019; 135:110916. [PMID: 31669601 DOI: 10.1016/j.fct.2019.110916] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes for 13 proteins involved in the oxidative phosphorylation (OXPHOS) process. In liver, genetic or acquired impairment of mtDNA homeostasis can reduce ATP output but also decrease fatty acid oxidation, thus leading to different hepatic lesions including massive necrosis and microvesicular steatosis. Hence, a severe impairment of mtDNA homeostasis can lead to liver failure and death. An increasing number of investigations report that some drugs can induce mitochondrial dysfunction and drug-induced liver injury (DILI) by altering mtDNA homeostasis. Some drugs such as ciprofloxacin, antiretroviral nucleoside reverse-transcriptase inhibitors and tacrine can inhibit hepatic mtDNA replication, thus inducing mtDNA depletion. Drug-induced reduced mtDNA levels can also be the consequence of reactive oxygen species-mediated oxidative damage to mtDNA, which triggers its degradation by mitochondrial nucleases. Such mechanism is suspected for acetaminophen and troglitazone. Other pharmaceuticals such as linezolid and tetracyclines can impair mtDNA translation, thus selectively reducing the synthesis of the 13 mtDNA-encoded proteins. Lastly, some drugs might alter the mtDNA methylation status but the pathophysiological consequences of such alteration are still unclear. Drug-induced impairment of mtDNA homeostasis is probably under-recognized since preclinical and post-marketing safety studies do not classically investigate mtDNA levels, mitochondrial protein synthesis and mtDNA oxidative damage.
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23
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Sharma N, Pasala MS, Prakash A. Mitochondrial DNA: Epigenetics and environment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:668-682. [PMID: 31335990 PMCID: PMC6941438 DOI: 10.1002/em.22319] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 05/22/2023]
Abstract
Maintenance of the mitochondrial genome is essential for proper cellular function. For this purpose, mitochondrial DNA (mtDNA) needs to be faithfully replicated, transcribed, translated, and repaired in the face of constant onslaught from endogenous and environmental agents. Although only 13 polypeptides are encoded within mtDNA, the mitochondrial proteome comprises over 1500 proteins that are encoded by nuclear genes and translocated to the mitochondria for the purpose of maintaining mitochondrial function. Regulation of mtDNA and mitochondrial proteins by epigenetic changes and post-translational modifications facilitate crosstalk between the nucleus and the mitochondria and ultimately lead to the maintenance of cellular health and homeostasis. DNA methyl transferases have been identified in the mitochondria implicating that methylation occurs within this organelle; however, the extent to which mtDNA is methylated has been debated for many years. Mechanisms of demethylation within this organelle have also been postulated, but the exact mechanisms and their outcomes is still an active area of research. Mitochondrial dysfunction in the form of altered gene expression and ATP production, resulting from epigenetic changes, can lead to various conditions including aging-related neurodegenerative disorders, altered metabolism, changes in circadian rhythm, and cancer. Here, we provide an overview of the epigenetic regulation of mtDNA via methylation, long and short noncoding RNAs, and post-translational modifications of nucleoid proteins (as mitochondria lack histones). We also highlight the influence of xenobiotics such as airborne environmental pollutants, contamination from heavy metals, and therapeutic drugs on mtDNA methylation. Environ. Mol. Mutagen., 60:668-682, 2019. © 2019 Wiley Periodicals, Inc.
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24
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Luo H, Wang L, Bao D, Wang L, Zhao H, Lian Y, Yan M, Mohan C, Li QZ. Novel Autoantibodies Related to Cell Death and DNA Repair Pathways in Systemic Lupus Erythematosus. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:248-259. [PMID: 31494269 PMCID: PMC6818352 DOI: 10.1016/j.gpb.2018.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/16/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune syndrome characterized by various co-existing autoantibodies (autoAbs) in patients’ blood. However, the full spectrum of autoAbs in SLE has not been comprehensively elucidated. In this study, a commercial platform bearing 9400 antigens (ProtoArray) was used to identify autoAbs that were significantly elevated in the sera of SLE patients. By comparing the autoAb profiles of SLE patients with those of healthy controls, we identified 437 IgG and 1213 IgM autoAbs that the expression levels were significantly increased in SLE (P < 0.05). Use of the ProtoArray platform uncovered over 300 novel autoAbs targeting a broad range of nuclear, cytoplasmic, and membrane antigens. Molecular interaction network analysis revealed that the antigens targeted by the autoAbs were most significantly enriched in cell death, cell cycle, and DNA repair pathways. A group of autoAbs associated with cell apoptosis and DNA repair function, including those targeting APEX1, AURKA, POLB, AGO1, HMGB1, IFIT5, MAPKAPK3, PADI4, RGS3, SRP19, UBE2S, and VRK1, were further validated by ELISA and Western blot in a larger cohort. In addition, the levels of autoAbs against APEX1, HMGB1, VRK1, AURKA, PADI4, and SRP19 were positively correlated with the level of anti-dsDNA in SLE patients. Comprehensive autoAb screening has identified novel autoAbs, which may shed light on potential pathogenic pathways leading to lupus.
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Affiliation(s)
- Hui Luo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ling Wang
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Nephrology, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, China
| | - Ding Bao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Li Wang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yun Lian
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mei Yan
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, TX 77004, USA
| | - Quan-Zhen Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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25
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Ferrando B, Furlanetto ALDM, Gredilla R, Havelund JF, Hebelstrup KH, Møller IM, Stevnsner T. DNA repair in plant mitochondria - a complete base excision repair pathway in potato tuber mitochondria. PHYSIOLOGIA PLANTARUM 2019; 166:494-512. [PMID: 30035320 DOI: 10.1111/ppl.12801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/05/2018] [Accepted: 07/11/2018] [Indexed: 05/07/2023]
Abstract
Mitochondria are one of the major sites of reactive oxygen species (ROS) production in the plant cell. ROS can damage DNA, and this damage is in many organisms mainly repaired by the base excision repair (BER) pathway. We know very little about DNA repair in plants especially in the mitochondria. Combining proteomics, bioinformatics, western blot and enzyme assays, we here demonstrate that the complete BER pathway is found in mitochondria isolated from potato (Solanum tuberosum) tubers. The enzyme activities of three DNA glycosylases and an apurinic/apyrimidinic (AP) endonuclease (APE) were characterized with respect to Mg2+ dependence and, in the case of the APE, temperature sensitivity. Evidence for the presence of the DNA polymerase and the DNA ligase, which complete the repair pathway by replacing the excised base and closing the gap, was also obtained. We tested the effect of oxidative stress on the mitochondrial BER pathway by incubating potato tubers under hypoxia. Protein carbonylation increased significantly in hypoxic tuber mitochondria indicative of increased oxidative stress. The activity of two BER enzymes increased significantly in response to this oxidative stress consistent with the role of the BER pathway in the repair of oxidative damage to mitochondrial DNA.
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Affiliation(s)
- Beatriz Ferrando
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Ana L D M Furlanetto
- Department of Biochemistry and Molecular Biology, Life sciences Sector, Federal University of Paraná, 81531-990, Curitiba, Puerto Rico, Brazil
| | - Ricardo Gredilla
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
- Department of Physiology, Faculty of Medicine, Complutense University, 28040, Madrid, Spain
| | - Jesper F Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense, Denmark
| | - Kim H Hebelstrup
- Department of Molecular Biology and Genetics, Aarhus University, DK-4200, Slagelse, Denmark
| | - Ian M Møller
- Department of Molecular Biology and Genetics, Aarhus University, DK-4200, Slagelse, Denmark
| | - Tinna Stevnsner
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
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26
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Liu J, Zheng B, Li Y, Yuan Y, Xing C. Genetic Polymorphisms of DNA Repair Pathways in Sporadic Colorectal Carcinogenesis. J Cancer 2019; 10:1417-1433. [PMID: 31031852 PMCID: PMC6485219 DOI: 10.7150/jca.28406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
DNA repair systems play a critical role in maintaining the integrity and stability of the genome, which mainly include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR) and double-strand break repair (DSBR). The polymorphisms in different DNA repair genes that are mainly represented by single-nucleotide polymorphisms (SNPs) can potentially modulate the individual DNA repair capacity and therefore exert an impact on individual genetic susceptibility to cancer. Sporadic colorectal cancer arises from the colorectum without known contribution from germline causes or significant family history of cancer or inflammatory bowel disease. In recent years, emerging studies have investigated the association between polymorphisms of DNA repair system genes and sporadic CRC. Here, we review recent insights into the polymorphisms of DNA repair pathway genes, not only individual gene polymorphism but also gene-gene and gene-environment interactions, in sporadic colorectal carcinogenesis.
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Affiliation(s)
- Jingwei Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Bowen Zheng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Ying Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
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27
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Chocron ES, Munkácsy E, Pickering AM. Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease. Biochim Biophys Acta Mol Basis Dis 2019; 1865:285-297. [PMID: 30419337 PMCID: PMC6310633 DOI: 10.1016/j.bbadis.2018.09.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome (mtDNA) represents a tiny fraction of the whole genome, comprising just 16.6 kilobases encoding 37 genes involved in oxidative phosphorylation and the mitochondrial translation machinery. Despite its small size, much interest has developed in recent years regarding the role of mtDNA as a determinant of both aging and age-associated diseases. A number of studies have presented compelling evidence for key roles of mtDNA in age-related pathology, although many are correlative rather than demonstrating cause. In this review we will evaluate the evidence supporting and opposing a role for mtDNA in age-associated functional declines and diseases. We provide an overview of mtDNA biology, damage and repair as well as the influence of mitochondrial haplogroups, epigenetics and maternal inheritance in aging and longevity.
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Affiliation(s)
- E Sandra Chocron
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Erin Munkácsy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Andrew M Pickering
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA; Department of Molecular Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA.
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28
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Naeem MM, Sondheimer N. Heteroplasmy Shifting as Therapy for Mitochondrial Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:257-267. [PMID: 31452145 DOI: 10.1007/978-981-13-8367-0_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial disease can arise due to pathogenic sequence variants in the mitochondrial DNA (mtDNA) that prevent cells from meeting their energy demands. Mitochondrial diseases are often fatal and currently there are no treatments directed towards the underlying cause of disease. Pathogenic variants in mtDNA often exist in a state of heteroplasmy, with coexistence of pathogenic and wild type mtDNA. The load of heteroplasmy, defined as the relative amount of pathogenic mtDNA to wild type mtDNA, corresponds to timing and symptom severity. Thus, changing the heteroplasmy load may lead to a shift in disease onset and symptom severity. Here we review techniques aimed at preventing inheritance of pathogenic mtDNA via mitochondrial replacement therapy (MRT) and strategies geared toward shifting of heteroplasmy in individuals with active mitochondrial disease. MRT strategies seek to create embryos with the nuclear genetic makeup of the intended parents and wild type mtDNA from a donor in order to avoid known maternal pathogenic variants. Heteroplasmy shift approaches in patients are of two categories: nuclease dependent and nuclease independent strategies. Despite initial success in mouse models and patient cells, these techniques have not reached clinical use. Translational attempts in this area are urgently needed to improve therapies for a currently untreatable set of disorders.
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Affiliation(s)
- Mansur M Naeem
- Institute of Medical Science, The University of Toronto, Toronto, ON, Canada
| | - Neal Sondheimer
- Institute of Medical Science, The University of Toronto, Toronto, ON, Canada.
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29
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Beard WA, Wilson SH. DNA polymerase beta and other gap-filling enzymes in mammalian base excision repair. Enzymes 2019; 45:1-26. [PMID: 31627875 DOI: 10.1016/bs.enz.2019.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA polymerase β plays a central role in the base excision DNA repair pathway that cleanses the genome of apurinic/apyrimidinic (AP) sites. AP sites arise in DNA from spontaneous base loss and DNA damage-specific glycosylases that hydrolyze the N-glycosidic bond between the deoxyribose and damaged base. AP sites are deleterious lesions because they can be mutagenic and/or cytotoxic. DNA polymerase β contributes two enzymatic activities, DNA synthesis and lyase, during the repair of AP sites; these activities reside on carboxyl- and amino-terminal domains, respectively. Accordingly, its cellular, structural, and kinetic attributes have been extensively characterized and it serves as model enzyme for the nucleotidyl transferase reaction utilized by other replicative, repair, and trans-lesion DNA polymerases.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Durham, NC, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Durham, NC, United States.
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