The Role of DNA Damage and Repair in Idiopathic Pulmonary Fibrosis

The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Given that the lung is exposed to the external environment, it is likely that oxidative stress, especially the stimulation of DNA, would be of particular importance in pulmonary fibrosis. DNA damage is known to play an important role in idiopathic pulmonary fibrosis initiation, so DNA repair systems targeting damage are also crucial for the survival of lung cells. Although many contemporary reports have summarized the role of individual DNA damage and repair pathways in their hypotheses, they have not focused on idiopathic pulmonary fibrosis. This review, therefore, aims to provide a concise overview for researchers to understand the pathways of DNA damage and repair and their roles in IPF.

[1]  Zijun Wu,et al.  TH5487, a small molecule inhibitor of OGG1, attenuates pulmonary fibrosis by NEDD4L-mediated OGG1 degradation. , 2022, Chemico-biological interactions.

[2]  C. Scotton,et al.  The Role of Herpes Viruses in Pulmonary Fibrosis , 2021, Frontiers in Medicine.

[3]  Lin Fu,et al.  Tauroursodeoxycholic acid alleviates pulmonary endoplasmic reticulum stress and epithelial-mesenchymal transition in bleomycin-induced lung fibrosis , 2021, BMC Pulmonary Medicine.

[4]  J. Charbonnier,et al.  The Multifaceted Roles of Ku70/80 , 2021, International journal of molecular sciences.

[5]  S. Raghavan,et al.  20 years of DNA Polymerase μ, the polymerase that still surprises , 2021, The FEBS journal.

[6]  S. Raghavan,et al.  Nonhomologous end joining: new accessory factors fine tune the machinery. , 2021, Trends in genetics : TIG.

[7]  Ansuman T. Satpathy,et al.  Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions , 2021, Cell.

[8]  S. Mori,et al.  Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types , 2022, JCO precision oncology.

[9]  Huaiyong Chen,et al.  Macrophages in Lung Injury, Repair, and Fibrosis , 2021, Cells.

[10]  K. Floro,et al.  The role of DNA damage and repair in liver cancer. , 2020, Biochimica et biophysica acta. Reviews on cancer.

[11]  E. Atabati,et al.  Association of COVID-19 and other viral infections with interstitial lung diseases, pulmonary fibrosis, and pulmonary hypertension: A narrative review , 2020, Canadian journal of respiratory therapy : CJRT = Revue canadienne de la therapie respiratoire : RCTR.

[12]  V. Bohr,et al.  DNA Damage and Mitochondria in Cancer and Aging. , 2020, Carcinogenesis.

[13]  Y. Nakabeppu,et al.  MUTYH Deficiency Is Associated with Attenuated Pulmonary Fibrosis in a Bleomycin-Induced Model , 2020, Oxidative medicine and cellular longevity.

[14]  Gang Liu,et al.  8‐Oxoguanine DNA glycosylase modulates the cell transformation process in pulmonary fibrosis by inhibiting Smad2/3 and interacting with Smad7 , 2020, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[15]  Natalie R. Gassman,et al.  Transcriptional dysregulation of base excision repair proteins in breast cancer. , 2020, DNA repair.

[16]  C. Mussolino,et al.  DNA Damage: From Threat to Treatment , 2020, Cells.

[17]  M. Dvir-Ginzberg,et al.  SIRT1 Deficiency, Specifically in Fibroblasts, Decreases Apoptosis Resistance and Is Associated with Resolution of Lung-Fibrosis , 2020, Biomolecules.

[18]  Nishant Singh,et al.  S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study , 2020, Translational Oncology.

[19]  Kacper Lechowicz,et al.  COVID-19: The Potential Treatment of Pulmonary Fibrosis Associated with SARS-CoV-2 Infection , 2020, Journal of clinical medicine.

[20]  A. Bast,et al.  Role of antioxidants in the treatment of gastroesophageal reflux disease-associated idiopathic pulmonary fibrosis. , 2020, Current opinion in pulmonary medicine.

[21]  Benjamin J. Polacco,et al.  A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing , 2020, Nature.

[22]  Trey Ideker,et al.  A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing , 2020, bioRxiv.

[23]  Alan B. Watts,et al.  Caveolin-1–derived peptide limits development of pulmonary fibrosis , 2019, Science Translational Medicine.

[24]  A. Jegga,et al.  Dysregulation of Mesenchymal Cell Survival Pathways in Severe Fibrotic Lung Disease: The Effect of Nintedanib Therapy , 2019, Front. Pharmacol..

[25]  E. Masini,et al.  Effects of PARP-1 Deficiency and Histamine H4 Receptor Inhibition in an Inflammatory Model of Lung Fibrosis in Mice , 2019, Front. Pharmacol..

[26]  U. Farooq,et al.  Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major , 2012, BMC Genomics.

[27]  R. Nho,et al.  Fibroblasts from patients with idiopathic pulmonary fibrosis are resistant to cisplatin-induced cell death via enhanced CK2-dependent XRCC1 activity , 2019, Apoptosis.

[28]  W. Zhou,et al.  AluYb8 insertion polymorphism in the MUTYH gene impairs mitochondrial DNA maintenance and affects the age of onset of IPF , 2019, Aging.

[29]  Bing Hu,et al.  P2X4R promotes airway remodeling by acting on the phenotype switching of bronchial smooth muscle cells in rats , 2018, Purinergic Signalling.

[30]  F. Xiang,et al.  Suppression of TGF-β1 enhances chemosensitivity of cisplatin-resistant lung cancer cells through the inhibition of drug-resistant proteins , 2018, Artificial cells, nanomedicine, and biotechnology.

[31]  Y. Janssen-Heininger,et al.  Oxidative stress in chronic lung disease: From mitochondrial dysfunction to dysregulated redox signaling. , 2018, Molecular aspects of medicine.

[32]  M. Weitzman,et al.  Virus DNA Replication and the Host DNA Damage Response. , 2018, Annual review of virology.

[33]  X. Yang,et al.  The regulatory role of APE1 in epithelial‐to‐mesenchymal transition and in determining EGFR‐TKI responsiveness in non‐small‐cell lung cancer , 2018, Cancer medicine.

[34]  W. Rom,et al.  Aldehydes are the predominant forces inducing DNA damage and inhibiting DNA repair in tobacco smoke carcinogenesis , 2018, Proceedings of the National Academy of Sciences.

[35]  L. Richeldi,et al.  Idiopathic pulmonary fibrosis: pathogenesis and management , 2018, Respiratory Research.

[36]  B. Schumacher,et al.  DNA damage responses and p53 in the aging process. , 2018, Blood.

[37]  P. Cejka,et al.  Main steps in DNA double-strand break repair: an introduction to homologous recombination and related processes , 2018, Chromosoma.

[38]  D. Knight,et al.  Divergent roles for Clusterin in Lung Injury and Repair , 2017, Scientific Reports.

[39]  W. Drake,et al.  Role of Microbial Agents in Pulmonary Fibrosis
 , 2017, The Yale journal of biology and medicine.

[40]  S. David,et al.  Repair of 8-oxoG:A mismatches by the MUTYH glycosylase: Mechanism, metals and medicine. , 2017, Free radical biology & medicine.

[41]  M. Lieber,et al.  Non-homologous DNA end joining and alternative pathways to double-strand break repair , 2017, Nature Reviews Molecular Cell Biology.

[42]  S. Zha,et al.  Regulation of the DNA Damage Response by DNA-PKcs Inhibitory Phosphorylation of ATM. , 2017, Molecular cell.

[43]  E. Masini,et al.  HYDAMTIQ, a selective PARP‐1 inhibitor, improves bleomycin‐induced lung fibrosis by dampening the TGF‐β/SMAD signalling pathway , 2016, Journal of cellular and molecular medicine.

[44]  Nayoung Kim,et al.  Protective Effect of Proton Pump Inhibitor for Survival in Patients with Gastroesophageal Reflux Disease and Idiopathic Pulmonary Fibrosis , 2016, Journal of neurogastroenterology and motility.

[45]  Shenmin Zhang,et al.  Prediction of survival prognosis of non-small cell lung cancer by APE1 through regulation of epithelial-mesenchymal transition , 2016, Oncotarget.

[46]  D. Durocher,et al.  A mechanism for the suppression of homologous recombination in G1 cells , 2015, Nature.

[47]  S. Kowalczykowski An Overview of the Molecular Mechanisms of Recombinational DNA Repair. , 2015, Cold Spring Harbor perspectives in biology.

[48]  M. Blasco,et al.  Mice with Pulmonary Fibrosis Driven by Telomere Dysfunction. , 2015, Cell reports.

[49]  O. Inanami,et al.  Downregulation of the DNA repair enzyme apurinic/apyrimidinic endonuclease 1 stimulates transforming growth factor-β1 production and promotes actin rearrangement. , 2015, Biochemical and biophysical research communications.

[50]  W. Seeger,et al.  Streptococcus pneumoniae triggers progression of pulmonary fibrosis through pneumolysin , 2015, Thorax.

[51]  S. Lees-Miller,et al.  The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis. , 2015, Progress in biophysics and molecular biology.

[52]  Tom L. Blundell,et al.  PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair , 2015, Science.

[53]  A. Brasier,et al.  8-Oxoguanine DNA glycosylase-1-mediated DNA repair is associated with Rho GTPase activation and α-smooth muscle actin polymerization. , 2014, Free radical biology & medicine.

[54]  J. Hoeijmakers,et al.  Understanding nucleotide excision repair and its roles in cancer and ageing , 2014, Nature Reviews Molecular Cell Biology.

[55]  A. Boulares,et al.  Poly (ADP‐ribose) polymerase‐1 is a key mediator of liver inflammation and fibrosis , 2014, Hepatology.

[56]  David J. Chen,et al.  DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. , 2014, DNA repair.

[57]  H. Collard,et al.  Pathogenesis of idiopathic pulmonary fibrosis. , 2014, Annual review of pathology.

[58]  D. Roth,et al.  Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. , 2013, Annual review of genetics.

[59]  K. Erdélyi,et al.  Poly (ADP-ribose) Polymerase-1 is a Key Mediator of Liver Inflammation and Fibrosis , 2013, Free Radical Biology and Medicine.

[60]  L. Pearl,et al.  A Mechanism for the Inhibition of DNA-PK-Mediated DNA Sensing by a Virus , 2013, PLoS pathogens.

[61]  D. Kamp,et al.  Oxidative stress and pulmonary fibrosis. , 2013, Biochimica et biophysica acta.

[62]  Brent S. Pedersen,et al.  Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis , 2013, Nature Genetics.

[63]  D. Kamp,et al.  Molecular basis of asbestos-induced lung disease. , 2013, Annual review of pathology.

[64]  P. Hergert,et al.  Regulation of myofibroblast differentiation by poly(ADP-ribose) polymerase 1. , 2013, The American journal of pathology.

[65]  G. Verleden,et al.  The pathogenesis of pulmonary fibrosis: a moving target , 2012, European Respiratory Journal.

[66]  S. Mitra,et al.  Activation of Ras Signaling Pathway by 8-Oxoguanine DNA Glycosylase Bound to Its Excision Product, 8-Oxoguanine* , 2012, The Journal of Biological Chemistry.

[67]  Y. Kim,et al.  Overview of base excision repair biochemistry. , 2012, Current molecular pharmacology.

[68]  Ivana V. Yang,et al.  A common MUC5B promoter polymorphism and pulmonary fibrosis. , 2011, The New England journal of medicine.

[69]  A. Woodcock,et al.  Ganciclovir Antiviral Therapy in Advanced Idiopathic Pulmonary Fibrosis: An Open Pilot Study , 2011, Pulmonary medicine.

[70]  D. Kamp,et al.  Molecular mechanisms of asbestos-induced lung epithelial cell apoptosis. , 2010, Chemico-biological interactions.

[71]  W. Coward,et al.  The pathogenesis of idiopathic pulmonary fibrosis , 2010, Therapeutic advances in respiratory disease.

[72]  T. Oury,et al.  Oxidative stress, extracellular matrix targets, and idiopathic pulmonary fibrosis. , 2010, Free radical biology & medicine.

[73]  Bing-Hua Jiang,et al.  Phosphatidylinositol-3-kinase/akt regulates bleomycin-induced fibroblast proliferation and collagen production. , 2010, American journal of respiratory cell and molecular biology.

[74]  B. Willis,et al.  N-acetylcysteine inhibits alveolar epithelial-mesenchymal transition. , 2009, American journal of physiology. Lung cellular and molecular physiology.

[75]  J. Egly,et al.  Molecular insights into the recruitment of TFIIH to sites of DNA damage , 2009, The EMBO journal.

[76]  P. Cramer,et al.  Molecular Basis of Transcriptional Mutagenesis at 8-Oxoguanine* , 2009, The Journal of Biological Chemistry.

[77]  Shanshan Song,et al.  Effect of silicon dioxide on expression of poly (ADP‐Ribose) polymerase mRNA and protein , 2009, Cell biology international.

[78]  Eleni P. Mimitou,et al.  Nucleases and helicases take center stage in homologous recombination. , 2009, Trends in biochemical sciences.

[79]  D. Zharkov Base excision DNA repair , 2008, Cellular and Molecular Life Sciences.

[80]  Marietta Y. W. T. Lee,et al.  Sequential recruitment of the repair factors during NER: the role of XPG in initiating the resynthesis step , 2008, The EMBO journal.

[81]  M. Hottiger,et al.  The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases. , 2008, Frontiers in bioscience : a journal and virtual library.

[82]  J. Egly,et al.  Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair. , 2007, Molecular cell.

[83]  P. Lansdorp,et al.  Telomerase mutations in families with idiopathic pulmonary fibrosis. , 2007, The New England journal of medicine.

[84]  T. Noll,et al.  The role of poly(ADP-ribose) polymerase (PARP) in the autonomous proliferative response of endothelial cells to hypoxia. , 2007, Cardiovascular research.

[85]  R. Costa,et al.  Chk2 Mediates Stabilization of the FoxM1 Transcription Factor To Stimulate Expression of DNA Repair Genes , 2006, Molecular and Cellular Biology.

[86]  A. Lu,et al.  MutY and MutY homologs (MYH) in genome maintenance. , 2006, Frontiers in bioscience : a journal and virtual library.

[87]  Wolf-Dietrich Heyer,et al.  Rad54: the Swiss Army knife of homologous recombination? , 2006, Nucleic acids research.

[88]  J. Dent,et al.  The Montreal Definition and Classification of Gastroesophageal Reflux Disease: A Global Evidence-Based Consensus , 2006, The American Journal of Gastroenterology.

[89]  D. Coultas,et al.  Is idiopathic pulmonary fibrosis an environmental disease? , 2006, Proceedings of the American Thoracic Society.

[90]  S. Bennett,et al.  Physical and functional interaction of human nuclear uracil-DNA glycosylase with proliferating cell nuclear antigen. , 2005, DNA repair.

[91]  I. Cousineau,et al.  BRCA2 regulates homologous recombination in response to DNA damage: implications for genome stability and carcinogenesis. , 2005, Cancer research.

[92]  E. Mazzon,et al.  Inhibitors of Poly(ADP-Ribose) Polymerase Modulate Signal Transduction Pathways and the Development of Bleomycin-Induced Lung Injury , 2005, Journal of Pharmacology and Experimental Therapeutics.

[93]  J. Błasiak,et al.  [Base excision repair]. , 2005, Postepy biochemii.

[94]  L. Symington,et al.  Recombination proteins in yeast. , 2004, Annual review of genetics.

[95]  G. Achanta,et al.  Role of p53 in Sensing Oxidative DNA Damage in Response to Reactive Oxygen Species-Generating Agents , 2004, Cancer Research.

[96]  N. Larebeke,et al.  Endogenous DNA damage in humans: a review of quantitative data , 2004 .

[97]  N. Van Larebeke,et al.  Endogenous DNA damage in humans: a review of quantitative data. , 2004, Mutagenesis.

[98]  A. Durandy,et al.  Repair of U/G and U/A in DNA by UNG2-associated repair complexes takes place predominantly by short-patch repair both in proliferating and growth-arrested cells. , 2004, Nucleic acids research.

[99]  M. Dizdaroglu Substrate specificities and excision kinetics of DNA glycosylases involved in base-excision repair of oxidative DNA damage. , 2003, Mutation research.

[100]  J. Eshleman,et al.  Human MutY: gene structure, protein functions and interactions, and role in carcinogenesis , 2003, Cellular and Molecular Life Sciences CMLS.

[101]  S. Hazen,et al.  Oxidative and nitrosative events in asthma. , 2003, Free radical biology & medicine.

[102]  Stephen C. West,et al.  Molecular views of recombination proteins and their control , 2003, Nature Reviews Molecular Cell Biology.

[103]  D. Spandidos,et al.  MYCL1, FHIT, SPARC, p16INK4 and TP53 genes associated to lung cancer in idiopathic pulmonary fibrosis , 2002, Journal of cellular and molecular medicine.

[104]  T. Kuroki,et al.  Hyperplastic epithelial foci in honeycomb lesions in idiopathic pulmonary fibrosis , 2002, Virchows Archiv.

[105]  C. Szabó,et al.  Activation of poly(ADP-ribose) polymerase contributes to development of doxorubicin-induced heart failure. , 2002, The Journal of pharmacology and experimental therapeutics.

[106]  M. Gallucci,et al.  Tumor specific modulation of KU70/80 DNA binding activity in breast and bladder human tumor biopsies , 2001, Oncogene.

[107]  M. Kelley,et al.  Going APE over ref-1. , 2000, Mutation research.

[108]  D. Spandidos,et al.  Frequent genetic alterations at the microsatellite level in cytologic sputum samples of patients with idiopathic pulmonary fibrosis. , 2000, American journal of respiratory and critical care medicine.

[109]  M. West,et al.  XRCC1 keeps DNA from getting stranded. , 2000, Mutation research.

[110]  Andreas D. Baxevanis,et al.  MLH3: a DNA mismatch repair gene associated with mammalian microsatellite instability , 2000, Nature Genetics.

[111]  A. Tomkinson,et al.  Reconstitution of Proliferating Cell Nuclear Antigen-dependent Repair of Apurinic/Apyrimidinic Sites with Purified Human Proteins* , 1999, The Journal of Biological Chemistry.

[112]  G. Morris,et al.  p53-Mediated Regulation of Proliferating Cell Nuclear Antigen Expression in Cells Exposed to Ionizing Radiation , 1999, Molecular and Cellular Biology.

[113]  G. Raghu,et al.  Increased prevalence of gastroesophageal reflux in patients with idiopathic pulmonary fibrosis. , 1998, American journal of respiratory and critical care medicine.

[114]  C B Harley,et al.  Telomerase catalytic subunit homologs from fission yeast and human. , 1997, Science.

[115]  G. Morris,et al.  Inhaled asbestos fibers induce p53 expression in the rat lung. , 1997, American journal of respiratory cell and molecular biology.

[116]  June Corwin,et al.  Telomerase Catalytic Subunit Homologs from Fission Yeast and Human , 1997 .

[117]  A. Grollman,et al.  Incision Activity of Human Apurinic Endonuclease (Ape) at Abasic Site Analogs in DNA (*) , 1995, The Journal of Biological Chemistry.

[118]  G. Hannon,et al.  The p21 inhibitor of cyclin-dependent kinases controls DNA replication by interaction with PCNA , 1994, Nature.

[119]  T. Lindahl Instability and decay of the primary structure of DNA , 1993, Nature.

[120]  A. Carrano,et al.  Molecular cloning of the human XRCC1 gene, which corrects defective DNA strand break repair and sister chromatid exchange , 1990, Molecular and cellular biology.

[121]  R. Cunningham,et al.  The enzymology of apurinic/apyrimidinic endonucleases. , 1990, Mutation research.

[122]  Carol W. Greider,et al.  Identification of a specific telomere terminal transferase activity in tetrahymena extracts , 1985, Cell.

[123]  T. Nakayama,et al.  Cigarette smoke induces DNA single-strand breaks in human cells , 1985, Nature.