140
Views
1
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

DNA Repair Mechanisms are Activated in Circulating Lymphocytes of Hospitalized Covid-19 Patients

ORCID Icon, , , ORCID Icon, , , ORCID Icon, ORCID Icon, , , , , ORCID Icon, , , , , , ORCID Icon & show all
Pages 6629-6644 | Received 30 Jun 2022, Accepted 20 Oct 2022, Published online: 07 Dec 2022

References

  • Kay J, Thadhani E, Samson L, Engelward B. Inflammation-induced DNA damage, mutations and cancer. DNA Repair (Amst). 2019;83:102673. doi:10.1016/j.dnarep.2019.102673
  • Rodier F, Coppe JP, Patil CK, et al. Persistent DNA damage signalling triggers senescence-associated inflammatory cytokine secretion. Nat Cell Biol. 2009;11(8):973–979. doi:10.1038/ncb1909
  • Cavanagh MM, Weyand CM, Goronzy JJ. Chronic inflammation and aging: DNA damage tips the balance. Curr Opin Immunol. 2012;24(4):488–493. doi:10.1016/j.coi.2012.04.003
  • Kang C, Xu Q, Martin TD, et al. The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4. Science. 2015;349(6255):aaa5612. doi:10.1126/science.aaa5612
  • Chernyak BV, Popova EN, Prikhodko AS, Grebenchikov OA, Zinovkina LA, Zinovkin RA. COVID-19 and Oxidative Stress. Biochemistry (Mosc). 2020;85(12):1543–1553. doi:10.1134/S0006297920120068
  • Cecchini R, Cecchini AL. SARS-CoV-2 infection pathogenesis is related to oxidative stress as a response to aggression. Med Hypotheses. 2020;143:110102. doi:10.1016/j.mehy.2020.110102
  • Suhail S, Zajac J, Fossum C, et al. Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: a Review. Protein J. 2020;39(6):644–656. doi:10.1007/s10930-020-09935-8
  • Laforge M, Elbim C, Frere C, et al. Tissue damage from neutrophil-induced oxidative stress in COVID-19. Nat Rev Immunol. 2020;20(9):515–516. doi:10.1038/s41577-020-0407-1
  • Shabrish S, Mittra I. Cytokine Storm as a Cellular Response to dsDNA Breaks: a New Proposal. Front Immunol. 2021;12:622738. doi:10.3389/fimmu.2021.622738
  • Lorente L, Martin MM, Gonzalez-Rivero AF, et al. DNA and RNA Oxidative Damage and Mortality of Patients With COVID-19. Am J Med Sci. 2021;361(5):585–590. doi:10.1016/j.amjms.2021.02.012
  • Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020;382(8):727–733. doi:10.1056/NEJMoa2001017
  • Osuchowski MF, Winkler MS, Skirecki T, et al. The COVID-19 puzzle: deciphering pathophysiology and phenotypes of a new disease entity. Lancet Respir Med. 2021;9(6):622–642. doi:10.1016/S2213-2600(21
  • Krokan HE, Bjoras M. Base excision repair. Cold Spring Harb Perspect Biol. 2013;5(4):a012583. doi:10.1101/cshperspect.a012583
  • Schwer B, Wei PC, Chang AN, et al. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A. 2016;113(8):2258–2263. doi:10.1073/pnas.1525564113
  • Puget N, Miller KM, Legube G. Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: roadblocks or Bona fide repair intermediates? DNA Repair (Amst). 2019;81:102661. doi:10.1016/j.dnarep.2019.102661
  • Scully R, Panday A, Elango R, Willis NA. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat Rev Mol Cell Biol. 2019;20(11):698–714. doi:10.1038/s41580-019-0152-0
  • Christensen EE, Jorgensen MJ, Nore KG, et al. Critical COVID-19 is associated with distinct leukocyte phenotypes and transcriptome patterns. J Intern Med. 2021;290(3):677–692. doi:10.1111/joim.13310
  • Barratt-Due A, Olsen IC, Nezvalova-Henriksen K, et al. Evaluation of the Effects of Remdesivir and Hydroxychloroquine on Viral Clearance in COVID-19: a Randomized Trial. Ann Intern Med. 2021;174(9):1261–1269. doi:10.7326/M21-0653
  • Olsen MB, Hildrestrand GA, Scheffler K, et al. NEIL3-Dependent Regulation of Cardiac Fibroblast Proliferation Prevents Myocardial Rupture. Cell Rep. 2017;18(1):82–92. doi:10.1016/j.celrep.2016.12.009
  • Wessel D, Flugge UI. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem. 1984;138(1):141–143. doi:10.1016/0003-2697(84)
  • MacLean B, Tomazela DM, Shulman N, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010;26(7):966–968. doi:10.1093/bioinformatics/btq054
  • Quiles-Jimenez A, Gregersen I, Mittelstedt Leal de Sousa M, et al. N6-methyladenosine in RNA of atherosclerotic plaques: an epitranscriptomic signature of human carotid atherosclerosis. Biochem Biophys Res Commun. 2020;533(4):631–637. doi:10.1016/j.bbrc.2020.09.057
  • Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890. doi:10.1093/bioinformatics/bty560
  • Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417–419. doi:10.1038/nmeth.4197
  • Frankish A, Diekhans M, Ferreira AM, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019;47(D1):D766–D773. doi:10.1093/nar/gky955
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi:10.1186/s13059-014-0550-8
  • Soneson C, Love MI, Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res. 2015;4:1521. doi:10.12688/f1000research.7563.2
  • Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523. doi:10.1038/s41467-019-09234-6
  • Wilk AJ, Lee MJ, Wei B, et al. Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. J Exp Med. 2021;218(8):548. doi:10.1084/jem.20210582
  • Galvan-Pena S, Leon J, Chowdhary K, et al. Profound Treg perturbations correlate with COVID-19 severity. Proc Natl Acad Sci U S A. 2021;118(37):865. doi:10.1073/pnas.2111315118
  • McClain MT, Constantine FJ, Henao R, et al. Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. Nat Commun. 2021;12(1):1079. doi:10.1038/s41467-021-21289-y
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425. doi:10.1016/j.cels.2015.12.004
  • Charlson ME, Pompei P, Ales KL, MacKenzie CR. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. J Chronic Dis. 1987;40(5):373–383. doi:10.1016/0021-9681(87)
  • Wang L, Balmat TJ, Antonia AL, et al. An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility. Genome Med. 2021;13(1):83. doi:10.1186/s13073-021-00904-z
  • Gorbunova V, Seluanov A, Mao Z, Hine C. Changes in DNA repair during aging. Nucleic Acids Res. 2007;35(22):7466–7474. doi:10.1093/nar/gkm756
  • Besaratinia A, Caliri AW, Tommasi S. Hydroxychloroquine induces oxidative DNA damage and mutation in mammalian cells. DNA Repair (Amst). 2021;106:103180. doi:10.1016/j.dnarep.2021.103180
  • Ntouros PA, Vlachogiannis NI, Pappa M, et al. Effective DNA damage response after acute but not chronic immune challenge: SARS-CoV-2 vaccine versus Systemic Lupus Erythematosus. Clin Immunol. 2021;229:108765. doi:10.1016/j.clim.2021.108765
  • Rai P, Sobol RW. Mechanisms of MTH1 inhibition-induced DNA strand breaks: the slippery slope from the oxidized nucleotide pool to genotoxic damage. DNA Repair (Amst). 2019;77:18–26. doi:10.1016/j.dnarep.2019.03.001
  • Aukrust P, Luna L, Ueland T, et al. Impaired base excision repair and accumulation of oxidative base lesions in CD4+ T cells of HIV-infected patients. Blood. 2005;105(12):4730–4735. doi:10.1182/blood-2004-11-4272
  • Ranneberg-Nilsen T, Bjoras M, Luna L, et al. Human cytomegalovirus infection modulates DNA base excision repair in fibroblast cells. Virology. 2006;348(2):389–397. doi:10.1016/j.virol.2006.01.001
  • Mihaljevic O, Zivancevic-Simonovic S, Cupurdija V, et al. DNA damage in peripheral blood lymphocytes of severely ill COVID-19 patients in relation to inflammatory markers and parameters of hemostasis. Mutagenesis. 2022. doi:10.1093/mutage/geac011
  • Ray Chaudhuri A, Nussenzweig A. The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat Rev Mol Cell Biol. 2017;18(10):610–621. doi:10.1038/nrm.2017.53
  • Lee S, Yu Y, Trimpert J, et al. Virus-induced senescence is driver and therapeutic target in COVID-19. Nature. 2021. doi:10.1038/s41586-021-03995-1
  • Lekva T, Ueland T, Halvorsen B, et al. Markers of cellular senescence is associated with persistent pulmonary pathology after COVID-19 infection. Infect Dis. 2022:1–6. doi:10.1080/23744235.2022.2113135
  • Murray JM, Carr AM. Integrating DNA damage repair with the cell cycle. Curr Opin Cell Biol. 2018;52:120–125. doi:10.1016/j.ceb.2018.03.006
  • Bednarski JJ, Sleckman BP. At the intersection of DNA damage and immune responses. Nat Rev Immunol. 2019;19(4):231–242. doi:10.1038/s41577-019-0135-6
  • Azzouz D, Khan MA, Palaniyar N. ROS induces NETosis by oxidizing DNA and initiating DNA repair. Cell Death Discov. 2021;7(1):113. doi:10.1038/s41420-021-00491-3
  • Panico P, Ostrosky-Wegman P, Salazar AM. The potential role of COVID-19 in the induction of DNA damage. Mutat Res Rev Mutat Res. 2022;789:108411. doi:10.1016/j.mrrev.2022.108411
  • Laphanuwat P, Jirawatnotai S. Immunomodulatory Roles of Cell Cycle Regulators. Front Cell Dev Biol. 2019;7:23. doi:10.3389/fcell.2019.00023
  • Troseid M, Dahl TB, Holter JC, et al. Persistent T-cell exhaustion in relation to prolonged pulmonary pathology and death after severe COVID-19: results from two Norwegian cohort studies. J Intern Med. 2022. doi:10.1111/joim.13549
  • Mah LJ, El-Osta A, Karagiannis TC. gammaH2AX: a sensitive molecular marker of DNA damage and repair. Leukemia. 2010;24(4):679–686. doi:10.1038/leu.2010.6