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Ghaderi-Zefrehi H, Rezaei M, Sadeghi F, Heiat M. Genetic polymorphisms in DNA repair genes and hepatocellular carcinoma risk. DNA Repair (Amst) 2021; 107:103196. [PMID: 34416543 DOI: 10.1016/j.dnarep.2021.103196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/23/2021] [Accepted: 07/26/2021] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent types of tumors worldwide. Its occurrence and development have been related to various risk factors, such as chronic infection with hepatitis B or C viruses and alcohol addiction. DNA repair systems play a critical role in maintaining the integrity of the genome. Defects in these systems have been related to increased susceptibility to various types of cancer. Multiple genetic polymorphisms in genes of DNA repair systems have been reported that may affect DNA repair capacity (DRC) and modulate risk to cancer. Several studies have been conducted to assess the role of polymorphisms of DNA repair genes on the HCC risk. Identifying these polymorphisms and their association with HCC risk may help to improve prevention and treatment strategies. In this study, we review investigations that evaluated the association between genetic polymorphisms of DNA repair genes and risk of HCC.
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Affiliation(s)
- Hossein Ghaderi-Zefrehi
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Franceschi S, Spugnesi L, Aretini P, Lessi F, Scarpitta R, Galli A, Congregati C, Caligo MA, Mazzanti CM. Whole-exome analysis of a Li-Fraumeni family trio with a novel TP53 PRD mutation and anticipation profile. Carcinogenesis 2017; 38:938-943. [PMID: 28911001 DOI: 10.1093/carcin/bgx069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Li-Fraumeni syndrome is a clinically heterogeneous familial cancer predisposition syndrome with autosomal-dominant inheritance caused by heterozygous germline mutations in the TP53 gene. We here analyze the genetic background of a family with a 4-year-proband presented with a Li-Fraumeni tumor. The mother developed breast cancer at age 37 and the proband died at age 8. We performed Sanger sequencing and whole-exome sequencing on peripheral blood DNA from proband and relatives. Data analysis selected only high-quality score and depth reads, rare variants and protein impact involving missense, non-sense, frameshift and splice disrupt mutations. Disease implicated variants and predicted deleterious alterations were also chosen. TP53 genetic testing revealed a never reported TP53 deletion arose as de novo mutation in the mother and inherited by the proband. We then performed whole-exome analysis of the trio to uncover inherited variants from the father that potentially worsen the already altered genetic background in the proband. No pathogenic variants were inherited in autosomal recessive, de novo dominant or X-linked recessive manner. Comparing proband and father exome we detected 25 predicted deleterious variants including a nonsense mutation in ERCC3. Those inherited mutations are possible candidate modifiers linked to TP53, explaining the proband accelerated tumor onset compared to the mother and providing a possible explanation of the genetic anticipation event in this Li-Fraumeni family.
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Affiliation(s)
| | - Laura Spugnesi
- Section of Genetic Oncology, Department of Laboratory Medicine, University Hospital of Pisa, Pisa 56100, Italy
| | - Paolo Aretini
- FPS - Fondazione Pisana per la Scienza, Pisa 56121, Italy
| | | | - Rosa Scarpitta
- Section of Genetic Oncology, Department of Laboratory Medicine, University Hospital of Pisa, Pisa 56100, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Pisa 56124, Italy
| | - Caterina Congregati
- Cytogenetics and Molecular Genetic Unit, University Hospital of Pisa, Pisa 56100, Italy
| | - Maria Adelaide Caligo
- UO Medical Genetics, Department of Laboratory Medicine, University Hospital of Pisa, Pisa 56100, Italy
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Baharoglu Z, Babosan A, Mazel D. Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase. Nucleic Acids Res 2013; 42:2366-79. [PMID: 24319148 PMCID: PMC3936754 DOI: 10.1093/nar/gkt1259] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.
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Affiliation(s)
- Zeynep Baharoglu
- Département Génomes et Génétique, Unité Plasticité du Génome Bactérien, Institut Pasteur, 75015 Paris, France and Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France
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Ruczinski I, Jorgensen TJ, Shugart YY, Schaad YB, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao W, Wheless L, Francis L, Alani RM, Strickland PT, Smith MW, Alberg AJ. A population-based study of DNA repair gene variants in relation to non-melanoma skin cancer as a marker of a cancer-prone phenotype. Carcinogenesis 2012; 33:1692-8. [PMID: 22581838 PMCID: PMC3514896 DOI: 10.1093/carcin/bgs170] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 11/13/2022] Open
Abstract
For unknown reasons, non-melanoma skin cancer (NMSC) is associated with increased risk of other malignancies. Focusing solely on DNA repair or DNA repair-related genes, this study tested the hypothesis that DNA repair gene variants contribute to the increased cancer risk associated with a personal history of NMSC. From the parent CLUE II cohort study, established in 1989 in Washington County, MD, the study consisted of a cancer-free control group (n 5 2296) compared with three mutually exclusive groups of cancer cases ascertained through 2007: (i) Other (non-NMSC) cancer only (n 5 2349); (ii) NMSC only (n 5 694) and (iii) NMSC plus other cancer (n 5 577). The frequency of minor alleles in 759 DNA repair gene single nucleotide polymorphisms (SNPs) was compared in these four groups. Comparing those with both NMSC and other cancer versus those with no cancer, 10 SNPs had allelic trend P-values <0.01. The two top-ranked SNPs were both within the thymine DNA glycosylase gene (TDG). One was a non-synonymous coding SNP (rs2888805) [per allele odds ratio (OR) 1.40, 95% confidence interval (CI) 1.16-1.70; P-value 5 0.0006] and the other was an intronic SNP in high linkage disequilibrium with rs2888805 (rs4135150). None of the associations had a P-value <6.6310(-5), the threshold for statistical significance after correcting for multiple comparisons. The results pinpoint DNA repair genes most likely to contribute to the NMSC cancer-prone phenotype. A promising lead is genetic variants in TDG, important not only in base excision repair but also in regulating the epigenome and gene expression, which may contribute to the NMSC-associated increase in overall cancer risk.
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Affiliation(s)
- Ingo Ruczinski
- Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- These authors contributed equally to this work
| | - Timothy J. Jorgensen
- Department of Radiation Medicine, Georgetown University School of MedicineWashington, DC, USA,
- These authors contributed equally to this work
| | - Yin Yao Shugart
- Division of Intramural Research Program, National Institute of Mental HealthBethesda, MD, USA
| | - Yvette Berthier Schaad
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
- Laboratory of Genomic Diversity, SAIC-Frederick, NCI-FrederickFrederick, MD
| | - Bailey Kessing
- Laboratory of Genomic Diversity, SAIC-Frederick, NCI-FrederickFrederick, MD
| | - Judith Hoffman-Bolton
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
- George W. Comstock Center for Public Health Research and PreventionWashington County, MD, USA,
| | | | - W.H.Linda Kao
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
| | - Lee Wheless
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South CarolinaCharleston, SC, USA,
| | - Lesley Francis
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South CarolinaCharleston, SC, USA,
| | - Rhoda M. Alani
- Department of Dermatology, Boston University School of MedicineBoston, MA, USA
| | - Paul T. Strickland
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
- Department of Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
| | - Michael W. Smith
- Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, Inc., NCI-FrederickFrederick, MD, USA
| | - Anthony J. Alberg
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South CarolinaCharleston, SC, USA,
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Gan H, Lin X, Zhang Z, Zhang W, Liao S, Wang L, Han C. piRNA profiling during specific stages of mouse spermatogenesis. RNA (NEW YORK, N.Y.) 2011; 17:1191-203. [PMID: 21602304 PMCID: PMC3138557 DOI: 10.1261/rna.2648411] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/01/2011] [Indexed: 05/19/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small RNAs abundantly expressed in animal gonads. piRNAs that map to retrotransposons are generated by a "ping-pong" amplification loop to suppress the activity of retrotransposons. However, the biogenesis and function of other categories of piRNAs have yet to be investigated. In this study, we first profiled the expression of small RNAs in type A spermatogonia, pachytene spermatocytes, and round spermatids by deep sequencing. We then focused on the computational analysis of the potential piRNAs generated in the present study as well as other published sets. piRNAs mapping to retrotransposons, mRNAs, and intergenic regions had different length distributions and were differentially regulated in spermatogenesis. piRNA-generating mRNAs (PRMRs), whose expression positively correlated with their piRNA products, constituted one-third of the protein-coding genes and were evolutionarily conserved and enriched with splicing isoforms and antisense transcripts. PRMRs with piRNAs preferentially mapped to CDSs and 3' UTRs partitioned into three clusters differentially expressed during spermatogenesis and enriched with unique sets of functional annotation terms related to housekeeping activities as well as spermatogenesis-specific processes. Intergenic piRNAs were divided into 2992 clusters probably representing novel transcriptional units that have not been reported. The transcripts of a large number of genes involved in spermatogenesis are the precursors of piRNAs, and these genes are intricately regulated by alternative splicing and antisense transcripts. piRNAs, whose regulatory role in gene expression awaits to be identified, are clearly products of a novel regulatory process that needs to be defined.
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Affiliation(s)
- Haiyun Gan
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiwen Lin
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Shangying Liao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Lixian Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunsheng Han
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Corresponding author.E-mail .
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Gopalakrishnan K, Low GKM, Ting APL, Srikanth P, Slijepcevic P, Hande MP. Hydrogen peroxide induced genomic instability in nucleotide excision repair-deficient lymphoblastoid cells. Genome Integr 2010; 1:16. [PMID: 21176161 PMCID: PMC3022891 DOI: 10.1186/2041-9414-1-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 12/22/2010] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Nucleotide Excision Repair (NER) pathway specialises in UV-induced DNA damage repair. Inherited defects in the NER can predispose individuals to Xeroderma Pigmentosum (XP). UV-induced DNA damage cannot account for the manifestation of XP in organ systems not directly exposed to sunlight. While the NER has recently been implicated in the repair of oxidative DNA lesions, it is not well characterised. Therefore we sought to investigate the role of NER factors Xeroderma Pigmentosum A (XPA), XPB and XPD in oxidative DNA damage-repair by subjecting lymphoblastoid cells from patients suffering from XP-A, XP-D and XP-B with Cockayne Syndrome to hydrogen peroxide (H2O2). RESULTS Loss of functional XPB or XPD but not XPA led to enhanced sensitivity towards H2O2-induced cell death. XP-deficient lymphoblastoid cells exhibited increased susceptibility to H2O2-induced DNA damage with XPD showing the highest susceptibility and lowest repair capacity. Furthermore, XPB- and XPD-deficient lymphoblastoid cells displayed enhanced DNA damage at the telomeres. XPA- and XPB-deficient lymphoblastoid cells also showed differential regulation of XPD following H2O2 treatment. CONCLUSIONS Taken together, our data implicate a role for the NER in H2O2-induced oxidative stress management and further corroborates that oxidative stress is a significant contributing factor in XP symptoms. Resistance of XPA-deficient lymphoblastoid cells to H2O2-induced cell death while harbouring DNA damage poses a potential cancer risk factor for XPA patients. Our data implicate XPB and XPD in the protection against oxidative stress-induced DNA damage and telomere shortening, and thus premature senescence.
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Affiliation(s)
- Kalpana Gopalakrishnan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Grace Kah Mun Low
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Aloysius Poh Leong Ting
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Prarthana Srikanth
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Predrag Slijepcevic
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University, Uxbridge UB8 3PH, UK
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
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