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Kumari R, Roy U, Desai S, Mondal AS, Nair RR, Nilavar N, Choudhary B, Raghavan SC. MicroRNA, miR-501 regulate the V(D)J recombination in B cells. Biochem J 2023; 480:2061-2077. [PMID: 38084601 DOI: 10.1042/bcj20230250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
The stringent regulation of RAGs (Recombination activating genes), the site-specific endonuclease responsible for V(D)J recombination, is important to prevent genomic rearrangements and chromosomal translocations in lymphoid cells. In the present study, we identify a microRNA, miR-501, which can regulate the expression of RAG1 in lymphoid cells. Overexpression of the pre-miRNA construct led to the generation of mature miRNAs and a concomitant reduction in RAG1 expression, whereas inhibition using anti-miRs resulted in its enhanced expression. The direct interaction of the 3'UTR of miR-501 with RAG1 was confirmed by the reporter assay. Importantly, overexpression of miRNAs led to inhibition of V(D)J recombination in B cells, revealing their impact on the physiological function of RAGs. Of interest is the inverse correlation observed for miR-501 with RAG1 in various leukemia patients and lymphoid cell lines, suggesting its possible use in cancer therapy. Thus, our results reveal the regulation of RAG1 by miR-501-3p in B cells and thus V(D)J recombination and its possible implications on immunoglobulin leukemogenesis.
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Affiliation(s)
- Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Arannya S Mondal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Rajshree R Nair
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Namrata Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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2
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Kumari N, Das K, Sharma S, Dahal S, Desai SS, Roy U, Sharma A, Manjunath M, Gopalakrishnan V, Retheesh ST, Javadekar SM, Choudhary B, Raghavan SC. Evaluation of potential role of R-loop and G-quadruplex DNA in the fragility of c-MYC during chromosomal translocation associated with Burkitt's lymphoma. J Biol Chem 2023; 299:105431. [PMID: 37926284 PMCID: PMC10704377 DOI: 10.1016/j.jbc.2023.105431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
t(8;14) translocation is the hallmark of Burkitt's lymphoma and results in c-MYC deregulation. During the translocation, c-MYC gene on chromosome 8 gets juxtaposed to the Ig switch regions on chromosome 14. Although the promoter of c-MYC has been investigated for its mechanism of fragility, little is known about other c-MYC breakpoint regions. We have analyzed the translocation break points at the exon 1/intron 1 of c-MYC locus from patients with Burkitt's lymphoma. Results showed that the breakpoint region, when present on a plasmid, could fold into an R-loop confirmation in a transcription-dependent manner. Sodium bisulfite modification assay revealed significant single-strandedness on chromosomal DNA of Burkitt's lymphoma cell line, Raji, and normal lymphocytes, revealing distinct R-loops covering up to 100 bp region. Besides, ChIP-DRIP analysis reveals that the R-loop antibody can bind to the breakpoint region. Further, we show the formation of stable parallel intramolecular G-quadruplex on non-template strand of the genome. Finally, incubation of purified AID in vitro or overexpression of AID within the cells led to enhanced mutation frequency at the c-MYC breakpoint region. Interestingly, anti-γH2AX can bind to DSBs generated at the c-MYC breakpoint region within the cells. The formation of R-loop and G-quadruplex was found to be mutually exclusive. Therefore, our results suggest that AID can bind to the single-stranded region of the R-loop and G4 DNA, leading to the deamination of cytosines to uracil and induction of DNA breaks in one of the DNA strands, leading to double-strand break, which could culminate in t(8;14) chromosomal translocation.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Kohal Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Anju Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Department of Zoology, St Joseph's College, Irinjalakuda, Kerala, India
| | - S T Retheesh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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3
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Kumari N, Antil H, Kumari S, Raghavan SC. Deficiency of ligase IV leads to reduced NHEJ, accumulation of DNA damage, and can sensitize cells to cancer therapeutics. Genomics 2023; 115:110731. [PMID: 37871849 DOI: 10.1016/j.ygeno.2023.110731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/14/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Ligase IV is a key enzyme involved during DNA double-strand breaks (DSBs) repair through nonhomologous end joining (NHEJ). However, in contrast to Ligase IV deficient mouse cells, which are embryonic lethal, Ligase IV deficient human cells, including pre-B cells, are viable. Using CRISPR-Cas9 mediated genome editing, we have generated six different LIG4 mutants in cervical cancer and normal kidney epithelial cell lines. While the LIG4 mutant cells showed a significant reduction in NHEJ, joining mediated through microhomology-mediated end joining (MMEJ) and homologous recombination (HR) were significantly high. The reduced NHEJ joining activity was restored by adding purified Ligase IV/XRCC4. Accumulation of DSBs and reduced cell viability were observed in LIG4 mutant cells. LIG4 mutant cells exhibited enhanced sensitivity towards DSB-inducing agents such as ionizing radiation (IR) and etoposide. More importantly, the LIG4 mutant of cervical cancer cells showed increased sensitivity towards FDA approved drugs such as Carboplatin, Cisplatin, Paclitaxel, Doxorubicin, and Bleomycin used for cervical cancer treatment. These drugs, in combination with IR showed enhanced cancer cell death in the background of LIG4 gene mutation. Thus, our study reveals that mutation in LIG4 results in compromised NHEJ, leading to sensitization of cervical cancer cells towards currently used cancer therapeutics.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Himanshu Antil
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Susmita Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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4
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Yusoff NA, Abd Hamid Z, Budin SB, Taib IS. Linking Benzene, in Utero Carcinogenicity and Fetal Hematopoietic Stem Cell Niches: A Mechanistic Review. Int J Mol Sci 2023; 24:ijms24076335. [PMID: 37047305 PMCID: PMC10094243 DOI: 10.3390/ijms24076335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Previous research reported that prolonged benzene exposure during in utero fetal development causes greater fetal abnormalities than in adult-stage exposure. This phenomenon increases the risk for disease development at the fetal stage, particularly carcinogenesis, which is mainly associated with hematological malignancies. Benzene has been reported to potentially act via multiple modes of action that target the hematopoietic stem cell (HSCs) niche, a complex microenvironment in which HSCs and multilineage hematopoietic stem and progenitor cells (HSPCs) reside. Oxidative stress, chromosomal aberration and epigenetic modification are among the known mechanisms mediating benzene-induced genetic and epigenetic modification in fetal stem cells leading to in utero carcinogenesis. Hence, it is crucial to monitor exposure to carcinogenic benzene via environmental, occupational or lifestyle factors among pregnant women. Benzene is a well-known cause of adult leukemia. However, proof of benzene involvement with childhood leukemia remains scarce despite previously reported research linking incidences of hematological disorders and maternal benzene exposure. Furthermore, accumulating evidence has shown that maternal benzene exposure is able to alter the developmental and functional properties of HSPCs, leading to hematological disorders in fetus and children. Since HSPCs are parental blood cells that regulate hematopoiesis during the fetal and adult stages, benzene exposure that targets HSPCs may induce damage to the population and trigger the development of hematological diseases. Therefore, the mechanism of in utero carcinogenicity by benzene in targeting fetal HSPCs is the primary focus of this review.
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Ray U, Gopinatha VK, Sharma S, Goyary L, Choudhary B, Mantelingu K, Rangappa KS, Raghavan SC. Identification and characterization of mercaptopyrimidine-based small molecules as inhibitors of nonhomologous DNA end joining. FEBS J 2023; 290:796-820. [PMID: 36048168 DOI: 10.1111/febs.16615] [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: 05/10/2022] [Revised: 07/21/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023]
Abstract
Mercaptopyrimidine derivatives are heterocyclic compounds with potent biological activities including antiproliferative, antibacterial, and anti-inflammatory properties. The present study describes the synthesis and characterization of several mercaptopyrimidine derivatives through condensation of 5,6-diamino-2-mercaptopyrimidin-4-ol with various heterocyclic and aromatic aldehydes. Previous studies have shown that SCR7, synthesized from 5,6-diamino-2-mercaptopyrimidin-4-ol, induced cytotoxicity by targeting cancer cells by primarily inhibiting DNA Ligase IV involved in nonhomologous end joining, one of the major DNA double-strand break repair pathways. Inhibition of DNA repair pathways is considered as an important strategy for cancer therapy. Due to limitations of SCR7 in terms of IC50 in cancer cells, here we have designed, synthesized, and characterized potent derivatives of SCR7 using 5,6-diamino-2-mercaptopyrimidin-4-ol as the starting material. Several synthesized imine compounds exhibited significant improvement in inhibition of end joining and cytotoxicity up to 27-fold lower concentrations than SCR7. Among these, two compounds, SCR116 and SCR132, showed increased cancer cell death in a Ligase IV-dependent manner. Treatment with the compounds also led to reduction in V(D)J recombination efficiency, cell cycle arrest at G2/M phase, accumulation of double-strand breaks inside cells, and improved anti-cancer potential when combined with γ-radiation and radiomimetic drugs. Thus, we describe novel inhibitors of NHEJ with higher efficacy and potential, which can be developed as cancer therapeutics.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Department of Studies in Chemistry, University of Mysore, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Laijau Goyary
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | | | - Kanchugarakoppal S Rangappa
- Department of Studies in Chemistry, University of Mysore, India.,Institution of Excellence, Vijnana Bhavana, University of Mysore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Sharma A, Kaninathan A, Dahal S, Kumari S, Choudhary B, Raghavan SC. Exposure to endosulfan can cause long term effects on general biology, including the reproductive system of mice. Front Genet 2022; 13:1047746. [PMID: 36506329 PMCID: PMC9729358 DOI: 10.3389/fgene.2022.1047746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
Increased infertility in humans is attributed to the increased use of environmental chemicals in the last several decades. Various studies have identified pesticides as one of the causes of reproductive toxicity. In a previous study, infertility was observed in male mice due to testicular atrophy and decreased sperm count when a sublethal dose of endosulfan (3 mg/kg) with a serum concentration of 23 μg/L was used. However, the serum concentration of endosulfan was much higher (up to 500 μg/L) in people living in endosulfan-exposed areas compared to the one used in the investigation. To mimic the situation in an experimental setup, mice were exposed to 5 mg/kg body weight of endosulfan, and reproductive toxicity and long-term impact on the general biology of animals were examined. HPLC analysis revealed a serum concentration of ∼50 μg/L of endosulfan after 24 h endosulfan exposure affected the normal physiology of mice. Histopathological studies suggest a persistent, severe effect on reproductive organs where vacuole degeneration of basal germinal epithelial cells and degradation of the interstitial matrix were observed in testes. Ovaries showed a reduction in the number of mature Graafian follicles. At the same time, mild vacuolation in liver hepatocytes and changes in the architecture of the lungs were observed. Endosulfan exposure induced DNA damage and mutations in germ cells at the molecular level. Interestingly, even after 8 months of endosulfan exposure, we observed increased DNA breaks in reproductive tissues. An increased DNA Ligase III expression was also observed, consistent with reported elevated levels of MMEJ-mediated repair. Further, we observed the generation of tumors in a few of the treated mice with time. Thus, the study not only explores the changes in the general biology of the mice upon exposure to endosulfan but also describes the molecular mechanism of its long-term effects.
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Affiliation(s)
- Anju Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Susmita Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India,*Correspondence: Sathees C. Raghavan,
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A novel KU70-mutant human leukemic cell line generated using CRISPR-Cas9 shows increased sensitivity to DSB inducing agents and reduced NHEJ activity. Biochim Biophys Acta Gen Subj 2022; 1866:130246. [PMID: 36162731 DOI: 10.1016/j.bbagen.2022.130246] [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: 06/27/2022] [Revised: 09/10/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022]
Abstract
KU70 (XRCC6 gene in humans) is one of the proteins in the KU70-KU80 heterodimer which is the first component recruited to broken DNA ends during DNA double-strand break repair through nonhomologous end joining (NHEJ). Previous studies have shown that Ku70 deficient mouse cells are defective in NHEJ and V(D)J recombination. In contrast, heterozygous KU70 mutant human cell lines did not show any significant change in cell viability and sensitivity towards ionizing radiation. In this study, we used CRISPR-Cas9 technique to generate a KU70 mutant (heterozygous) human pre-B leukemic cell line (N6-KU70-2-DG). We observed that the N6-KU70-2-DG cells showed a prominent reduction in the expression of both KU70 mRNA and protein. The mutant cells showed reduced cell viability, increased sensitivity to DSB inducing agents such as ionizing radiation (IR) and etoposide, and increased number of unrepaired DSBs after exposure to IR. In addition, the mutant cells showed a reduction in the NHEJ activity and increased rate of microhomology mediated joining (MMEJ) activity. KU70 mutant cells also revealed enhanced level of senescence markers following irradiation. Thus, we report a novel KU70-mutant leukemic cell line (heterozygous) with reduced NHEJ, which is sensitive to DNA damaging agents, unlike the previously reported other KU heterozygous mutant cell lines.
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8
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Holmes TH, Winn LM. DNA damage, DNA repair gene expression, and topoisomerase IIα activity in CD-1 mice following in utero benzene exposure. Toxicol Lett 2022; 368:47-55. [PMID: 35963423 DOI: 10.1016/j.toxlet.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/16/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022]
Abstract
Benzene is an environmental toxicant and known human carcinogen. Recent epidemiological studies show a relationship between exposure to benzene in pregnant women and increased incidence of childhood leukemias. Studies in murine models demonstrate a relationship between carcinogenicity and in utero benzene exposure which was sex dependent, thus the cellular mechanisms of benzene toxicity by sex require further studies. A hypothesized mechanism of benzene-induced in utero carcinogenicity is through increased DNA damage and reduced fetal DNA repair capacity. This includes the potential inhibition of topoisomerase IIα (topo IIα), in part, to generate double stranded DNA (dsDNA) breaks and induction of error-prone DNA repair. Using a mouse model of transplacental benzene carcinogenicity, gestational day (GD) 14 fetal livers were harvested 2, 6, and 24 h following maternal exposure to 200 mg/kg benzene and used to assess DNA damage, DNA repair gene expression and topo IIα activity. DNA damage, measured by levels of modified histone H2AX (γH2AX), is significantly increased in benzene exposed pups, with sex-dependent significance seen only in female pups. Comet assay results confirmed that benzene exposure in utero induces dsDNA damage in the GD14 fetal liver. Genes involved in DNA repair were assessed, and DNA repair gene expression changes were observed after 24 h in genes related to nucleotide excision repair, homologous recombination, and non-homologous end-joining. There were no significant differences in topo IIα activity in GD14 fetal livers at any timepoint, or between sexes. Overall, this study shows that 200 mg/kg benzene exposure induces dsDNA damage and alters fetal DNA repair gene expression in utero, without perturbing fetal topo IIα in CD-1 mice.
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Affiliation(s)
- Trent H Holmes
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Louise M Winn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada; School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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9
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Depletion of RNASEH2 Activity Leads to Accumulation of DNA Double-strand Breaks and Reduced Cellular Survivability in T Cell Leukemia. J Mol Biol 2022; 434:167617. [DOI: 10.1016/j.jmb.2022.167617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/15/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022]
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10
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Pugsley K, Scherer SW, Bellgrove MA, Hawi Z. Environmental exposures associated with elevated risk for autism spectrum disorder may augment the burden of deleterious de novo mutations among probands. Mol Psychiatry 2022; 27:710-730. [PMID: 34002022 PMCID: PMC8960415 DOI: 10.1038/s41380-021-01142-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022]
Abstract
Although the full aetiology of autism spectrum disorder (ASD) is unknown, familial and twin studies demonstrate high heritability of 60-90%, indicating a predominant role of genetics in the development of the disorder. The genetic architecture of ASD consists of a complex array of rare and common variants of all classes of genetic variation usually acting additively to augment individual risk. The relative contribution of heredity in ASD persists despite selective pressures against the classic autistic phenotype; a phenomenon thought to be explained, in part, by the incidence of spontaneous (or de novo) mutations. Notably, environmental exposures attributed as salient risk factors for ASD may play a causal role in the emergence of deleterious de novo variations, with several ASD-associated agents having significant mutagenic potential. To explore this hypothesis, this review article assesses published epidemiological data with evidence derived from assays of mutagenicity, both in vivo and in vitro, to determine the likely role such agents may play in augmenting the genetic liability in ASD. Broadly, these exposures were observed to elicit genomic alterations through one or a combination of: (1) direct interaction with genetic material; (2) impaired DNA repair; or (3) oxidative DNA damage. However, the direct contribution of these factors to the ASD phenotype cannot be determined without further analysis. The development of comprehensive prospective birth cohorts in combination with genome sequencing is essential to forming a causal, mechanistic account of de novo mutations in ASD that links exposure, genotypic alterations, and phenotypic consequences.
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Affiliation(s)
- Kealan Pugsley
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC Australia
| | - Stephen W. Scherer
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Mark A. Bellgrove
- grid.1002.30000 0004 1936 7857Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
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Kumari R, Roy U, Desai S, Nilavar NM, Van Nieuwenhuijze A, Paranjape A, Radha G, Bawa P, Srivastava M, Nambiar M, Balaji KN, Liston A, Choudhary B, Raghavan SC. MicroRNA miR-29c regulates RAG1 expression and modulates V(D)J recombination during B cell development. Cell Rep 2021; 36:109390. [PMID: 34260911 DOI: 10.1016/j.celrep.2021.109390] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 03/07/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Recombination activating genes (RAGs), consisting of RAG1 and RAG2, are stringently regulated lymphoid-specific genes, which initiate V(D)J recombination in developing lymphocytes. We report the regulation of RAG1 through a microRNA (miRNA), miR-29c, in a B cell stage-specific manner in mice and humans. Various lines of experimentation, including CRISPR-Cas9 genome editing, demonstrate the target specificity and direct interaction of miR-29c to RAG1. Modulation of miR-29c levels leads to change in V(D)J recombination efficiency in pre-B cells. The miR-29c expression is inversely proportional to RAG1 in a B cell developmental stage-specific manner, and miR-29c null mice exhibit a reduction in mature B cells. A negative correlation of miR-29c and RAG1 levels is also observed in leukemia patients, suggesting the potential use of miR-29c as a biomarker and a therapeutic target. Thus, our results reveal the role of miRNA in the regulation of RAG1 and its relevance in cancer.
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Affiliation(s)
- Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Namrata M Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Amita Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Gudapureddy Radha
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pushpinder Bawa
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Mrinal Srivastava
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR), Hyderabad 500046, India
| | - Mridula Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | | | - Adrian Liston
- Immunology Programme, Babraham Institute, Cambridge, United Kingdom
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India.
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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12
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Dahal S, Siddiqua H, Katapadi VK, Iyer D, Raghavan SC. Characterization of G4 DNA formation in mitochondrial DNA and their potential role in mitochondrial genome instability. FEBS J 2021; 289:163-182. [PMID: 34228888 DOI: 10.1111/febs.16113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022]
Abstract
Mitochondria possess their own genome which can be replicated independently of nuclear DNA. Mitochondria being the powerhouse of the cell produce reactive oxygen species, due to which the mitochondrial genome is frequently exposed to oxidative damage. Previous studies have demonstrated an association of mitochondrial deletions to aging and human disorders. Many of these deletions were present adjacent to non-B DNA structures. Thus, we investigate noncanonical structures associated with instability in mitochondrial genome. In silico studies revealed the presence of > 100 G-quadruplex motifs (of which 5 have the potential to form 3-plate G4 DNA), 23 inverted repeats, and 3 mirror repeats in the mitochondrial DNA (mtDNA). Further analysis revealed that among the deletion breakpoints from patients with mitochondrial disorders, majority are located at G4 DNA motifs. Interestingly, ~ 50% of the deletions were at base-pair positions 8271-8281, ~ 35% were due to deletion at 12362-12384, and ~ 12% due to deletion at 15516-15545. Formation of 3-plate G-quadruplex DNA structures at mitochondrial fragile regions was characterized using electromobility shift assay, circular dichroism (CD), and Taq polymerase stop assay. All 5 regions could fold into both intramolecular and intermolecular G-quadruplex structures in a KCl-dependent manner. G4 DNA formation was in parallel orientation, which was abolished in the presence of LiCl. The formation of G4 DNA affected both replication and transcription. Finally, immunolocalization of BG4 with MitoTracker confirmed the formation of G-quadruplex in mitochondrial genome. Thus, we characterize the formation of 5 different G-quadruplex structures in human mitochondrial region, which may contribute toward formation of mitochondrial deletions.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Humaira Siddiqua
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vijeth K Katapadi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Divyaanka Iyer
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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13
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Ghosh D, Raghavan SC. Nonhomologous end joining: new accessory factors fine tune the machinery. Trends Genet 2021; 37:582-599. [PMID: 33785198 DOI: 10.1016/j.tig.2021.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major DNA double-strand break (DSB) repair pathways in eukaryotes. The well-known critical proteins involved in NHEJ include Ku70/80, DNA-PKcs, Artemis, DNA pol λ/μ, DNA ligase IV-XRCC4, and XLF. Recent studies have added a number of new proteins to the NHEJ repertoire namely paralog of XRCC4 and XLF (PAXX), modulator of retroviral infection (MRI)/ cell cycle regulator of NHEJ (CYREN), transactivation response DNA-binding protein (TARDBP) of 43 kDa (TDP-43), intermediate filament family orphan (IFFO1), ERCC excision repair 6 like 2 (ERCC6L2), and RNase H2. PAXX acts as a stabilizing factor for the main NHEJ components. MRI/CYREN seems to play a dual role stimulating NHEJ in the G1 phase of the cell cycle, while inhibiting the pathway in the S and G2 phases. TDP-43 can recruit the ligase IV-XRCC4 complex to the DSB sites and stimulate ligation in neuronal cells. RNase H2 excises out the ribonucleotides inserted during repair by DNA polymerase μ/TdT. This review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ.
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Affiliation(s)
- Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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14
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Vindya K. Gopinatha, Ray U, Mantelingu K, Raghavan SC, Rangappa KS. Synthesis and Biological Evaluation of Theophylline Methyl 1,3,4-Oxadiazole as Anticancer Agents. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816202005009x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Znc2 module of RAG1 contributes towards structure-specific nuclease activity of RAGs. Biochem J 2020; 477:3567-3582. [PMID: 32886094 DOI: 10.1042/bcj20200361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
Recombination activating genes (RAGs), consisting of RAG1 and RAG2 have ability to perform spatially and temporally regulated DNA recombination in a sequence specific manner. Besides, RAGs also cleave at non-B DNA structures and are thought to contribute towards genomic rearrangements and cancer. The nonamer binding domain of RAG1 binds to the nonamer sequence of the signal sequence during V(D)J recombination. However, deletion of NBD did not affect RAG cleavage on non-B DNA structures. In the present study, we investigated the involvement of other RAG domains when RAGs act as a structure-specific nuclease. Studies using purified central domain (CD) and C-terminal domain (CTD) of the RAG1 showed that CD of RAG1 exhibited high affinity and specific binding to heteroduplex DNA, which was irrespective of the sequence of single-stranded DNA, unlike CTD which showed minimal binding. Furthermore, we show that ZnC2 of RAG1 is crucial for its binding to DNA structures as deletion and point mutations abrogated the binding of CD to heteroduplex DNA. Our results also provide evidence that unlike RAG cleavage on RSS, central domain of RAG1 is sufficient to cleave heteroduplex DNA harbouring pyrimidines, but not purines. Finally, we show that a point mutation in the DDE catalytic motif is sufficient to block the cleavage of CD on heteroduplex DNA. Therefore, in the present study we demonstrate that the while ZnC2 module in central domain of RAG1 is required for binding to non-B DNA structures, active site amino acids are important for RAGs to function as a structure-specific nuclease.
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16
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Abstract
Small molecule inhibitors targeting BCL2 are explored as anticancer therapeutics. Previously, we have reported identification and characterization of a novel BCL2 inhibitor, Disarib. Disarib induced cancer cell death in a BCL2 dependent manner in different cancer cell lines and mouse tumor models when it was administered intraperitoneally. In the present study, using two syngeneic mouse models, breast adenocarcinoma (EAC) and Dalton’s lymphoma (DLA), we show that oral administration of Disarib resulted in significant tumor regression in a concentration dependent manner. Importantly, tumor developed in both female and male mice were equally sensitive to Disarib. Further, we have investigated the toxicity of Disarib in normal cells. Single dose toxicity analysis of Disarib in male and female mice after oral administration revealed no significant variations compared to control group for parameters such as body weight, food and water consumption and behavioural changes which were analysed for the entire period of study. Haematological and histopathological analyses also did not show any significant difference from the control groups. Thus, our results reveal safe use of Disarib as a small molecule inhibitor and provide the foundation for investigation of other preclinical studies.
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17
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Ray U, Raul SK, Gopinatha VK, Ghosh D, Rangappa KS, Mantelingu K, Raghavan SC. Identification and characterization of novel SCR7-based small-molecule inhibitor of DNA end-joining, SCR130 and its relevance in cancer therapeutics. Mol Carcinog 2020; 59:618-628. [PMID: 32189406 DOI: 10.1002/mc.23186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
Abstract
Targeting DNA repair with small-molecule inhibitors is an attractive strategy for cancer therapy. Majority of DNA double-strand breaks in mammalian cells are repaired through nonhomologous end-joining (NHEJ). It has been shown that small-molecule inhibitors of NHEJ can block efficient repair inside cancer cells, leading to cell death. Previously, we have reported that SCR7, an inhibitor of NHEJ can induce tumor regression in mice. Later studies have shown that different forms of SCR7 can inhibit DNA end-joining in Ligase IV-dependent manner. Recently, we have derivatized SCR7 by introducing spiro ring into core structure. Here, we report the identification of a novel inhibitor of NHEJ, named SCR130 with 20-fold higher efficacy in inducing cytotoxicity in cancer cell lines. SCR130 inhibited DNA end-joining catalyzed by rat tissue extract. Specificity analysis revealed that while SCR130 was specific to Ligase IV, it showed minimal or no effect on Ligase III and Ligase I mediated joining. Importantly, SCR130 exhibited the least cytotoxicity in Ligase IV-null cell line as compared with wild type, confirming Ligase IV-specificity. Furthermore, we demonstrate that SCR130 can potentiate the effect of radiation in cancer cells when used in combination with γ-radiation. Various cellular assays in conjunction with Western blot analysis revealed that treatment with SCR130 led to loss of mitochondrial membrane potential leading to cell death by activating both intrinsic and extrinsic pathways of apoptosis. Thus, we describe a novel inhibitor of NHEJ with higher efficacy and may have the potential to be developed as cancer therapeutic.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sanjay Kumar Raul
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vindya K Gopinatha
- Department of Studies in Chemistry, ManasaganFindo-frgotri, University of Mysore, Mysuru, India
| | - Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Kempegowda Mantelingu
- Department of Studies in Chemistry, ManasaganFindo-frgotri, University of Mysore, Mysuru, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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18
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Holmes TH, Winn LM. DNA Damage and Perturbed Topoisomerase IIα as a Target of 1,4-Benzoquinone Toxicity in Murine Fetal Liver Cells. Toxicol Sci 2019; 171:339-346. [PMID: 31340051 DOI: 10.1093/toxsci/kfz158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/28/2019] [Accepted: 07/11/2019] [Indexed: 01/10/2023] Open
Abstract
Benzene is a ubiquitous environmental pollutant. Recent studies have shown a link between the development of childhood leukemias and maternal benzene exposure, suggesting that these leukemias may be initiated in utero. Benzene crosses the placental barrier however the mechanisms behind in utero benzene toxicity have not been well elucidated. This study is the first to show that the benzene metabolite, benzoquinone (BQ), perturbs fetal topoisomerase IIα (Topo IIα), an enzyme essential for DNA repair. Using cultured murine CD-1 fetal liver cells, this study shows that Topo IIα activity decreases following 24 hours of exposure to BQ (12.5 and 15.625 µM), with the 12.5 µM confirmed to disrupt the c-kit+Lin-Sca-1-Il7rα- population of cells in culture. Pre-treatment with the antioxidant, N-acetylcysteine did not prevent the inhibtion of Topo IIα by BQ. An increase in Topo IIα-DNA covalent adducts was detected following 24-hour exposures to BQ (12.5 and 50 µM). Interestingly, BQ (12.5 µM) exposure did not significantly increase levels of 4-hydroxynonenal (4-HNE), a marker of oxidative stress after 24 hours. However, increased levels of the double-stranded DNA break marker γH2AX were detected following 24 hours of BQ exposure, confirming that Topo IIα-induced breaks are increased in BQ treated cells. This study shows that fetal Topo IIα is perturbed by BQ and suggests that this protein is a target of benzene and may be implicated with in utero benzene toxicity.
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Affiliation(s)
- Trent H Holmes
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Louise M Winn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.,School of Environmental Studies, Queen's University, Kingston, Ontario, Canada
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19
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Gopalakrishnan V, Dahal S, Radha G, Sharma S, Raghavan SC, Choudhary B. Characterization of DNA double-strand break repair pathways in diffuse large B cell lymphoma. Mol Carcinog 2018; 58:219-233. [DOI: 10.1002/mc.22921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/18/2018] [Accepted: 10/07/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Vidya Gopalakrishnan
- Institute of Bioinformatics and Applied Biotechnology; Electronics City; Bangalore India
- Manipal Academy of Higher Education; Manipal Karnataka India
| | - Sumedha Dahal
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Gudapureddy Radha
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Shivangi Sharma
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology; Electronics City; Bangalore India
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20
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Vartak SV, Swarup HA, Gopalakrishnan V, Gopinatha VK, Ropars V, Nambiar M, John F, Kothanahally SKS, Kumari R, Kumari N, Ray U, Radha G, Dinesh D, Pandey M, Ananda H, Karki SS, Srivastava M, Charbonnier JB, Choudhary B, Mantelingu K, Raghavan SC. Autocyclized and oxidized forms of SCR7 induce cancer cell death by inhibiting nonhomologous DNA end joining in a Ligase IV dependent manner. FEBS J 2018; 285:3959-3976. [PMID: 30230716 DOI: 10.1111/febs.14661] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/23/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022]
Abstract
Nonhomologous DNA end joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals. Previously, we have described a small molecule inhibitor, SCR7, which can inhibit NHEJ in a Ligase IV-dependent manner. Administration of SCR7 within the cells resulted in the accumulation of DNA breaks, cell death, and inhibition of tumor growth in mice. In the present study, we report that parental SCR7, which is unstable, can be autocyclized into a stable form. Both parental SCR7 and cyclized SCR7 possess the same molecular weight (334.09) and molecular formula (C18 H14 N4 OS), whereas its oxidized form, SCR7-pyrazine, possesses a different molecular formula (C18 H12 N4 OS), molecular weight (332.07), and structure. While cyclized form of SCR7 showed robust inhibition of NHEJ in vitro, both forms exhibited efficient cytotoxicity. Cyclized and oxidized forms of SCR7 inhibited DNA end joining catalyzed by Ligase IV, whereas their impact was minimal on Ligase III, Ligase I, and T4 DNA Ligase-mediated joining. Importantly, both forms inhibited V(D)J recombination, although the effect was more pronounced for SCR7-cyclized. Both forms blocked NHEJ in a Ligase IV-dependent manner leading to the accumulation of DSBs within the cells. Although cytotoxicity due to SCR7-cyclized was Ligase IV specific, the pyrazine form exhibited nonspecific cytotoxicity at higher concentrations in Ligase IV-null cells. Finally, we demonstrate that both forms can potentiate the effect of radiation. Thus, we report that cyclized and oxidized forms of SCR7 can inhibit NHEJ in a Ligase IV-dependent manner, although SCR7-pyrazine is less specific to Ligase IV inside the cell.
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Affiliation(s)
- Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Vidya Gopalakrishnan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Univ Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Mridula Nambiar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Franklin John
- Department of Chemistry, Sacred Heart College, Kochi, India
| | | | - Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Gudapureddy Radha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Depina Dinesh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Monica Pandey
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Hanumappa Ananda
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Department of Chemistry, University of Mysore, India
| | - Subhas S Karki
- KLE Academy of Higher Education and Research, KLE College of Pharmacy, Rajajinagar, Bengaluru, India
| | - Mrinal Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Jean Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Univ Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | | | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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21
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Dahal S, Dubey S, Raghavan SC. Homologous recombination-mediated repair of DNA double-strand breaks operates in mammalian mitochondria. Cell Mol Life Sci 2018; 75:1641-1655. [PMID: 29116362 PMCID: PMC11105789 DOI: 10.1007/s00018-017-2702-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 10/23/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA is frequently exposed to oxidative damage, as compared to nuclear DNA. Previously, we have shown that while microhomology-mediated end joining can account for DNA deletions in mitochondria, classical nonhomologous DNA end joining, the predominant double-strand break (DSB) repair pathway in nucleus, is undetectable. In the present study, we investigated the presence of homologous recombination (HR) in mitochondria to maintain its genomic integrity. Biochemical studies revealed that HR-mediated repair of DSBs is more efficient in the mitochondria of testes as compared to that of brain, kidney and spleen. Interestingly, a significant increase in the efficiency of HR was observed when a DSB was introduced. Analyses of the clones suggest that most of the recombinants were generated through reciprocal exchange, while ~ 30% of recombinants were due to gene conversion in testicular extracts. Colocalization and immunoblotting studies showed the presence of RAD51 and MRN complex proteins in the mitochondria and immunodepletion of MRE11, RAD51 or NIBRIN suppressed the HR-mediated repair. Thus, our results reveal importance of homologous recombination in the maintenance of mitochondrial genome stability.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Shubham Dubey
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India.
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22
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Liu XL, Wu RY, Sun XF, Cheng SF, Zhang RQ, Zhang TY, Zhang XF, Zhao Y, Shen W, Li L. Mycotoxin zearalenone exposure impairs genomic stability of swine follicular granulosa cells in vitro. Int J Biol Sci 2018; 14:294-305. [PMID: 29559847 PMCID: PMC5859475 DOI: 10.7150/ijbs.23898] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/30/2017] [Indexed: 01/15/2023] Open
Abstract
Zearalenone (ZEA), a metabolite of Fusarium fungi, is commonly found on moldy grains. Because it can competitively combine to estrogen receptor to disrupt estrogenic signaling, it has been reported to have serious adverse effects on animal reproduction systems. In order to explore the genotoxic effects of ZEA exposure on ovarian somatic cells, porcine granulosa cells were exposed to 10 μM and 30 μM ZEA for 24 or 72 h in vitro. The results showed that ZEA exposure for 24 h remarkably reduced the proliferation of porcine granulosa cells in a dose-dependent manner as determined by MTT analysis and flow cytometry. Furthermore, exposure to ZEA for 72 h induced apoptosis, and RNA sequence analysis also revealed that the expression of apoptosis related genes were altered. RT-qPCR, immunofluorescence and western blot analysis further confirmed the expression of DNA damage and repair related genes (γ-H2AX, BRCA1, RAD51 and PRKDC) were increased in ZEA exposed granulosa cells. When the estrogen antagonist, tamoxifen, was added with ZEA in the culture medium, the DNA damage and repairment by ZEA returned to normal level. Collectively, these results illustrate that ZEA disrupts genome stability and inhibits growth of porcine granulosa cells via the estrogen receptors which may promote granulosa cell apoptosis when the DNA repair system is not enough to rescue this serious damage.
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Affiliation(s)
- Xue-Lian Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Rui-Ying Wu
- Center for Reproductive Medicine, Qingdao Women's and Children's Hospital, Qingdao University, Qingdao 266034, China
| | - Xiao-Feng Sun
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Shun-Feng Cheng
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.,College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Rui-Qian Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Tian-Yu Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Xi-Feng Zhang
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yong Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.,College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Shen
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.,Center for Reproductive Medicine, Qingdao Women's and Children's Hospital, Qingdao University, Qingdao 266034, China.,College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lan Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.,College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
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23
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Srivastava S, Dahal S, Naidu SJ, Anand D, Gopalakrishnan V, Kooloth Valappil R, Raghavan SC. DNA double-strand break repair in Penaeus monodon is predominantly dependent on homologous recombination. DNA Res 2017; 24:117-128. [PMID: 28431013 PMCID: PMC5397610 DOI: 10.1093/dnares/dsw059] [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: 08/08/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) are mostly repaired by nonhomologous end joining (NHEJ) and homologous recombination (HR) in higher eukaryotes. In contrast, HR-mediated DSB repair is the major double-strand break repair pathway in lower order organisms such as bacteria and yeast. Penaeus monodon, commonly known as black tiger shrimp, is one of the economically important crustaceans facing large-scale mortality due to exposure to infectious diseases. The animals can also get exposed to chemical mutagens under the culture conditions as well as in wild. Although DSB repair mechanisms have been described in mammals and some invertebrates, its mechanism is unknown in the shrimp species. In the present study, we show that HR-mediated DSB repair is the predominant mode of repair in P. monodon. Robust repair was observed at a temperature of 30 °C, when 2 µg of cell-free extract derived from hepatopancreas was used for the study. Although HR occurred through both reciprocal recombination and gene conversion, the latter was predominant when the bacterial colonies containing recombinants were evaluated. Unlike mammals, NHEJ-mediated DSB repair was undetectable in P. monodon. However, we could detect evidence for an alternative mode of NHEJ that uses microhomology, termed as microhomology-mediated end joining (MMEJ). Interestingly, unlike HR, MMEJ was predominant at lower temperatures. Therefore, the results suggest that, while HR is major DSB repair pathway in shrimp, MMEJ also plays a role in ensuring the continuity and stability of the genome.
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Affiliation(s)
- Shikha Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sharanya J Naidu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Deepika Anand
- ICAR-Central Institute of Fisheries Education, Mumbai 400 061, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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24
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Zimmerlin L, Park TS, Zambidis ET. Capturing Human Naïve Pluripotency in the Embryo and in the Dish. Stem Cells Dev 2017; 26:1141-1161. [PMID: 28537488 DOI: 10.1089/scd.2017.0055] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although human embryonic stem cells (hESCs) were first derived almost 20 years ago, it was only recently acknowledged that they share closer molecular and functional identity to postimplantation lineage-primed murine epiblast stem cells than to naïve preimplantation inner cell mass-derived mouse ESCs (mESCs). A myriad of transcriptional, epigenetic, biochemical, and metabolic attributes have now been described that distinguish naïve and primed pluripotent states in both rodents and humans. Conventional hESCs and human induced pluripotent stem cells (hiPSCs) appear to lack many of the defining hallmarks of naïve mESCs. These include important features of the naïve ground state murine epiblast, such as an open epigenetic architecture, reduced lineage-primed gene expression, and chimera and germline competence following injection into a recipient blastocyst-stage embryo. Several transgenic and chemical methods were recently reported that appear to revert conventional human PSCs to mESC-like ground states. However, it remains unclear if subtle deviations in global transcription, cell signaling dependencies, and extent of epigenetic/metabolic shifts in these various human naïve-reverted pluripotent states represent true functional differences or alternatively the existence of distinct human pluripotent states along a spectrum. In this study, we review the current understanding and developmental features of various human pluripotency-associated phenotypes and discuss potential biological mechanisms that may support stable maintenance of an authentic epiblast-like ground state of human pluripotency.
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Affiliation(s)
- Ludovic Zimmerlin
- 1 Institute for Cell Engineering, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , Baltimore, Maryland
| | - Tea Soon Park
- 1 Institute for Cell Engineering, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , Baltimore, Maryland
| | - Elias T Zambidis
- 1 Institute for Cell Engineering, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , Baltimore, Maryland
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25
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Vartak SV, Iyer D, Santhoshkumar T, Sharma S, Mishra A, Goldsmith G, Srivastava M, Srivastava S, Karki SS, Surolia A, Choudhary B, Raghavan SC. Novel BCL2 inhibitor, Disarib induces apoptosis by disruption of BCL2-BAK interaction. Biochem Pharmacol 2017; 131:16-28. [DOI: 10.1016/j.bcp.2017.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 02/16/2017] [Indexed: 11/28/2022]
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26
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Regulation of non-homologous end joining via post-translational modifications of components of the ligation step. Curr Genet 2016; 63:591-605. [PMID: 27915381 DOI: 10.1007/s00294-016-0670-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks are the most serious type of DNA damage and non-homologous end joining (NHEJ) is an important pathway for their repair. In Saccharomyces cerevisiae, three complexes mediate the canonical NHEJ pathway, Ku (Ku70/Ku80), MRX (Mre11/Rad50/Xrs2) and DNA ligase IV (Dnl4/Lif1). Mammalian NHEJ is more complex, primarily as a consequence of the fact that more factors are involved in the process, and also because higher chromatin organization and more complex regulatory networks exist in mammals. In addition, a stronger interconnection between the NHEJ and DNA damage response (DDR) pathways seems to occur in mammals compared to yeast. DDR employs multiple post-translational modifications (PTMs) of the target proteins and mutual crosstalk among them to ensure highly efficient down-stream effects. Checkpoint-mediated phosphorylation is the best understood PTM that regulates DDR, although recently SUMOylation has also been shown to be involved. Both phosphorylation and SUMOylation affect components of NHEJ. In this review, we discuss a role of these two PTMs in regulation of NHEJ via targeting the components of the ligation step.
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27
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Sebastian R, Raghavan SC. Induction of DNA damage and erroneous repair can explain genomic instability caused by endosulfan. Carcinogenesis 2016; 37:929-40. [PMID: 27492056 DOI: 10.1093/carcin/bgw081] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/30/2016] [Indexed: 12/15/2022] Open
Abstract
Endosulfan (ES) is an organochlorine pesticide, speculated to be associated with chromosomal abnormalities and diseases in humans. However, very little is known about the mechanism of its genotoxicity. Using in vivo, ex vivo and in vitro model systems, we show that exposure to ES induces reactive oxygen species (ROS) in a concentration and time-dependent manner. The generation of ROS results in DNA double-strand breaks either directly or in a replication-dependent manner, both in mice and human cells. Importantly, ES-induced DNA damage evokes DNA damage response, resulting in elevated levels of classical non-homologous DNA endjoining (NHEJ), the predominant double-strand break repair pathway in higher eukaryotes. Sequence analyses of NHEJ junctions revealed that ES treatment results in extensive processing of broken DNA, culminating in increased and long junctional deletions, thereby favoring erroneous repair. We also find that exposure to ES leads to significant increase in microhomology-mediated end joining (MMEJ), a LIGASE III-dependent alternative repair pathway. Therefore, we demonstrate that ES induces DNA damage and genomic instability, alters DNA damage response thereby promoting erroneous DNA repair.
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Affiliation(s)
- Robin Sebastian
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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Tadi SK, Sebastian R, Dahal S, Babu RK, Choudhary B, Raghavan SC. Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions. Mol Biol Cell 2015; 27:223-35. [PMID: 26609070 PMCID: PMC4713127 DOI: 10.1091/mbc.e15-05-0260] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 11/18/2015] [Indexed: 12/13/2022] Open
Abstract
Repair of double-strand breaks in mammalian mitochondria depends on microhomology-mediated end joining (MMEJ). Classical NHEJ is not detectable in mitochondria. DNA ligase III, but not ligase IV or ligase I, is involved in mitochondrial MMEJ. The protein machinery involved in miitochondrial MMEJ includes CtIP, FEN1, ligase III, MRE11, and PARP1. Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.
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Affiliation(s)
- Satish Kumar Tadi
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Robin Sebastian
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Ravi K Babu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560 100, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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Exposure to Endosulfan can result in male infertility due to testicular atrophy and reduced sperm count. Cell Death Discov 2015; 1:15020. [PMID: 27551453 PMCID: PMC4979443 DOI: 10.1038/cddiscovery.2015.20] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/11/2022] Open
Abstract
Endosulfan (ES) is a widely used organochlorine pesticide and is speculated to be detrimental to human health. However, very little is known about mechanism of its genotoxicity. Using mouse model system, we show that exposure to ES affected physiology and cellular architecture of organs and tissues. Among all organs, damage to testes was extensive and it resulted in death of different testicular-cell populations. We find that the damage in testes resulted in qualitative and quantitative defects during spermatogenesis in a time-dependent manner, increasing epididymal reactive oxygen species levels, affecting sperm chromatin integrity. This further culminated in reduced number of epididymal sperms and actively motile sperms. Finally, we show that ES exposure affected fertility in male but not in female mice. Therefore, we demonstrate that ES exerts pathophysiological changes in mice, induces testicular atrophy, affects spermatogenesis, reduces quantity and vigour of epididymal sperm and leads to infertility in males.
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Philbrook NA, Winn LM. Benzoquinone toxicity is not prevented by sulforaphane in CD-1 mouse fetal liver cells. J Appl Toxicol 2015; 36:1015-24. [DOI: 10.1002/jat.3251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/06/2015] [Accepted: 09/06/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Nicola A. Philbrook
- Department of Biomedical and Molecular Sciences, Graduate Program in Pharmacology and Toxicology; Queen's University; Kingston ON Canada K7L3N6
| | - Louise M. Winn
- School of Environmental Studies; Queen's University; Kingston ON Canada K7L3N6
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31
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Vartak SV, Raghavan SC. Inhibition of nonhomologous end joining to increase the specificity of CRISPR/Cas9 genome editing. FEBS J 2015; 282:4289-94. [PMID: 26290158 DOI: 10.1111/febs.13416] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/02/2015] [Accepted: 08/04/2015] [Indexed: 12/22/2022]
Abstract
DNA repair, one of the fundamental processes occurring in a cell, safeguards the genome and maintains its integrity. Among various DNA lesions, double-strand breaks are considered to be the most deleterious, as they can lead to potential loss of genetic information, if not repaired. Nonhomologous end joining (NHEJ) and homologous recombination are two major double-strand break repair pathways. SCR7, a DNA ligase IV inhibitor, was recently identified and characterized as a potential anticancer compound. Interestingly, SCR7 was shown to have several applications, owing to its unique property as an NHEJ inhibitor. Here, we focus on three main areas of research in which SCR7 is actively being used, and discuss one of the applications, i.e. genome editing via CRISPR/Cas, in detail. In the past year, different studies have shown that SCR7 significantly increases the efficiency of precise genome editing by inhibiting NHEJ, and favouring the error-free homologous recombination pathway, both in vitro and in vivo. Overall, we discuss the current applications of SCR7 to shed light on the unique property of the small molecule of having distinct applications in normal and cancer cells, when used at different cellular concentrations.
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Affiliation(s)
- Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Sharma S, Javadekar SM, Pandey M, Srivastava M, Kumari R, Raghavan SC. Homology and enzymatic requirements of microhomology-dependent alternative end joining. Cell Death Dis 2015; 6:e1697. [PMID: 25789972 PMCID: PMC4385936 DOI: 10.1038/cddis.2015.58] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 12/24/2014] [Accepted: 02/09/2015] [Indexed: 01/19/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major double-strand break (DSB) repair pathways in higher eukaryotes. Recently, it has been shown that alternative NHEJ (A-NHEJ) occurs in the absence of classical NHEJ and is implicated in chromosomal translocations leading to cancer. In the present study, we have developed a novel biochemical assay system utilizing DSBs flanked by varying lengths of microhomology to study microhomology-mediated alternative end joining (MMEJ). We show that MMEJ can operate in normal cells, when microhomology is present, irrespective of occurrence of robust classical NHEJ. Length of the microhomology determines the efficiency of MMEJ, 5 nt being obligatory. Using this biochemical approach, we show that products obtained are due to MMEJ, which is dependent on MRE11, NBS1, LIGASE III, XRCC1, FEN1 and PARP1. Thus, we define the enzymatic machinery and microhomology requirements of alternative NHEJ using a well-defined biochemical system.
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Affiliation(s)
- S Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - S M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - M Pandey
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - M Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - R Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - S C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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Ganesan S, Keating AF. Phosphoramide mustard exposure induces DNA adduct formation and the DNA damage repair response in rat ovarian granulosa cells. Toxicol Appl Pharmacol 2014; 282:252-8. [PMID: 25497287 DOI: 10.1016/j.taap.2014.11.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 11/15/2022]
Abstract
Phosphoramide mustard (PM), the ovotoxic metabolite of the anti-cancer agent cyclophosphamide (CPA), destroys rapidly dividing cells by forming NOR-G-OH, NOR-G and G-NOR-G adducts with DNA, potentially leading to DNA damage. A previous study demonstrated that PM induces ovarian DNA damage in rat ovaries. To investigate whether PM induces DNA adduct formation, DNA damage and induction of the DNA repair response, rat spontaneously immortalized granulosa cells (SIGCs) were treated with vehicle control (1% DMSO) or PM (3 or 6μM) for 24 or 48h. Cell viability was reduced (P<0.05) after 48h of exposure to 3 or 6μM PM. The NOR-G-OH DNA adduct was detected after 24h of 6μM PM exposure, while the more cytotoxic G-NOR-G DNA adduct was formed after 48h by exposure to both PM concentrations. Phosphorylated H2AX (γH2AX), a marker of DNA double stranded break occurrence, was also increased by PM exposure, coincident with DNA adduct formation. Additionally, induction of genes (Atm, Parp1, Prkdc, Xrcc6, and Brca1) and proteins (ATM, γH2AX, PARP-1, PRKDC, XRCC6, and BRCA1) involved in DNA repair were observed in both a time- and dose-dependent manner. These data support that PM induces DNA adduct formation in ovarian granulosa cells, induces DNA damage and elicits the ovarian DNA repair response.
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Affiliation(s)
- Shanthi Ganesan
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
| | - Aileen F Keating
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
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Ganesan S, Nteeba J, Keating AF. Enhanced susceptibility of ovaries from obese mice to 7,12-dimethylbenz[a]anthracene-induced DNA damage. Toxicol Appl Pharmacol 2014; 281:203-10. [PMID: 25448685 DOI: 10.1016/j.taap.2014.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/03/2014] [Accepted: 10/05/2014] [Indexed: 01/10/2023]
Abstract
7,12-Dimethylbenz[a]anthracene (DMBA) depletes ovarian follicles and induces DNA damage in extra-ovarian tissues, thus, we investigated ovarian DMBA-induced DNA damage. Additionally, since obesity is associated with increased offspring birth defect incidence, we hypothesized that a DMBA-induced DNA damage response (DDR) is compromised in ovaries from obese females. Wild type (lean) non agouti (a/a) and KK.Cg-Ay/J heterozygote (obese) mice were dosed with sesame oil or DMBA (1mg/kg; intraperitoneal injection) at 18weeks of age, for 14days. Total ovarian RNA and protein were isolated and abundance of Ataxia telangiectasia mutated (Atm), X-ray repair complementing defective repair in Chinese hamster cells 6 (Xrcc6), breast cancer type 1 (Brca1), Rad 51 homolog (Rad51), poly [ADP-ribose] polymerase 1 (Parp1) and protein kinase, DNA-activated, catalytic polypeptide (Prkdc) were quantified by RT-PCR or Western blot. Phosphorylated histone H2AX (γH2AX) level was determined by Western blotting. Obesity decreased (P<0.05) basal protein abundance of PRKDC and BRCA1 proteins but increased (P<0.05) γH2AX and PARP1 proteins. Ovarian ATM, XRCC6, PRKDC, RAD51 and PARP1 proteins were increased (P<0.05) by DMBA exposure in lean mice. A blunted DMBA-induced increase (P<0.05) in XRCC6, PRKDC, RAD51 and BRCA1 was observed in ovaries from obese mice, relative to lean counterparts. Taken together, DMBA exposure induced γH2AX as well as the ovarian DDR, supporting that DMBA causes ovarian DNA damage. Additionally, ovarian DDR was partially attenuated in obese females raising concern that obesity may be an additive factor during chemical-induced ovotoxicity.
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Affiliation(s)
- Shanthi Ganesan
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
| | - Jackson Nteeba
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
| | - Aileen F Keating
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
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Lamparter C, Winn LM. Tissue-specific effects of valproic acid on DNA repair genes and apoptosis in postimplantation mouse embryos. Toxicol Sci 2014; 141:59-67. [PMID: 24913804 PMCID: PMC4833099 DOI: 10.1093/toxsci/kfu105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/21/2014] [Indexed: 11/13/2022] Open
Abstract
Exposure to the anticonvulsant drug valproic acid (VPA) is associated with an increased risk of congenital malformations. Although the mechanisms contributing to its teratogenicity are poorly understood, VPA has been shown to induce DNA double strand breaks (DSB) and to increase homologous recombination in vitro. The objective of the present study was to determine whether in utero exposure to VPA alters the frequency of intrachromosomal recombination and the expression of several genes involved in DSB repair in pKZ1 mouse embryos. Pregnant pKZ1 transgenic mice (GD 9.0) were administered VPA (500 mg/kg s.c.) and embryos were extracted and microdissected into the head, heart, and trunk regions 1, 3, 6, and 24 h after injection. Quantitative PCR was used to measure the tissue-specific expression of lacZ, a surrogate measure of recombination, Xrcc4, Rad51, Brca1, and Brca2, with Western blotting used to quantify Rad51, cleaved caspase-3 and cleaved-PARP protein. Increased recombination was only observed in the embryonic head following 6-h VPA exposure. VPA had no effect on Xrcc4 expression. Rad51, Brca1, and Brca2 expression rapidly decreased in head and trunk tissues after 1-h VPA exposure, followed by a subsequent increase in all tissues, although it was generally attenuated in the head and not due to differences in endogenous levels. Cleaved caspase-3 and cleaved-PARP expression was increased in all tissues 3 h following VPA exposure. This study indicates that the tissue-specific expression of several genes involved in DSB repair is altered following exposure to VPA and may be contributing to increased apoptosis.
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Affiliation(s)
- Christina Lamparter
- Graduate Program in Pharmacology and Toxicology, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Louise M Winn
- Graduate Program in Pharmacology and Toxicology, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada School of Environmental Studies, Queen's University, Kingston, Ontario, Canada
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Abstract
DNA strand breaks arise continuously in cells and can lead to chromosome rearrangements and genome instability or cell death. The commonest DNA breaks are DNA single-strand breaks, which arise at a frequency of tens-of-thousands per cell each day and which can block the progression of RNA/DNA polymerases and disrupt gene transcription and genome duplication. If not rapidly repaired, SSBs can be converted into DNA double-strand breaks (DSBs) during genome duplication, eliciting a complex series of DNA damage responses that attempt to protect cells from irreversible replication fork collapse. DSBs are the most cytotoxic and clastogenic type of DNA breaks, and can also arise independently of DNA replication, albeit at a frequency several orders of magnitude lower than SSBs. Here, I discuss the evidence that DNA single- and double -strand break repair pathways, and cellular tolerance mechanisms for protecting replication forks during genome duplication, utilize signalling by protein ADP-ribosyltransferases to protect cells from the harmful impact of DNA strand breakage.
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Affiliation(s)
- K W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brigton BN1 9RQ, United Kingdom.
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Frit P, Barboule N, Yuan Y, Gomez D, Calsou P. Alternative end-joining pathway(s): bricolage at DNA breaks. DNA Repair (Amst) 2014; 17:81-97. [PMID: 24613763 DOI: 10.1016/j.dnarep.2014.02.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/01/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years.
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Affiliation(s)
- Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France.
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The role of microhomology in genomic structural variation. Trends Genet 2014; 30:85-94. [PMID: 24503142 DOI: 10.1016/j.tig.2014.01.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/03/2014] [Accepted: 01/05/2014] [Indexed: 02/06/2023]
Abstract
Genomic structural variation, which can be defined as differences in the copy number, orientation, or location of relatively large DNA segments, is not only crucial in evolution, but also gives rise to genomic disorders. Whereas the major mechanisms that generate structural variation have been well characterised, insights into additional mechanisms are emerging from the identification of short regions of DNA sequence homology, also known as microhomology, at chromosomal breakpoints. In addition, functional studies are elucidating the characteristics of microhomology-mediated pathways, which are mutagenic. Here, we describe the features and mechanistic models of microhomology-mediated events, discuss their physiological and pathological significance, and highlight recent advances in this rapidly evolving field of research.
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Ganesan S, Bhattacharya P, Keating AF. 7,12-Dimethylbenz[a]anthracene exposure induces the DNA repair response in neonatal rat ovaries. Toxicol Appl Pharmacol 2013; 272:690-6. [PMID: 23969067 DOI: 10.1016/j.taap.2013.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 11/29/2022]
Abstract
7,12-Dimethylbenz[a]anthracene (DMBA) destroys ovarian follicles at all stages of development. This study investigated DMBA-induced DNA double strand break (DSB) formation with subsequent activation of the ovarian DNA repair response in models of pre-antral or pre-ovulatory follicle loss. Postnatal day (PND) 4 Fisher 344 (F344) rat ovaries were cultured for 4 days followed by single exposures of vehicle control (1% DMSO) or DMBA (12.5 nM or 75 nM) and maintained in culture for 4 or 8 days. Alternately, PND4 F344 rat ovaries were exposed to 1 μM DMBA at the start of culture for 2 days. Total RNA or protein was isolated, followed by qPCR or Western blotting to quantify mRNA or protein level, respectively. γH2AX and phosphorylated ATM were localized and quantified using immunofluorescence staining. DMBA exposure increased caspase 3 and γH2AX protein. Additionally, DMBA (12.5 nM and 1 μM) increased levels of mRNA encoding Atm, Xrcc6, Brca1 and Rad51. In contrast, Parp1 mRNA was decreased on d4 and increased on d8 of DMBA exposure, while PARP1 protein increased after 8 days of DMBA exposure. Total ATM increased in a concentration-dependent temporal pattern (75 nM d4; 12.5 nM d8), while pATM was localized in large primary and secondary follicles and increased after 8 days of 75 nM DMBA exposure compared to both control and 12.5 nM DMBA. These findings support that, despite some concentration effects, DMBA induces ovarian DNA damage and that DNA repair mechanisms are induced as a potential mechanism to prevent follicle loss.
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Affiliation(s)
- Shanthi Ganesan
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
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Rodrigues PMG, Grigaravicius P, Remus M, Cavalheiro GR, Gomes AL, Martins MR, Frappart L, Reuss D, McKinnon PJ, von Deimling A, Martins RAP, Frappart PO. Nbn and atm cooperate in a tissue and developmental stage-specific manner to prevent double strand breaks and apoptosis in developing brain and eye. PLoS One 2013; 8:e69209. [PMID: 23935957 PMCID: PMC3728324 DOI: 10.1371/journal.pone.0069209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/06/2013] [Indexed: 01/30/2023] Open
Abstract
Nibrin (NBN or NBS1) and ATM are key factors for DNA Double Strand Break (DSB) signaling and repair. Mutations in NBN or ATM result in Nijmegen Breakage Syndrome and Ataxia telangiectasia. These syndromes share common features such as radiosensitivity, neurological developmental defects and cancer predisposition. However, the functional synergy of Nbn and Atm in different tissues and developmental stages is not yet understood. Here, we show in vivo consequences of conditional inactivation of both genes in neural stem/progenitor cells using Nestin-Cre mice. Genetic inactivation of Atm in the central nervous system of Nbn-deficient mice led to reduced life span and increased DSBs, resulting in increased apoptosis during neural development. Surprisingly, the increase of DSBs and apoptosis was found only in few tissues including cerebellum, ganglionic eminences and lens. In sharp contrast, we showed that apoptosis associated with Nbn deletion was prevented by simultaneous inactivation of Atm in developing retina. Therefore, we propose that Nbn and Atm collaborate to prevent DSB accumulation and apoptosis during development in a tissue- and developmental stage-specific manner.
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Affiliation(s)
- Paulo M. G. Rodrigues
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulius Grigaravicius
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Remus
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriel R. Cavalheiro
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anielle L. Gomes
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauricio R. Martins
- Programa de Pós Graduação em Biofísica, IBCCF, Universidade Federal do Rio de Janeiro, CCS, Rio de Janeiro, Brazil
| | - Lucien Frappart
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - David Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Peter J. McKinnon
- Department of Genetics, St.Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Rodrigo A. P. Martins
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (POF); (RAPM)
| | - Pierre-Olivier Frappart
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail: (POF); (RAPM)
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Chiruvella KK, Liang Z, Birkeland SR, Basrur V, Wilson TE. Saccharomyces cerevisiae DNA ligase IV supports imprecise end joining independently of its catalytic activity. PLoS Genet 2013; 9:e1003599. [PMID: 23825968 PMCID: PMC3694833 DOI: 10.1371/journal.pgen.1003599] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/16/2013] [Indexed: 12/22/2022] Open
Abstract
DNA ligase IV (Dnl4 in budding yeast) is a specialized ligase used in non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Although point and truncation mutations arise in the human ligase IV syndrome, the roles of Dnl4 in DSB repair have mainly been examined using gene deletions. Here, Dnl4 catalytic point mutants were generated that were severely defective in auto-adenylation in vitro and NHEJ activity in vivo, despite being hyper-recruited to DSBs and supporting wild-type levels of Lif1 interaction and assembly of a Ku- and Lif1-containing complex at DSBs. Interestingly, residual levels of especially imprecise NHEJ were markedly higher in a deletion-based assay with Dnl4 catalytic mutants than with a gene deletion strain, suggesting a role of DSB-bound Dnl4 in supporting a mode of NHEJ catalyzed by a different ligase. Similarly, next generation sequencing of repair joints in a distinct single-DSB assay showed that dnl4-K466A mutation conferred a significantly different imprecise joining profile than wild-type Dnl4 and that such repair was rarely observed in the absence of Dnl4. Enrichment of DNA ligase I (Cdc9 in yeast) at DSBs was observed in wild-type as well as dnl4 point mutant strains, with both Dnl4 and Cdc9 disappearing from DSBs upon 5' resection that was unimpeded by the presence of catalytically inactive Dnl4. These findings indicate that Dnl4 can promote mutagenic end joining independently of its catalytic activity, likely by a mechanism that involves Cdc9.
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Affiliation(s)
- Kishore K. Chiruvella
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Zhuobin Liang
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Ann Arbor, Michigan, United States of America
| | - Shanda R. Birkeland
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas E. Wilson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Chiruvella KK, Liang Z, Wilson TE. Repair of double-strand breaks by end joining. Cold Spring Harb Perspect Biol 2013; 5:a012757. [PMID: 23637284 DOI: 10.1101/cshperspect.a012757] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonhomologous end joining (NHEJ) refers to a set of genome maintenance pathways in which two DNA double-strand break (DSB) ends are (re)joined by apposition, processing, and ligation without the use of extended homology to guide repair. Canonical NHEJ (c-NHEJ) is a well-defined pathway with clear roles in protecting the integrity of chromosomes when DSBs arise. Recent advances have revealed much about the identity, structure, and function of c-NHEJ proteins, but many questions exist regarding their concerted action in the context of chromatin. Alternative NHEJ (alt-NHEJ) refers to more recently described mechanism(s) that repair DSBs in less-efficient backup reactions. There is great interest in defining alt-NHEJ more precisely, including its regulation relative to c-NHEJ, in light of evidence that alt-NHEJ can execute chromosome rearrangements. Progress toward these goals is reviewed.
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Somasagara RR, Hegde M, Chiruvella KK, Musini A, Choudhary B, Raghavan SC. Extracts of strawberry fruits induce intrinsic pathway of apoptosis in breast cancer cells and inhibits tumor progression in mice. PLoS One 2012; 7:e47021. [PMID: 23071702 PMCID: PMC3468438 DOI: 10.1371/journal.pone.0047021] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 09/07/2012] [Indexed: 01/25/2023] Open
Abstract
Background The consumption of berry fruits, including strawberries, has been suggested to have beneficial effects against oxidative stress mediated diseases. Berries contain multiple phenolic compounds and secondary metabolites that contribute to their biological properties. Methodology/Principal Findings Current study investigates the anticancer activity of the methanolic extract of strawberry (MESB) fruits in leukaemia (CEM) and breast cancer (T47D) cell lines ex vivo, and its cancer therapeutic and chemopreventive potential in mice models. Results of MTT, trypan blue and LDH assays suggested that MESB can induce cytotoxicity in cancer cells, irrespective of origin, in a concentration- and time-dependent manner. Treatment of mice bearing breast adenocarcinoma with MESB blocked the proliferation of tumor cells in a time-dependent manner and resulted in extended life span. Histological and immunohistochemical studies suggest that MESB treatment affected tumor cell proliferation by activating apoptosis and did not result in any side effects. Finally, we show that MESB can induce intrinsic pathway of apoptosis by activating p73 in breast cancer cells, when tumor suppressor gene p53 is mutated. Conclusions/Significance The present study reveals that strawberry fruits possess both cancer preventive and therapeutic values and we discuss the mechanism by which it is achieved.
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Affiliation(s)
| | - Mahesh Hegde
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Kishore K. Chiruvella
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Anjaneyulu Musini
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, Karnataka, India
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail:
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