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Zhang F, Zhang B, Cui T, Chen S, Zhang C, Wang Z, Liu X. The novel roles of RNA m6A modification in regulating the development, infection, and oxidative DNA damage repair of Phytophthora sojae. PLoS Pathog 2024; 20:e1012553. [PMID: 39312577 PMCID: PMC11449341 DOI: 10.1371/journal.ppat.1012553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 10/03/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024] Open
Abstract
N6-methyladenosine (m6A), a vital post-transcriptional regulator, is among the most prevalent RNA modifications in eukaryotes. Nevertheless, the biological functions of m6A in oomycetes remain poorly understood. Here, we showed that the PsMTA1 and PsMTA2 genes are orthologs of human METTL4, while the PsMET16 gene is an ortholog of human METTL16. These genes are implicated in m6A modification and play a critical role in the production of sporangia and oospores, the release of zoospores, and the virulence of Phytophthora sojae. In P. sojae, m6A modifications are predominantly enriched in the coding sequence and the 3' untranslated region. Notably, the PsMTA1 knockout mutant exhibited reduced virulence, attributed to impaired tolerance to host defense-generated ROS stress. Mechanistically, PsMTA1-mediated m6A modification positively regulates the mRNA lifespan of DNA damage response (DDR) genes in reaction to plant ROS stress during infection. Consequently, the mRNA abundance of the DDR gene PsRCC1 was reduced in the single m6A site mutant ΔRCC1/RCC1A2961C, resulting in compromised DNA damage repair and reduced ROS adaptation-associated virulence in P. sojae. Overall, these results indicate that m6A-mediated RNA metabolism is associated with the development and pathogenicity of P. sojae, underscoring the roles of epigenetic markers in the adaptive flexibility of Phytophthora during infection.
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Affiliation(s)
- Fan Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Borui Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Tongshan Cui
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanshan Chen
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Can Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhiwen Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xili Liu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
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2
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Di Giorgio E, Dalla E, Tolotto V, D’Este F, Paluvai H, Ranzino L, Brancolini C. HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair. Nucleic Acids Res 2024; 52:8218-8240. [PMID: 38874468 PMCID: PMC11317144 DOI: 10.1093/nar/gkae501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX. It also affects H2BK120ac levels, which are increased in DNA-damaged regions that accumulate during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Francesca D’Este
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Harikrishnareddy Paluvai
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
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3
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Sogari A, Rovera E, Grasso G, Mariella E, Reilly NM, Lamba S, Mauri G, Durinikova E, Vitiello PP, Lorenzato A, Avolio M, Piumatti E, Bonoldi E, Aquilano MC, Arena S, Sartore-Bianchi A, Siena S, Trusolino L, Donalisio M, Russo M, Di Nicolantonio F, Lembo D, Bardelli A. Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells. Cell Rep Med 2024; 5:101376. [PMID: 38228147 PMCID: PMC10897517 DOI: 10.1016/j.xcrm.2023.101376] [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: 04/16/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024]
Abstract
The bacterial genotoxin colibactin promotes colorectal cancer (CRC) tumorigenesis, but systematic assessment of its impact on DNA repair is lacking, and its effect on response to DNA-damaging chemotherapeutics is unknown. We find that CRC cell lines display differential response to colibactin on the basis of homologous recombination (HR) proficiency. Sensitivity to colibactin is induced by inhibition of ATM, which regulates DNA double-strand break repair, and blunted by HR reconstitution. Conversely, CRC cells chronically infected with colibactin develop a tolerant phenotype characterized by restored HR activity. Notably, sensitivity to colibactin correlates with response to irinotecan active metabolite SN38, in both cell lines and patient-derived organoids. Moreover, CRC cells that acquire colibactin tolerance develop cross-resistance to SN38, and a trend toward poorer response to irinotecan is observed in a retrospective cohort of CRCs harboring colibactin genomic island. Our results shed insight into colibactin activity and provide translational evidence on its chemoresistance-promoting role in CRC.
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Affiliation(s)
- Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Emanuele Rovera
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Gaia Grasso
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Elisa Mariella
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | | | - Simona Lamba
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Gianluca Mauri
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Pietro Paolo Vitiello
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Marco Avolio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Eleonora Piumatti
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Emanuela Bonoldi
- Department of Pathology, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Sabrina Arena
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Torino, 10060 Candiolo, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Division of Clinical Research and Innovation, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Torino, 10060 Candiolo, Italy
| | - Manuela Donalisio
- Department of Clinical and Biological Sciences, University of Torino, 10043 Orbassano, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Torino, 10060 Candiolo, Italy
| | - David Lembo
- Department of Clinical and Biological Sciences, University of Torino, 10043 Orbassano, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy.
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4
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Sobanski T, Suraweera A, Burgess JT, Richard I, Cheong CM, Dave K, Rose M, Adams MN, O'Byrne KJ, Richard DJ, Bolderson E. The fructose-bisphosphate, Aldolase A (ALDOA), facilitates DNA-PKcs and ATM kinase activity to regulate DNA double-strand break repair. Sci Rep 2023; 13:15171. [PMID: 37704669 PMCID: PMC10499815 DOI: 10.1038/s41598-023-41133-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Glucose metabolism and DNA repair are fundamental cellular processes frequently dysregulated in cancer. In this study, we define a direct role for the glycolytic Aldolase A (ALDOA) protein in DNA double-strand break (DSB) repair. ALDOA is a fructose biphosphate Aldolase that catalyses fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP), during glycolysis. Here, we show that upon DNA damage induced by ionising radiation (IR), ALDOA translocates from the cytoplasm into the nucleus, where it partially co-localises with the DNA DSB marker γ-H2AX. DNA damage was shown to be elevated in ALDOA-depleted cells prior to IR and following IR the damage was repaired more slowly. Consistent with this, cells depleted of ALDOA exhibited decreased DNA DSB repair via non-homologous end-joining and homologous recombination. In support of the defective repair observed in its absence, ALDOA was found to associate with the major DSB repair effector kinases, DNA-dependent Protein Kinase (DNA-PK) and Ataxia Telangiectasia Mutated (ATM) and their autophosphorylation was decreased when ALDOA was depleted. Together, these data establish a role for an essential metabolic protein, ALDOA in DNA DSB repair and suggests that targeting ALDOA may enable the concurrent targeting of cancer metabolism and DNA repair to induce tumour cell death.
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Affiliation(s)
- Thais Sobanski
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Amila Suraweera
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Joshua T Burgess
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Iain Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Chee Man Cheong
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Keyur Dave
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Maddison Rose
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Mark N Adams
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
| | - Kenneth J O'Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia
- Princess Alexandra Hospital, Ipswich Road, Woolloongabba, Brisbane, QLD, 4102, Australia
| | - Derek J Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia.
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Brisbane, Australia.
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5
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Liang S, Wang H, Tian H, Xu Z, Wu M, Hua D, Li C. The prognostic biological markers of immunotherapy for non-small cell lung cancer: current landscape and future perspective. Front Immunol 2023; 14:1249980. [PMID: 37753089 PMCID: PMC10518408 DOI: 10.3389/fimmu.2023.1249980] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
The emergence of immunotherapy, particularly programmed cell death 1 (PD-1) and programmed cell death ligand-1 (PD-L1) produced profound transformations for treating non-small cell lung cancer (NSCLC). Nevertheless, not all NSCLC patients can benefit from immunotherapy in clinical practice. In addition to limited response rates, exorbitant treatment costs, and the substantial threats involved with immune-related adverse events, the intricate interplay between long-term survival outcomes and early disease progression, including early immune hyperprogression, remains unclear. Consequently, there is an urgent imperative to identify robust predictive and prognostic biological markers, which not only possess the potential to accurately forecast the therapeutic efficacy of immunotherapy in NSCLC but also facilitate the identification of patient subgroups amenable to personalized treatment approaches. Furthermore, this advancement in patient stratification based on certain biological markers can also provide invaluable support for the management of immunotherapy in NSCLC patients. Hence, in this review, we comprehensively examine the current landscape of individual biological markers, including PD-L1 expression, tumor mutational burden, hematological biological markers, and gene mutations, while also exploring the potential of combined biological markers encompassing radiological and radiomic markers, as well as prediction models that have the potential to better predict responders to immunotherapy in NSCLC with an emphasis on some directions that warrant further investigation which can also deepen the understanding of clinicians and provide a reference for clinical practice.
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Affiliation(s)
- Shuai Liang
- Department of Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Hanyu Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Haixia Tian
- Department of Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Zhicheng Xu
- Department of Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Min Wu
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Dong Hua
- Department of Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Chengming Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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6
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Hu C, Nagaraj AB, Shimelis H, Montalban G, Lee KY, Huang H, Lumby CA, Na J, Susswein LR, Roberts ME, Marshall ML, Hiraki S, LaDuca H, Chao E, Yussuf A, Pesaran T, Neuhausen SL, Haiman CA, Kraft P, Lindstrom S, Palmer JR, Teras LR, Vachon CM, Yao S, Ong I, Nathanson KL, Weitzel JN, Boddicker N, Gnanaolivu R, Polley EC, Mer G, Cui G, Karam R, Richardson ME, Domchek SM, Yadav S, Hruska KS, Dolinsky J, Weroha SJ, Hart SN, Simard J, Masson JY, Pang YP, Couch FJ. Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C. Cancer Res 2023; 83:2557-2571. [PMID: 37253112 PMCID: PMC10390864 DOI: 10.1158/0008-5472.can-22-2319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/07/2022] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C-/- cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case-control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18-7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71-30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers. SIGNIFICANCE Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants.
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Affiliation(s)
| | | | | | - Gemma Montalban
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | | | | | | | - Jie Na
- Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | | | | | | | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lauren R. Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irene Ong
- University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques Simard
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Jean Yves Masson
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
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7
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Tan J, Wang W, Liu X, Xu J, Che Y, Liu Y, Hu J, Hu L, Li J, Zhou Q. C11orf54 promotes DNA repair via blocking CMA-mediated degradation of HIF1A. Commun Biol 2023; 6:606. [PMID: 37277441 DOI: 10.1038/s42003-023-04957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
C11orf54 is an ester hydrolase highly conserved across different species. C11orf54 has been identified as a biomarker protein of renal cancers, but its exact function remains poorly understood. Here we demonstrate that C11orf54 knockdown decreases cell proliferation and enhances cisplatin-induced DNA damage and apoptosis. On the one hand, loss of C11orf54 reduces Rad51 expression and nuclear accumulation, which results in suppression of homologous recombination repair. On the other hand, C11orf54 and HIF1A competitively interact with HSC70, knockdown of C11orf54 promotes HSC70 binding to HIF1A to target it for degradation via chaperone-mediated autophagy (CMA). C11orf54 knockdown-mediated HIF1A degradation reduces the transcription of ribonucleotide reductase regulatory subunit M2 (RRM2), which is a rate-limiting RNR enzyme for DNA synthesis and DNA repair by producing dNTPs. Supplement of dNTPs can partially rescue C11orf54 knockdown-mediated DNA damage and cell death. Furthermore, we find that Bafilomycin A1, an inhibitor of both macroautophagy and chaperone-mediated autophagy, shows similar rescue effects as dNTP treatment. In summary, we uncover a role of C11orf54 in regulating DNA damage and repair through CMA-mediated decreasing of HIF1A/RRM2 axis.
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Affiliation(s)
- Junyang Tan
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Wenjun Wang
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Xinjie Liu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Jinhong Xu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Yaping Che
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Yanyan Liu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Jiaqiao Hu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Liubing Hu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China
| | - Jianshuang Li
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China.
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China.
| | - Qinghua Zhou
- The Sixth Affiliated Hospital of Jinan University, Jinan University, 523573, Dongguan, Guangdong, China.
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, 510632, Guangzhou, Guangdong, China.
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8
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Sharma AK, Fitieh AM, Locke AJ, Ali JYH, Ismail IH. Quantification of protein enrichment at site-specific DNA double-strand breaks by chromatin immunoprecipitation in cultured human cells. STAR Protoc 2023; 4:101917. [PMID: 36520630 PMCID: PMC9758495 DOI: 10.1016/j.xpro.2022.101917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Here, we present a chromatin-immunoprecipitation-based protocol to quantify the recruitment of proteins adjacent to site-specific DNA double-strand breaks (DSBs), such as proteins involved in DSB repair. We describe steps to induce DSBs in U2OS osteosarcoma cells stably expressing the restriction endonucleases FokI or AsiSI. We then detail the procedures of chromatin isolation and immunoprecipitation, followed by protein elution and quantitative-PCR-based quantification of DNA. This protocol cannot be used on DSBs generated at random loci by DNA damaging agents. For complete details on the use and execution of this protocol, please refer to Fitieh et al. (2022).1.
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Affiliation(s)
- Ajit K Sharma
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Amira Mohammed Fitieh
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada; Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Andrew J Locke
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Jana Yasser Hafez Ali
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Ismail Hassan Ismail
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada; Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt.
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9
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Vergara X, Schep R, Medema RH, van Steensel B. From fluorescent foci to sequence: Illuminating DNA double strand break repair by high-throughput sequencing technologies. DNA Repair (Amst) 2022; 118:103388. [PMID: 36037787 DOI: 10.1016/j.dnarep.2022.103388] [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: 06/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
Technologies to study DNA double-strand break (DSB) repair have traditionally mostly relied on fluorescence read-outs, either by microscopy or flow cytometry. The advent of high throughput sequencing (HTS) has created fundamentally new opportunities to study the mechanisms underlying DSB repair. Here, we review the suite of HTS-based assays that are used to study three different aspects of DNA repair: detection of broken ends, protein recruitment and pathway usage. We highlight new opportunities that HTS technology offers towards a better understanding of the DSB repair process.
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Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, the Netherlands.
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10
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Halder S, Ranjha L, Taglialatela A, Ciccia A, Cejka P. Strand annealing and motor driven activities of SMARCAL1 and ZRANB3 are stimulated by RAD51 and the paralog complex. Nucleic Acids Res 2022; 50:8008-8022. [PMID: 35801922 PMCID: PMC9371921 DOI: 10.1093/nar/gkac583] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
SMARCAL1, ZRANB3 and HLTF are required for the remodeling of replication forks upon stress to promote genome stability. RAD51, along with the RAD51 paralog complex, were also found to have recombination-independent functions in fork reversal, yet the underlying mechanisms remained unclear. Using reconstituted reactions, we build upon previous data to show that SMARCAL1, ZRANB3 and HLTF have unequal biochemical capacities, explaining why they have non-redundant functions. SMARCAL1 uniquely anneals RPA-coated ssDNA, which depends on its direct interaction with RPA, but not on ATP. SMARCAL1, along with ZRANB3, but not HLTF efficiently employ ATPase driven translocase activity to rezip RPA-covered bubbled DNA, which was proposed to mimic elements of fork reversal. In contrast, ZRANB3 and HLTF but not SMARCAL1 are efficient in branch migration that occurs downstream in fork remodeling. We also show that low concentrations of RAD51 and the RAD51 paralog complex, RAD51B–RAD51C–RAD51D–XRCC2 (BCDX2), directly stimulate the motor-driven activities of SMARCAL1 and ZRANB3 but not HLTF, and the interplay is underpinned by physical interactions. Our data provide a possible mechanism explaining previous cellular experiments implicating RAD51 and BCDX2 in fork reversal.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
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11
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Al-Soodani AT, Wu X, Kelp NC, Brown AJ, Roberts SA, Her C. hMSH5 Regulates NHEJ and Averts Excessive Nucleotide Alterations at Repair Joints. Genes (Basel) 2022; 13:genes13040673. [PMID: 35456479 PMCID: PMC9026759 DOI: 10.3390/genes13040673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/05/2023] Open
Abstract
Inappropriate repair of DNA double-strand breaks (DSBs) leads to genomic instability, cell death, or malignant transformation. Cells minimize these detrimental effects by selectively activating suitable DSB repair pathways in accordance with their underlying cellular context. Here, we report that hMSH5 down-regulates NHEJ and restricts the extent of DSB end processing before rejoining, thereby reducing “excessive” deletions and insertions at repair joints. RNAi-mediated knockdown of hMSH5 led to large nucleotide deletions and longer insertions at the repair joints, while at the same time reducing the average length of microhomology (MH) at repair joints. Conversely, hMSH5 overexpression reduced end-joining activity and increased RPA foci formation (i.e., more stable ssDNA at DSB ends). Furthermore, silencing of hMSH5 delayed 53BP1 chromatin spreading, leading to increased end resection at DSB ends.
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12
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Banday S, Pandita RK, Mushtaq A, Bacolla A, Mir US, Singh DK, Jan S, Bhat KP, Hunt CR, Rao G, Charaka VK, Tainer JA, Pandita TK, Altaf M. Autism-Associated Vigilin Depletion Impairs DNA Damage Repair. Mol Cell Biol 2021; 41:e0008221. [PMID: 33941620 PMCID: PMC8224237 DOI: 10.1128/mcb.00082-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/17/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Vigilin (Vgl1) is essential for heterochromatin formation, chromosome segregation, and mRNA stability and is associated with autism spectrum disorders and cancer: vigilin, for example, can suppress proto-oncogene c-fms expression in breast cancer. Conserved from yeast to humans, vigilin is an RNA-binding protein with 14 tandemly arranged nonidentical hnRNP K-type homology (KH) domains. Here, we report that vigilin depletion increased cell sensitivity to cisplatin- or ionizing radiation (IR)-induced cell death and genomic instability due to defective DNA repair. Vigilin depletion delayed dephosphorylation of IR-induced γ-H2AX and elevated levels of residual 53BP1 and RIF1 foci, while reducing Rad51 and BRCA1 focus formation, DNA end resection, and double-strand break (DSB) repair. We show that vigilin interacts with the DNA damage response (DDR) proteins RAD51 and BRCA1, and vigilin depletion impairs their recruitment to DSB sites. Transient hydroxyurea (HU)-induced replicative stress in vigilin-depleted cells increased replication fork stalling and blocked restart of DNA synthesis. Furthermore, histone acetylation promoted vigilin recruitment to DSBs preferentially in the transcriptionally active genome. These findings uncover a novel vigilin role in DNA damage repair with implications for autism and cancer-related disorders.
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Affiliation(s)
- Shahid Banday
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Raj K. Pandita
- Houston Methodist Research Institute, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
| | - Arjamand Mushtaq
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Ulfat Syed Mir
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | | | - Sadaf Jan
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Krishna P. Bhat
- Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | | | - Ganesh Rao
- Baylor College of Medicine, Houston, Texas, USA
| | | | - John A. Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
- Department of Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Tej K. Pandita
- Houston Methodist Research Institute, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
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13
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Burgess JT, Cheong CM, Suraweera A, Sobanski T, Beard S, Dave K, Rose M, Boucher D, Croft LV, Adams MN, O'Byrne K, Richard DJ, Bolderson E. Barrier-to-autointegration-factor (Banf1) modulates DNA double-strand break repair pathway choice via regulation of DNA-dependent kinase (DNA-PK) activity. Nucleic Acids Res 2021; 49:3294-3307. [PMID: 33660778 PMCID: PMC8034644 DOI: 10.1093/nar/gkab110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/04/2021] [Accepted: 02/23/2021] [Indexed: 01/07/2023] Open
Abstract
DNA repair pathways are essential to maintain the integrity of the genome and prevent cell death and tumourigenesis. Here, we show that the Barrier-to-Autointegration Factor (Banf1) protein has a role in the repair of DNA double-strand breaks. Banf1 is characterized as a nuclear envelope protein and mutations in Banf1 are associated with the severe premature aging syndrome, Néstor–Guillermo Progeria Syndrome. We have previously shown that Banf1 directly regulates the activity of PARP1 in the repair of oxidative DNA lesions. Here, we show that Banf1 also has a role in modulating DNA double-strand break repair through regulation of the DNA-dependent Protein Kinase catalytic subunit, DNA-PKcs. Specifically, we demonstrate that Banf1 relocalizes from the nuclear envelope to sites of DNA double-strand breaks. We also show that Banf1 can bind to and directly inhibit the activity of DNA-PKcs. Supporting this, cellular depletion of Banf1 leads to an increase in non-homologous end-joining and a decrease in homologous recombination, which our data suggest is likely due to unrestrained DNA-PKcs activity. Overall, this study identifies how Banf1 regulates double-strand break repair pathway choice by modulating DNA-PKcs activity to control genome stability within the cell.
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Affiliation(s)
- Joshua T Burgess
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Chee Man Cheong
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Amila Suraweera
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Thais Sobanski
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Sam Beard
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Keyur Dave
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Maddison Rose
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Didier Boucher
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Laura V Croft
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Mark N Adams
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Kenneth O'Byrne
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia.,Princess Alexandra Hospital, Ipswich Road, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Derek J Richard
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Emma Bolderson
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
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14
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DNA double-strand break repair: Putting zinc fingers on the sore spot. Semin Cell Dev Biol 2021; 113:65-74. [DOI: 10.1016/j.semcdb.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
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15
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Tye S, Ronson GE, Morris JR. A fork in the road: Where homologous recombination and stalled replication fork protection part ways. Semin Cell Dev Biol 2021; 113:14-26. [PMID: 32653304 PMCID: PMC8082280 DOI: 10.1016/j.semcdb.2020.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
In response to replication hindrances, DNA replication forks frequently stall and are remodelled into a four-way junction. In such a structure the annealed nascent strand is thought to resemble a DNA double-strand break and remodelled forks are vulnerable to nuclease attack by MRE11 and DNA2. Proteins that promote the recruitment, loading and stabilisation of RAD51 onto single-stranded DNA for homology search and strand exchange in homologous recombination (HR) repair and inter-strand cross-link repair also act to set up RAD51-mediated protection of nascent DNA at stalled replication forks. However, despite the similarities of these pathways, several lines of evidence indicate that fork protection is not simply analogous to the RAD51 loading step of HR. Protection of stalled forks not only requires separate functions of a number of recombination proteins, but also utilises nucleases important for the resection steps of HR in alternative ways. Here we discuss how fork protection arises and how its differences with HR give insights into the differing contexts of these two pathways.
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Affiliation(s)
- Stephanie Tye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - George E Ronson
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK.
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16
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COMMD4 functions with the histone H2A-H2B dimer for the timely repair of DNA double-strand breaks. Commun Biol 2021; 4:484. [PMID: 33875784 PMCID: PMC8055684 DOI: 10.1038/s42003-021-01998-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genomic stability is critical for normal cellular function and its deregulation is a universal hallmark of cancer. Here we outline a previously undescribed role of COMMD4 in maintaining genomic stability, by regulation of chromatin remodelling at sites of DNA double-strand breaks. At break-sites, COMMD4 binds to and protects histone H2B from monoubiquitination by RNF20/RNF40. DNA damage-induced phosphorylation of the H2A-H2B heterodimer disrupts the dimer allowing COMMD4 to preferentially bind H2A. Displacement of COMMD4 from H2B allows RNF20/40 to monoubiquitinate H2B and for remodelling of the break-site. Consistent with this critical function, COMMD4-deficient cells show excessive elongation of remodelled chromatin and failure of both non-homologous-end-joining and homologous recombination. We present peptide-mapping and mutagenesis data for the potential molecular mechanisms governing COMMD4-mediated chromatin regulation at DNA double-strand breaks. Amila Suraweera et al. use a range of biochemical and in vitro cellular assays to examine the role of the COMMD4 in DNA repair. Their results suggest that COMMD4 interacts with the histone H2A-H2B during repair of double-stranded DNA breaks, thereby maintaining genomic stability by regulating chromatin structure.
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17
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Han T, Jing X, Bao J, Zhao L, Zhang A, Miao R, Guo H, Zhou B, Zhang S, Sun J, Shi J. H. pylori infection alters repair of DNA double-strand breaks via SNHG17. J Clin Invest 2021; 130:3901-3918. [PMID: 32538894 DOI: 10.1172/jci125581] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/14/2020] [Indexed: 12/15/2022] Open
Abstract
Chronic infections can lead to carcinogenesis through inflammation-related mechanisms. Chronic infection of the human gastric mucosa with Helicobacter pylori is a well-known risk factor for gastric cancer. However, the mechanisms underlying H. pylori-induced gastric carcinogenesis are incompletely defined. We aimed to screen and clarify the functions of long noncoding RNAs (lncRNAs) that are differentially expressed in H. pylori-related gastric cancer. We found that lncRNA SNHG17 was upregulated by H. pylori infection and markedly increased the levels of double-strand breaks (DSBs). SNHG17 overexpression correlated with poor overall survival in patients with gastric cancer. The recruitment of NONO by overabundant nuclear SNHG17, along with the role of cytoplasmic SNHG17 as a decoy for miR-3909, which regulates Rad51 expression, shifted the DSB repair balance from homologous recombination toward nonhomologous end joining. Notably, during chronic H. pylori infection, SNHG17 knockdown inhibited chromosomal aberrations. Our findings suggest that spatially independent deregulation of the SNHG17/NONO and SNHG17/miR-3909/RING1/Rad51 pathways upon H. pylori infection promotes tumorigenesis in gastric cancer by altering the DNA repair system, which is critical for the maintenance of genomic stability. Upregulation of SNHG17 by H. pylori infection might be an undefined link between cancer and inflammation.
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Affiliation(s)
- Taotao Han
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohui Jing
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiayu Bao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianmei Zhao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Research Center, Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Aidong Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Renling Miao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Guo
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoguo Zhou
- Department of General Surgery, First Affiliated Hospital of Harbin Medical University, Heilongjiang, China
| | - Shang Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiazeng Sun
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Juan Shi
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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18
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Turan V, Oktay K. BRCA-related ATM-mediated DNA double-strand break repair and ovarian aging. Hum Reprod Update 2020; 26:43-57. [PMID: 31822904 DOI: 10.1093/humupd/dmz043] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Oocyte aging has significant clinical consequences, and yet no treatment exists to address the age-related decline in oocyte quality. The lack of progress in the treatment of oocyte aging is due to the fact that the underlying molecular mechanisms are not sufficiently understood. BRCA1 and 2 are involved in homologous DNA recombination and play essential roles in ataxia telangiectasia mutated (ATM)-mediated DNA double-strand break (DSB) repair. A growing body of laboratory, translational and clinical evidence has emerged within the past decade indicating a role for BRCA function and ATM-mediated DNA DSB repair in ovarian aging. OBJECTIVE AND RATIONALE Although there are several competing or complementary theories, given the growing evidence tying BRCA function and ATM-mediated DNA DSB repair mechanisms in general to ovarian aging, we performed this review encompassing basic, translational and clinical work to assess the current state of knowledge on the topic. A clear understanding of the mechanisms underlying oocyte aging may result in targeted treatments to preserve ovarian reserve and improve oocyte quality. SEARCH METHODS We searched for published articles in the PubMed database containing key words, BRCA, BRCA1, BRCA2, Mutations, Fertility, Ovarian Reserve, Infertility, Mechanisms of Ovarian Aging, Oocyte or Oocyte DNA Repair, in the English-language literature until May 2019. We did not include abstracts or conference proceedings, with the exception of our own. OUTCOMES Laboratory studies provided robust and reproducible evidence that BRCA1 function and ATM-mediated DNA DSB repair, in general, weakens with age in oocytes of multiple species including human. In both women with BRCA mutations and BRCA-mutant mice, primordial follicle numbers are reduced and there is accelerated accumulation of DNA DSBs in oocytes. In general, women with BRCA1 mutations have lower ovarian reserves and experience earlier menopause. Laboratory evidence also supports critical role for BRCA1 and other ATM-mediated DNA DSB repair pathway members in meiotic function. When laboratory, translational and clinical evidence is considered together, BRCA-related ATM-mediated DNA DSB repair function emerges as a likely regulator of ovarian aging. Moreover, DNA damage and repair appear to be key features in chemotherapy-induced ovarian aging. WIDER IMPLICATIONS The existing data suggest that the BRCA-related ATM-mediated DNA repair pathway is a strong candidate to be a regulator of oocyte aging, and the age-related decline of this pathway likely impairs oocyte health. This knowledge may create an opportunity to develop targeted treatments to reverse or prevent physiological or chemotherapy-induced oocyte aging. On the immediate practical side, women with BRCA or similar mutations may need to be specially counselled for fertility preservation.
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Affiliation(s)
- Volkan Turan
- Department of Obstetrics and Gynecology, Uskudar University School of Medicine, Istanbul, Turkey.,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Kutluk Oktay
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
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19
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Saito Y, Kobayashi J, Kanemaki MT, Komatsu K. RIF1 controls replication initiation and homologous recombination repair in a radiation dose-dependent manner. J Cell Sci 2020; 133:jcs240036. [PMID: 32434870 PMCID: PMC7328141 DOI: 10.1242/jcs.240036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/29/2020] [Indexed: 01/13/2023] Open
Abstract
RIF1 controls both DNA replication timing and the DNA double-strand break (DSB) repair pathway to maintain genome integrity. However, it remains unclear how RIF1 links these two processes following exposure to ionizing radiation (IR). Here, we show that inhibition of homologous recombination repair (HRR) by RIF1 occurs in a dose-dependent manner and is controlled via DNA replication. RIF1 inhibits both DNA end resection and RAD51 accumulation after exposure to high doses of IR. Contrastingly, HRR inhibition by RIF1 is antagonized by BRCA1 after a low-dose IR exposure. At high IR doses, RIF1 suppresses replication initiation by dephosphorylating MCM helicase. Notably, the dephosphorylation of MCM helicase inhibits both DNA end resection and HRR, even without RIF1. Thus, our data show the importance of active DNA replication for HRR and suggest a common suppression mechanism for DNA replication and HRR at high IR doses, both of which are controlled by RIF1.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yuichiro Saito
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junya Kobayashi
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Kenshi Komatsu
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
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20
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Sato K, Brandsma I, van Rossum-Fikkert SE, Verkaik N, Oostra AB, Dorsman JC, van Gent DC, Knipscheer P, Kanaar R, Zelensky AN. HSF2BP negatively regulates homologous recombination in DNA interstrand crosslink repair. Nucleic Acids Res 2020; 48:2442-2456. [PMID: 31960047 PMCID: PMC7049687 DOI: 10.1093/nar/gkz1219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/06/2023] Open
Abstract
The tumor suppressor BRCA2 is essential for homologous recombination (HR), replication fork stability and DNA interstrand crosslink (ICL) repair in vertebrates. We show that ectopic production of HSF2BP, a BRCA2-interacting protein required for meiotic HR during mouse spermatogenesis, in non-germline human cells acutely sensitize them to ICL-inducing agents (mitomycin C and cisplatin) and PARP inhibitors, resulting in a phenotype characteristic of cells from Fanconi anemia (FA) patients. We biochemically recapitulate the suppression of ICL repair and establish that excess HSF2BP compromises HR by triggering the removal of BRCA2 from the ICL site and thereby preventing the loading of RAD51. This establishes ectopic expression of a wild-type meiotic protein in the absence of any other protein-coding mutations as a new mechanism that can lead to an FA-like cellular phenotype. Naturally occurring elevated production of HSF2BP in tumors may be a source of cancer-promoting genomic instability and also a targetable vulnerability.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Inger Brandsma
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Sari E van Rossum-Fikkert
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Nicole Verkaik
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anneke B Oostra
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Dik C van Gent
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
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21
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Palmer N, Kaldis P. Less-well known functions of cyclin/CDK complexes. Semin Cell Dev Biol 2020; 107:54-62. [PMID: 32386818 DOI: 10.1016/j.semcdb.2020.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinases (CDKs) are activated by cyclins, which play important roles in dictating the actions of CDK/cyclin complexes. Cyclin binding influences the substrate specificity of these complexes in addition to their susceptibility to inhibition or degradation. CDK/cyclin complexes are best known to promote cell cycle progression in the mitotic cell cycle but are also crucial for important cellular processes not strictly associated with cellular division. This chapter primarily explores the understudied topic of CDK/cyclin complex functionality during the DNA damage response. We detail how CDK/cyclin complexes perform dual roles both as targets of DNA damage checkpoint signaling as well as effectors of DNA repair. Additionally, we discuss the potential CDK-independent roles of cyclins in these processes and the impact of such roles in human diseases such as cancer. Our goal is to place the spotlight on these important functions of cyclins either acting as independent entities or within CDK/cyclin complexes which have attracted less attention in the past. We consider that this will be important for a more complete understanding of the intricate functions of cell cycle proteins in the DNA damage response.
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Affiliation(s)
- Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore; Department of Clinical Sciences, Lund University, Clinical Research Centre (CRC), Box 50332, SE-202 13, Malmö, Sweden.
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22
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Guerreiro IM, Barros-Silva D, Lopes P, Cantante M, Cunha AL, Lobo J, Antunes L, Rodrigues A, Soares M, Henrique R, Jerónimo C. RAD51Bme Levels as a Potential Predictive Biomarker for PD-1 Blockade Response in Non-Small Cell Lung Cancer. J Clin Med 2020; 9:jcm9041000. [PMID: 32252414 PMCID: PMC7230458 DOI: 10.3390/jcm9041000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Lung cancer (LC) cells frequently express high levels of programmed death-ligand 1 (PD-L1). Although these levels grossly correlate with the likelihood of response to specific checkpoint inhibitors, the response prediction is rather imperfect, and more accurate predictive biomarkers are mandatory. We examined the methylation profile of RAD51B (RAD51Bme) as a candidate predictive biomarker for anti-PD-1 therapy efficacy in non-small cell lung cancer (NSCLC), correlating with patients’ outcome. PD-L1 immunoexpression and RAD51Bme levels were analysed in NSCLC samples obtained from patients not treated with anti-PD-1 (Untreated Cohort (#1)) and patients treated with PD-1 blockade (Treated Cohort (#2)). Of a total of 127 patients assessed, 58.3% depicted PD-L1 positivity (PD-L1+). RAD51Bme levels were significantly associated with PD-L1 immunoexpression. Patients with PD-1 blockade clinical benefit disclosed higher RAD51Bme levels (p = 0.0390) and significantly lower risk of disease progression (HR 0.37; 95% CI: 0.15–0.88; p = 0.025). Combining RAD51Bme+ with PD-L1+ improved the sensitivity of the test to predict immunotherapy response. PD-L1+ was also associated with lower risk of death (HR 0.35; 95% CI: 0.15–0.81; p = 0.014). Thus, RAD51Bme levels might be combined with validated predictive biomarker PD-L1 immunostaining to select patients who will most likely experience clinical benefit from PD-1 blockade. The predictive value of RAD51Bme should be confirmed in prospective studies.
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Affiliation(s)
- Inês Maria Guerreiro
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
- Correspondence: (I.M.G.); (C.J.); Tel.: +351-225-084-000 (I.M.G.); Fax: +351-225-084-001 (I.M.G.)
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
| | - Paula Lopes
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ana Luísa Cunha
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Luís Antunes
- Cancer Epidemiology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
| | - Ana Rodrigues
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
| | - Marta Soares
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Correspondence: (I.M.G.); (C.J.); Tel.: +351-225-084-000 (I.M.G.); Fax: +351-225-084-001 (I.M.G.)
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23
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Hohmann T, Kessler J, Vordermark D, Dehghani F. Evaluation of machine learning models for automatic detection of DNA double strand breaks after irradiation using a γH2AX foci assay. PLoS One 2020; 15:e0229620. [PMID: 32101565 PMCID: PMC7043763 DOI: 10.1371/journal.pone.0229620] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
Ionizing radiation induces amongst other the most critical type of DNA damage: double-strand breaks (DSBs). Efficient repair of such damage is crucial for cell survival and genomic stability. The analysis of DSB associated foci assays is often performed manually or with automatic systems. Manual evaluation is time consuming and subjective, while most automatic approaches are prone to changes in experimental conditions or to image artefacts. Here, we examined multiple machine learning models, namely a multi-layer perceptron classifier (MLP), linear support vector machine classifier (SVM), complement naive bayes classifier (cNB) and random forest classifier (RF), to correctly classify γH2AX foci in manually labeled images containing multiple types of artefacts. All models yielded reasonable agreements to the manual rating on the training images (Matthews correlation coefficient >0.4). Afterwards, the best performing models were applied on images obtained under different experimental conditions. Thereby, the MLP model produced the best results with an F1 Score >0.9. As a consequence, we have demonstrated that the used approach is sufficient to mimic manual counting and is robust against image artefacts and changes in experimental conditions.
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Affiliation(s)
- Tim Hohmann
- Institute of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Germany
- * E-mail:
| | - Jacqueline Kessler
- Department of Radiotherapy, Martin Luther University Halle-Wittenberg, Germany
| | - Dirk Vordermark
- Department of Radiotherapy, Martin Luther University Halle-Wittenberg, Germany
| | - Faramarz Dehghani
- Institute of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Germany
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24
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Mohan M, Akula D, Dhillon A, Goyal A, Anindya R. Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase. Nucleic Acids Res 2019; 47:11729-11745. [PMID: 31642493 PMCID: PMC7145530 DOI: 10.1093/nar/gkz938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/31/2022] Open
Abstract
The integrity of our DNA is challenged daily by a variety of chemicals that cause DNA base alkylation. DNA alkylation repair is an essential cellular defence mechanism to prevent the cytotoxicity or mutagenesis from DNA alkylating chemicals. Human oxidative demethylase ALKBH3 is a central component of alkylation repair, especially from single-stranded DNA. However, the molecular mechanism of ALKBH3-mediated damage recognition and repair is less understood. We report that ALKBH3 has a direct protein-protein interaction with human RAD51 paralogue RAD51C. We also provide evidence that RAD51C-ALKBH3 interaction stimulates ALKBH3-mediated repair of methyl-adduct located within 3'-tailed DNA, which serves as a substrate for the RAD51 recombinase. We further show that the lack of RAD51C-ALKBH3 interaction affects ALKBH3 function in vitro and in vivo. Our data provide a molecular mechanism underlying upstream events of alkyl adduct recognition and repair by ALKBH3.
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Affiliation(s)
- Monisha Mohan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, India
| | - Deepa Akula
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, India
| | - Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Roy Anindya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, India
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25
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Li F, Sun Q, Liu K, Han H, Lin N, Cheng Z, Cai Y, Tian F, Mao Z, Tong T, Zhao W. The deubiquitinase OTUD5 regulates Ku80 stability and non-homologous end joining. Cell Mol Life Sci 2019; 76:3861-3873. [PMID: 30980112 PMCID: PMC11105630 DOI: 10.1007/s00018-019-03094-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 02/03/2023]
Abstract
The ability of cells to repair DNA double-strand breaks (DSBs) is important for maintaining genome stability and eliminating oncogenic DNA lesions. Two distinct and complementary pathways, non-homologous end joining (NHEJ) and homologous recombination (HR), are employed by mammalian cells to repair DNA DSBs. Each pathway is tightly controlled in response to increased DSBs. The Ku heterodimer has been shown to play a regulatory role in NHEJ repair. Ku80 ubiquitination contributes to the selection of a DSB repair pathway by causing the removal of Ku heterodimers from DSB sites. However, whether Ku80 deubiquitination also plays a role in regulating DSB repair is unknown. To address this question, we performed a comprehensive study of the deubiquitinase specific for Ku80, and our study showed that the deubiquitinase OTUD5 serves as an important regulator of NHEJ repair by increasing the stability of Ku80. Further studies revealed that OTUD5 depletion impaired NHEJ repair, and hence reduced overall DSB repair. Furthermore, OTUD5-depleted cells displayed excess end resection; as a result, HR repair was facilitated by OTUD5 depletion during the S/G2 phase. In summary, our study demonstrates that OTUD5 is a specific deubiquitinase for Ku80 and establishes OTUD5 as an important and positive regulator of NHEJ repair.
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Affiliation(s)
- Fangzhou Li
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Qianqian Sun
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Kun Liu
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Haichao Han
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Ning Lin
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab, Co. Ltd, Hangzhou Economic and Technological Development Area, Hangzhou, 310018, China
| | - Yueming Cai
- Rheumatic Immunology Department, Peking University Shenzhen Hospital, Shenzhen, 518035, China
| | - Feng Tian
- Department of Laboratory Animal Science, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Zebin Mao
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Tanjun Tong
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China
| | - Wenhui Zhao
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, 38 Xueyuan Road, Beijing, 100191, China.
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26
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Garcin EB, Gon S, Sullivan MR, Brunette GJ, Cian AD, Concordet JP, Giovannangeli C, Dirks WG, Eberth S, Bernstein KA, Prakash R, Jasin M, Modesti M. Differential Requirements for the RAD51 Paralogs in Genome Repair and Maintenance in Human Cells. PLoS Genet 2019; 15:e1008355. [PMID: 31584931 PMCID: PMC6795472 DOI: 10.1371/journal.pgen.1008355] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/16/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A cells. Underlining their importance for genomic stability, mutant cell lines display variable growth defects, impaired sister chromatid recombination, reduced levels of stable RAD51 nuclear foci, and hyper-sensitivity to mitomycin C and olaparib, with the weakest phenotypes observed in RAD51B-deficient cells. Altogether these observations underscore the contributions of RAD51 paralogs in diverse DNA repair processes, and demonstrate essential differences in different cell types. Finally, this study will provide useful reagents to analyze patient-derived mutations and to investigate mechanisms of chemotherapeutic resistance deployed by cancers.
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Affiliation(s)
- Edwige B. Garcin
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
| | - Stéphanie Gon
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
| | - Meghan R. Sullivan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Gregory J. Brunette
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Anne De Cian
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Jean-Paul Concordet
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Carine Giovannangeli
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Wilhelm G. Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kara A. Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Mauro Modesti
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
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Horikoshi N, Sharma D, Leonard F, Pandita RK, Charaka VK, Hambarde S, Horikoshi NT, Gaur Khaitan P, Chakraborty S, Cote J, Godin B, Hunt CR, Pandita TK. Pre-existing H4K16ac levels in euchromatin drive DNA repair by homologous recombination in S-phase. Commun Biol 2019; 2:253. [PMID: 31286070 PMCID: PMC6611875 DOI: 10.1038/s42003-019-0498-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/29/2019] [Indexed: 12/22/2022] Open
Abstract
The homologous recombination (HR) repair pathway maintains genetic integrity after DNA double-strand break (DSB) damage and is particularly crucial for maintaining fidelity of expressed genes. Histone H4 acetylation on lysine 16 (H4K16ac) is associated with transcription, but how pre-existing H4K16ac directly affects DSB repair is not known. To answer this question, we used CRISPR/Cas9 technology to introduce I-SceI sites, or repair pathway reporter cassettes, at defined locations within gene-rich (high H4K16ac/euchromatin) and gene-poor (low H4K16ac/heterochromatin) regions. The frequency of DSB repair by HR is higher in gene-rich regions. Interestingly, artificially targeting H4K16ac at specific locations using gRNA/dCas9-MOF increases HR frequency in euchromatin. Finally, inhibition/depletion of RNA polymerase II or Cockayne syndrome B protein leads to decreased recruitment of HR factors at DSBs. These results indicate that the pre-existing H4K16ac status at specific locations directly influences the repair of local DNA breaks, favoring HR in part through the transcription machinery.
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Affiliation(s)
- Nobuo Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
- Present Address: Department of Radiation Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Dharmendra Sharma
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Fransisca Leonard
- Department of Nanomedicine, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Raj K. Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Vijaya K. Charaka
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Shashank Hambarde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Nobuko T. Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Puja Gaur Khaitan
- Department of Surgery, The Houston Methodist Research Institute, Houston, TX 77030 USA
- Present Address: Department of Surgery, Medstar Washington Hospital Center, Washington, DC 20010 USA
| | - Sharmistha Chakraborty
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Jacques Cote
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Quebec City, QC G1V4G2 Canada
| | - Biana Godin
- Department of Nanomedicine, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Clayton R. Hunt
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Tej K. Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
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28
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Andreyeva EN, Ogienko AA, Dubatolova TD, Oshchepkova AL, Kozhevnikova EN, Ivankin AV, Pavlova GA, Kopyl SA, Pindyurin AV. A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism. BMC Genet 2019; 20:31. [PMID: 30885138 PMCID: PMC6421639 DOI: 10.1186/s12863-019-0726-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreover, our knowledge of the functions of the CNDP2 orthologs in well-established model organisms is scarce. In particular, the function of the D. melanogaster ortholog of CNDP2, encoded by the CG17337 gene (hereafter referred to as dCNDP2), is still unknown. Results This study was aimed at developing a set of genetic and molecular tools to study the roles of dCNDP2. We generated a dCNDP2 null mutation (hereafter ∆dCNDP2) using CRISPR/Cas9-mediated homologous recombination (HR) and found that the ∆dCNDP2 mutants are homozygous viable, morphologically normal and fertile. We also generated transgenic fly lines expressing eGFP-tagged and non-tagged dCNDP2 protein, all under the control of the UAS promoter, as well as polyclonal antibodies specific to dCNDP2. Using these tools, we demonstrate that only one of the two predicted dCNDP2 isoforms is expressed throughout the different tissues tested. dCNDP2 was detected in both the cytoplasm and the nucleus, and was found to be associated with multiple sites in the salivary gland polytene chromosomes. Conclusions The dCNDP2 gene is not essential for fly viability under standard laboratory conditions. The subcellular localization pattern of dCNDP2 suggests that this protein might have roles in both the cytoplasm and the nucleus. The genetic and molecular tools developed in this study will allow further functional characterization of the conserved CNDP2 protein using D. melanogaster as a model system. Electronic supplementary material The online version of this article (10.1186/s12863-019-0726-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Anna A Ogienko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Tatiana D Dubatolova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anastasiya L Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Elena N Kozhevnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anton V Ivankin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Gera A Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Sergei A Kopyl
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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29
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Chromatin control in double strand break repair. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019. [PMID: 30798938 DOI: 10.1016/bs.apcsb.2018.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
DNA double strand breaks (DSB) are the most deleterious type of damage inflicted on DNA by various environmental factors and as consequences of normal cellular metabolism. The multistep nature of DSB repair and the need to assemble large protein complexes at repair sites necessitate multiple chromatin changes there. This review focuses on the key findings of how chromatin regulators exert temporal and spatial control on DSB repair. These mechanisms coordinate repair with cell cycle progression, lead to DSB repair pathway choice, provide accessibility of repair machinery to damaged sites and move the lesions to nuclear environments permissive for repair.
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30
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Abstract
XRCC2 is one of five somatic RAD51 paralogs, all of which have Walker A and B ATPase motifs. Each of the paralogs, including XRCC2, has a function in DNA double-strand break repair by homologous recombination (HR). However, their individual roles are not as well understood as that of RAD51 itself. The XRCC2 protein forms a complex (BCDX2) with three other RAD51 paralogs, RAD51B, RAD51C and RAD51D. It is believed that the BCDX2 complex mediates HR downstream of BRCA2 but upstream of RAD51, as XRCC2 is involved in the assembly of RAD51 into DNA damage foci. XRCC2 can bind DNA and, along with RAD51D, can promote homologous pairing in vitro. Consistent with its role in HR, XRCC2-deficient cells have increased levels of spontaneous chromosome instability, and exhibit hypersensitivity to DNA interstrand crosslinking agents such as mitomycin C and cisplatin as well as ionizing radiation, alkylating agents and aldehydes. XRCC2 also functions in promoting DNA replication and chromosome segregation. Biallelic mutation of XRCC2 (FANCU) causes the FA-U subtype of FA, while heterozygosity for deleterious mutations in XRCC2 may be associated with an increased breast cancer risk. XRCC2 appears to function 'downstream' in the FA pathway, since it is not required for FANCD2 monoubiquitination, which is the central step in the FA pathway. Clinically, the only known FA-U patient in the world exhibits severe congenital abnormalities, but had not developed, by seven years of age, the bone marrow failure and cancer that are often seen in patients from other FA complementation groups.
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Affiliation(s)
- Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA; (PRA); Department of Pediatrics III, University Children's Hospital Essen, University Duisburg-Essen, Essen Germany; (HH)
| | - Helmut Hanenberg
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA; (PRA); Department of Pediatrics III, University Children's Hospital Essen, University Duisburg-Essen, Essen Germany; (HH)
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31
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Fu Q, Wang J, Huang T. The effect of hyperthermia on the DNA damage response induced by γ-rays, as determined through in situ cell tracking. JOURNAL OF RADIATION RESEARCH 2018; 59:577-582. [PMID: 30085098 PMCID: PMC6151638 DOI: 10.1093/jrr/rry057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Hyperthermia (HT) acts as a cancer treatment by direct cell killing, radiosensitization, and promotion of tumor reoxygenation. The sensor proteins of the DNA damage response (DDR) are the direct targets of HT. However, the spatiotemporal properties of sensor proteins under HT are still unclear. Therefore, investigating the impact of HT on sensor proteins is of great importance. In the present study, the human fibrosarcoma cell line HT1080 stably transfected with 53BP1-GFP [the DDR protein 53BP1 fused to green fluorescent protein (GFP)] was used to investigate the real-time cellular response to DNA double-strand breaks (DSBs) induced by γ-rays. Using live-cell imaging combined with HT treatment, the spatiotemporal properties of the 53BP1 protein were directly monitored and quantitatively studied. We found that HT could delay and decrease the formation of 53BP1 ionizing radiation-induced foci (IRIF). Moreover, through the in situ tracking of individual IRIF, it was found that HT resulted in more unrepaired IRIF over the period of observation compared with IR alone. Additionally, the unrepaired IRIF had a larger area, higher intensity, and slower repair rate. Indeed, almost every cell treated with HT had unrepaired IRIF, and the majority of these IRIF increased in area individually, while the rest increased in area by the merging of adjacent IRIF. In summary, our study demonstrated that HT could perturb the primary event in the DDR induced by IR, and this may have important implications for cancer treatment and heat radiosensitization.
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Affiliation(s)
- Qibin Fu
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Tang Jia Wan, Zhuhai, P. R. China
| | - Jing Wang
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing, P. R. China
| | - Tuchen Huang
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Tang Jia Wan, Zhuhai, P. R. China
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32
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Wang L, Ma J, Yang B, Jing F, Hu Y. XRCC2 Polymorphisms and Environmental Factors Predict High Risk of Colorectal Cancer. Med Sci Monit 2018; 24:2858-2863. [PMID: 29748531 PMCID: PMC5961417 DOI: 10.12659/msm.904935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background This case-control study aimed to analyze the association of XRCC2 polymorphisms (rs3218408 and rs3218384) with colorectal cancer (CRC) risk. The interaction of XRCC2 polymorphisms with environmental factors was investigated as well. Material/Methods We enrolled 147 CRC patients and 114 healthy individuals into the study. Polymerase chain reaction (PCR)-sequencing method was performed to detect rs3218408 and rs3218384 polymorphisms. Hardy-Weinberg equilibrium (HWE) was checked in the control group. Odds ratio (OR) with 95% confidence interval (CI) represented the risk of CRC. Cross-table method was used in analyzing the interaction effects. Results Compared to the control group, the frequency of smokers was much higher in the case group (P<0.001). A similar result was observed in drinkers (55.8% vs. 40.4%, P=0.013). Dietary habits of all subjects were investigated as well, showing that CRC patients ate fewer vegetables than did healthy controls (P<0.001). In the analysis of polymorphisms, rs3218408 appeared to be an independent risk factor of CRC (GG: OR=2.048, 95%CI=1.032–4.061; G allele: OR=1.445, 95%CI=1.019–2.049). There were 68 (76.4%) C allele carriers (rs3218384) among smokers, which was higher than the number of G allele carriers (P<0.001). A similar outcome was observed for alcohol drinkers (P=0.048), which suggests a relationship of rs3218384 with smoking and drinking. Further analysis indicated that interaction of rs3218384 with smoking increased the risk of CRC (GG and smoking: OR=3.250, 95%CI=1.235–8.556; GC+CC and smoking: OR=2.167, 95%CI=1.175–3.996). Conclusions We found that rs3218408 was related with increased risk of CRC, and the interaction of rs3218384 with smoking increased the risk of CRC.
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Affiliation(s)
- Lijie Wang
- Department of Oncology, Chinese PLA General Hospital, Beijing, China (mainland)
| | - Junxun Ma
- Department of Oncology, Chinese PLA General Hospital, Beijing, China (mainland)
| | - Bo Yang
- Department of Oncology, Chinese PLA General Hospital, Beijing, China (mainland)
| | - Fangfang Jing
- Department of Oncology, Chinese PLA General Hospital, Beijing, China (mainland)
| | - Yi Hu
- Department of Oncology, Chinese PLA General Hospital, Beijing, China (mainland)
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Chakraborty S, Pandita RK, Hambarde S, Mattoo AR, Charaka V, Ahmed KM, Iyer SP, Hunt CR, Pandita TK. SMARCAD1 Phosphorylation and Ubiquitination Are Required for Resection during DNA Double-Strand Break Repair. iScience 2018; 2:123-135. [PMID: 29888761 PMCID: PMC5993204 DOI: 10.1016/j.isci.2018.03.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/16/2018] [Accepted: 02/28/2018] [Indexed: 02/08/2023] Open
Abstract
The chromatin remodeling factor SMARCAD1, an SWI/SNF ATPase family member, has a role in 5' end resection at DNA double-strand breaks (DSBs) to produce single-strand DNA (ssDNA), a critical step for subsequent checkpoint and repair factor loading to remove DNA damage. However, the mechanistic details of SMARCAD1 coupling to the DNA damage response and repair pathways remains unknown. Here we report that SMARCAD1 is recruited to DNA DSBs through an ATM-dependent process. Depletion of SMARCAD1 reduces ionizing radiation (IR)-induced repairosome foci formation and DSB repair by homologous recombination (HR). IR induces SMARCAD1 phosphorylation at a conserved T906 by ATM kinase, a modification essential for SMARCAD1 recruitment to DSBs. Interestingly, T906 phosphorylation is also important for SMARCAD1 ubiquitination by RING1 at K905. Both these post-translational modifications are critical for regulating the role of SMARCAD1 in DNA end resection, HR-mediated repair, and cell survival after DNA damage.
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Affiliation(s)
- Sharmistha Chakraborty
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA.
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Shashank Hambarde
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Abid R Mattoo
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Vijaya Charaka
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Kazi M Ahmed
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Swaminathan P Iyer
- Department of Hematology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA.
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34
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β1-Integrin Impacts Rad51 Stability and DNA Double-Strand Break Repair by Homologous Recombination. Mol Cell Biol 2018; 38:MCB.00672-17. [PMID: 29463647 DOI: 10.1128/mcb.00672-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/15/2018] [Indexed: 01/04/2023] Open
Abstract
The molecular mechanisms underlying resistance to radiotherapy in breast cancer cells remain elusive. Previously, we reported that elevated β1-integrin is associated with enhanced breast cancer cell survival postirradiation, but how β1-integrin conferred radioresistance was unclear. Ionizing radiation (IR) induced cell killing correlates with the efficiency of DNA double-strand break (DSB) repair, and we found that nonmalignant breast epithelial (S1) cells with low β1-integrin expression have a higher frequency of S-phase-specific IR-induced chromosomal aberrations than the derivative malignant breast (T4-2) cells with high β1-integrin expression. In addition, there was an increased frequency of IR-induced homologous recombination (HR) repairosome focus formation in T4-2 cells compared with that of S1 cells. Cellular levels of Rad51 in T4-2 cells, a critical factor in HR-mediated DSB repair, were significantly higher. Blocking or depleting β1-integrin activity in T4-2 cells reduced Rad51 levels, while ectopic expression of β1-integrin in S1 cells correspondingly increased Rad51 levels, suggesting that Rad51 is regulated by β1-integrin. The low level of Rad51 protein in S1 cells was found to be due to rapid degradation by the ubiquitin proteasome pathway (UPP). Furthermore, the E3 ubiquitin ligase RING1 was highly upregulated in S1 cells compared to T4-2 cells. Ectopic β1-integrin expression in S1 cells reduced RING1 levels and increased Rad51 accumulation. In contrast, β1-integrin depletion in T4-2 cells significantly increased RING1 protein levels and potentiated Rad51 ubiquitination. These data suggest for the first time that elevated levels of the extracellular matrix receptor β1-integrin can increase tumor cell radioresistance by decreasing Rad51 degradation through a RING1-mediated proteasomal pathway.
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35
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Andriuskevicius T, Kotenko O, Makovets S. Putting together and taking apart: assembly and disassembly of the Rad51 nucleoprotein filament in DNA repair and genome stability. Cell Stress 2018; 2:96-112. [PMID: 31225474 PMCID: PMC6551702 DOI: 10.15698/cst2018.05.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Homologous recombination is a key mechanism providing both genome stability and genetic diversity in all living organisms. Recombinases play a central role in this pathway: multiple protein subunits of Rad51 or its orthologues bind single-stranded DNA to form a nucleoprotein filament which is essential for initiating recombination events. Multiple factors are involved in the regulation of this step, both positively and negatively. In this review, we discuss Rad51 nucleoprotein assembly and disassembly, how it is regulated and what functional significance it has in genome maintenance.
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Affiliation(s)
| | - Oleksii Kotenko
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh
| | - Svetlana Makovets
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh
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36
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Rieke DT, Ochsenreither S, Klinghammer K, Seiwert TY, Klauschen F, Tinhofer I, Keilholz U. Methylation of RAD51B, XRCC3 and other homologous recombination genes is associated with expression of immune checkpoints and an inflammatory signature in squamous cell carcinoma of the head and neck, lung and cervix. Oncotarget 2018; 7:75379-75393. [PMID: 27683114 PMCID: PMC5342748 DOI: 10.18632/oncotarget.12211] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/07/2016] [Indexed: 12/29/2022] Open
Abstract
Immune checkpoints are emerging treatment targets, but mechanisms underlying checkpoint expression are poorly understood. Since alterations in DNA repair genes have been connected to the efficacy of checkpoint inhibitors, we investigated associations between methylation of DNA repair genes and CTLA4 and CD274 (PD-L1) expression.A list of DNA repair genes (179 genes) was selected from the literature, methylation status and expression of inflammation-associated genes (The Cancer Genome Atlas data) was correlated in head and neck squamous cell carcinoma (HNSCC), cervical and lung squamous cell carcinoma.A significant positive correlation of the methylation status of 15, 3 and 2 genes with checkpoint expression was identified, respectively. RAD51B methylation was identified in all cancer subtypes. In HNSCC and cervical cancer, there was significant enrichment for homologous recombination genes. Methylation of the candidate genes was also associated with expression of other checkpoints, ligands, MHC- and T-cell associated genes as well as an interferon-inflammatory immune gene signature, predictive for the efficacy of PD-1 inhibition in HNSCC.Homologous recombination deficiency might therefore be mediated by DNA repair gene hypermethylation and linked to an immune-evasive phenotype in SCC. The methylation status of these genes could represent a new predictive biomarker for immune checkpoint inhibition.
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Affiliation(s)
- Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Ochsenreither
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tanguy Y Seiwert
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Frederick Klauschen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
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37
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Horikoshi N, Pandita RK, Mujoo K, Hambarde S, Sharma D, Mattoo AR, Chakraborty S, Charaka V, Hunt CR, Pandita TK. β2-spectrin depletion impairs DNA damage repair. Oncotarget 2018; 7:33557-70. [PMID: 27248179 PMCID: PMC5085102 DOI: 10.18632/oncotarget.9677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/20/2016] [Indexed: 12/22/2022] Open
Abstract
β2-Spectrin (β2SP/SPTBN1, gene SPTBN1) is a key TGF-β/SMAD3/4 adaptor and transcriptional cofactor that regulates TGF-β signaling and can contribute to liver cancer development. Here we report that cells deficient in β2-Spectrin (β2SP) are moderately sensitive to ionizing radiation (IR) and extremely sensitive to agents that cause interstrand cross-links (ICLs) or replication stress. In response to treatment with IR or ICL agents (formaldehyde, cisplatin, camptothecin, mitomycin), β2SP deficient cells displayed a higher frequency of cells with delayed γ-H2AX removal and a higher frequency of residual chromosome aberrations. Following hydroxyurea (HU)-induced replication stress, β2SP-deficient cells displayed delayed disappearance of γ-H2AX foci along with defective repair factor recruitment (MRE11, CtIP, RAD51, RPA, and FANCD2) as well as defective restart of stalled replication forks. Repair factor recruitment is a prerequisite for initiation of DNA damage repair by the homologous recombination (HR) pathway, which was also defective in β2SP deficient cells. We propose that β2SP is required for maintaining genomic stability following replication fork stalling, whether induced by either ICL damage or replicative stress, by facilitating fork regression as well as DNA damage repair by homologous recombination.
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Affiliation(s)
- Nobuo Horikoshi
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Kalpana Mujoo
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Shashank Hambarde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dharmendra Sharma
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Abid R Mattoo
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Sharmistha Chakraborty
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Vijaya Charaka
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
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38
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Liu X, Kumar M, Yang L, Molkentine DP, Valdecanas D, Yu S, Meyn RE, Heymach JV, Skinner HD. BAP1 Is a Novel Target in HPV-Negative Head and Neck Cancer. Clin Cancer Res 2017; 24:600-607. [PMID: 29113987 DOI: 10.1158/1078-0432.ccr-17-1573] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/03/2017] [Accepted: 11/03/2017] [Indexed: 02/05/2023]
Abstract
Purpose: This study examined the potential role of the nuclear deubiquitinating enzyme BRCA1-associated protein-1 (BAP1) in radioresistance in head and neck squamous cell cancer (HNSCC).Experimental Design: We overexpressed, knocked down, and rescued BAP1 expression in six HNSCC cell lines, three human papillomavirus (HPV)-negative and three HPV-positive, and examined the effects on radiosensitivity in vitro and in an HNSCC mouse xenograft model. Radiosensitivity was assessed by clonogenic cell survival and tumor growth delay assays; changes in protein expression were analyzed by immunofluorescence staining and Western blotting. We also analyzed The Cancer Genome Atlas HNSCC database to test for associations between BAP1 expression and outcome in patients.Results: Overexpression of BAP1 induced radioresistance in both cell lines and xenograft models; conversely, BAP1 knockdown led to increased ubiquitination of histone H2A, which has been implicated in DNA repair. We further found that BAP1 depletion suppressed the assembly of constitutive BRCA1 foci, which are associated with homologous recombination (HR), but had minimal effect on γ-H2AX foci and did not affect proteins associated with nonhomologous end joining, suggesting that BAP1 affects radiosensitivity in HNSCC by modifying HR. Finally, in patients with HNSCC, overexpression of BAP1 was associated with higher failure rates after radiotherapy.Conclusions: BAP1 can induce radioresistance in HNSCC cells, possibly via deubiquitination of H2Aub and modulation of HR, and was associated with poor outcomes in patients with HNSCC. BAP1 may be a potential therapeutic target in HNSCC. Clin Cancer Res; 24(3); 600-7. ©2017 AACR.
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Affiliation(s)
- Xiyou Liu
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Manish Kumar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Liangpeng Yang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David P Molkentine
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Valdecanas
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shiying Yu
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Raymond E Meyn
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Heath D Skinner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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39
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Laugeray A, Oummadi A, Jourdain C, Feat J, Meyer-Dilhet G, Menuet A, Plé K, Gay M, Routier S, Mortaud S, Guillemin GJ. Perinatal Exposure to the Cyanotoxin β-N-Méthylamino-L-Alanine (BMAA) Results in Long-Lasting Behavioral Changes in Offspring-Potential Involvement of DNA Damage and Oxidative Stress. Neurotox Res 2017; 33:87-112. [PMID: 28879461 DOI: 10.1007/s12640-017-9802-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/25/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
Abstract
We recently demonstrated that perinatal exposure to the glutamate-related herbicide, glufosinate ammonium, has deleterious effects on neural stem cell (NSC) homeostasis within the sub-ventricular zone (SVZ), probably leading to ASD-like symptoms in offspring later in life. In the present study, we aimed to investigate whether perinatal exposure to another glutamate-related toxicant, the cyanobacterial amino acid β-N-methylamino-L-alanine (BMAA), might also trigger neurodevelopmental disturbances. With this aim, female mice were intranasally exposed to low doses of BMAA, 50 mg kg-1 three times a week from embryonic days 7-10 to postnatal day 21. Behavioral analyses were performed during the offspring's early life and during adulthood. Developmental analyses revealed that perinatal exposure to BMAA hastened the appearance of some reflexes and communicative skills. BMAA-exposed offspring displayed sex-dependent changes in emotional cognition shortly after exposure. Later in life, the female offspring continued to express emotional defects and to display abnormal sociability, while males were less affected. To assess whether early exposure to BMAA had deleterious effects on NSC homeostasis, we exposed mice NSCs to 1 and 3 mM BMAA during 24 h. We found that BMAA-exposed NSCs produced high levels of ROS, highlighting the ability of BMAA to induce oxidative stress. We also showed that BMAA exposure increased the number of γH2AX/53BP1 foci per nucleus, suggesting that BMAA-induced DNA damage in NSCs. Collectively, this data strongly suggests that perinatal exposure to the cyanobacteria BMAA, even at low doses, results in neurobehavioral disturbances during both the postnatal period and adulthood. This is considered to be underpinned at the cellular level through dysregulation of NSC homeostasis in the developing brain.
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Affiliation(s)
- Anthony Laugeray
- Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355, Centre National de la Recherche Scientifique, 3b, rue de la Férollerie, 45071, Orléans, France. .,University of Orléans, Orléans, France.
| | | | | | - Justyne Feat
- Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355, Centre National de la Recherche Scientifique, 3b, rue de la Férollerie, 45071, Orléans, France
| | - Géraldine Meyer-Dilhet
- Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355, Centre National de la Recherche Scientifique, 3b, rue de la Férollerie, 45071, Orléans, France
| | - Arnaud Menuet
- Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355, Centre National de la Recherche Scientifique, 3b, rue de la Férollerie, 45071, Orléans, France.,University of Orléans, Orléans, France
| | - Karen Plé
- University of Orléans, Orléans, France.,Institute de Chimie Organique et Analytique, UMR 7311, Center National de la Recherche Scientifique, Orléans, France
| | - Marion Gay
- University of Orléans, Orléans, France.,Institute de Chimie Organique et Analytique, UMR 7311, Center National de la Recherche Scientifique, Orléans, France
| | - Sylvain Routier
- University of Orléans, Orléans, France.,Institute de Chimie Organique et Analytique, UMR 7311, Center National de la Recherche Scientifique, Orléans, France
| | - Stéphane Mortaud
- Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355, Centre National de la Recherche Scientifique, 3b, rue de la Férollerie, 45071, Orléans, France. .,University of Orléans, Orléans, France.
| | - Gilles J Guillemin
- Neuroinflammation Group, MND and Neurodegenerative Diseases Research Center, Macquarie University, Sydney, NSW, 2109, Australia.
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40
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Molecular targeting of hypoxia in radiotherapy. Adv Drug Deliv Rev 2017; 109:45-62. [PMID: 27771366 DOI: 10.1016/j.addr.2016.10.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/02/2016] [Accepted: 10/15/2016] [Indexed: 12/21/2022]
Abstract
Hypoxia (low O2) is an essential microenvironmental driver of phenotypic diversity in human solid cancers. Hypoxic cancer cells hijack evolutionarily conserved, O2- sensitive pathways eliciting molecular adaptations that impact responses to radiotherapy, tumor recurrence and patient survival. In this review, we summarize the radiobiological, genetic, epigenetic and metabolic mechanisms orchestrating oncogenic responses to hypoxia. In addition, we outline emerging hypoxia- targeting strategies that hold promise for individualized cancer therapy in the context of radiotherapy and drug delivery.
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41
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Sadik H, Korangath P, Nguyen NK, Gyorffy B, Kumar R, Hedayati M, Teo WW, Park S, Panday H, Munoz TG, Menyhart O, Shah N, Pandita RK, Chang JC, DeWeese T, Chang HY, Pandita TK, Sukumar S. HOXC10 Expression Supports the Development of Chemotherapy Resistance by Fine Tuning DNA Repair in Breast Cancer Cells. Cancer Res 2016; 76:4443-56. [PMID: 27302171 DOI: 10.1158/0008-5472.can-16-0774] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/25/2016] [Indexed: 11/16/2022]
Abstract
Development of drug resistance is a major factor limiting the continued success of cancer chemotherapy. To overcome drug resistance, understanding the underlying mechanism(s) is essential. We found that HOXC10 is overexpressed in primary carcinomas of the breast, and even more significantly in distant metastasis arising after failed chemotherapy. High HOXC10 expression correlates with shorter recurrence-free and overall survival in patients with estrogen receptor-negative breast cancer undergoing chemotherapy. We found that HOXC10 promotes survival in cells treated with doxorubicin, paclitaxel, or carboplatin by suppressing apoptosis and upregulating NF-κB Overexpressed HOXC10 increases S-phase-specific DNA damage repair by homologous recombination (HR) and checkpoint recovery in cells at three important phases. For double-strand break repair, HOXC10 recruits HR proteins at sites of DNA damage. It enhances resection and lastly, it resolves stalled replication forks, leading to initiation of DNA replication following DNA damage. We show that HOXC10 facilitates, but is not directly involved in DNA damage repair mediated by HR. HOXC10 achieves integration of these functions by binding to, and activating cyclin-dependent kinase, CDK7, which regulates transcription by phosphorylating the carboxy-terminal domain of RNA polymerase II. Consistent with these findings, inhibitors of CDK7 reverse HOXC10-mediated drug resistance in cultured cells. Blocking HOXC10 function, therefore, presents a promising new strategy to overcome chemotherapy resistance in breast cancer. Cancer Res; 76(15); 4443-56. ©2016 AACR.
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Affiliation(s)
- Helen Sadik
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Preethi Korangath
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nguyen K Nguyen
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Balazs Gyorffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary. 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Rakesh Kumar
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mohammad Hedayati
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wei Wen Teo
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sunju Park
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hardik Panday
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Teresa Gonzalez Munoz
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Otilia Menyhart
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary. 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Nilay Shah
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Raj K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas
| | - Jenny C Chang
- Methodist Cancer Center, The Houston Methodist Research Institute, Houston, Texas
| | - Theodore DeWeese
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Howard Y Chang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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42
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Ismail IH, Gagné JP, Genois MM, Strickfaden H, McDonald D, Xu Z, Poirier GG, Masson JY, Hendzel MJ. The RNF138 E3 ligase displaces Ku to promote DNA end resection and regulate DNA repair pathway choice. Nat Cell Biol 2015; 17:1446-57. [PMID: 26502055 DOI: 10.1038/ncb3259] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 09/22/2015] [Indexed: 12/30/2022]
Abstract
DNA double-strand breaks (DSBs) are repaired mainly by non-homologous end joining or homologous recombination (HR). Cell cycle stage and DNA end resection are believed to regulate the commitment to HR repair. Here we identify RNF138 as a ubiquitin E3 ligase that regulates the HR pathway. RNF138 is recruited to DNA damage sites through zinc fingers that have a strong preference for DNA with 5'- or 3'-single-stranded overhangs. RNF138 stimulates DNA end resection and promotes ATR-dependent signalling and DSB repair by HR, thereby contributing to cell survival on exposure to DSB-inducing agents. Finally, we establish that RNF138-dependent Ku removal from DNA breaks is one mechanism whereby RNF138 can promote HR. These results establish RNF138 as an important regulator of DSB repair pathway choice.
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Affiliation(s)
- Ismail Hassan Ismail
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue Edmonton, Alberta T6G 1Z2, Canada.,Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, 2705 boul. Laurier Québec city, Québec G1V 4G2, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, Québec G1V 0A6, Canada
| | - Marie-Michelle Genois
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, Québec G1V 0A6, Canada.,Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon Québec City, Québec G1R 2J6, Canada
| | - Hilmar Strickfaden
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue Edmonton, Alberta T6G 1Z2, Canada
| | - Darin McDonald
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue Edmonton, Alberta T6G 1Z2, Canada
| | - Zhizhong Xu
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue Edmonton, Alberta T6G 1Z2, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, 2705 boul. Laurier Québec city, Québec G1V 4G2, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, Québec G1V 0A6, Canada
| | - Jean-Yves Masson
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, Québec G1V 0A6, Canada.,Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon Québec City, Québec G1R 2J6, Canada
| | - Michael J Hendzel
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue Edmonton, Alberta T6G 1Z2, Canada
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43
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Somyajit K, Saxena S, Babu S, Mishra A, Nagaraju G. Mammalian RAD51 paralogs protect nascent DNA at stalled forks and mediate replication restart. Nucleic Acids Res 2015; 43:9835-55. [PMID: 26354865 PMCID: PMC4787763 DOI: 10.1093/nar/gkv880] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/23/2015] [Indexed: 12/22/2022] Open
Abstract
Mammalian RAD51 paralogs are implicated in the repair of collapsed replication forks by homologous recombination. However, their physiological roles in replication fork maintenance prior to fork collapse remain obscure. Here, we report on the role of RAD51 paralogs in short-term replicative stress devoid of DSBs. We show that RAD51 paralogs localize to nascent DNA and common fragile sites upon replication fork stalling. Strikingly, RAD51 paralogs deficient cells exhibit elevated levels of 53BP1 nuclear bodies and increased DSB formation, the latter being attributed to extensive degradation of nascent DNA at stalled forks. RAD51C and XRCC3 promote the restart of stalled replication in an ATP hydrolysis dependent manner by disengaging RAD51 and other RAD51 paralogs from the halted forks. Notably, we find that Fanconi anemia (FA)-like disorder and breast and ovarian cancer patient derived mutations of RAD51C fails to protect replication fork, exhibit under-replicated genomic regions and elevated micro-nucleation. Taken together, RAD51 paralogs prevent degradation of stalled forks and promote the restart of halted replication to avoid replication fork collapse, thereby maintaining genomic integrity and suppressing tumorigenesis.
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Affiliation(s)
- Kumar Somyajit
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Sneha Saxena
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Sharath Babu
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Anup Mishra
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
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44
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Role of the Exocyst Complex Component Sec6/8 in Genomic Stability. Mol Cell Biol 2015; 35:3633-45. [PMID: 26283729 DOI: 10.1128/mcb.00768-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 11/20/2022] Open
Abstract
The exocyst is a heterooctomeric complex well appreciated for its role in the dynamic assembly of specialized membrane domains. Accumulating evidence indicates that this macromolecular machine also serves as a physical platform that coordinates regulatory cascades supporting biological systems such as host defense signaling, cell fate, and energy homeostasis. The isolation of multiple components of the DNA damage response (DDR) as exocyst-interacting proteins, together with the identification of Sec8 as a suppressor of the p53 response, suggested functional interactions between the exocyst and the DDR. We found that exocyst perturbation resulted in resistance to ionizing radiation (IR) and accelerated resolution of DNA damage. This occurred at the expense of genomic integrity, as enhanced recombination frequencies correlated with the accumulation of aberrant chromatid exchanges. Sec8 perturbation resulted in the accumulation of ATF2 and RNF20 and the promiscuous accumulation of DDR-associated chromatin marks and Rad51 repairosomes. Thus, the exocyst supports DNA repair fidelity by limiting the formation of repair chromatin in the absence of DNA damage.
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45
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Bashir N, Sana S, Mahjabeen I, Kayani MA. Association of reduced XRCC2 expression with lymph node metastasis in breast cancer tissues. Fam Cancer 2015; 13:611-7. [PMID: 25159888 DOI: 10.1007/s10689-014-9745-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The main purpose of this study was to evaluate the association between reduction in XRCC2 gene and involvement of lymph node metastasis in breast cancer. In first part of the study, meta-analysis of 14 published XRCC2 studies was performed to define the role of XRCC2 gene as diagnostic marker and in second part of the study XRCC2 gene expression was observed using real time PCR in study cohort of 100 females (50 breast cancer patients and 50 controls). A statistically significant down regulation of XRCC2 (p < 0.04) and up-regulation of ki-67 (p < 0.05) was observed in breast cancer tissues compared to non-cancerous healthy tissues. In order to explore gene-gene and gene-clinicopathological parameters relationship Spearmen correlation was performed. We observed a significantly negative correlation between XRCC2 and Ki-67 expression (r = -0.376**, p < 0.01). In case of gene-clinicopathological parameters relationship, we observed a significant correlation between XRCC2 expression and lymph node status (r = -0.521***, p < 0.002) and metastatic status (r = -0.303*, p < 0.04) of breast cancer patients. Our data suggests that deregulation of XRCC2 in breast cancer has the potential to predict lymph node metastasis and may serve as a therapeutic target for breast cancer patients at risk of metastasis.
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Affiliation(s)
- Nabiha Bashir
- Cancer Genetics Lab, Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chakshazad, Islamabad, Pakistan
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46
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Wu J, Starr S. Low-fidelity compensatory backup alternative DNA repair pathways may unify current carcinogenesis theories. Future Oncol 2015; 10:1239-53. [PMID: 24947263 DOI: 10.2217/fon.13.272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The somatic mutation carcinogenesis theory has dominated for decades. The alternative theory, tissue organization field theory, argues that the development of cancer is determined by the surrounding microenvironment. However, neither theory can explain all features of cancer. As cancers share the features of uncontrolled proliferation and genomic instability, they are likely to have the same pathogenesis. It has been found that various DNA repair pathways within a cell crosstalk with one another, forming a DNA repair network. When one DNA repair pathways is defective, the others may work as compensatory backups. The latter pathways are explored for synthetic lethal anticancer therapy. In this article, we extend the concept of compensatory alternative DNA repair to unify the theories. We propose that the microenvironmental stress can activate low-fidelity compensatory alternative DNA repair, causing mutations. If the mutation occurs to a DNA repair gene, this secondarily mutated gene can lead to even more mutated genes, including those related to other DNA repair pathways, eventually destabilizing the genome. Therefore, the low-fidelity compensatory alternative DNA repair may mediate microenvironment-dependent carcinogenesis. The proposal seems consistent with the view of evolution: the environmental stress causes mutations to adapt to the changing environment.
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Affiliation(s)
- Jiaxi Wu
- Central Laboratories, Xuhui Central Hospital, Shanghai Clinical Research Center, Chinese Academy of Sciences, 966 Middle Huaihai Road, Shanghai 200031, China
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47
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Genois MM, Plourde M, Éthier C, Roy G, Poirier GG, Ouellette M, Masson JY. Roles of Rad51 paralogs for promoting homologous recombination in Leishmania infantum. Nucleic Acids Res 2015; 43:2701-15. [PMID: 25712090 PMCID: PMC4357719 DOI: 10.1093/nar/gkv118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 12/28/2022] Open
Abstract
To achieve drug resistance Leishmania parasite alters gene copy number by using its repeated sequences widely distributed through the genome. Even though homologous recombination (HR) is ascribed to maintain genome stability, this eukaryote exploits this potent mechanism driven by the Rad51 recombinase to form beneficial extrachromosomal circular amplicons. Here, we provide insights on the formation of these circular amplicons by analyzing the functions of the Rad51 paralogs. We purified three Leishmania infantum Rad51 paralogs homologs (LiRad51-3, LiRad51-4 and LiRad51-6) all of which directly interact with LiRad51. LiRad51-3, LiRad51-4 and LiRad51-6 show differences in DNA binding and annealing capacities. Moreover, it is also noteworthy that LiRad51-3 and LiRad51-4 are able to stimulate Rad51-mediated D-loop formation. In addition, we succeed to inactivate the LiRad51-4 gene and report a decrease of circular amplicons in this mutant. The LiRad51-3 gene was found to be essential for cell viability. Thus, we propose that the LiRad51 paralogs play crucial functions in extrachromosomal circular DNA amplification to circumvent drug actions and preserve survival.
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Affiliation(s)
- Marie-Michelle Genois
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada Centre de Recherche en Infectiologie, CHUL, 2705 boul. Laurier, Quebec, Quebec G1V 4G2, Canada
| | - Marie Plourde
- Centre de Recherche en Infectiologie, CHUL, 2705 boul. Laurier, Quebec, Quebec G1V 4G2, Canada
| | - Chantal Éthier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, 2705 boul. Laurier, Quebec city, Quebec, G1V 4G2, Canada
| | - Gaétan Roy
- Centre de Recherche en Infectiologie, CHUL, 2705 boul. Laurier, Quebec, Quebec G1V 4G2, Canada
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, 2705 boul. Laurier, Quebec city, Quebec, G1V 4G2, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, CHUL, 2705 boul. Laurier, Quebec, Quebec G1V 4G2, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
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48
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Pandita RK, Chow TT, Udayakumar D, Bain AL, Cubeddu L, Hunt CR, Shi W, Horikoshi N, Zhao Y, Wright WE, Khanna KK, Shay JW, Pandita TK. Single-strand DNA-binding protein SSB1 facilitates TERT recruitment to telomeres and maintains telomere G-overhangs. Cancer Res 2015; 75:858-69. [PMID: 25589350 DOI: 10.1158/0008-5472.can-14-2289] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proliferating mammalian stem and cancer cells express telomerase [telomerase reverse transcriptase (TERT)] in an effort to extend chromosomal G-overhangs and maintain telomere ends. Telomerase-expressing cells also have higher levels of the single-stranded DNA-binding protein SSB1, which has a critical role in DNA double-strand break (DSB) repair. Here, we report that SSB1 binds specifically to G-strand telomeric DNA in vitro and associates with telomeres in vivo. SSB1 interacts with the TERT catalytic subunit and regulates its interaction with telomeres. Deletion of SSB1 reduces TERT interaction with telomeres and leads to G-overhang loss. Although SSB1 is recruited to DSB sites, we found no corresponding change in TERT levels at these sites, implying that SSB1-TERT interaction relies upon a specific chromatin structure or context. Our findings offer an explanation for how telomerase is recruited to telomeres to facilitate G-strand DNA extension, a critical step in maintaining telomere ends and cell viability in all cancer cells. Cancer Res; 75(5); 858-69. ©2015 AACR.
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Affiliation(s)
- Raj K Pandita
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas. Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas
| | - Tracy T Chow
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Durga Udayakumar
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas. Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Amanda L Bain
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Liza Cubeddu
- School of Science and Health, University of Western Sydney, Sydney, Australia
| | - Clayton R Hunt
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas. Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Wei Shi
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Nobuo Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas. Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yong Zhao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas. Center for Excellence in Genomics Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas. Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas.
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49
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Uringa EJ, Baldeyron C, Odijk H, Wassenaar E, van Cappellen WA, Maas A, Hoeijmakers JHJ, Baarends WM, Kanaar R, Essers J. A mRad51-GFP antimorphic allele affects homologous recombination and DNA damage sensitivity. DNA Repair (Amst) 2014; 25:27-40. [PMID: 25463395 DOI: 10.1016/j.dnarep.2014.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
Accurate DNA double-strand break repair through homologous recombination is essential for preserving genome integrity. Disruption of the gene encoding RAD51, the protein that catalyzes DNA strand exchange during homologous recombination, results in lethality of mammalian cells. Proteins required for homologous recombination, also play an important role during DNA replication. To explore the role of RAD51 in DNA replication and DSB repair, we used a knock-in strategy to express a carboxy-terminal fusion of green fluorescent protein to mouse RAD51 (mRAD51-GFP) in mouse embryonic stem cells. Compared to wild-type cells, heterozygous mRad51(+/wt-GFP) embryonic stem cells showed increased sensitivity to DNA damage induced by ionizing radiation and mitomycin C. Moreover, gene targeting was found to be severely impaired in mRad51(+/wt-GFP) embryonic stem cells. Furthermore, we found that mRAD51-GFP foci were not stably associated with chromatin. From these experiments we conclude that this mRad51-GFP allele is an antimorphic allele. When this allele is present in a heterozygous condition over wild-type mRad51, embryonic stem cells are proficient in DNA replication but display defects in homologous recombination and DNA damage repair.
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Affiliation(s)
- Evert-Jan Uringa
- Department of Reproduction and Development, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Céline Baldeyron
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Hanny Odijk
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Evelyne Wassenaar
- Department of Reproduction and Development, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Alex Maas
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Reproduction and Development, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Surgical Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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50
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Somyajit K, Mishra A, Jameei A, Nagaraju G. Enhanced non-homologous end joining contributes toward synthetic lethality of pathological RAD51C mutants with poly (ADP-ribose) polymerase. Carcinogenesis 2014; 36:13-24. [PMID: 25292178 DOI: 10.1093/carcin/bgu211] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) inhibitors are actively under clinical trials for the treatment of breast and ovarian cancers that arise due to mutations in BRCA1 and BRCA2. The RAD51 paralog RAD51C has been identified as a breast and ovarian cancer susceptibility gene. The pathological RAD51C mutants that were identified in cancer patients are hypomorphic with partial repair function. However, targeting cancer cells that express hypomorphic mutants of RAD51C is highly challenging. Here, we report that RAD51C-deficient cells can be targeted by a 'synthetic lethal' approach using PARP inhibitor and this sensitivity was attributed to accumulation of cells in the G2/M and chromosomal aberrations. In addition, spontaneous hyperactivation of PARP1 was evident in RAD51C-deficient cells. Interestingly, RAD51C-negative cells exhibited enhanced recruitment of non-homologous end joining (NHEJ) proteins onto chromatin and this accumulation correlated with increased activity of error-prone NHEJ as well as genome instability leading to cell death. Notably, inhibition of DNA-PKcs or depletion of KU70 or Ligase IV rescued this phenotype. Strikingly, stimulation of NHEJ by low dose of ionizing radiation (IR) in the PARP inhibitor-treated RAD51C-deficient cells and cells expressing pathological RAD51C mutants induced enhanced toxicity 'synergistically'. These results demonstrate that cancer cells arising due to hypomorphic mutations in RAD51C can be specifically targeted by a 'synergistic approach' and imply that this strategy can be potentially applied to cancers with hypomorphic mutations in other homologous recombination pathway genes.
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Affiliation(s)
- Kumar Somyajit
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Anup Mishra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Aida Jameei
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
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