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Marshall S, Navarro MVAS, Ascenҫão CFR, Dibitetto D, Smolka MB. In-depth mapping of DNA-PKcs signaling uncovers noncanonical features of its kinase specificity. J Biol Chem 2024; 300:107513. [PMID: 38945450 PMCID: PMC11327452 DOI: 10.1016/j.jbc.2024.107513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via nonhomologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation, and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here, we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a noncanonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Sequence and structural analyses of the DNA-PKcs substrate recognition pocket revealed unique features compared to closely related phosphatidylinositol 3-kinase-related kinases that may explain its broader substrate preference. These findings expand the repertoire of DNA-PKcs and ATM substrates while establishing a novel preferential phosphorylation motif for DNA-PKcs.
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Affiliation(s)
- Shannon Marshall
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Marcos V A S Navarro
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil.
| | - Carolline F R Ascenҫão
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Diego Dibitetto
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
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2
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Wang Y, Sun Y, Tan M, Lin X, Tai P, Huang X, Jin Q, Yuan D, Xu T, He B. Association Between Polymorphisms in DNA Damage Repair Pathway Genes and Female Breast Cancer Risk. DNA Cell Biol 2024; 43:219-231. [PMID: 38634815 DOI: 10.1089/dna.2023.0331] [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] [Indexed: 04/19/2024] Open
Abstract
Breast cancer risk have been discussed to be associated with polymorphisms in genes as well as abnormal DNA damage repair function. This study aims to assess the relationship between genes single nucleotide polymorphisms (SNPs) related to DNA damage repair and female breast cancer risk in Chinese population. A case-control study containing 400 patients and 400 healthy controls was conducted. Genotype was identified using the sequence MassARRAY method and expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER-2) in tumor tissues was analyzed by immunohistochemistry assay. The results revealed that ATR rs13091637 decreased breast cancer risk influenced by ER, PR (CT/TT vs. CC: adjusted odds ratio [OR] = 1.54, 95% confidence interval [CI]: 1.04-2.27, p = 0.032; CT/TT vs. CC: adjusted OR = 1.63, 95%CI: 1.14-2.35, p = 0.008) expression. Stratified analysis revealed that PALB2 rs16940342 increased breast cancer risk in response to menstrual status (AG/GG vs. AA: adjusted OR = 1.72, 95%CI: 1.13-2.62, p = 0.011) and age of menarche (AG/GG vs. AA: adjusted OR = 1.54, 95%CI: 1.03-2.31, p = 0.037), whereas ATM rs611646 and Ku70 rs132793 were associated with reduced breast cancer risk influenced by menarche (GA/AA vs. GG: adjusted OR = 0.50, 95%CI: 0.30-0.95, p = 0.033). In a summary, PALB2 rs16940342, ATR rs13091637, ATM rs611646, and Ku70 rs132793 were associated with breast cancer risk.
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Affiliation(s)
- Ying Wang
- School of Basic-Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yalan Sun
- School of Basic-Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Mingjuan Tan
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Lin
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ping Tai
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Huang
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Qing Jin
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Dan Yuan
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Tao Xu
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bangshun He
- School of Basic-Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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3
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Marshall S, Navarro MV, Ascenҫão CF, Smolka MB. IN-DEPTH MAPPING OF DNA-PKcs SIGNALING UNCOVERS CONSERVED FEATURES OF ITS KINASE SPECIFICITY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576037. [PMID: 38293078 PMCID: PMC10827184 DOI: 10.1101/2024.01.17.576037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Cross-species analysis in mouse pre-B and human HCT116 cell lines revealed splicing factors and transcriptional regulators phosphorylated at this novel motif, several of which contain SAP domains. These findings expand the list of DNA-PKcs and ATM substrates and establish a novel preferential phosphorylation motif for DNA-PKcs that connects it to proteins involved in nucleotide processes and interactions.
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Affiliation(s)
- Shannon Marshall
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcos V.A.S. Navarro
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- 2. IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos - SP, 13566-590, Brazil
| | - Carolline F.R. Ascenҫão
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcus B. Smolka
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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4
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Fulneček J, Klimentová E, Cairo A, Bukovcakova SV, Alexiou P, Prokop Z, Riha K. The SAP domain of Ku facilitates its efficient loading onto DNA ends. Nucleic Acids Res 2023; 51:11706-11716. [PMID: 37850645 PMCID: PMC10681742 DOI: 10.1093/nar/gkad850] [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: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/19/2023] Open
Abstract
The evolutionarily conserved DNA repair complex Ku serves as the primary sensor of free DNA ends in eukaryotic cells. Its rapid association with DNA ends is crucial for several cellular processes, including non-homologous end joining (NHEJ) DNA repair and telomere protection. In this study, we conducted a transient kinetic analysis to investigate the impact of the SAP domain on individual phases of the Ku-DNA interaction. Specifically, we examined the initial binding, the subsequent docking of Ku onto DNA, and sliding of Ku along DNA. Our findings revealed that the C-terminal SAP domain of Ku70 facilitates the initial phases of the Ku-DNA interaction but does not affect the sliding process. This suggests that the SAP domain may either establish the first interactions with DNA, or stabilize these initial interactions during loading. To assess the biological role of the SAP domain, we generated Arabidopsis plants expressing Ku lacking the SAP domain. Intriguingly, despite the decreased efficiency of the ΔSAP Ku complex in loading onto DNA, the mutant plants exhibited full proficiency in classical NHEJ and telomere maintenance. This indicates that the speed with which Ku loads onto telomeres or DNA double-strand breaks is not the decisive factor in stabilizing these DNA structures.
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Affiliation(s)
| | | | | | | | | | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Karel Riha
- CEITEC Masaryk University, Brno, Czech Republic
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5
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Prabhu D, Ray U, Rajeev A, Joy R, George AT, George J, Raghavan SC, John F. Design and Synthesis of Ketenimine Sulfonamide Conjugates through Multicomponent Reactions; A Combined Cytotoxic Analysis and Computational Exploration. ACS OMEGA 2023; 8:38619-38631. [PMID: 37867708 PMCID: PMC10586297 DOI: 10.1021/acsomega.3c05816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023]
Abstract
Multicomponent reactions involving zwitterion generated from dimethyl acetylenedicarboxylate, aryl sulfonamide, and isocyanide to generate sulfonamide-conjugated ketenimines is reported. The synthetic strategy adopted is highly atom economical and stereoselective. Ketenimine sulfonamide analogues are key intermediates for further synthetic conversions to generate a combinatorial library of compounds. Furthermore, sulfonamide compounds are known to possess a broad spectrum of biological applications. All the novel molecules synthesized exhibit the potential to target the nonhomologous DNA end-joining (NHEJ) pathway with cytotoxic ability. Computational studies compliment the in vitro biological assays of the 8 small-molecule inhibitors. DNA double-strand breaks (DSBs) are considered as the most lethal among different DNA damages. NHEJ repairs about 70% of the DSBs generated in cells within mammals. The DNA-dependent protein kinase catalytic subunit is one of the PI3 kinases associated with NHEJ. Compounds DK01-DK08 were investigated for their ability to induce cancer cell death by treating with two leukemic cell lines where NHEJ is high. Results showed that bromoaryl (DK04)- and nitroaryl (DK05)-conjugated molecules showed excellent biological activity, having IC50 values of ∼2 μM in Nalm6 cell lines.
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Affiliation(s)
- Deepak
J. Prabhu
- Post
Graduate Research Department of Chemistry, Maharajas College, Ernakulam, Ernakulam, Kerala 682011, India
| | - Ujjayinee Ray
- Department
of Microbiology, Techno India University,
Kolkata, West Bengal 700091, India
| | - Anjaly Rajeev
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Reshma Joy
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Abi Thoppilan George
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Jinu George
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Sathees C. Raghavan
- Department
of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Franklin John
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
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6
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Timmins J. Recognition of DNA Lesions. Int J Mol Sci 2023; 24:ijms24119682. [PMID: 37298630 DOI: 10.3390/ijms24119682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The average human cell suffers from approximately 104-105 DNA lesions per day [...].
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Affiliation(s)
- Joanna Timmins
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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7
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Extended DNA binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks. J Biol Chem 2022; 298:102268. [PMID: 35850305 PMCID: PMC9399289 DOI: 10.1016/j.jbc.2022.102268] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Elevated DNA replication stress causes instability of the DNA replication fork and increased DNA mutations, which underlies tumorigenesis. The DNA replication stress regulator silencing-defective 2 (SDE2) is known to bind to TIMELESS (TIM), a protein of the fork protection complex, and enhances its stability, thereby supporting replisome activity at DNA replication forks. However, the DNA-binding activity of SDE2 is not well defined. Here, we structurally and functionally characterize a new conserved DNA-binding motif related to the SAP (SAF-A/B, Acinus, PIAS) domain in human SDE2 and establish its preference for ssDNA. Our NMR solution structure of the SDE2SAP domain reveals a helix-extended loop-helix core with the helices aligned parallel to each other, consistent with known canonical SAP folds. Notably, we have shown that the DNA interaction of this SAP domain extends beyond the core SAP domain and is augmented by two lysine residues in the C-terminal tail, which is uniquely positioned adjacent to the SAP motif and conserved in the pre-mRNA splicing factor SF3A3. Furthermore, we found that mutation in the SAP domain and extended C terminus not only disrupts ssDNA binding but also impairs TIM localization at replication forks, thus inhibiting efficient fork progression. Taken together, our results establish SDE2SAP as an essential element for SDE2 to exert its role in preserving replication fork integrity via fork protection complex regulation and highlight the structural diversity of the DNA–protein interactions achieved by a specialized DNA-binding motif.
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8
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Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 262] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
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9
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Zahid S, Seif El Dahan M, Iehl F, Fernandez-Varela P, Le Du MH, Ropars V, Charbonnier JB. The Multifaceted Roles of Ku70/80. Int J Mol Sci 2021; 22:ijms22084134. [PMID: 33923616 PMCID: PMC8073936 DOI: 10.3390/ijms22084134] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
DNA double-strand breaks (DSBs) are accidental lesions generated by various endogenous or exogenous stresses. DSBs are also genetically programmed events during the V(D)J recombination process, meiosis, or other genome rearrangements, and they are intentionally generated to kill cancer during chemo- and radiotherapy. Most DSBs are processed in mammalian cells by the classical nonhomologous end-joining (c-NHEJ) pathway. Understanding the molecular basis of c-NHEJ has major outcomes in several fields, including radiobiology, cancer therapy, immune disease, and genome editing. The heterodimer Ku70/80 (Ku) is a central actor of the c-NHEJ as it rapidly recognizes broken DNA ends in the cell and protects them from nuclease activity. It subsequently recruits many c-NHEJ effectors, including nucleases, polymerases, and the DNA ligase 4 complex. Beyond its DNA repair function, Ku is also involved in several other DNA metabolism processes. Here, we review the structural and functional data on the DNA and RNA recognition properties of Ku implicated in DNA repair and in telomeres maintenance.
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