1
|
Ferdoush J, Kadir RA, Ogle M, Saha A. Regulation of eukaryotic transcription initiation in response to cellular stress. Gene 2024; 924:148616. [PMID: 38795856 DOI: 10.1016/j.gene.2024.148616] [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: 11/22/2023] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Transcription initiation is a vital step in the regulation of eukaryotic gene expression. It can be dysregulated in response to various cellular stressors which is associated with numerous human diseases including cancer. Transcription initiation is facilitated via many gene-specific trans-regulatory elements such as transcription factors, activators, and coactivators through their interactions with transcription pre-initiation complex (PIC). These trans-regulatory elements can uniquely facilitate PIC formation (hence, transcription initiation) in response to cellular nutrient stress. Cellular nutrient stress also regulates the activity of other pathways such as target of rapamycin (TOR) pathway. TOR pathway exhibits distinct regulatory mechanisms of transcriptional activation in response to stress. Like TOR pathway, the cell cycle regulatory pathway is also found to be linked to transcriptional regulation in response to cellular stress. Several transcription factors such as p53, C/EBP Homologous Protein (CHOP), activating transcription factor 6 (ATF6α), E2F, transforming growth factor (TGF)-β, Adenomatous polyposis coli (APC), SMAD, and MYC have been implicated in regulation of transcription of target genes involved in cell cycle progression, apoptosis, and DNA damage repair pathways. Additionally, cellular metabolic and oxidative stressors have been found to regulate the activity of long non-coding RNAs (lncRNA). LncRNA regulates transcription by upregulating or downregulating the transcription regulatory proteins involved in metabolic and cell signaling pathways. Numerous human diseases, triggered by chronic cellular stressors, are associated with abnormal regulation of transcription. Hence, understanding these mechanisms would help unravel the molecular regulatory insights with potential therapeutic interventions. Therefore, here we emphasize the recent advances of regulation of eukaryotic transcription initiation in response to cellular stress.
Collapse
Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Matthew Ogle
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Ayan Saha
- Department of Bioinformatics and Biotechnology, Asian University for Women, Chattogram, Bangladesh
| |
Collapse
|
2
|
Toprani SM, Scheibler C, Mordukhovich I, McNeely E, Nagel ZD. Cosmic Ionizing Radiation: A DNA Damaging Agent That May Underly Excess Cancer in Flight Crews. Int J Mol Sci 2024; 25:7670. [PMID: 39062911 PMCID: PMC11277465 DOI: 10.3390/ijms25147670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
In the United States, the Federal Aviation Administration has officially classified flight crews (FC) consisting of commercial pilots, cabin crew, or flight attendants as "radiation workers" since 1994 due to the potential for cosmic ionizing radiation (CIR) exposure at cruising altitudes originating from solar activity and galactic sources. Several epidemiological studies have documented elevated incidence and mortality for several cancers in FC, but it has not yet been possible to establish whether this is attributable to CIR. CIR and its constituents are known to cause a myriad of DNA lesions, which can lead to carcinogenesis unless DNA repair mechanisms remove them. But critical knowledge gaps exist with regard to the dosimetry of CIR, the role of other genotoxic exposures among FC, and whether possible biological mechanisms underlying higher cancer rates observed in FC exist. This review summarizes our understanding of the role of DNA damage and repair responses relevant to exposure to CIR in FC. We aimed to stimulate new research directions and provide information that will be useful for guiding regulatory, public health, and medical decision-making to protect and mitigate the risks for those who travel by air.
Collapse
Affiliation(s)
- Sneh M. Toprani
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
| | - Christopher Scheibler
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
| | - Irina Mordukhovich
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
- Sustainability and Health Initiative (SHINE), Department of Environmental Health, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Eileen McNeely
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
- Sustainability and Health Initiative (SHINE), Department of Environmental Health, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Zachary D. Nagel
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
| |
Collapse
|
3
|
Kyle AH, Karan T, Baker JHE, Püspöky Banáth J, Wang T, Liu A, Mendez C, Peter Petric M, Duzenli C, Minchinton AI. Detection of FLASH-radiotherapy tissue sparing in a 3D-spheroid model using DNA damage response markers. Radiother Oncol 2024; 196:110326. [PMID: 38735536 DOI: 10.1016/j.radonc.2024.110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/07/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
PURPOSE The oxygen depletion hypothesis has been proposed as a rationale to explain the observed phenomenon of FLASH-radiotherapy (FLASH-RT) sparing normal tissues while simultaneously maintaining tumor control. In this study we examined the distribution of DNA Damage Response (DDR) markers in irradiated 3D multicellular spheroids to explore the relationship between FLASH-RT protection and radiolytic-oxygen-consumption (ROC) in tissues. METHODS Studies were performed using a Varian Truebeam linear accelerator delivering 10 MeV electrons with an average dose rate above 50 Gy/s. Irradiations were carried out on 3D spheroids maintained under a range of O2 and temperature conditions to control O2 consumption and create gradients representative of in vivo tissues. RESULTS Staining for pDNA-PK (Ser2056) produced a linear radiation dose response whereas γH2AX (Ser139) showed saturation with increasing dose. Using the pDNA-PK staining, radiation response was then characterised for FLASH compared to standard-dose-rates as a function of depth into the spheroids. At 4 °C, chosen to minimize the development of metabolic oxygen gradients within the tissues, FLASH protection could be observed at all distances under oxygen conditions of 0.3-1 % O2. Whereas at 37 °C a FLASH-protective effect was limited to the outer cell layers of tissues, an effect only observed at 3 % O2. Modelling of changes in the pDNA-PK-based oxygen enhancement ratio (OER) yielded a tissue ROC g0-value estimate of 0.73 ± 0.25 µM/Gy with a km of 5.4 µM at FLASH dose rates. CONCLUSIONS DNA damage response markers are sensitive to the effects of transient oxygen depletion during FLASH radiotherapy. Findings support the rationale that well-oxygenated tissues would benefit more from FLASH-dose-rate protection relative to poorly-oxygenated tissues.
Collapse
Affiliation(s)
| | | | | | | | | | - Anam Liu
- BC Cancer Research Institute, Vancouver, Canada
| | | | | | | | | |
Collapse
|
4
|
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 DOI: 10.1016/j.jbc.2024.107513] [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: 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.
Collapse
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.
| |
Collapse
|
5
|
Li Y, Mu L, Li Y, Mi Y, Hu Y, Li X, Tao D, Qin J. Golgi dispersal in cancer stem cells promotes chemoresistance of colorectal cancer via the Golgi stress response. Cell Death Dis 2024; 15:417. [PMID: 38879509 PMCID: PMC11180190 DOI: 10.1038/s41419-024-06817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/19/2024]
Abstract
Chemotherapy is a crucial treatment for colorectal tumors. However, its efficacy is restricted by chemoresistance. Recently, Golgi dispersal has been suggested to be a potential response to chemotherapy, particularly to drugs that induce DNA damage. However, the underlying mechanisms by which Golgi dispersal enhances the capacity to resist DNA-damaging agents remain unclear. Here, we demonstrated that DNA-damaging agents triggered Golgi dispersal in colorectal cancer (CRC), and cancer stem cells (CSCs) possessed a greater degree of Golgi dispersal compared with differentiated cancer cells (non-CSCs). We further revealed that Golgi dispersal conferred resistance against the lethal effects of DNA-damaging agents. Momentously, Golgi dispersal activated the Golgi stress response via the PKCα/GSK3α/TFE3 axis, resulting in enhanced protein and vesicle trafficking, which facilitated drug efflux through ABCG2. Identification of Golgi dispersal indicated an unexpected pathway regulating chemoresistance in CRC.
Collapse
Affiliation(s)
- Yangkun Li
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Lei Mu
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yanqi Li
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yulong Mi
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Surgical Oncology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350013, Fujian, China
| | - Yibing Hu
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Breast Surgery, Peking University Shenzhen Hospital, Shenzhen, 518000, Guangdong, China
| | - Xiaolan Li
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Deding Tao
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jichao Qin
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Department of Gastrointestinal Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
| |
Collapse
|
6
|
Lohberger B, Barna S, Glänzer D, Eck N, Leithner A, Georg D. DNA-PKcs Inhibition Sensitizes Human Chondrosarcoma Cells to Carbon Ion Irradiation via Cell Cycle Arrest and Telomere Capping Disruption. Int J Mol Sci 2024; 25:6179. [PMID: 38892366 PMCID: PMC11173223 DOI: 10.3390/ijms25116179] [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: 05/03/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
In order to overcome the resistance to radiotherapy in human chondrosarcoma cells, the prevention from efficient DNA repair with a combined treatment with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) inhibitor AZD7648 was explored for carbon ion (C-ion) as well as reference photon (X-ray) irradiation (IR) using gene expression analysis, flow cytometry, protein phosphorylation, and telomere length shortening. Proliferation markers and cell cycle distribution changed significantly after combined treatment, revealing a prominent G2/M arrest. The expression of the G2/M checkpoint genes cyclin B, CDK1, and WEE1 was significantly reduced by IR alone and the combined treatment. While IR alone showed no effects, additional AZD7648 treatment resulted in a dose-dependent reduction in AKT phosphorylation and an increase in Chk2 phosphorylation. Twenty-four hours after IR, the key genes of DNA repair mechanisms were reduced by the combined treatment, which led to impaired DNA repair and increased radiosensitivity. A time-dependent shortening of telomere length was observed in both cell lines after combined treatment with AZD7648 and 8 Gy X-ray/C-ion IR. Our data suggest that the inhibition of DNA-PKcs may increase sensitivity to X-rays and C-ion IR by impairing its functional role in DNA repair mechanisms and telomere end protection.
Collapse
Affiliation(s)
- Birgit Lohberger
- Department of Orthopedics and Trauma, Medical University of Graz, Auenbruggerplatz 5-7, 8036 Graz, Austria; (D.G.); (N.E.); (A.L.)
| | - Sandra Barna
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (S.B.); (D.G.)
- MedAustron-Ion Therapy Center, Viktor-Kaplan Strasse 2, 2700 Wiener Neustadt, Austria
| | - Dietmar Glänzer
- Department of Orthopedics and Trauma, Medical University of Graz, Auenbruggerplatz 5-7, 8036 Graz, Austria; (D.G.); (N.E.); (A.L.)
| | - Nicole Eck
- Department of Orthopedics and Trauma, Medical University of Graz, Auenbruggerplatz 5-7, 8036 Graz, Austria; (D.G.); (N.E.); (A.L.)
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, Auenbruggerplatz 5-7, 8036 Graz, Austria; (D.G.); (N.E.); (A.L.)
| | - Dietmar Georg
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (S.B.); (D.G.)
- MedAustron-Ion Therapy Center, Viktor-Kaplan Strasse 2, 2700 Wiener Neustadt, Austria
| |
Collapse
|
7
|
Kim DY, Yun H, You JE, Lee JU, Kang DH, Ryu YS, Koh DI, Jin DH. Inactivation of VRK1 sensitizes ovarian cancer to PARP inhibition through regulating DNA-PK stability. Exp Cell Res 2024; 438:114036. [PMID: 38614421 DOI: 10.1016/j.yexcr.2024.114036] [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: 11/27/2023] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/15/2024]
Abstract
Ovarian cancer is the leading cause of gynecologic cancer death. Among the most innovative anti-cancer approaches, the genetic concept of synthetic lethality is that mutations in multiple genes work synergistically to effect cell death. Previous studies found that although vaccinia-related kinase-1 (VRK1) associates with DNA damage repair proteins, its underlying mechanisms remain unclear. Here, we found high VRK1 expression in ovarian tumors, and that VRK1 depletion can significantly promote apoptosis and cell cycle arrest. The effect of VRK1 knockdown on apoptosis was manifested by increased DNA damage, genomic instability, and apoptosis, and also blocked non-homologous end joining (NHEJ) by destabilizing DNA-PK. Further, we verified that VRK1 depletion enhanced sensitivity to a PARP inhibitor (PARPi), olaparib, promoting apoptosis through DNA damage, especially in ovarian cancer cell lines with high VRK1 expression. Proteins implicated in DNA damage responses are suitable targets for the development of new anti-cancer therapeutic strategies, and their combination could represent an alternative form of synthetic lethality. Therefore, normal protective DNA damage responses are impaired by combining olaparib with elimination of VRK1 and could be used to reduce drug dose and its associated toxicity. In summary, VRK1 represents both a potential biomarker for PARPi sensitivity, and a new DDR-associated therapeutic target, in ovarian cancer.
Collapse
Affiliation(s)
- Do Yeon Kim
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Hyeseon Yun
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Ji-Eun You
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Ji-U Lee
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-Hee Kang
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Yea Seong Ryu
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-In Koh
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-Hoon Jin
- Department of Convergence Medicine, Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
| |
Collapse
|
8
|
Hermantara R, Richmond L, Taqi AF, Chilaka S, Jeantet V, Guerrini I, West K, West A. Improving CRISPR-Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration. J Biomed Sci 2024; 31:32. [PMID: 38532479 DOI: 10.1186/s12929-024-01020-x] [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: 10/08/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR-Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency. METHOD Here we report the development of a multicolour fluorescence assay for studying CRISPR-Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR-Cas9 strategies. RESULT We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration. CONCLUSION Our results highlight the need for a more stringent assessment of CRISPR-Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
Collapse
Affiliation(s)
- Rio Hermantara
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
| | - Laura Richmond
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Aqeel Faisal Taqi
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sabari Chilaka
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Valentine Jeantet
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ileana Guerrini
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katherine West
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Adam West
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
9
|
Westover KR, Jin P, Yao B. Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics 2024; 16:589-608. [PMID: 38530068 PMCID: PMC11160457 DOI: 10.2217/epi-2023-0379] [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: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.
Collapse
Affiliation(s)
- Katherine R Westover
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
10
|
Gonzáles-Córdova RA, Dos Santos TR, Gachet-Castro C, Andrade Vieira J, Trajano-Silva LAM, Sakamoto-Hojo ET, Baqui MMA. Trypanosoma cruzi infection induces DNA double-strand breaks and activates DNA damage response pathway in host epithelial cells. Sci Rep 2024; 14:5225. [PMID: 38433244 PMCID: PMC10909859 DOI: 10.1038/s41598-024-53589-w] [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: 05/24/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, invades many cell types affecting numerous host-signalling pathways. During the T. cruzi infection, we demonstrated modulations in the host RNA polymerase II activity with the downregulation of ribonucleoproteins affecting host transcription and splicing machinery. These alterations could be a result of the initial damage to the host DNA caused by the presence of the parasite, however, the mechanisms are not well understood. Herein, we examined whether infection by T. cruzi coincided with enhanced DNA damage in the host cell. We studied the engagement of the DNA damage response (DDR) pathways at the different time points (0-24 h post-infection, hpi) by T. cruzi in LLC-MK2 cells. In response to double-strand breaks (DSB), maximum phosphorylation of the histone variant H2AX is observed at 2hpi and promotes recruitment of the DDR p53-binding protein (53BP1). During T. cruzi infection, Ataxia-telangiectasia mutated protein (ATM) and DNA-PK protein kinases remained active in a time-dependent manner and played roles in regulating the host response to DSB. The host DNA lesions caused by the infection are likely orchestrated by the non-homologous end joining (NHEJ) pathway to maintain the host genome integrity.
Collapse
Affiliation(s)
- Raul Alexander Gonzáles-Córdova
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Thamires Rossi Dos Santos
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Camila Gachet-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Johnathan Andrade Vieira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Lays Adrianne Mendonça Trajano-Silva
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Elza Tiemi Sakamoto-Hojo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
- Department of Biology, Faculty of Philosophy Sciences and Letters at Ribeirão Preto, University of São Paulo, São Paulo, 14040-901, Brazil
| | - Munira Muhammad Abdel Baqui
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil.
| |
Collapse
|
11
|
Leal AF, Herreno-Pachón AM, Benincore-Flórez E, Karunathilaka A, Tomatsu S. Current Strategies for Increasing Knock-In Efficiency in CRISPR/Cas9-Based Approaches. Int J Mol Sci 2024; 25:2456. [PMID: 38473704 PMCID: PMC10931195 DOI: 10.3390/ijms25052456] [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: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
Collapse
Affiliation(s)
- Andrés Felipe Leal
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angelica María Herreno-Pachón
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Eliana Benincore-Flórez
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
| | - Amali Karunathilaka
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shunji Tomatsu
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19144, USA
| |
Collapse
|
12
|
Klieber N, Hildebrand LS, Faulhaber E, Symank J, Häck N, Härtl A, Fietkau R, Distel LV. Different Impacts of DNA-PK and mTOR Kinase Inhibitors in Combination with Ionizing Radiation on HNSCC and Normal Tissue Cells. Cells 2024; 13:304. [PMID: 38391917 PMCID: PMC10887161 DOI: 10.3390/cells13040304] [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: 01/20/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
Despite substantial advancements in understanding the pathomechanisms of head and neck squamous cell carcinoma (HNSCC), effective therapy remains challenging. The application of kinase inhibitors (KIs) in HNSCC, specifically mTOR and DNA-PK inhibitors, can increase radiosensitivity and therefore presents a promising strategy when used simultaneously with ionizing radiation (IR) in cancer treatment. Our study focused on the selective DNA-PK-inhibitor AZD7648; the selective mTOR-inhibitor Sapanisertib; and CC-115, a dual inhibitor targeting both mTOR and DNA-PK. The impact of these KIs on HNSCC and normal tissue cells was assessed using various analytical methods including cell death studies, cell cycle analysis, real-time microscopy, colony-forming assays and immunohistochemical staining for γH2AX and downstream mTOR protein p-S6. We detected a strong inhibition of IR-induced DNA double-strand break (DSB) repair, particularly in AZD7648-treated HNSCC, whereas normal tissue cells repaired DNA DSB more efficiently. Additionally, AZD7648 + IR treatment showed a synergistic decline in cell proliferation and clonogenicity, along with an elevated G2/M arrest and cell death in the majority of HNSCC cell lines. CC-115 + IR treatment led to an elevation in G2/M arrest, increased cell death, and a synergistic reduction in cell proliferation, though the effect was notably lower compared to the AZD7648 + IR- treated group. Sapanisertib led to a high cellular toxicity in both HNSCC and normal tissue cells, even in non-irradiated cells. Regarding cell proliferation and the induction of apoptosis and necrosis, Sapanisertib + IR was beneficial only in HPV+ HNSCC. Overall, this study highlights the potential of AZD7648 as a radiosensitizing agent in advanced-stage HPV-positive and negative HNSCC, offering a promising therapeutic strategy. However, the dual mTOR/DNA-PK-I CC-115 did not provide a distinct advantage over the use of selective KIs in our investigations, suggesting limited benefits for its application in KI + IR therapy. Notably, the selective mTOR-inhibitor Sapanisertib was only beneficial in HPV+ HNSCC and should not be applied in HPV- cases.
Collapse
Affiliation(s)
- Nina Klieber
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Laura S. Hildebrand
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Eva Faulhaber
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Julia Symank
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Nicole Häck
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Annamaria Härtl
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Luitpold V. Distel
- Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsstr. 27, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Liu K, Yuan X, Yang T, Deng D, Chen Y, Tang M, Zhang C, Zou Y, Zhang S, Li D, Shi M, Guo Y, Zhou Y, Zhao M, Yang Z, Chen L. Discovery, Optimization, and Evaluation of Potent and Selective DNA-PK Inhibitors in Combination with Chemotherapy or Radiotherapy for the Treatment of Malignancies. J Med Chem 2024; 67:245-271. [PMID: 38117951 DOI: 10.1021/acs.jmedchem.3c01338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Given the multifaceted biological functions of DNA-PK encompassing DNA repair pathways and beyond, coupled with the susceptibility of DNA-PK-deficient cells to DNA-damaging agents, significant strides have been made in the pursuit of clinical potential for DNA-PK inhibitors as synergistic adjuncts to chemo- or radiotherapy. Nevertheless, although substantial progress has been made with the discovery of potent inhibitors of DNA-PK, the clinical trial landscape requires even more potent and selective molecules. This necessitates further endeavors to expand the repertoire of clinically accessible DNA-PK inhibitors for the ultimate benefit of patients. Described herein are the obstacles that were encountered and the solutions that were found, which eventually led to the identification of compound 31t. This compound exhibited a remarkable combination of robust potency and exceptional selectivity along with favorable in vivo profiles as substantiated by pharmacokinetic studies in rats and pharmacodynamic assessments in H460, BT474, and A549 xenograft models.
Collapse
Affiliation(s)
- Kongjun Liu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xue Yuan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Dexin Deng
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yong Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Minghai Tang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chufeng Zhang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yurong Zou
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shunjie Zhang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Dan Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Mingsong Shi
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yong Guo
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yanting Zhou
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Min Zhao
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Zhuang Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
- Chengdu Zenitar Biomedical Technology Co., Ltd., Chengdu 610041, China
| |
Collapse
|
15
|
Liu MY, Lin KR, Chien YL, Yang BZ, Tsui LY, Chu HP, Wu CSP. ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress. Nucleic Acids Res 2024; 52:204-222. [PMID: 37930853 PMCID: PMC10783509 DOI: 10.1093/nar/gkad973] [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: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
Aberrant DNA/RNA hybrids (R-loops) formed during transcription and replication disturbances pose threats to genome stability. DHX9 is an RNA helicase involved in R-loop resolution, but how DHX9 is regulated in response to genotoxic stress remains unclear. Here we report that DHX9 is phosphorylated at S321 and S688, with S321 phosphorylation primarily induced by ATR after DNA damage. Phosphorylation of DHX9 at S321 promotes its interaction with γH2AX, BRCA1 and RPA, and is required for its association with R-loops under genotoxic stress. Inhibition of ATR or expression of the non-phosphorylatable DHX9S321A prevents DHX9 from interacting with RPA and R-loops, leading to the accumulation of stress-induced R-loops. Furthermore, depletion of RPA reduces the association between DHX9 and γH2AX, and in vitro binding analysis confirms a direct interaction between DHX9 and RPA. Notably, cells with the non-phosphorylatable DHX9S321A variant exhibit hypersensitivity to genotoxic stress, while those expressing the phosphomimetic DHX9S321D variant prevent R-loop accumulation and display resistance to DNA damage agents. In summary, we uncover a new mechanism by which ATR directly regulates DHX9 through phosphorylation to eliminate stress-induced R-loops.
Collapse
Affiliation(s)
- Mei-Yin Liu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Keng-Ru Lin
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Yuh-Ling Chien
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Bing-Ze Yang
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Li-Yu Tsui
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | | | - Ching-Shyi Peter Wu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| |
Collapse
|
16
|
Studstill CJ, Mac M, Moody CA. Interplay between the DNA damage response and the life cycle of DNA tumor viruses. Tumour Virus Res 2023; 16:200272. [PMID: 37918513 PMCID: PMC10685005 DOI: 10.1016/j.tvr.2023.200272] [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: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023] Open
Abstract
Approximately 20 % of human cancers are associated with virus infection. DNA tumor viruses can induce tumor formation in host cells by disrupting the cell's DNA replication and repair mechanisms. Specifically, these viruses interfere with the host cell's DNA damage response (DDR), which is a complex network of signaling pathways that is essential for maintaining the integrity of the genome. DNA tumor viruses can disrupt these pathways by expressing oncoproteins that mimic or inhibit various DDR components, thereby promoting genomic instability and tumorigenesis. Recent studies have highlighted the molecular mechanisms by which DNA tumor viruses interact with DDR components, as well as the ways in which these interactions contribute to viral replication and tumorigenesis. Understanding the interplay between DNA tumor viruses and the DDR pathway is critical for developing effective strategies to prevent and treat virally associated cancers. In this review, we discuss the current state of knowledge regarding the mechanisms by which human papillomavirus (HPV), merkel cell polyomavirus (MCPyV), Kaposi's sarcoma-associated herpesvirus (KSHV), and Epstein-Barr virus (EBV) interfere with DDR pathways to facilitate their respective life cycles, and the consequences of such interference on genomic stability and cancer development.
Collapse
Affiliation(s)
- Caleb J Studstill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Michelle Mac
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Cary A Moody
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
| |
Collapse
|
17
|
Zhou Y, Börcsök J, Adib E, Kamran SC, Neil AJ, Stawiski K, Freeman D, Stormoen DR, Sztupinszki Z, Samant A, Nassar A, Bekele RT, Hanlon T, Valentine H, Epstein I, Sharma B, Felt K, Abbosh P, Wu CL, Efstathiou JA, Miyamoto DT, Anderson W, Szallasi Z, Mouw KW. ATM deficiency confers specific therapeutic vulnerabilities in bladder cancer. SCIENCE ADVANCES 2023; 9:eadg2263. [PMID: 37992168 PMCID: PMC10664985 DOI: 10.1126/sciadv.adg2263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Ataxia-telangiectasia mutated (ATM) plays a central role in the cellular response to DNA damage and ATM alterations are common in several tumor types including bladder cancer. However, the specific impact of ATM alterations on therapy response in bladder cancer is uncertain. Here, we combine preclinical modeling and clinical analyses to comprehensively define the impact of ATM alterations on bladder cancer. We show that ATM loss is sufficient to increase sensitivity to DNA-damaging agents including cisplatin and radiation. Furthermore, ATM loss drives sensitivity to DNA repair-targeted agents including poly(ADP-ribose) polymerase (PARP) and Ataxia telangiectasia and Rad3 related (ATR) inhibitors. ATM loss alters the immune microenvironment and improves anti-PD1 response in preclinical bladder models but is not associated with improved anti-PD1/PD-L1 response in clinical cohorts. Last, we show that ATM expression by immunohistochemistry is strongly correlated with response to chemoradiotherapy. Together, these data define a potential role for ATM as a predictive biomarker in bladder cancer.
Collapse
Affiliation(s)
- Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Börcsök
- Danish Cancer Institute, Copenhagen, Denmark
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Elio Adib
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sophia C. Kamran
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander J. Neil
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Konrad Stawiski
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Dory Freeman
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dag Rune Stormoen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Amruta Samant
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, USA
| | - Raie T. Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henkel Valentine
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ilana Epstein
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bijaya Sharma
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen Felt
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Philip Abbosh
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Albert Einstein Medical Center, Philadelphia, PA, USA
| | - Chin-Lee Wu
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Jason A. Efstathiou
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - David T. Miyamoto
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William Anderson
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group and Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Kent W. Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, MA, USA
| |
Collapse
|
18
|
Lal S, Bhola NE, Sun BC, Chen Y, Huang T, Morton V, Chen KX, Xia S, Zhang H, Parikh NS, Ye Q, Veiby OP, Bellovin DI, Ji Y. Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor. CANCER RESEARCH COMMUNICATIONS 2023; 3:1731-1742. [PMID: 37663435 PMCID: PMC10473160 DOI: 10.1158/2767-9764.crc-23-0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023]
Abstract
DNA-dependent protein kinase (DNA-PK), a driver of the non-homologous end-joining (NHEJ) DNA damage response pathway, plays an instrumental role in repairing double-strand breaks (DSB) induced by DNA-damaging poisons. We evaluate ZL-2201, an orally bioavailable, highly potent, and selective pharmacologic inhibitor of DNA-PK activity, for the treatment of human cancerous malignancies. ZL-2201 demonstrated greater selectivity for DNA-PK and effectively inhibited DNA-PK autophosphorylation in a concentration- and time-dependent manner. Initial data suggested a potential correlation between ataxia-telangiectasia mutated (ATM) deficiency and ZL-2201 sensitivity. More so, ZL-2201 showed strong synergy with topoisomerase II inhibitors independent of ATM status in vitro. In vivo oral administration of ZL-2201 demonstrated dose-dependent antitumor activity in the NCI-H1703 xenograft model and significantly enhanced the activity of approved DNA-damaging agents in A549 and FaDu models. From a phosphoproteomic mass spectrometry screen, we identified and validated that ZL-2201 and PRKDC siRNA decreased Ser108 phosphorylation of MCM2, a key DNA replication factor. Collectively, we have characterized a potent and selective DNA-PK inhibitor with promising monotherapy and combinatory therapeutic potential with approved DNA-damaging agents. More importantly, we identified phospho-MCM2 (Ser108) as a potential proximal biomarker of DNA-PK inhibition that warrants further preclinical and clinical evaluation. Significance ZL-2201, a potent and selective DNA-PK inhibitor, can target tumor models in combination with DNA DSB-inducing agents such as radiation or doxorubicin, with potential to improve recurrent therapies in the clinic.
Collapse
Affiliation(s)
- Shruti Lal
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Neil E. Bhola
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Bee-Chun Sun
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Yuping Chen
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Tom Huang
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Vivian Morton
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | | | | | | | - Nehal S. Parikh
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Qiuping Ye
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - O. Petter Veiby
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | | | - Yuhua Ji
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| |
Collapse
|
19
|
Head PE, Kapoor-Vazirani P, Nagaraju GP, Zhang H, Rath S, Luong N, Haji-Seyed-Javadi R, Sesay F, Wang SY, Duong D, Daddacha W, Minten E, Song B, Danelia D, Liu X, Li S, Ortlund E, Seyfried N, Smalley D, Wang Y, Deng X, Dynan W, El-Rayes B, Davis A, Yu D. DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining. Nucleic Acids Res 2023; 51:7972-7987. [PMID: 37395399 PMCID: PMC10450170 DOI: 10.1093/nar/gkad549] [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: 02/15/2022] [Revised: 06/02/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) plays a critical role in non-homologous end joining (NHEJ), the predominant pathway that repairs DNA double-strand breaks (DSB) in response to ionizing radiation (IR) to govern genome integrity. The interaction of the catalytic subunit of DNA-PK (DNA-PKcs) with the Ku70/Ku80 heterodimer on DSBs leads to DNA-PK activation; however, it is not known if upstream signaling events govern this activation. Here, we reveal a regulatory step governing DNA-PK activation by SIRT2 deacetylation, which facilitates DNA-PKcs localization to DSBs and interaction with Ku, thereby promoting DSB repair by NHEJ. SIRT2 deacetylase activity governs cellular resistance to DSB-inducing agents and promotes NHEJ. SIRT2 furthermore interacts with and deacetylates DNA-PKcs in response to IR. SIRT2 deacetylase activity facilitates DNA-PKcs interaction with Ku and localization to DSBs and promotes DNA-PK activation and phosphorylation of downstream NHEJ substrates. Moreover, targeting SIRT2 with AGK2, a SIRT2-specific inhibitor, augments the efficacy of IR in cancer cells and tumors. Our findings define a regulatory step for DNA-PK activation by SIRT2-mediated deacetylation, elucidating a critical upstream signaling event initiating the repair of DSBs by NHEJ. Furthermore, our data suggest that SIRT2 inhibition may be a promising rationale-driven therapeutic strategy for increasing the effectiveness of radiation therapy.
Collapse
Affiliation(s)
- PamelaSara E Head
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Priya Kapoor-Vazirani
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Ganji P Nagaraju
- School of Medicine, Division of Hematology and Medical Oncology, University of Alabama, Birmingham, AL 35233, USA
| | - Hui Zhang
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Sandip K Rath
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Nho C Luong
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Ramona Haji-Seyed-Javadi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Fatmata Sesay
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Shi-Ya Wang
- Department of Radiation Oncology, UT Southwestern Medical School, Dallas, TX 75390, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Waaqo Daddacha
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA
| | - Elizabeth V Minten
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Boying Song
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Diana Danelia
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shuyi Li
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David M Smalley
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ya Wang
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - Xingming Deng
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| | - William S Dynan
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bassel El-Rayes
- School of Medicine, Division of Hematology and Medical Oncology, University of Alabama, Birmingham, AL 35233, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical School, Dallas, TX 75390, USA
| | - David S Yu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine,Atlanta, GA 30322, USA
| |
Collapse
|
20
|
Urushihara Y, Hashimoto T, Fujishima Y, Hosoi Y. AMPK/FOXO3a Pathway Increases Activity and/or Expression of ATM, DNA-PKcs, Src, EGFR, PDK1, and SOD2 and Induces Radioresistance under Nutrient Starvation. Int J Mol Sci 2023; 24:12828. [PMID: 37629008 PMCID: PMC10454868 DOI: 10.3390/ijms241612828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Most solid tumors contain hypoxic and nutrient-deprived microenvironments. The cancer cells in these microenvironments have been reported to exhibit radioresistance. We have previously reported that nutrient starvation increases the expression and/or activity of ATM and DNA-PKcs, which are involved in the repair of DNA double-strand breaks induced by ionizing radiation. In the present study, to elucidate the molecular mechanisms underlying these phenomena, we investigated the roles of AMPK and FOXO3a, which play key roles in the cellular response to nutrient starvation. Nutrient starvation increased clonogenic cell survival after irradiation and increased the activity and/or expression of AMPKα, FOXO3a, ATM, DNA-PKcs, Src, EGFR, PDK1, and SOD2 in MDA-MB-231 cells. Knockdown of AMPKα using siRNA suppressed the activity and/or expression of FOXO3a, ATM, DNA-PKcs, Src, EGFR, PDK1, and SOD2 under nutrient starvation. Knockdown of FOXO3a using siRNA suppressed the activity and/or expression of AMPKα, ATM, DNA-PKcs, FOXO3a, Src, EGFR, PDK1, and SOD2 under nutrient starvation. Nutrient starvation decreased the incidence of apoptosis after 8 Gy irradiation. Knockdown of FOXO3a increased the incidence of apoptosis after irradiation under nutrient starvation. AMPK and FOXO3a appear to be key molecules that induce radioresistance under nutrient starvation and may serve as targets for radiosensitization.
Collapse
Affiliation(s)
- Yusuke Urushihara
- Department of Radiation Biology, School of Medicine, Tohoku University, Sendai 980-8575, Japan
- Kobe Research Lab, Oncolys BioPharma Inc., Kobe 650-0047, Japan
| | - Takuma Hashimoto
- Department of Radiation Biology, School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Yohei Fujishima
- Department of Radiation Biology, School of Medicine, Tohoku University, Sendai 980-8575, Japan
- Department of Risk Analysis and Biodosimetry, Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki 036-8562, Japan
| | - Yoshio Hosoi
- Department of Radiation Biology, School of Medicine, Tohoku University, Sendai 980-8575, Japan
| |
Collapse
|
21
|
Lu H, Zhang Q, Laverty DJ, Puncheon AC, Augustine M, Williams G, Nagel Z, Chen BC, Davis A. ATM phosphorylates the FATC domain of DNA-PKcs at threonine 4102 to promote non-homologous end joining. Nucleic Acids Res 2023; 51:6770-6783. [PMID: 37309889 PMCID: PMC10359628 DOI: 10.1093/nar/gkad505] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
Ataxia-telangiectasia mutated (ATM) drives the DNA damage response via modulation of multiple signal transduction and DNA repair pathways. Previously, ATM activity was implicated in promoting the non-homologous end joining (NHEJ) pathway to repair a subset of DNA double-stranded breaks (DSBs), but how ATM performs this function is still unclear. In this study, we identified that ATM phosphorylates the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a core NHEJ factor, at its extreme C-terminus at threonine 4102 (T4102) in response to DSBs. Ablating phosphorylation at T4102 attenuates DNA-PKcs kinase activity and this destabilizes the interaction between DNA-PKcs and the Ku-DNA complex, resulting in decreased assembly and stabilization of the NHEJ machinery at DSBs. Phosphorylation at T4102 promotes NHEJ, radioresistance, and increases genomic stability following DSB induction. Collectively, these findings establish a key role for ATM in NHEJ-dependent repair of DSBs through positive regulation of DNA-PKcs.
Collapse
Affiliation(s)
- Huiming Lu
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX75390, USA
| | - Qin Zhang
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX75390, USA
| | - Daniel J Laverty
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA02115, USA
| | - Andrew C Puncheon
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX75390, USA
| | - Mathew M Augustine
- Division of Surgical Oncology, Department of Surgery, UT Southwestern Medical Center, Dallas, TX75390, USA
- Department of Surgery, North Texas VA Medical Center, Dallas, TX75216, USA
| | - Gareth J Williams
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA02115, USA
| | - Benjamin P C Chen
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX75390, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX75390, USA
| |
Collapse
|
22
|
Obata H, Ogawa M, Zalutsky MR. DNA Repair Inhibitors: Potential Targets and Partners for Targeted Radionuclide Therapy. Pharmaceutics 2023; 15:1926. [PMID: 37514113 PMCID: PMC10384049 DOI: 10.3390/pharmaceutics15071926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The present review aims to explore the potential targets/partners for future targeted radionuclide therapy (TRT) strategies, wherein cancer cells often are not killed effectively, despite receiving a high average tumor radiation dose. Here, we shall discuss the key factors in the cancer genome, especially those related to DNA damage response/repair and maintenance systems for escaping cell death in cancer cells. To overcome the current limitations of TRT effectiveness due to radiation/drug-tolerant cells and tumor heterogeneity, and to make TRT more effective, we propose that a promising strategy would be to target the DNA maintenance factors that are crucial for cancer survival. Considering their cancer-specific DNA damage response/repair ability and dysregulated transcription/epigenetic system, key factors such as PARP, ATM/ATR, amplified/overexpressed transcription factors, and DNA methyltransferases have the potential to be molecular targets for Auger electron therapy; moreover, their inhibition by non-radioactive molecules could be a partnering component for enhancing the therapeutic response of TRT.
Collapse
Affiliation(s)
- Honoka Obata
- Department of Advanced Nuclear Medicine Sciences, National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Department of Molecular Imaging and Theranostics, National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Departments of Radiology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Mikako Ogawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Michael R Zalutsky
- Departments of Radiology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
| |
Collapse
|
23
|
Li Z, Jiao X, Robertson AG, Di Sante G, Ashton AW, DiRocco A, Wang M, Zhao J, Addya S, Wang C, McCue PA, South AP, Cordon-Cardo C, Liu R, Patel K, Hamid R, Parmar J, DuHadaway JB, Jones SJM, Casimiro MC, Schultz N, Kossenkov A, Phoon LY, Chen H, Lan L, Sun Y, Iczkowski KA, Rui H, Pestell RG. The DACH1 gene is frequently deleted in prostate cancer, restrains prostatic intraepithelial neoplasia, decreases DNA damage repair, and predicts therapy responses. Oncogene 2023; 42:1857-1873. [PMID: 37095257 PMCID: PMC10238272 DOI: 10.1038/s41388-023-02668-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/26/2023]
Abstract
Prostate cancer (PCa), the second leading cause of death in American men, includes distinct genetic subtypes with distinct therapeutic vulnerabilities. The DACH1 gene encodes a winged helix/Forkhead DNA-binding protein that competes for binding to FOXM1 sites. Herein, DACH1 gene deletion within the 13q21.31-q21.33 region occurs in up to 18% of human PCa and was associated with increased AR activity and poor prognosis. In prostate OncoMice, prostate-specific deletion of the Dach1 gene enhanced prostatic intraepithelial neoplasia (PIN), and was associated with increased TGFβ activity and DNA damage. Reduced Dach1 increased DNA damage in response to genotoxic stresses. DACH1 was recruited to sites of DNA damage, augmenting recruitment of Ku70/Ku80. Reduced Dach1 expression was associated with increased homology directed repair and resistance to PARP inhibitors and TGFβ kinase inhibitors. Reduced Dach1 expression may define a subclass of PCa that warrants specific therapies.
Collapse
Affiliation(s)
- Zhiping Li
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, VSZ 4S6, Canada
- Dxige Research, Courtenay, BC, V9N 1C2, Canada
| | - Gabriele Di Sante
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Anthony W Ashton
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
- Lankenau Institute for Medical Research, 100 East Lancaster Avenue, Wynnewood, PA, 19096, USA
- Division of Perinatal Research, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW, 2065, Australia
- Sydney Medical School Northern, University of Sydney, Sydney, NSW, 2006, Australia
| | - Agnese DiRocco
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Min Wang
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Jun Zhao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Sankar Addya
- Department of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - Peter A McCue
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Mt. Sinai, Hospital, 1468 Madison Ave., Floor 15, New York, NY, 10029, USA
| | - Runzhi Liu
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Kishan Patel
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Rasha Hamid
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Jorim Parmar
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - James B DuHadaway
- Lankenau Institute for Medical Research, 100 East Lancaster Avenue, Wynnewood, PA, 19096, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, VSZ 4S6, Canada
| | - Mathew C Casimiro
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
- Abraham Baldwin Agricultural College, Department of Science and Mathematics, Box 15, 2802 Moore Highway, Tifton, GA, 31794, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce St., Philadelphia, PA, 19104, USA
| | - Lai Yee Phoon
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Hao Chen
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Li Lan
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Yunguang Sun
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Richard G Pestell
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA.
- The Wistar Cancer Center, Philadelphia, PA, 19104, USA.
| |
Collapse
|
24
|
Chae K, Overcash JM, Dawson C, Valentin C, Tsujimoto H, Myles KM, Adelman ZN. CRISPR-based gene editing of non-homologous end joining factors biases DNA repair pathway choice toward single-strand annealing in Aedes aegypti. CURRENT RESEARCH IN BIOTECHNOLOGY 2023; 5:100133. [PMID: 37475832 PMCID: PMC10357993 DOI: 10.1016/j.crbiot.2023.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
To maintain genome stability, eukaryotic cells orchestrate DNA repair pathways to process DNA double-strand breaks (DSBs) that result from diverse developmental or environmental stimuli. Bias in the selection of DSB repair pathways, either non-homologous end joining (NHEJ) or homology-directed repair (HDR), is also critical for efficient gene editing and for homing-based gene drive approaches developed for the control of disease-transmitting vector mosquitoes. However, little is understood about DNA repair homeostasis in the mosquito genome. Here, we utilized CRISPR/Cas9 to generate indel mutant strains for core NHEJ factors ku80, DNA ligase IV (lig4), and DNA-PKcs in the mosquito Aedes aegypti and evaluated the corresponding effects on DNA repair. In a plasmid-based assay, disruption of ku80 or lig4, but not DNA-PKcs, reduced both NHEJ and SSA. However, a transgenic reporter strain-based test revealed that those mutations significantly biased DNA repair events toward SSA. Interestingly, ku80 mutation also significantly increased the end joining rate by a yet-characterized mechanism in males. Our study provides evidence that the core NHEJ factors have an antagonistic effect on SSA-based DSB repair of the Ae. aegypti genome. Down-modulating the NHEJ pathway can enhance the efficiency of nuclease-based genetic control approaches, as most of those operate by homology-based repair processes along with extensive DNA end resection that is antagonized by NHEJ.
Collapse
Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Justin M. Overcash
- U.S. Department of Agriculture-Animal and Plant Health Inspection Service (USDA-APHIS), Biotechnology Regulatory Services, Riverdale, MD 20737, United States
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Collin Valentin
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Hitoshi Tsujimoto
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Kevin M. Myles
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Zach N. Adelman
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| |
Collapse
|
25
|
Lee YR, Kang GS, Oh T, Jo HJ, Park HJ, Ahn GO. DNA-Dependent Protein Kinase Catalytic Subunit (DNA-PKcs): Beyond the DNA Double-Strand Break Repair. Mol Cells 2023; 46:200-205. [PMID: 36756777 PMCID: PMC10086554 DOI: 10.14348/molcells.2023.2164] [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: 10/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 02/10/2023] Open
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase related kinase family is a well-known player in repairing DNA double strand break through non-homologous end joining pathway. This mechanism has allowed us to understand its critical role in T and B cell development through V(D)J recombination and class switch recombination, respectively. We have also learned that the defects in these mechanisms lead to severely combined immunodeficiency (SCID). Here we highlight some of the latest evidence where DNA-PKcs has been shown to localize not only in the nucleus but also in the cytoplasm, phosphorylating various proteins involved in cellular metabolism and cytokine production. While it is an exciting time to unveil novel functions of DNA-PKcs, one should carefully choose experimental models to study DNA-PKcs as the experimental evidence has been shown to differ between cells of defective DNA-PKcs and those of DNA-PKcs knockout. Moreover, while there are several DNA-PK inhibitors currently being evaluated in the clinical trials in attempt to increase the efficacy of radiotherapy or chemotherapy, multiple functions and subcellular localization of DNA-PKcs in various types of cells may further complicate the effects at the cellular and organismal level.
Collapse
Affiliation(s)
- Ye-Rim Lee
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Gi-Sue Kang
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Taerim Oh
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hye-Ju Jo
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hye-Joon Park
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - G-One Ahn
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
26
|
Chen W, Chiang J, Shang Z, Palchik G, Newman C, Zhang Y, Davis AJ, Lee H, Chen BPC. DNA-PKcs and ATM modulate mitochondrial ADP-ATP exchange as an oxidative stress checkpoint mechanism. EMBO J 2023; 42:e112094. [PMID: 36727301 PMCID: PMC10015379 DOI: 10.15252/embj.2022112094] [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: 07/11/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 02/03/2023] Open
Abstract
DNA-PKcs is a key regulator of DNA double-strand break repair. Apart from its canonical role in the DNA damage response, DNA-PKcs is involved in the cellular response to oxidative stress (OS), but its exact role remains unclear. Here, we report that DNA-PKcs-deficient human cells display depolarized mitochondria membrane potential (MMP) and reoriented metabolism, supporting a role for DNA-PKcs in oxidative phosphorylation (OXPHOS). DNA-PKcs directly interacts with mitochondria proteins ANT2 and VDAC2, and formation of the DNA-PKcs/ANT2/VDAC2 (DAV) complex supports optimal exchange of ADP and ATP across mitochondrial membranes to energize the cell via OXPHOS and to maintain MMP. Moreover, we demonstrate that the DAV complex temporarily dissociates in response to oxidative stress to attenuate ADP-ATP exchange, a rate-limiting step for OXPHOS. Finally, we found that dissociation of the DAV complex is mediated by phosphorylation of DNA-PKcs at its Thr2609 cluster by ATM kinase. Based on these findings, we propose that the coordination between the DAV complex and ATM serves as a novel oxidative stress checkpoint to decrease ROS production from mitochondrial OXPHOS and to hasten cellular recovery from OS.
Collapse
Affiliation(s)
- Wei‐Min Chen
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
- Department of Life ScienceNational Taiwan UniversityTaipeiTaiwan
| | - Jui‐Chung Chiang
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
- Department of Life ScienceNational Taiwan UniversityTaipeiTaiwan
| | - Zengfu Shang
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
| | - Guillermo Palchik
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
| | - Ciara Newman
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
| | - Yuanyuan Zhang
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
| | - Hsinyu Lee
- Department of Life ScienceNational Taiwan UniversityTaipeiTaiwan
| | - Benjamin PC Chen
- Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical Center at DallasDallasTXUSA
| |
Collapse
|
27
|
Lu H, Zhang Q, Laverty DJ, Puncheon AC, Williams GJ, Nagel ZD, Chen BP, Davis AJ. ATM phosphorylates the FATC domain of DNA-PK cs at threonine 4102 to promote non-homologous end joining. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526879. [PMID: 36778257 PMCID: PMC9915669 DOI: 10.1101/2023.02.02.526879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ataxia-telangiectasia mutated (ATM) drives the DNA damage response via modulation of multiple signal transduction and DNA repair pathways. Previously, ATM activity was implicated in promoting the non-homologous end joining (NHEJ) pathway to repair a subset of DNA double strand breaks (DSBs), but how ATM performs this function is still unclear. In this study, we identified that ATM phosphorylates the DNA-dependent protein kinase catalytic subunit (DNA-PK cs ), a core NHEJ factor, at its extreme C-terminus at threonine 4102 (T4102) in response to DSBs. Phosphorylation at T4102 stabilizes the interaction between DNA-PK cs and the Ku-DNA complex and promotes assembly and stabilization of the NHEJ machinery at DSBs. Ablating phosphorylation at this site results in decreased NHEJ, radiosensitivity, and increased radiation-induced genomic instability. Collectively, these findings establish a key role for ATM in NHEJ-dependent repair of DSBs through positive regulation of DNA-PK cs .
Collapse
|
28
|
DNA Double-Strand Break-Related Competitive Endogenous RNA Network of Noncoding RNA in Bovine Cumulus Cells. Genes (Basel) 2023; 14:genes14020290. [PMID: 36833217 PMCID: PMC9956238 DOI: 10.3390/genes14020290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
(1) Background: DNA double strand breaks (DSBs) are the most serious form of DNA damage that affects oocyte maturation and the physiological state of follicles and ovaries. Non-coding RNAs (ncRNAs) play a crucial role in DNA damage and repair. This study aims to analyze and establish the network of ncRNAs when DSB occurs and provide new ideas for next research on the mechanism of cumulus DSB. (2) Methods: Bovine cumulus cells (CCs) were treated with bleomycin (BLM) to construct a DSB model. We detected the changes of the cell cycle, cell viability, and apoptosis to determine the effect of DSBs on cell biology, and further evaluated the relationship between the transcriptome and competitive endogenous RNA (ceRNA) network and DSBs. (3) Results: BLM increased γH2AX positivity in CCs, disrupted the G1/S phase, and decreased cell viability. Totals of 848 mRNAs, 75 long noncoding RNAs (lncRNAs), 68 circular RNAs (circRNAs), and 71 microRNAs (miRNAs) in 78 groups of lncRNA-miRNA-mRNA regulatory networks, 275 groups of circRNA-miRNA-mRNA regulatory networks, and five groups of lncRNA/circRNA-miRNA-mRNA co-expression regulatory networks were related to DSBs. Most differentially expressed ncRNAs were annotated to cell cycle, p53, PI3K-AKT, and WNT signaling pathways. (4) Conclusions: The ceRNA network helps to understand the effects of DNA DSBs activation and remission on the biological function of CCs.
Collapse
|
29
|
Li Z, Jiao X, Robertson AG, Sante GD, Ashton AW, DiRocco A, Wang M, Zhao J, Addya S, Wang C, McCue PA, South AP, Cordon-Cardo C, Liu R, Patel K, Hamid R, Parmar J, DuHadaway JB, Jones SJ, Casimiro MC, Schultz N, Kossenkov A, Phoon LY, Chen H, Lan L, Sun Y, Iczkowski KA, Rui H, Pestell RG. The DACH1 gene is frequently deleted in prostate cancer, restrains prostatic intraepithelial neoplasia, decreases DNA damage repair, and predicts therapy responses. RESEARCH SQUARE 2023:rs.3.rs-2423179. [PMID: 36712010 PMCID: PMC9882663 DOI: 10.21203/rs.3.rs-2423179/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Prostate cancer (PCa), the second leading cause of death in American men, includes distinct genetic subtypes with distinct therapeutic vulnerabilities. The DACH1 gene encodes a winged helix/Forkhead DNA-binding protein that competes for binding to FOXM1 sites. Herein, DACH1 gene deletion within the 13q21.31-q21.33 region occurs in up to 18% of human PCa and was associated with increased AR activity and poor prognosis. In prostate OncoMice, prostate-specific deletion of the Dach1 gene enhanced prostatic intraepithelial neoplasia (PIN), and was associated with increased TGFb activity and DNA damage. Reduced Dach1 increased DNA damage in response to genotoxic stresses. DACH1 was recruited to sites of DNA damage, augmenting recruitment of Ku70/Ku80. Reduced Dach1 expression was associated with increased homology directed repair and resistance to PARP inhibitors and TGFb kinase inhibitors. Reduced Dach1 expression may define a subclass of PCa that warrants specific therapies.
Collapse
Affiliation(s)
- Zhiping Li
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - A. Gordon Robertson
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Gabriele Di Sante
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Anthony W. Ashton
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
- Division of Perinatal Research, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW, 2065, Australia; Sydney Medical School Northern, University of Sydney, NSW, 2006, Australia
- Lankenau Institute for Medical Research, 100 East Lancaster Avenue, Wynnewood, PA 19096
| | - Agnese DiRocco
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Min Wang
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Jun Zhao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Sankar Addya
- Department of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10 Street, Philadelphia, PA 19107
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10 Street, Philadelphia, PA 19107
| | - Peter A. McCue
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10 Street, Philadelphia, PA 19107
| | - Andrew P. South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10 Street, Philadelphia, PA 19107
| | - Carlos Cordon-Cardo
- Department of Pathology, Mt. Sinai, Hospital, 1468 Madison Ave., Floor 15, New York, NY, 10029
| | - Runzhi Liu
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Kishan Patel
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Rasha Hamid
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - Jorim Parmar
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
| | - James B. DuHadaway
- Lankenau Institute for Medical Research, 100 East Lancaster Avenue, Wynnewood, PA 19096
| | - Steven J. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Mathew C. Casimiro
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
- Abraham Baldwin Agricultural College, Department of Science and Mathematics, Box 15, 2802 Moore Highway, Tifton, GA, 31794
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA
| | - Lai Yee Phoon
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA, and Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Hao Chen
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA, and Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Li Lan
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA, and Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Yunguang Sun
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Richard G. Pestell
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902 Pennsylvania
- The Wistar Cancer Center, Philadelphia, PA 19107
| |
Collapse
|
30
|
The lncRNA LUCAT1 is elevated in inflammatory disease and restrains inflammation by regulating the splicing and stability of NR4A2. Proc Natl Acad Sci U S A 2023; 120:e2213715120. [PMID: 36577072 PMCID: PMC9910463 DOI: 10.1073/pnas.2213715120] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nuclear long non-coding RNA LUCAT1 has previously been identified as a negative feedback regulator of type I interferon and inflammatory cytokine expression in human myeloid cells. Here, we define the mechanistic basis for the suppression of inflammatory gene expression by LUCAT1. Using comprehensive identification of RNA-binding proteins by mass spectrometry as well as RNA immunoprecipitation, we identified proteins important in processing and alternative splicing of mRNAs as LUCAT1-binding proteins. These included heterogeneous nuclear ribonucleoprotein C, M, and A2B1. Consistent with this finding, cells lacking LUCAT1 have altered splicing of selected immune genes. In particular, upon lipopolysaccharide stimulation, the splicing of the nuclear receptor 4A2 (NR4A2) gene was particularly affected. As a consequence, expression of NR4A2 was reduced and delayed in cells lacking LUCAT1. NR4A2-deficient cells had elevated expression of immune genes. These observations suggest that LUCAT1 is induced to control the splicing and stability of NR4A2, which is in part responsible for the anti-inflammatory effect of LUCAT1. Furthermore, we analyzed a large cohort of patients with inflammatory bowel disease as well as asthma and chronic obstructive pulmonary disease. In these patients, LUCAT1 levels were elevated and in both diseases, positively correlated with disease severity. Collectively, these studies define a key molecular mechanism of LUCAT1-dependent immune regulation through post-transcriptional regulation of mRNAs highlighting its role in the regulation of inflammatory disease.
Collapse
|
31
|
Krämer OH, Diehl T, Roos WP. Assessing the Effect of Histone Deacetylase Inhibitors on DNA Double-Strand Break Repair by Nonhomologous End Joining. Methods Mol Biol 2023; 2589:293-302. [PMID: 36255632 DOI: 10.1007/978-1-0716-2788-4_19] [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: 06/16/2023]
Abstract
This book chapter describes a plasmid-based reporter method, first described by Bennardo et al. (2008) that we use in our laboratory for determining the activity of the repair of DNA double-strand breaks by nonhomologous end joining. This method can be used to measure the impact of epigenetic modifiers of the histone deacetylase family on this DNA repair pathway by flow cytometry.
Collapse
Affiliation(s)
- Oliver H Krämer
- Institute of Toxicology, University Medical Center Mainz, Mainz, Germany
| | - Tamara Diehl
- Institute of Toxicology, University Medical Center Mainz, Mainz, Germany
| | - Wynand P Roos
- Institute of Toxicology, University Medical Center Mainz, Mainz, Germany.
| |
Collapse
|
32
|
Naeem M, Alkhodairy HF, Ashraf I, Khalil AB. CRISPR/Cas System Toward the Development of Next-Generation Recombinant Vaccines: Current Scenario and Future Prospects. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2023; 48:1-11. [PMID: 36185592 PMCID: PMC9510529 DOI: 10.1007/s13369-022-07266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
The initially developed vaccines were relying mostly on attenuation and inactivation of pathogens. The use of recombinant DNA technology allows the targeting of immune responses focused against a few protective antigens. The conventional recombination methods for generating vaccines are time-consuming, laborious, and less efficient. To overcome these limitations, a new precise CRISPR/Cas9 with high efficacy, specificity, and low-cost properties has solved a lot of current problems of recombinant vaccines that intrigued the inspiration for novel recombinant vaccine development. CRISPR/Cas9 system was discovered as a bacterial adaptive immune system. In the domain of virology, CRISPR/Cas9 is used to engineer the virus genome to understand the fundamentals of viral pathogenesis, gene therapy, and virus-host interactions. One step ahead CRISPR/Cass9 bypassed the vaccine to precisely engineer the B-cells to secrete the specific antibodies against deadly viral pathogens. There is a critical literature review gap especially in the use of CRISPR/Cas9 to generate recombinant vaccines against viral diseases and its prospective application to engineering the B-cells in immunocompromised people. This review heights the application of CRISPR/Cas9 compared to conventional approaches for the development of recombinant vaccine vectors, editing the genes of B-cells, and challenges that need to be overcome. The factors affecting CRISPR/Cas9-edited recombinant vaccines and prospects in the context of viral genome editing for the development of vaccines will be discussed.
Collapse
Affiliation(s)
- Muhammad Naeem
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261 Saudi Arabia
| | - Hanoof Fahd Alkhodairy
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261 Saudi Arabia
| | - Iqra Ashraf
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Amjad Bajes Khalil
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261 Saudi Arabia
| |
Collapse
|
33
|
Novotny JP, Mariño-Enríquez A, Fletcher JA. Targeting DNA-PK. Cancer Treat Res 2023; 186:299-312. [PMID: 37978142 DOI: 10.1007/978-3-031-30065-3_16] [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: 11/19/2023]
Abstract
This chapter explores the multifaceted roles of DNA-PK with particular focus on its functions in non-homologous end-joining (NHEJ) DNA repair. DNA-PK is the primary orchestrator of NHEJ but also regulates other biologic processes. The growing understanding of varied DNA-PK biologic roles highlights new avenues for cancer treatment. However, these multiple roles also imply challenges, particularly in combination therapies, with perhaps a higher risk of clinical toxicities than was previously envisioned. These considerations underscore the need for compelling and innovative strategies to accomplish effective clinical translation.
Collapse
|
34
|
Mouawad R, Neamati N. Inhibition of Protein Disulfide Isomerase (PDIA1) Leads to Proteasome-Mediated Degradation of Ubiquitin-like PHD and RING Finger Domain-Containing Protein 1 (UHRF1) and Increased Sensitivity of Glioblastoma Cells to Topoisomerase II Inhibitors. ACS Pharmacol Transl Sci 2022; 6:100-114. [PMID: 36654750 PMCID: PMC9841782 DOI: 10.1021/acsptsci.2c00186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Glioblastoma (GBM) is the most aggressive brain tumor, and the prognosis remains poor with current available treatments. PDIA1 is considered a promising therapeutic target in GBM. In this study, we demonstrate that targeting PDIA1 results in increased GBM cell death by topoisomerase II (Top-II) inhibitors resulting in proteasome-mediated degradation of the oncogenic protein UHRF1. Combination of the PDIA1 inhibitor, bepristat-2a, produces strong synergy with doxorubicin, etoposide, and mitoxantrone in GBM and other cancer cell lines. Our bioinformatics analysis of multiple datasets revealed downregulation of UHRF1, upon PDIA1 inhibition. In addition, PDIA1 inhibition results in proteasome-mediated degradation of UHRF1 protein. Interestingly, treatment of GBM cells with bepristat-2a results in increased apoptosis and resistance to ferroptosis. Our findings emphasize the importance of PDIA1 as a therapeutic target in GBM and present a promising new therapeutic approach using Top-II inhibitors for GBM treatment.
Collapse
|
35
|
Li Z, Zhou Z, Tian S, Zhang K, An G, Zhang Y, Ma R, Sheng B, Wang T, Yang H, Yang L. RPRM deletion preserves hematopoietic regeneration by promoting EGFR-dependent DNA repair and hematopoietic stem cell proliferation post ionizing radiation. Cell Biol Int 2022; 46:2158-2172. [PMID: 36041213 PMCID: PMC9804513 DOI: 10.1002/cbin.11900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/28/2022] [Accepted: 08/22/2022] [Indexed: 01/05/2023]
Abstract
Reprimo (RPRM), a target gene of p53, is a known tumor suppressor. DNA damage induces RPRM, which triggers p53-dependent G2 arrest by inhibiting cyclin B1/Cdc2 complex activation and promotes DNA damage-induced apoptosis. RPRM negatively regulates ataxia-telangiectasia mutated by promoting its nuclear-cytoplasmic translocation and degradation, thus inhibiting DNA damage. Therefore, RPRM plays a crucial role in DNA damage response. Moreover, the loss of RPRM confers radioresistance in mice, which enables longer survival and less severe intestinal injury after radiation exposure. However, the role of RPRM in radiation-induced hematopoietic system injury remains unknown. Herein, utilizing a RPRM-knockout mouse model, we found that RPRM deletion did not affect steady-state hematopoiesis in mice. However, RPRM knockout significantly alleviated radiation-induced hematopoietic system injury and preserved mouse hematopoietic regeneration in hematopoietic stem cells (HSCs) against radiation-induced DNA damage. Further mechanistic studies showed that RPRM loss significantly increased EGFR expression and phosphorylation in HSCs to activate STAT3 and DNA-PKcs, thus promoting HSC DNA repair and proliferation. These findings reveal the critical role of RPRM in radiation-induced hematopoietic system injury, confirming our hypothesis that RPRM may serve as a novel target for radiation protection.
Collapse
Affiliation(s)
- Zixuan Li
- State Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouJiangsuChina,School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University/Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhouJiangsuChina,Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Zhou Zhou
- State Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouJiangsuChina,School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University/Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhouJiangsuChina
| | - Shuaiyu Tian
- Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Kailu Zhang
- Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Gangli An
- Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Yarui Zhang
- State Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouJiangsuChina,School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University/Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhouJiangsuChina
| | - Renyuxue Ma
- Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Binjie Sheng
- Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Tian Wang
- State Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouJiangsuChina,School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University/Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhouJiangsuChina,Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| | - Hongying Yang
- State Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouJiangsuChina,School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University/Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhouJiangsuChina
| | - Lin Yang
- State Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouJiangsuChina,School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University/Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsSoochow UniversitySuzhouJiangsuChina,Cyrus Tang Medical Institute, Collaborative Innovation Center of HematologySoochow UniversitySuzhouJiangsuChina
| |
Collapse
|
36
|
Kim H, Kim D, Choi H, Shin G, Lee JK. Deubiquitinase USP2 stabilizes the MRE11-RAD50-NBS1 complex at DNA double-strand break sites by counteracting the ubiquitination of NBS1. J Biol Chem 2022; 299:102752. [PMID: 36436562 PMCID: PMC9758435 DOI: 10.1016/j.jbc.2022.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex plays essential roles in the cellular response to DNA double-strand breaks (DSBs), which are the most cytotoxic DNA lesions, and is a target of various modifications and controls. Recently, lysine 48-linked ubiquitination of NBS1, resulting in premature disassembly of the MRN complex from DSB sites, was observed in cells lacking RECQL4 helicase activity. However, the role and control of this ubiquitination during the DSB response in cells with intact RECQL4 remain unknown. Here, we showed that USP2 counteracts this ubiquitination and stabilizes the MRN complex during the DSB response. By screening deubiquitinases that increase the stability of the MRN complex in RECQL4-deficient cells, USP2 was identified as a new deubiquitinase that acts at DSB sites to counteract NBS1 ubiquitination. We determined that USP2 is recruited to DSB sites in a manner dependent on ATM, a major checkpoint kinase against DSBs, and stably interacts with NBS1 and RECQL4 in immunoprecipitation experiments. Phosphorylation of two critical residues in the N terminus of USP2 by ATM is required for its recruitment to DSBs and its interaction with RECQL4. While inactivation of USP2 alone does not substantially influence the DSB response, we found that inactivation of USP2 and USP28, another deubiquitinase influencing NBS1 ubiquitination, results in premature disassembly of the MRN complex from DSB sites as well as defects in ATM activation and homologous recombination repair abilities. These results suggest that deubiquitinases counteracting NBS1 ubiquitination are essential for the stable maintenance of the MRN complex and proper cellular response to DSBs.
Collapse
Affiliation(s)
- Hyunsup Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Dongmin Kim
- Department of Biology Education, Seoul National University, Seoul, Korea
| | - Hyemin Choi
- Department of Biology Education, Seoul National University, Seoul, Korea
| | - Gwangsu Shin
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Joon-Kyu Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea; Department of Biology Education, Seoul National University, Seoul, Korea.
| |
Collapse
|
37
|
The Role of DNA Damage and Repair in Idiopathic Pulmonary Fibrosis. Antioxidants (Basel) 2022; 11:antiox11112292. [PMID: 36421478 PMCID: PMC9687113 DOI: 10.3390/antiox11112292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Given that the lung is exposed to the external environment, it is likely that oxidative stress, especially the stimulation of DNA, would be of particular importance in pulmonary fibrosis. DNA damage is known to play an important role in idiopathic pulmonary fibrosis initiation, so DNA repair systems targeting damage are also crucial for the survival of lung cells. Although many contemporary reports have summarized the role of individual DNA damage and repair pathways in their hypotheses, they have not focused on idiopathic pulmonary fibrosis. This review, therefore, aims to provide a concise overview for researchers to understand the pathways of DNA damage and repair and their roles in IPF.
Collapse
|
38
|
The relationship between MUC19 copy number variation and growth traits of Chinese cattle. Gene 2022; 851:147010. [DOI: 10.1016/j.gene.2022.147010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/04/2022]
|
39
|
R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage. EPIGENOMES 2022; 6:epigenomes6030026. [PMID: 36135313 PMCID: PMC9498298 DOI: 10.3390/epigenomes6030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/24/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is thought to employ a strategy of exclusively transcribing meiotic or post-meiotic genes before their use. Recent studies have shown that R-loops, three-stranded DNA/RNA hybrid nucleotide structures formed during transcription, play a crucial role in transcription and genome integrity. Although our knowledge about the function of R-loops during meiosis is limited, recent findings in mouse models have suggested that they play crucial roles in meiosis. Given that defective formation of an R-loop can cause abnormal transcription and transcription-coupled DNA damage, the precise regulatory network of R-loops may be essential in vivo for the faithful progression of mammalian meiosis and gametogenesis.
Collapse
|
40
|
Xiao H, Li F, Mladenov E, Soni A, Mladenova V, Pan B, Dueva R, Stuschke M, Timmermann B, Iliakis G. Increased Resection at DSBs in G2-Phase Is a Unique Phenotype Associated with DNA-PKcs Defects That Is Not Shared by Other Factors of c-NHEJ. Cells 2022; 11:cells11132099. [PMID: 35805183 PMCID: PMC9265841 DOI: 10.3390/cells11132099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
The load of DNA double-strand breaks (DSBs) induced in the genome of higher eukaryotes by different doses of ionizing radiation (IR) is a key determinant of DSB repair pathway choice, with homologous recombination (HR) and ATR substantially gaining ground at doses below 0.5 Gy. Increased resection and HR engagement with decreasing DSB-load generate a conundrum in a classical non-homologous end-joining (c-NHEJ)-dominated cell and suggest a mechanism adaptively facilitating resection. We report that ablation of DNA-PKcs causes hyper-resection, implicating DNA-PK in the underpinning mechanism. However, hyper-resection in DNA-PKcs-deficient cells can also be an indirect consequence of their c-NHEJ defect. Here, we report that all tested DNA-PKcs mutants show hyper-resection, while mutants with defects in all other factors of c-NHEJ fail to do so. This result rules out the model of c-NHEJ versus HR competition and the passive shift from c-NHEJ to HR as the causes of the increased resection and suggests the integration of DNA-PKcs into resection regulation. We develop a model, compatible with the results of others, which integrates DNA-PKcs into resection regulation and HR for a subset of DSBs. For these DSBs, we propose that the kinase remains at the break site, rather than the commonly assumed autophosphorylation-mediated removal from DNA ends.
Collapse
Affiliation(s)
- Huaping Xiao
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Fanghua Li
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Department of Particle Therapy, University Hospital Essen, West German Proton Therapy Centre Essen (WPE), West German Cancer Center (WTZ), German Cancer Consortium (DKTK), 45147 Essen, Germany;
| | - Emil Mladenov
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Aashish Soni
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Veronika Mladenova
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Bing Pan
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Rositsa Dueva
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, German Cancer Research Center (DKFZ), 45147 Essen, Germany
| | - Beate Timmermann
- Department of Particle Therapy, University Hospital Essen, West German Proton Therapy Centre Essen (WPE), West German Cancer Center (WTZ), German Cancer Consortium (DKTK), 45147 Essen, Germany;
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, German Cancer Research Center (DKFZ), 45147 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
- Correspondence: ; Tel.: +49-201-723-4152
| |
Collapse
|
41
|
Small-molecule enhancers of CRISPR-induced homology-directed repair in gene therapy: A medicinal chemist's perspective. Drug Discov Today 2022; 27:2510-2525. [PMID: 35738528 DOI: 10.1016/j.drudis.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/19/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022]
Abstract
CRISPR technologies are increasingly being investigated and utilized for the treatment of human genetic diseases via genome editing. CRISPR-Cas9 first generates a targeted DNA double-stranded break, and a functional gene can then be introduced to replace the defective copy in a precise manner by templated repair via the homology-directed repair (HDR) pathway. However, this is challenging owing to the relatively low efficiency of the HDR pathway compared with a rival random repair pathway known as non-homologous end joining (NHEJ). Small molecules can be employed to increase the efficiency of HDR and decrease that of NHEJ to improve the efficiency of precise knock-in genome editing. This review discusses the potential usage of such small molecules in the context of gene therapy and their drug-likeness, from a medicinal chemist's perspective.
Collapse
|
42
|
Chughtai AA, Pannhausen J, Dinger P, Wirtz J, Knüchel R, Gaisa NT, Eble MJ, Rose M. Effective Radiosensitization of Bladder Cancer Cells by Pharmacological Inhibition of DNA-PK and ATR. Biomedicines 2022; 10:biomedicines10061277. [PMID: 35740300 PMCID: PMC9220184 DOI: 10.3390/biomedicines10061277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/09/2022] Open
Abstract
This study aims at analyzing the impact of the pharmacological inhibition of DNA damage response (DDR) targets (DNA-PK and ATR) on radiosensitization of bladder cancer cell lines of different molecular/histological subtypes. Applying DNA-PK (AZD7648) and ATR (Ceralasertib) inhibitors on SCaBER, J82 and VMCUB-1 bladder cancer cell lines, we revealed sensitization upon ionizing radiation (IR), i.e., the IC50 for each drug shifted to a lower drug concentration with increased IR doses. In line with this, drug exposure retarded DNA repair after IR-induced DNA damage visualized by a neutral comet assay. Western blot analyses confirmed specific inhibition of targeted DDR pathways in the analyzed bladder cancer cell lines, i.e., drugs blocked DNA-PK phosphorylation at Ser2056 and the ATR downstream mediator CHK1 at Ser317. Interestingly, clonogenic survival assays indicated a cell-line-dependent synergism of combined DDR inhibition upon IR. Calculating combined index (CI) values, with and without IR, according to the Chou–Talalay method, confirmed drug- and IR-dose-specific synergistic CI values. Thus, we provide functional evidence that DNA-PK and ATR inhibitors specifically target corresponding DDR pathways retarding the DNA repair process at nano-molar concentrations. This, in turn, leads to a strong radiosensitizing effect and impairs the survival of bladder cancer cells.
Collapse
Affiliation(s)
- Ahmed Ali Chughtai
- Department of Radiation Oncology, RWTH Aachen University, 52074 Aachen, Germany;
- Correspondence: (A.A.C.); (M.R.); Tel.: +49-241-8036863 (A.A.C.); +49-241-8089715 (M.R.); Fax: +49-241-8082425 (A.A.C.); +49-241-8082439 (M.R.)
| | - Julia Pannhausen
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Pia Dinger
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Julia Wirtz
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Ruth Knüchel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Nadine T. Gaisa
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Michael J. Eble
- Department of Radiation Oncology, RWTH Aachen University, 52074 Aachen, Germany;
| | - Michael Rose
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
- Correspondence: (A.A.C.); (M.R.); Tel.: +49-241-8036863 (A.A.C.); +49-241-8089715 (M.R.); Fax: +49-241-8082425 (A.A.C.); +49-241-8082439 (M.R.)
| |
Collapse
|
43
|
Lu H, Guan J, Wang SY, Li GM, Bohr VA, Davis AJ. DNA-PKcs-dependent phosphorylation of RECQL4 promotes NHEJ by stabilizing the NHEJ machinery at DNA double-strand breaks. Nucleic Acids Res 2022; 50:5635-5651. [PMID: 35580045 PMCID: PMC9178012 DOI: 10.1093/nar/gkac375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Non-homologous end joining (NHEJ) is the major pathway that mediates the repair of DNA double-strand breaks (DSBs) generated by ionizing radiation (IR). Previously, the DNA helicase RECQL4 was implicated in promoting NHEJ, but its role in the pathway remains unresolved. In this study, we report that RECQL4 stabilizes the NHEJ machinery at DSBs to promote repair. Specifically, we find that RECQL4 interacts with the NHEJ core factor DNA-PKcs and the interaction is increased following IR. RECQL4 promotes DNA end bridging mediated by DNA-PKcs and Ku70/80 in vitro and the accumulation/retention of NHEJ factors at DSBs in vivo. Moreover, interaction between DNA-PKcs and the other core NHEJ proteins following IR treatment is attenuated in the absence of RECQL4. These data indicate that RECQL4 promotes the stabilization of the NHEJ factors at DSBs to support formation of the NHEJ long-range synaptic complex. In addition, we observed that the kinase activity of DNA-PKcs is required for accumulation of RECQL4 to DSBs and that DNA-PKcs phosphorylates RECQL4 at six serine/threonine residues. Blocking phosphorylation at these sites reduced the recruitment of RECQL4 to DSBs, attenuated the interaction between RECQL4 and NHEJ factors, destabilized interactions between the NHEJ machinery, and resulted in decreased NHEJ. Collectively, these data illustrate reciprocal regulation between RECQL4 and DNA-PKcs in NHEJ.
Collapse
Affiliation(s)
- Huiming Lu
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junhong Guan
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shih-Ya Wang
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guo-Min Li
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vilhelm A Bohr
- DNA Repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
44
|
Black Phosphorus Quantum Dots Enhance the Radiosensitivity of Human Renal Cell Carcinoma Cells through Inhibition of DNA-PKcs Kinase. Cells 2022; 11:cells11101651. [PMID: 35626687 PMCID: PMC9139844 DOI: 10.3390/cells11101651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/03/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Renal cell carcinoma (RCC) is one of the most aggressive urological malignancies and has a poor prognosis, especially in patients with metastasis. Although RCC is traditionally considered to be radioresistant, radiotherapy (RT) is still a common treatment for palliative management of metastatic RCC. Novel approaches are urgently needed to overcome radioresistance of RCC. Black phosphorus quantum dots (BPQDs) have recently received great attention due to their unique physicochemical properties and good biocompatibility. In the present study, we found that BPQDs enhance ionizing radiation (IR)-induced apoptotic cell death of RCC cells. BPQDs treatment significantly increases IR-induced DNA double-strand breaks (DSBs), as indicated by the neutral comet assay and the DSBs biomarkers γH2AX and 53BP1. Mechanistically, BPQDs can interact with purified DNA–protein kinase catalytic subunit (DNA-PKcs) and promote its kinase activity in vitro. BPQDs impair the autophosphorylation of DNA-PKcs at S2056, and this site phosphorylation is essential for efficient DNA DSBs repair and the release of DNA-PKcs from the damage sites. Consistent with this, BPQDs suppress nonhomologous end-joining (NHEJ) repair and lead to sustained high levels of autophosphorylated DNA-PKcs on the damaged sites. Moreover, animal experiments indicate that the combined approach with both BPQDs and IR displays better efficacy than monotreatment. These findings demonstrate that BPQDs have potential applications in radiosensitizing RCC cells.
Collapse
|
45
|
Subsets of Slow Dynamic Modes Reveal Global Information Sources as Allosteric Sites. J Mol Biol 2022; 434:167644. [DOI: 10.1016/j.jmb.2022.167644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023]
|
46
|
Hu C, Wallace N. Beta HPV Deregulates Double-Strand Break Repair. Viruses 2022; 14:v14050948. [PMID: 35632690 PMCID: PMC9146468 DOI: 10.3390/v14050948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Beta human papillomavirus (beta HPV) infections are common in adults. Certain types of beta HPVs are associated with nonmelanoma skin cancer (NMSC) in immunocompromised individuals. However, whether beta HPV infections promote NMSC in the immunocompetent population is unclear. They have been hypothesized to increase genomic instability stemming from ultraviolet light exposure by disrupting DNA damage responses. Implicit in this hypothesis is that the virus encodes one or more proteins that impair DNA repair signaling. Fluorescence-based reporters, next-generation sequencing, and animal models have been used to test this primarily in cells expressing beta HPV E6/E7. Of the two, beta HPV E6 appears to have the greatest ability to increase UV mutagenesis, by attenuating two major double-strand break (DSB) repair pathways, homologous recombination, and non-homologous end-joining. Here, we review this dysregulation of DSB repair and emerging approaches that can be used to further these efforts.
Collapse
|
47
|
Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
Collapse
Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
| |
Collapse
|
48
|
Dylgjeri E, Kothari V, Shafi AA, Semenova G, Gallagher PT, Guan YF, Pang A, Goodwin JF, Irani S, McCann JJ, Mandigo AC, Chand S, McNair CM, Vasilevskaya I, Schiewer MJ, Lallas CD, McCue PA, Gomella LG, Seifert EL, Carroll JS, Butler LM, Holst J, Kelly WK, Knudsen KE. A Novel Role for DNA-PK in Metabolism by Regulating Glycolysis in Castration-Resistant Prostate Cancer. Clin Cancer Res 2022; 28:1446-1459. [PMID: 35078861 PMCID: PMC9365345 DOI: 10.1158/1078-0432.ccr-21-1846] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/22/2021] [Accepted: 01/20/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE DNA-dependent protein kinase catalytic subunit (DNA-PKcs, herein referred as DNA-PK) is a multifunctional kinase of high cancer relevance. DNA-PK is deregulated in multiple tumor types, including prostate cancer, and is associated with poor outcomes. DNA-PK was previously nominated as a therapeutic target and DNA-PK inhibitors are currently undergoing clinical investigation. Although DNA-PK is well studied in DNA repair and transcriptional regulation, much remains to be understood about the way by which DNA-PK drives aggressive disease phenotypes. EXPERIMENTAL DESIGN Here, unbiased proteomic and metabolomic approaches in clinically relevant tumor models uncovered a novel role of DNA-PK in metabolic regulation of cancer progression. DNA-PK regulation of metabolism was interrogated using pharmacologic and genetic perturbation using in vitro cell models, in vivo xenografts, and ex vivo in patient-derived explants (PDE). RESULTS Key findings reveal: (i) the first-in-field DNA-PK protein interactome; (ii) numerous DNA-PK novel partners involved in glycolysis; (iii) DNA-PK interacts with, phosphorylates (in vitro), and increases the enzymatic activity of glycolytic enzymes ALDOA and PKM2; (iv) DNA-PK drives synthesis of glucose-derived pyruvate and lactate; (v) DNA-PK regulates glycolysis in vitro, in vivo, and ex vivo; and (vi) combination of DNA-PK inhibitor with glycolytic inhibitor 2-deoxyglucose leads to additive anti-proliferative effects in aggressive disease. CONCLUSIONS Findings herein unveil novel DNA-PK partners, substrates, and function in prostate cancer. DNA-PK impacts glycolysis through direct interaction with glycolytic enzymes and modulation of enzymatic activity. These events support energy production that may contribute to generation and/or maintenance of DNA-PK-mediated aggressive disease phenotypes.
Collapse
Affiliation(s)
- Emanuela Dylgjeri
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vishal Kothari
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ayesha A. Shafi
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Galina Semenova
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Peter T. Gallagher
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Yi F. Guan
- School of Medical Sciences and Prince of Wales Clinical School, UNSW Sydney, Sydney, Australia
| | - Angel Pang
- School of Medical Sciences and Prince of Wales Clinical School, UNSW Sydney, Sydney, Australia
| | - Jonathan F. Goodwin
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Swati Irani
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School and Freemasons Foundation Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, South Australia
| | - Jennifer J. McCann
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Amy C. Mandigo
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Saswati Chand
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christopher M. McNair
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Irina Vasilevskaya
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Matthew J. Schiewer
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Costas D. Lallas
- Department of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Peter A. McCue
- Department of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Leonard G. Gomella
- Department of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Erin L. Seifert
- Department of Pathology, Anatomy and Cell Biology and MitoCare Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jason S. Carroll
- Cancer Research UK Cambridge Research Institute, England, United Kingdom
| | - Lisa M. Butler
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School and Freemasons Foundation Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, South Australia
| | - Jeff Holst
- School of Medical Sciences and Prince of Wales Clinical School, UNSW Sydney, Sydney, Australia
| | - William K. Kelly
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E. Knudsen
- Department of Cancer Biology at Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| |
Collapse
|
49
|
Han Y, Huang X, Cao X, Li Y, Gao L, Jia J, Li G, Guo H, Liu X, Zhao H, Guan H, Zhou P, Gao S. SENP3-mediated TIP60 deSUMOylation is required for DNA-PKcs activity and DNA damage repair. MedComm (Beijing) 2022; 3:e123. [PMID: 35356800 PMCID: PMC8941250 DOI: 10.1002/mco2.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/13/2022] Open
Abstract
The activation of DNA-dependent kinase (DNA-PKcs) upon DNA damage contains a cascade of reactions, covering acetylation by TIP60, binding with Ku70/80, and autophosphorylation. However, how cells regulate TIP60-mediated acetylation of DNA-PKcs and the following DNA-PKcs activation upon DNA damage remains obscure. This present study reported that TIP60 is hyper-SUMOylated in normal conditions, but upon irradiation-induced DNA damage, small ubiquitin-like modifier (SUMO)-specific protease 3 (SENP3)-mediated deSUMOylation of TIP60 promoted its interaction with DNA-PKcs to form the TIP60-DNA-PKcs complex. We show that TIP60 SUMOylation is reduced quickly in response to DNA damage and the deSUMOylation of TIP60 by SENP3 is required for DNA-PKcs acetylation and its autophosphorylation. Comet and γH2AX immunofluorescence assay showed that knockdown of SENP3 impaired DNA damage repair. Using the NHEJ report system, we found that knockdown of SENP3 affected the efficiency of NHEJ. Further exploration using clonogenic survival assay, cell viability assay and cytoflow assay suggested that leaking SENP3 increased the sensitivity of tumour cells to serval DNA damage treatment. Overall, our findings revealed a previously unidentified role of SENP3 in regulating DNA-PKcs activity and DNA damage repair.
Collapse
Affiliation(s)
- Yang Han
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| | - Xin Huang
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| | - Xiaoyu Cao
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China.,School of life Sciences Hebei University Baoding China
| | - Yuchen Li
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China.,School of Medicine University of South China Hengyang China
| | - Lei Gao
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China.,School of life Sciences Hebei University Baoding China
| | - Jin Jia
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China.,School of Medicine University of South China Hengyang China
| | - Gang Li
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China.,School of Public Health Institute for Environmental Medicine and Radiation Hygiene University of South China Hengyang China
| | - Hejiang Guo
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| | - Xiaochang Liu
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| | - Hongling Zhao
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| | - Hua Guan
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| | - Pingkun Zhou
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China.,School of Medicine University of South China Hengyang China.,School of Public Health Institute for Environmental Medicine and Radiation Hygiene University of South China Hengyang China
| | - Shanshan Gao
- Department of Radiation Biology Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine Beijing China
| |
Collapse
|
50
|
Meng W, Palmer JD, Siedow M, Haque SJ, Chakravarti A. Overcoming Radiation Resistance in Gliomas by Targeting Metabolism and DNA Repair Pathways. Int J Mol Sci 2022; 23:ijms23042246. [PMID: 35216362 PMCID: PMC8880405 DOI: 10.3390/ijms23042246] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Gliomas represent a wide spectrum of brain tumors characterized by their high invasiveness, resistance to chemoradiotherapy, and both intratumoral and intertumoral heterogeneity. Recent advances in transomics studies revealed that enormous abnormalities exist in different biological layers of glioma cells, which include genetic/epigenetic alterations, RNA expressions, protein expression/modifications, and metabolic pathways, which provide opportunities for development of novel targeted therapeutic agents for gliomas. Metabolic reprogramming is one of the hallmarks of cancer cells, as well as one of the oldest fields in cancer biology research. Altered cancer cell metabolism not only provides energy and metabolites to support tumor growth, but also mediates the resistance of tumor cells to antitumor therapies. The interactions between cancer metabolism and DNA repair pathways, and the enhancement of radiotherapy sensitivity and assessment of radiation response by modulation of glioma metabolism are discussed herein.
Collapse
|