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Xu T, Liu F, He J, Xu P, Qu J, Wang H, Yue J, Yang Q, Wu W, Zeng G, Sun D, Chen X. Leveraging zebrafish models for advancing radiobiology: Mechanisms, applications, and future prospects in radiation exposure research. ENVIRONMENTAL RESEARCH 2024; 266:120504. [PMID: 39638026 DOI: 10.1016/j.envres.2024.120504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 11/12/2024] [Accepted: 12/01/2024] [Indexed: 12/07/2024]
Abstract
Ionizing radiation (IR) represents a significant risk to human health and societal stability. To effectively analyze the mechanisms of IR and enhance protective strategies, the development of more sophisticated animal models is imperative. The zebrafish, with its high degree of genomic homology to humans and the capacity for whole-body optical visualization and high-throughput screening, represents an invaluable model for the study of IR. This review examines the benefits of utilizing zebrafish as a model organism for research on IR, emphasizing recent advancements and applications. It presents a comprehensive overview of the methodologies for establishing IR models in zebrafish, addresses current challenges, and discusses future development trends. This paper provide theoretical support for elucidating the mechanisms of IR injury and developing effective treatment strategies.
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Affiliation(s)
- Ting Xu
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China; Department of Endocrinology, Yiwu Central Hospital, The Affiliated Yiwu Hospital of Wenzhou Medical University, Yiwu, 322000, China
| | - Fan Liu
- State and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, School of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Jiaxuan He
- State and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, School of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Peiye Xu
- State and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, School of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Junying Qu
- State and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, School of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, School of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Hanbing Wang
- Department of Biotechnology, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Jinghui Yue
- Nuclear Power Institute of China, Chengdu, 610200, China
| | - Qinsi Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325000, China
| | - Wei Wu
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Guoming Zeng
- Intelligent Construction Technology Application Service Center, School of Architecture and Engineering, Chongqing City Vocational College, Chongqing, 402160, China
| | - Da Sun
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China; Department of Endocrinology, Yiwu Central Hospital, The Affiliated Yiwu Hospital of Wenzhou Medical University, Yiwu, 322000, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, School of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
| | - Xia Chen
- Department of Endocrinology, Yiwu Central Hospital, The Affiliated Yiwu Hospital of Wenzhou Medical University, Yiwu, 322000, China.
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2
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Almohdar D, Kamble P, Basavannacharya C, Gulkis M, Calbay O, Huang S, Narayan S, Çağlayan M. Impact of DNA ligase inhibition on the nick sealing of polβ nucleotide insertion products at the downstream steps of base excision repair pathway. Mutagenesis 2024; 39:263-279. [PMID: 38736258 PMCID: PMC11529620 DOI: 10.1093/mutage/geae013] [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: 02/21/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024] Open
Abstract
DNA ligase (LIG) I and IIIα finalize base excision repair (BER) by sealing a nick product after nucleotide insertion by DNA polymerase (pol) β at the downstream steps. We previously demonstrated that a functional interplay between polβ and BER ligases is critical for efficient repair, and polβ mismatch or oxidized nucleotide insertions confound the final ligation step. Yet, how targeting downstream enzymes with small molecule inhibitors could affect this coordination remains unknown. Here, we report that DNA ligase inhibitors, L67 and L82-G17, slightly enhance hypersensitivity to oxidative stress-inducing agent, KBrO3, in polβ+/+ cells more than polβ-/- null cells. We showed less efficient ligation after polβ nucleotide insertions in the presence of the DNA ligase inhibitors. Furthermore, the mutations at the ligase inhibitor binding sites (G448, R451, A455) of LIG1 significantly affect nick DNA binding affinity and nick sealing efficiency. Finally, our results demonstrated that the BER ligases seal a gap repair intermediate by the effect of polβ inhibitor that diminishes gap filling activity. Overall, our results contribute to understand how the BER inhibitors against downstream enzymes, polβ, LIG1, and LIGIIIα, could impact the efficiency of gap filling and subsequent nick sealing at the final steps leading to the formation of deleterious repair intermediates.
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Affiliation(s)
- Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, United States
| | - Pradnya Kamble
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, United States
| | - Chandrakala Basavannacharya
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, United States
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, United States
| | - Ozlem Calbay
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, United States
| | - Shuang Huang
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, United States
| | - Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, United States
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, United States
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3
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Cameron M, Frame F, Maitland NJ, Hancock Y. Raman spectroscopy reveals oxidative stress-induced metabolic vulnerabilities in early-stage AR-negative prostate-cancer versus normal-prostate cell lines. Sci Rep 2024; 14:25388. [PMID: 39455589 PMCID: PMC11512068 DOI: 10.1038/s41598-024-70338-1] [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: 04/03/2024] [Accepted: 08/14/2024] [Indexed: 10/28/2024] Open
Abstract
Quantitative Raman spectroscopy provides information-rich imaging of complex tissues. To illustrate its ability to characterise early-stage disease, we compared live P4E6, a low-grade Gleason-3 prostate-cancer cell line, to PNT2-C2, a normal prostate cell-line equivalent, thereby elucidating key molecular and mechanistic differences. Spectral changes from statistically relevant population sampling show P4E6 is defined by reduced DNA/RNA signatures (primarily base-pair modifications), increased protein-related signatures (synthesis), decreased whole-cell measured saturated and unsaturated fatty acids, and increased cholesterol and cholesterol ester (lipid storage). Signatures in the live-cell disease state point to the Warburg effect for aerobic glycolysis as the mechanism for cellular energy generation. A follow-on study involving catastrophic desiccation showed a key survival pathway in the cancer state in the structural robustness of DNA/RNA. Metabolic changes, namely in Warburg-to-oxidative-phosphorylation rerouting and reduced protein synthesis, were also shown. Such modifications limit cancer's resistance to oxidative damage, and thus its ability to utilise a higher redox homeostasis for metabolic advantage. The results demonstrate the ability of quantitative Raman spectroscopy to uncover, with full molecular-heterogeneity capture, mechanistic vulnerabilities in lowest-grade tumorigenic prostate cancer, thereby revealing underlying targets for disease disruption at early stage.
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Affiliation(s)
- M Cameron
- School of Physics, Engineering and Technology, University of York, Heslington, York, YO10 5DD, UK
| | - F Frame
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
- York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - N J Maitland
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
- York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Y Hancock
- School of Physics, Engineering and Technology, University of York, Heslington, York, YO10 5DD, UK.
- York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK.
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4
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Bai B, Ma Y, Liu D, Zhang Y, Zhang W, Shi R, Zhou Q. DNA damage caused by chemotherapy has duality, and traditional Chinese medicine may be a better choice to reduce its toxicity. Front Pharmacol 2024; 15:1483160. [PMID: 39502534 PMCID: PMC11534686 DOI: 10.3389/fphar.2024.1483160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 10/14/2024] [Indexed: 11/08/2024] Open
Abstract
Background DNA damage induced by chemotherapy has duality. It affects the efficacy of chemotherapy and constrains its application. An increasing number of studies have shown that traditional Chinese medicine (TCM) is highly effective in reducing side-effects induced by chemotherapy due to its natural, non-toxic and many sourced from food. Recent advancements have demonstrated survival rates are improved attributable to effective chemotherapy. DNA damage is the principal mechanism underlying chemotherapy. However, not all instances of DNA damage are beneficial. Chemotherapy induces DNA damage in normal cells, leading to side effects. It affects the efficacy of chemotherapy and constrains its application. Objectives This review aims to summarize the dual nature of DNA damage induced by chemotherapy and explore how TCM can mitigate chemotherapy-induced side effects. Results The review summarized the latest research progress in DNA damage caused by chemotherapy and the effect of alleviating side effects by TCM. It focused on advantages and disadvantages of chemotherapy, the mechanism of drugs and providing insights for rational and effective clinical treatment and serving as a basis for experiment. In this review, we described the mechanisms of DNA damage, associated chemotherapeutics, and their toxicity. Furthermore, we explored Chinese herb that can alleviate chemotherapy-induced side-effects. Conclusion We highlight key mechanisms of DNA damage caused by chemotherapeutics and discuss specific TCM herbs that have shown potential in reducing these side effects. It can provide reference for clinical and basic research.
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Affiliation(s)
- Bufan Bai
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yingrui Ma
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Deng Liu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifei Zhang
- Department of Intensive Care Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weihong Zhang
- Breast Surgery Department, Baoshan Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Shi
- Department of Intensive Care Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qianmei Zhou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Dongfang Hospital Affiliated to Shanghai Tongji University, Shanghai, China
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5
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Zuo Y, He J, Zhou Z, Sun J, Ouyang C, Huang H, Wang Y, Liu H, Reed SH. Long non-coding RNA LIP interacts with PARP-1 influencing the efficiency of base excision repair. Noncoding RNA Res 2024; 9:649-658. [PMID: 38577022 PMCID: PMC10987297 DOI: 10.1016/j.ncrna.2024.03.010] [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: 12/11/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
In recent years, various long non-coding RNAs (lncRNAs) involved in DNA damage response (DDR) have been identified and studied to deepen our understanding. However, there are rare reports on the association between lncRNAs and base excision repair (BER). Our designed DNA microarray identified dozens of functionally unknown lncRNAs, and their transcription levels significantly increased upon exposure to DNA damage inducers. One of them, named LIP (Long noncoding RNA Interacts with PARP-1), exhibited a significant alteration in transcription in response to methyl methanesulfonate (MMS) and temozolomide (TMZ) treatments. LIP knockdown or knockout cell lines are sensitive to MMS and TMZ, indicating that LIP plays a crucial role in DDR. The loss or insufficiency of LIP significantly influences the efficiency of BER in human cells, and it suggests that LIP participates in the BER pathway. The interaction between LIP and a key factor in BER, poly (ADP-ribose) polymerase 1 (PARP-1), has been confirmed. We identified and characterized LIP, a lncRNA, which is involved in DDR, significantly influences BER efficiency, and interacts with the BER key factor PARP-1. This advances our understanding of the connection between lncRNAs and BER, presenting the potential for the discovery of new drug targets.
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Affiliation(s)
- You Zuo
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jiaqian He
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Zheng Zhou
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jingjing Sun
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Can Ouyang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Hui Huang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Yajuan Wang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Hairong Liu
- College of Material Science and Engineering, Hunan University, Changsha, 410082, PR China
| | - Simon H. Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
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6
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Gao Z, Luan X, Wang X, Han T, Li X, Li Z, Li P, Zhou Z. DNA damage response-related ncRNAs as regulators of therapy resistance in cancer. Front Pharmacol 2024; 15:1390300. [PMID: 39253383 PMCID: PMC11381396 DOI: 10.3389/fphar.2024.1390300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 08/14/2024] [Indexed: 09/11/2024] Open
Abstract
The DNA damage repair (DDR) pathway is a complex signaling cascade that can sense DNA damage and trigger cellular responses to DNA damage to maintain genome stability and integrity. A typical hallmark of cancer is genomic instability or nonintegrity, which is closely related to the accumulation of DNA damage within cancer cells. The treatment principles of radiotherapy and chemotherapy for cancer are based on their cytotoxic effects on DNA damage, which are accompanied by severe and unnecessary side effects on normal tissues, including dysregulation of the DDR and induced therapeutic tolerance. As a driving factor for oncogenes or tumor suppressor genes, noncoding RNA (ncRNA) have been shown to play an important role in cancer cell resistance to radiotherapy and chemotherapy. Recently, it has been found that ncRNA can regulate tumor treatment tolerance by altering the DDR induced by radiotherapy or chemotherapy in cancer cells, indicating that ncRNA are potential regulatory factors targeting the DDR to reverse tumor treatment tolerance. This review provides an overview of the basic information and functions of the DDR and ncRNAs in the tolerance or sensitivity of tumors to chemotherapy and radiation therapy. We focused on the impact of ncRNA (mainly microRNA [miRNA], long noncoding RNA [lncRNA], and circular RNA [circRNA]) on cancer treatment by regulating the DDR and the underlying molecular mechanisms of their effects. These findings provide a theoretical basis and new insights for tumor-targeted therapy and the development of novel drugs targeting the DDR or ncRNAs.
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Affiliation(s)
- Ziru Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xinchi Luan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xuezhe Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Tianyue Han
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiaoyuan Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Zeyang Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
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7
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Tao J, Zhang H, Weinfeld M, Le XC. Detection of Uracil-Excising DNA Glycosylases in Cancer Cell Samples Using a Three-Dimensional DNAzyme Walker. ACS MEASUREMENT SCIENCE AU 2024; 4:459-466. [PMID: 39184356 PMCID: PMC11342458 DOI: 10.1021/acsmeasuresciau.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 08/27/2024]
Abstract
DNA glycosylase dysregulation is implicated in carcinogenesis and therapeutic resistance of cancers. Thus, various DNA-based detection platforms have been developed by leveraging the base excision activity of DNA glycosylases. However, the efficacy of DNA-based methods is hampered due to nonspecific degradation by nucleases commonly present in cancer cells and during preparations of cell lysates. In this report, we describe a fluorescence-based assay using a specific and nuclease-resistant three-dimensional DNAzyme walker to investigate the activity of DNA glycosylases from cancer cell lysates. We focus on DNA glycosylases that excise uracil from deoxyuridine (dU) lesions, namely, uracil DNA glycosylase (UDG) and single-stranded monofunctional uracil DNA glycosylase (SMUG1). The limits of detection for detecting UDG and SMUG1 in the buffer were 3.2 and 3.0 pM, respectively. The DNAzyme walker detected uracil excision activity in diluted cancer cell lysate from as few as 48 A549 cells. The results of the UDG inhibitor experiments demonstrate that UDG is the predominant uracil-excising glycosylase in A549 cells. Approximately 500 nM of UDG is present in each A549 cell on average. No fluorescence was generated in the samples lacking DNAzyme activation, indicating that there was no nonspecific nuclease interference. The ability of the DNAzyme walker to respond to glycosylase activity illustrates the potential use of DNAzyme walker technology to monitor and study biochemical processes involving glycosylases.
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Affiliation(s)
- Jeffrey Tao
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Michael Weinfeld
- Division
of Experimental Oncology, Department of Oncology, Faculty of Medicine
and Dentistry, University of Alberta, Cross
Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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Velaiyan M, Muthusamy R, Kativa M, Annamalai A, Govindhan A, Punniyakotti P, Balupillai A. Gallic acid-loaded chitosan nanoparticles enhance the DNA damage and apoptotic features through inhibiting flap endonuclease-1 in triple-negative breast cancer cells. ENVIRONMENTAL TOXICOLOGY 2024; 39:4171-4183. [PMID: 38666519 DOI: 10.1002/tox.24293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/29/2023] [Accepted: 04/09/2024] [Indexed: 07/14/2024]
Abstract
This study investigated the fabrication of gallic acid-loaded chitosan nanoparticles (Gal-Chi-NPs) that enhanced the DNA damage and apoptotic features by inhibiting FEN-1 expressions in MDA-MB 231 cells. Gal-Chi-NPs were fabricated by the ionic gelation method, and it was characterized by several studies such as dynamic light spectroscopy, Fourier-transforms infrared spectroscopy, x-ray diffraction, scanning electron microscopy, energy-dispersive x-ray, atomic force microscopy, and thermogravimetric analysis. We have obtained that Gal-Chi-NPs displayed 182.2 nm with crystal, smooth surface, and heat stability in nature. Gal-Chi-NPs induce significant toxicity in MDA-MB-231 cells that compared with normal NIH-3T3 cells. A significant reactive oxygen species (ROS) overproduction was observed in Gal-Chi-NPs treated MDA-MB-231. Flap endonuclease-1 (FEN-1) is a crucial protein involved in long patch base excision repair that is involved in repairing the chemotherapeutic mediated DNA-damaged base. Therefore, inhibition of FEN-1 protein expression is a crucial target for enhancing chemotherapeutical efficacy. In this study, we have obtained that Gal-Chi-NPs treatment enhanced the DNA damage by observing increased p-H2AX, PARP1; and suppressed the expression of FEN-1 in MDA-MB-231 cells. Moreover, Gal-Chi-NPs inhibited the expression of tumor proliferating markers p-PI3K, AKT, cyclin-D1, PCNA, and BCL-2; induced proapoptotic proteins (Bax and caspase-3) in MDA-MB 231 cells. Thus, Gal-Chi-NPs induce DNA damage and apoptotic features and inhibit tumor proliferation by suppressing FEN-1 expression in triple-negative breast cancer cells.
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Affiliation(s)
- Monica Velaiyan
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Rajasekar Muthusamy
- Central Research Laboratory, Vinayaka Mission's Kirupananda Variyar Medical College and Hospitals, Salem, Tamil Nadu, India
| | - Miguel Kativa
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Asaikkutti Annamalai
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Annamalai Govindhan
- Department of Medicine, Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, Texas, USA
| | - Parthipan Punniyakotti
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Agilan Balupillai
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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10
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Li C, Xue Y, Wu J, Zhang L, Yang T, Ai M, Han J, Zheng X, Wang R, Boldogh I, Ba X. MTH1 inhibition synergizes with ROS-inducing agents to trigger cervical cancer cells undergoing parthanatos. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167190. [PMID: 38657912 DOI: 10.1016/j.bbadis.2024.167190] [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: 09/21/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Cervical cancer cells possess high levels of reactive oxygen species (ROS); thus, increasing oxidative stress above the toxicity threshold to induce cell death is a promising chemotherapeutic strategy. However, the underlying mechanisms of cell death are elusive, and efficacy and toxicity issues remain. Within DNA, 8-oxo-7,8-dihydroguanine (8-oxoG) is the most frequent base lesion repaired by 8-oxoguanine glycosylase 1 (OGG1)-initiated base excision repair. Cancer cells also express high levels of MutT homolog 1 (MTH1), which prevents DNA replication-induced incorporation of 8-oxoG into the genome by hydrolyzing 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP). Here, we revealed that ROS-inducing agents triggered cervical cancer to undergo parthanatos, which was mainly induced by massive DNA strand breaks resulting from overwhelming 8-oxoG excision by OGG1. Furthermore, the MTH1 inhibitor synergized with a relatively low dose of ROS-inducing agents by enhancing 8-oxoG loading in the DNA. In vivo, this drug combination suppressed the growth of tumor xenografts, and this inhibitory effect was significantly decreased in the absence of OGG1. Hence, the present study highlights the roles of base repair enzymes in cell death induction and suggests that the combination of lower doses of ROS-inducing agents with MTH1 inhibitors may be a more selective and safer strategy for cervical cancer chemotherapy.
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Affiliation(s)
- Chunshuang Li
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Yaoyao Xue
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Jiaxin Wu
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Lihong Zhang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Tianming Yang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Mengtao Ai
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Jinling Han
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Xu Zheng
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Ruoxi Wang
- Key Laboratory of Animal Resistance Biology of Shandong Province, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.
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11
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Zhao SJ, Prior D, Heske CM, Vasquez JC. Therapeutic Targeting of DNA Repair Pathways in Pediatric Extracranial Solid Tumors: Current State and Implications for Immunotherapy. Cancers (Basel) 2024; 16:1648. [PMID: 38730598 PMCID: PMC11083679 DOI: 10.3390/cancers16091648] [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: 04/05/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
DNA damage is fundamental to tumorigenesis, and the inability to repair DNA damage is a hallmark of many human cancers. DNA is repaired via the DNA damage repair (DDR) apparatus, which includes five major pathways. DDR deficiencies in cancers give rise to potential therapeutic targets, as cancers harboring DDR deficiencies become increasingly dependent on alternative DDR pathways for survival. In this review, we summarize the DDR apparatus, and examine the current state of research efforts focused on identifying vulnerabilities in DDR pathways that can be therapeutically exploited in pediatric extracranial solid tumors. We assess the potential for synergistic combinations of different DDR inhibitors as well as combinations of DDR inhibitors with chemotherapy. Lastly, we discuss the immunomodulatory implications of targeting DDR pathways and the potential for using DDR inhibitors to enhance tumor immunogenicity, with the goal of improving the response to immune checkpoint blockade in pediatric solid tumors. We review the ongoing and future research into DDR in pediatric tumors and the subsequent pediatric clinical trials that will be critical to further elucidate the efficacy of the approaches targeting DDR.
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Affiliation(s)
- Sophia J. Zhao
- Department of Pediatric Hematology/Oncology, Yale University School of Medicine, New Haven, CT 06510, USA; (S.J.Z.); (D.P.)
| | - Daniel Prior
- Department of Pediatric Hematology/Oncology, Yale University School of Medicine, New Haven, CT 06510, USA; (S.J.Z.); (D.P.)
| | - Christine M. Heske
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Juan C. Vasquez
- Department of Pediatric Hematology/Oncology, Yale University School of Medicine, New Haven, CT 06510, USA; (S.J.Z.); (D.P.)
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12
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Wei W, Yue D. CoGSPro-net:A graph neural network based on protein-protein interaction for classifying lung cancer-relatrd proteins. Comput Biol Med 2024; 172:108251. [PMID: 38508055 DOI: 10.1016/j.compbiomed.2024.108251] [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: 01/21/2024] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
This paper proposes a deep learning algorithm named CoGSPro for classifying lung cancer-related proteins. CoGSPro combines graph neural networks and attention mechanisms to extract key features from protein data and accurately classify proteins. It utilizes large-scale protein expression datasets to train and validate the model, enabling it to identify subtle patterns related to lung cancer. CoGSPro integrates protein-protein interaction network information to improve its predictive accuracy. The experimental results indicate that CoGSPro achieves cutting-edge performance, attaining an accuracy of 96.60% in the classification of lung cancer proteins, surpassing other baseline methods. Additionally, CoGSPro has uncovered new biomarkers for lung cancer, offering potential targets for early detection and treatment.
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Affiliation(s)
- Wei Wei
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Dongsheng Yue
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China.
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13
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Liu QW, Yang ZW, Tang QH, Wang WE, Chu DS, Ji JF, Fan QY, Jiang H, Yang QX, Zhang H, Liu XY, Xu XS, Wang XF, Liu JB, Fu D, Tao K, Yu H. The power and the promise of synthetic lethality for clinical application in cancer treatment. Biomed Pharmacother 2024; 172:116288. [PMID: 38377739 DOI: 10.1016/j.biopha.2024.116288] [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: 01/04/2024] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024] Open
Abstract
Synthetic lethality is a phenomenon wherein the simultaneous deficiency of two or more genes results in cell death, while the deficiency of any individual gene does not lead to cell death. In recent years, synthetic lethality has emerged as a significant topic in the field of targeted cancer therapy, with certain drugs based on this concept exhibiting promising outcomes in clinical trials. Nevertheless, the presence of tumor heterogeneity and the intricate DNA repair mechanisms pose challenges to the effective implementation of synthetic lethality. This review aims to explore the concepts, development, and ethical quandaries surrounding synthetic lethality. Additionally, it will provide an in-depth analysis of the clinical application and underlying mechanism of synthetic lethality.
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Affiliation(s)
- Qian-Wen Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhi-Wen Yang
- Department of Pharmacy, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, Shanghai 200050, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences, Hengyang Normal University, Hengyang, Hunan Province 421008, China
| | - Wen-Er Wang
- General Surgery, the Fourth Hospital Of Changsha, Changsha Hospital Of Hunan Normal University, Changsha, Hunan Province 410006, China
| | - Da-Sheng Chu
- Second Cadre Rest Medical and Health Center of Changning District, Shanghai Garrison, Shanghai226631, China
| | - Jin-Feng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu Province 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Hong Jiang
- Department of Thoracic Surgery, the 905th Hospital of Chinese People's Liberation Army Navy, Shanghai 200050, China
| | - Qin-Xin Yang
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Hui Zhang
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Xin-Yun Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Xiao-Sheng Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Feng Wang
- Department of Orthopedics, Xiamen Hospital, Zhongshan Hospital, Fudan University, Xiamen, Fujian Province 361015, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China.
| | - Da Fu
- General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Kun Tao
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Hong Yu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; Department of Pathology, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province 225300, China.
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14
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Farias TG, Rodrigues JA, Dos Santos MS, Mencalha AL, de Souza da Fonseca A. Effects of low‑power red laser and blue LED on mRNA levels from DNA repair genes in human breast cancer cells. Lasers Med Sci 2024; 39:56. [PMID: 38329547 DOI: 10.1007/s10103-024-04001-6] [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: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024]
Abstract
Photobiomodulation (PBM) induced by non-ionizing radiations emitted from low-power lasers and light-emitting diodes (LEDs) has been used for various therapeutic purposes due to its molecular, cellular, and systemic effects. At the molecular level, experimental data have suggested that PBM modulates base excision repair (BER), which is responsible for restoring DNA damage. There is a relationship between the misfunction of the BER DNA repair pathway and the development of tumors, including breast cancer. However, the effects of PBM on cancer cells have been controversial. Breast cancer (BC) is the main public health problem in the world and is the most diagnosed type of cancer among women worldwide. Therefore, the evaluation of new strategies, such as PBM, could increase knowledge about BC and improve therapies against BC. Thus, this work aims to evaluate the effects of low-power red laser (658 nm) and blue LED (470 nm) on the mRNA levels from BER genes in human breast cancer cells. MCF-7 and MDA-MB-231 cells were irradiated with a low-power red laser (69 J cm-2, 0.77 W cm-2) and blue LED (482 J cm-2, 5.35 W cm-2), alone or in combination, and the relative mRNA levels of the APTX, PolB, and PCNA genes were assessed by reverse transcription-quantitative polymerase chain reaction. The results suggested that exposure to low-power red laser and blue LED decreased the mRNA levels from APTX, PolB, and PCNA genes in human breast cancer cells. Our research shows that photobiomodulation induced by low-power red laser and blue LED decreases the mRNA levels of repair genes from the base excision repair pathway in MCF-7 and MDA-MB-231 cells.
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Affiliation(s)
- Thayssa Gomes Farias
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Boulevard 28 de Setembro, 87, Rio de Janeiro, 20551030, Brazil.
| | - Juliana Alves Rodrigues
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Boulevard 28 de Setembro, 87, Rio de Janeiro, 20551030, Brazil
| | - Márcia Soares Dos Santos
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Boulevard 28 de Setembro, 87, Rio de Janeiro, 20551030, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Boulevard 28 de Setembro, 87, Rio de Janeiro, 20551030, Brazil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Boulevard 28 de Setembro, 87, Rio de Janeiro, 20551030, Brazil
- Departamento de Ciências Fisiológicas, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rua Frei Caneca, 94, Rio de Janeiro, 20211040, Brazil
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15
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Paller CJ, Tukachinsky H, Maertens A, Decker B, Sampson JR, Cheadle JP, Antonarakis ES. Pan-Cancer Interrogation of MUTYH Variants Reveals Biallelic Inactivation and Defective Base Excision Repair Across a Spectrum of Solid Tumors. JCO Precis Oncol 2024; 8:e2300251. [PMID: 38394468 PMCID: PMC10901435 DOI: 10.1200/po.23.00251] [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: 05/21/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/25/2024] Open
Abstract
PURPOSE Biallelic germline pathogenic variants of the base excision repair (BER) pathway gene MUTYH predispose to colorectal cancer (CRC) and other cancers. The possible association of heterozygous variants with broader cancer susceptibility remains uncertain. This study investigated the prevalence and consequences of pathogenic MUTYH variants and MUTYH loss of heterozygosity (LOH) in a large pan-cancer analysis. MATERIALS AND METHODS Data from 354,366 solid tumor biopsies that were sequenced as part of routine clinical care were analyzed using a validated algorithm to distinguish germline from somatic MUTYH variants. RESULTS Biallelic germline pathogenic MUTYH variants were identified in 119 tissue biopsies. Most were CRCs and showed increased tumor mutational burden (TMB) and a mutational signature consistent with defective BER (COSMIC Signature SBS18). Germline heterozygous pathogenic variants were identified in 5,991 biopsies and their prevalence was modestly elevated in some cancer types. About 12% of these cancers (738 samples: including adrenal gland cancers, pancreatic islet cell tumors, nonglioma CNS tumors, GI stromal tumors, and thyroid cancers) showed somatic LOH for MUTYH, higher rates of chromosome 1p loss (where MUTYH is located), elevated genomic LOH, and higher COSMIC SBS18 signature scores, consistent with BER deficiency. CONCLUSION This analysis of MUTYH alterations in a large set of solid cancers suggests that in addition to the established role of biallelic pathogenic MUTYH variants in cancer predisposition, a broader range of cancers may possibly arise in MUTYH heterozygotes via a mechanism involving somatic LOH at the MUTYH locus and defective BER. However, the effect is modest and requires confirmation in additional studies before being clinically actionable.
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Affiliation(s)
- Channing J Paller
- Johns Hopkins University School of Medicine, Oncology, Baltimore, MD
| | | | - Alexandra Maertens
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing (CAAT), Baltimore, MD
| | | | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Jeremy P Cheadle
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Emmanuel S Antonarakis
- University of Minnesota Masonic Cancer Center, Division of Hematology, Oncology and Transplantation, Minneapolis, MN
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16
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Ferguson DT, Taka E, Tilghman SL, Womble T, Redmond BV, Gedeon S, Flores-Rozas H, Reed SL, Soliman KFA, Kanga KJW, Darling-Reed SF. The Anticancer Effects of the Garlic Organosulfide Diallyl Trisulfide through the Attenuation of B[a]P-Induced Oxidative Stress, AhR Expression, and DNA Damage in Human Premalignant Breast Epithelial (MCF-10AT1) Cells. Int J Mol Sci 2024; 25:923. [PMID: 38255999 PMCID: PMC10815401 DOI: 10.3390/ijms25020923] [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: 12/14/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Benzo[a]pyrene (B[a]P) is the most characterized polycyclic aromatic hydrocarbon associated with breast cancer. Our lab previously reported that the organosulfur compound (OSC), diallyl trisulfide (DATS), chemoprevention mechanism works through the induction of cell cycle arrest and a reduction in oxidative stress and DNA damage in normal breast epithelial cells. We hypothesize that DATS will inhibit B[a]P-induced cancer initiation in premalignant breast epithelial (MCF-10AT1) cells. In this study, we evaluated the ability of DATS to attenuate B[a]P-induced neoplastic transformation in MCF-10AT1 cells by measuring biological endpoints such as proliferation, clonogenicity, reactive oxygen species (ROS) formation, and 8-hydroxy-2-deoxyguanosine (8-OHdG) DNA damage levels, as well as DNA repair and antioxidant proteins. The results indicate that B[a]P induced proliferation, clonogenic formation, ROS formation, and 8-OHdG levels, as well as increasing AhR, ARNT/HIF-1β, and CYP1A1 protein expression compared with the control in MCF-10AT1 cells. B[a]P/DATS's co-treatment (CoTx) inhibited cell proliferation, clonogenic formation, ROS formation, AhR protein expression, and 8-OHdG levels compared with B[a]P alone and attenuated all the above-mentioned B[a]P-induced changes in protein expression, causing a chemopreventive effect. This study demonstrates, for the first time, that DATS prevents premalignant breast cells from undergoing B[a]P-induced neoplastic transformation, thus providing more evidence for its chemopreventive effects in breast cancer.
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Affiliation(s)
- Dominique T. Ferguson
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Equar Taka
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Syreeta L. Tilghman
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Tracy Womble
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Bryan V. Redmond
- Department of Neuroscience, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Shasline Gedeon
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Hernan Flores-Rozas
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Sarah L. Reed
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Karam F. A. Soliman
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
| | - Konan J. W. Kanga
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA;
| | - Selina F. Darling-Reed
- Pharmaceutical Sciences Division, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA; (D.T.F.); (E.T.); (S.L.T.); (T.W.); (S.G.); (H.F.-R.); (S.L.R.); (K.F.A.S.)
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17
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Magadeeva S, Qian X, Korff N, Flörkemeier I, Hedemann N, Rogmans C, Forster M, Arnold N, Maass N, Bauerschlag DO, Weimer JP. Assessing the Phenotype of a Homologous Recombination Deficiency Using High Resolution Array-Based Comparative Genome Hybridization in Ovarian Cancer. Int J Mol Sci 2023; 24:17467. [PMID: 38139296 PMCID: PMC10743768 DOI: 10.3390/ijms242417467] [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: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Ovarian cancer (OC) cells with homologous recombination deficiency (HRD) accumulate genomic scars (LST, TAI, and LOH) over a value of 42 in sum. PARP inhibitors can treat OC with HRD. The detection of HRD can be done directly by imaging these genomic scars, or indirectly by detecting mutations in the genes involved in HR. We show that HRD detection is also possible using high-resolution aCGH. A total of 30 OCs were analyzed retrospectively with high-resolution arrays as a test set and 19 OCs prospectively as a validation set. Mutation analysis was performed by HBOC TruRisk V2 panel to detect HR-relevant mutations. CNVs were clustered with respect to the involved HR genes versus the OC cases. In prospective validation, the HRD status determined by aCGH was compared with external HRD assessments. Two BRCA mutation carriers did not have HRD. OC could approximately differentiate into two groups with characteristic CNV patterns with different survival rates. Mutation frequencies have a linear regression on the HRD score. Mutations in individual HR-relevant genes do not always indicate HRD. This may depend on the mutation frequency in tumor cells. The aCGH shows the genomic scars of an HRD inexpensively and directly.
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Affiliation(s)
- Svetlana Magadeeva
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Xueqian Qian
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nadine Korff
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Inken Flörkemeier
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nina Hedemann
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Christoph Rogmans
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nicolai Maass
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Dirk O. Bauerschlag
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jörg P. Weimer
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
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Abstract
PURPOSE The transcription factor NF-E2-related factor 2 (NRF2) is a master regulator widely involved in essential cellular functions such as DNA repair. By clarifying the upstream and downstream links of NRF2 to DNA damage repair, we hope that attention will be drawn to the utilization of NRF2 as a target for cancer therapy. METHODS Query and summarize relevant literature on the role of NRF2 in direct repair, BER, NER, MMR, HR, and NHEJ in pubmed. Make pictures of Roles of NRF2 in DNA Damage Repair and tables of antioxidant response elements (AREs) of DNA repair genes. Analyze the mutation frequency of NFE2L2 in different types of cancer using cBioPortal online tools. By using TCGA, GTEx and GO databases, analyze the correlation between NFE2L2 mutations and DNA repair systems as well as the degree of changes in DNA repair systems as malignant tumors progress. RESULTS NRF2 plays roles in maintaining the integrity of the genome by repairing DNA damage, regulating the cell cycle, and acting as an antioxidant. And, it possibly plays roles in double stranded break (DSB) pathway selection following ionizing radiation (IR) damage. Whether pathways such as RNA modification, ncRNA, and protein post-translational modification affect the regulation of NRF2 on DNA repair is still to be determined. The overall mutation frequency of the NFE2L2 gene in esophageal carcinoma, lung cancer, and penile cancer is the highest. Genes (50 of 58) that are negatively correlated with clinical staging are positively correlated with NFE2L2 mutations or NFE2L2 expression levels. CONCLUSION NRF2 participates in a variety of DNA repair pathways and plays important roles in maintaining genome stability. NRF2 is a potential target for cancer treatment.
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Affiliation(s)
- Jiale Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
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19
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Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
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20
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Das D, Duncton MAJ, Georgiadis TM, Pellicena P, Clark J, Sobol RW, Georgiadis MM, King-Underwood J, Jobes DV, Chang C, Gao Y, Deacon AM, Wilson DM. A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1. Int J Mol Sci 2023; 24:16637. [PMID: 38068959 PMCID: PMC10706420 DOI: 10.3390/ijms242316637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM ("SAR by X-ray Poses Quickly") platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or "undruggable" targets, allows for (i) hit generation; (ii) the mapping of protein-ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.
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Affiliation(s)
- Debanu Das
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | | | | | | | - Jennifer Clark
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
- Department of Pathology & Laboratory Medicine, Warrant Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Millie M. Georgiadis
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - David V. Jobes
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Mid-Atlantic BioTherapeutics, Inc., Doylestown, PA 18902, USA
| | - Caleb Chang
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Yang Gao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashley M. Deacon
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | - David M. Wilson
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Biomedical Research Institute, Hasselt University, 3500 Diepenbeek, Belgium
- Belgium & Boost Scientific, 3550 Heusden-Zolder, Belgium
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21
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Melia E, Parsons J. DNA damage and repair dependencies of ionising radiation modalities. Biosci Rep 2023; 43:BSR20222586. [PMID: 37695845 PMCID: PMC10548165 DOI: 10.1042/bsr20222586] [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: 05/11/2023] [Revised: 08/18/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023] Open
Abstract
Radiotherapy is utilised in the treatment of ∼50% of all human cancers, which predominantly employs photon radiation. However, particle radiotherapy elicits significant benefits over conventional photons due to more precise dose deposition and increased linear energy transfer (LET) that generates an enhanced therapeutic response. Specifically, proton beam therapy (PBT) and carbon ion radiotherapy (CIRT) are characterised by a Bragg peak, which generates a low entrance radiation dose, with the majority of the energy deposition being defined within a small region which can be specifically targeted to the tumour, followed by a low exit dose. PBT is deemed relatively low-LET whereas CIRT is more densely ionising and therefore high LET. Despite the radiotherapy type, tumour cell killing relies heavily on the introduction of DNA damage that overwhelms the repair capacity of the tumour cells. It is known that DNA damage complexity increases with LET that leads to enhanced biological effectiveness, although the specific DNA repair pathways that are activated following the different radiation sources is unclear. This knowledge is required to determine whether specific proteins and enzymes within these pathways can be targeted to further increase the efficacy of the radiation. In this review, we provide an overview of the different radiation modalities and the DNA repair pathways that are responsive to these. We also provide up-to-date knowledge of studies examining the impact of LET and DNA damage complexity on DNA repair pathway choice, followed by evidence on how enzymes within these pathways could potentially be therapeutically exploited to further increase tumour radiosensitivity, and therefore radiotherapy efficacy.
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Affiliation(s)
- Emma Melia
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Jason L. Parsons
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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22
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Tao J, Zhang H, Weinfeld M, Le XC. Development of a DNAzyme Walker for the Detection of APE1 in Living Cancer Cells. Anal Chem 2023; 95:14990-14997. [PMID: 37725609 PMCID: PMC10568531 DOI: 10.1021/acs.analchem.3c02574] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
DNAzyme walker technology is a compelling option for bioanalytical and drug delivery applications. While nucleic acid and protein targets have been used to activate DNAzyme walkers, investigations into enzyme-triggered DNAzyme walkers in living cells are still in their early stages. The base excision repair (BER) pathway presents an array of enzymes that are overexpressed in cancer cells. Here, we introduce a DNAzyme walker system that sensitively and specifically detects the BER enzyme apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1). We constructed the DNAzyme walker on the surface of 20 nm-diameter gold nanoparticles. We achieved a detection limit of 160 fM of APE1 in a buffer and in whole cell lysate equivalent to the amount of APE1 in a single HeLa cell in a sample volume of 100 μL. Confocal imaging of the DNAzyme walking reveals a cytoplasmic distribution of APE1 in HeLa cells. Walking activity is tunable to exogenous Mn2+ concentrations and the uptake of the DNAzyme walker system does not require transfection assistance. We demonstrate the investigative potential of the DNAzyme walker for up-regulated or overactive enzyme biomarkers of the BER pathway in cancer cells.
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Affiliation(s)
- Jeffrey Tao
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
| | - Hongquan Zhang
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
| | - Michael Weinfeld
- Division
of Experimental Oncology, Department of Oncology, Faculty of Medicine
and Dentistry, University of Alberta, Cross
Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
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23
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Westwood MN, Pilarski A, Johnson C, Mamoud S, Meints GA. Backbone Conformational Equilibrium in Mismatched DNA Correlates with Enzyme Activity. Biochemistry 2023; 62:2816-2827. [PMID: 37699121 PMCID: PMC10552547 DOI: 10.1021/acs.biochem.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/25/2023] [Indexed: 09/14/2023]
Abstract
T:G mismatches in mammals arise primarily from the deamination of methylated CpG sites or the incorporation of improper nucleotides. The process by which repair enzymes such as thymine DNA glycosylase (TDG) identify a canonical DNA base in the incorrect pairing context remains a mystery. However, the abundant contacts of the repair enzymes with the DNA backbone suggest a role for protein-phosphate interaction in the recognition and repair processes, where conformational properties may facilitate the proper interactions. We have previously used 31P NMR to investigate the energetics of DNA backbone BI-BII interconversion and the effect of a mismatch or lesion compared to canonical DNA and found stepwise differences in ΔG of 1-2 kcal/mol greater than equivalent steps in unmodified DNA. We have currently compared our results to substrate dependence for TDG, MBD4, M. HhaI, and CEBPβ, testing for correlations to sequence and base-pair dependence. We found strong correlations of our DNA phosphate backbone equilibrium (Keq) to different enzyme kinetics or binding parameters of these varied enzymes, suggesting that the backbone equilibrium may play an important role in mismatch recognition and/or conformational rearrangement and energetics during nucleotide flipping or other aspects of enzyme interrogation of the DNA substrate.
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Affiliation(s)
- M. N. Westwood
- Biophysics
Program, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - A. Pilarski
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| | - C. Johnson
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| | - S. Mamoud
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
| | - G. A. Meints
- Department
of Chemistry and Biochemistry, Missouri
State University, 901 S. National Ave., Springfield, Missouri 65897, United States
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24
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Wu S, Jia S. Functional Diversity of SIRT7 Across Cellular Compartments: Insights and Perspectives. Cell Biochem Biophys 2023; 81:409-419. [PMID: 37581721 DOI: 10.1007/s12013-023-01162-z] [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: 05/16/2023] [Accepted: 08/05/2023] [Indexed: 08/16/2023]
Abstract
Posttranslational modifications (PTMs) play important roles in the regulation of protein function. Acetylation and deacetylation are among the most important PTMs. SIRT7 is a relatively understudied member of the sirtuin family, but recent studies have revealed that it plays a regulatory role in a variety of cellular activities, such as genome stabilization and repair, gene translation, ribosome production and other important processes. Here, we provide a list of the functions and mechanisms of SIRT7 in various organelles and show the important role of SIRT7 in maintaining normal cell function.
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Affiliation(s)
- Songtao Wu
- Zhejiang University School of Medicine, Hangzhou, China.
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
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25
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Tufail M. DNA repair pathways in breast cancer: from mechanisms to clinical applications. Breast Cancer Res Treat 2023:10.1007/s10549-023-06995-z. [PMID: 37289340 DOI: 10.1007/s10549-023-06995-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Breast cancer (BC) is a complex disease with various subtypes and genetic alterations that impact DNA repair pathways. Understanding these pathways is essential for developing effective treatments and improving patient outcomes. AREA COVERED This study investigates the significance of DNA repair pathways in breast cancer, specifically focusing on various pathways such as nucleotide excision repair, base excision repair, mismatch repair, homologous recombination repair, non-homologous end joining, fanconi anemia pathway, translesion synthesis, direct repair, and DNA damage tolerance. The study also examines the role of these pathways in breast cancer resistance and explores their potential as targets for cancer treatment. CONCLUSION Recent advances in targeted therapies have shown promise in exploiting DNA repair pathways for BC treatment. However, much research is needed to improve the efficacy of these therapies and identify new targets. Additionally, personalized treatments that target specific DNA repair pathways based on tumor subtype or genetic profile are being developed. Advances in genomics and imaging technologies can potentially improve patient stratification and identify biomarkers of treatment response. However, many challenges remain, including toxicity, resistance, and the need for more personalized treatments. Continued research and development in this field could significantly improve BC treatment.
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Affiliation(s)
- Muhammad Tufail
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China.
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26
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Xiong X, Song Q, Jing M, Yan W. Identification of PANoptosis-Based Prognostic Signature for Predicting Efficacy of Immunotherapy and Chemotherapy in Hepatocellular Carcinoma. Genet Res (Camb) 2023; 2023:6879022. [PMID: 37313428 PMCID: PMC10260314 DOI: 10.1155/2023/6879022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023] Open
Abstract
Background PANoptosis has been a research hotspot, but the role of PANoptosis in hepatocellular carcinoma (HCC) remains widely unknown. Drug resistance and low response rate are the main limitations of chemotherapy and immunotherapy in HCC. Thus, construction of a prognostic signature to predict prognosis and recognize ideal patients for corresponding chemotherapy and immunotherapy is necessary. Method The mRNA expression data of HCC patients was collected from TCGA database. Through LASSO and Cox regression, we developed a prognostic signature based on PANoptosis-related genes. KM analysis and ROC curve were implemented to evaluate the prognostic efficacy of this signature, and ICGC and GEO database were used as external validation cohorts. The immune cell infiltration, immune status, and IC50 of chemotherapeutic drugs were compared among different risk subgroups. The relationships between the signature and the efficacy of ICI therapy, sorafenib treatment, and transcatheter arterial chemoembolization (TACE) therapy were investigated. Result A 3-gene prognostic signature was constructed which divided the patients into low- and high-risk subgroups. Low-risk patients had better prognosis, and the risk score was proved to be an independent predictor of overall survival (OS), which had a well predictive effect. Patients in high-risk population had more immunosuppressive cells (Tregs, M0 macrophages, and MDSCs), higher TIDE score and TP53 mutation rate, and elevated activity of base excision repair (BER) pathways. Patients with low risk benefited more from ICI, TACE, and sorafenib therapy. The predictive value of the risk score was comparable with TIDE and MSI for OS under ICI therapy. The risk score could be a biomarker to predict the response to ICI, TACE, and sorafenib therapy. Conclusion The novel signature based on PANoptosis is a promising biomarker to distinguish the prognosis predict the benefit of ICI, TACE, and sorafenib therapy, and forecast the response to them.
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Affiliation(s)
- Xiaofeng Xiong
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianben Song
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengjia Jing
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Yang X, Xu L, Yang L. Recent advances in EZH2-based dual inhibitors in the treatment of cancers. Eur J Med Chem 2023; 256:115461. [PMID: 37156182 DOI: 10.1016/j.ejmech.2023.115461] [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: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
The enhancer of zeste homolog 2 (EZH2) protein is the catalytic subunit of one of the histone methyltransferases. EZH2 catalyzes the trimethylation of lysine 27 of histone H3 (H3K27me3) and further alters downstream target levels. EZH2 is upregulated in cancer tissues, wherein its levels correlate strongly with cancer genesis, progression, metastasis, and invasion. Consequently, it has emerged as a novel anticancer therapeutic target. Nonetheless, developing EZH2 inhibitors (EZH2i) has encountered numerous difficulties, such as pre-clinical drug resistance and poor therapeutic effect. The EZH2i synergistically suppresses cancers when used in combination with additional antitumor drugs, such as PARP inhibitors, HDAC inhibitors, BRD4 inhibitors, EZH1 inhibitors, and EHMT2 inhibitors. Typically, the use of dual inhibitors of two different targets mediated by one individual molecule has been recognized as the preferred approach for overcoming the limitations of EZH2 monotherapy. The present review discusses the theoretical basis for designing EZH2-based dual-target inhibitors, and also describes some in vitro and in vivo analysis results.
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Affiliation(s)
- Xiaojuan Yang
- School of Pharmacy, Xinxiang University, Xinxiang, 453003, China.
| | - Lu Xu
- School of Pharmacy, Xinxiang University, Xinxiang, 453003, China
| | - Li Yang
- School of Pharmacy, Xinxiang University, Xinxiang, 453003, China
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28
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Bardelčíková A, Šoltys J, Mojžiš J. Oxidative Stress, Inflammation and Colorectal Cancer: An Overview. Antioxidants (Basel) 2023; 12:antiox12040901. [PMID: 37107276 PMCID: PMC10135609 DOI: 10.3390/antiox12040901] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Colorectal cancer (CRC) represents the second leading cause of cancer-related deaths worldwide. The pathogenesis of CRC is a complex multistep process. Among other factors, inflammation and oxidative stress (OS) have been reported to be involved in the initiation and development of CRC. Although OS plays a vital part in the life of all organisms, its long-term effects on the human body may be involved in the development of different chronic diseases, including cancer diseases. Chronic OS can lead to the oxidation of biomolecules (nucleic acids, lipids and proteins) or the activation of inflammatory signaling pathways, resulting in the activation of several transcription factors or the dysregulation of gene and protein expression followed by tumor initiation or cancer cell survival. In addition, it is well known that chronic intestinal diseases such as inflammatory bowel disease (IBD) are associated with an increased risk of cancer, and a link between OS and IBD initiation and progression has been reported. This review focuses on the role of oxidative stress as a causative agent of inflammation in colorectal cancer.
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Affiliation(s)
- Annamária Bardelčíková
- Department of Pharmacology, Medical Faculty of University of Pavol Jozef Šafárik in Košice, Tr. SNP 1, 040 11 Košice, Slovakia
| | - Jindřich Šoltys
- Institute of Parasitology, Slovak Academy of Science, Hlinkova 3, 040 01 Košice, Slovakia
| | - Ján Mojžiš
- Department of Pharmacology, Medical Faculty of University of Pavol Jozef Šafárik in Košice, Tr. SNP 1, 040 11 Košice, Slovakia
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29
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Li P, Xiao X, Gong J, Zhang X, Cai K, Liang R, Wang D, Chen Y, Chen H, Xie Z, Liao Q. Pogostemon cablin (Blanco) Benth granule revealed a positive effect on improving intestinal barrier function and fecal microbiota in mice with irinotecan-induced intestinal mucositis. Arch Microbiol 2023; 205:179. [PMID: 37029820 DOI: 10.1007/s00203-023-03526-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023]
Abstract
Pogostemon cablin (Blanco) Benth (PCB), a medicinal and edible homologous Chinese herb, has a protective effect on the structure and function of intestine. In this study, we aimed to investigate the effect of PCB granule (PCBG) on the improvement of irinotecan-induced intestinal mucositis and the regulation of intestinal microorganisms in mice. Our results demonstrated that PCBG supplementation significantly improved diarrhea symptoms caused by irinotecan, as evidenced by inhibiting weight loss, reversing intestinal atrophy, protecting against splenomegaly and balancing oxidative stress. Furthermore, compared with the model group, PCBG restored the intestinal morphology and improved intestinal barrier dysfunction by promoting the expression of tight junction proteins and mucin. Moreover, high-throughput sequencing analysis revealed that PCBG improved the flora disorder caused by irinotecan and regulated microbial community structure, such as decreasing the relative abundance of Bacteroides as well as increasing the relative abundance of Lactobacillus. Meanwhile, the disordered microbial functions in intestinal mucositis mice were recovered more closely to the controls by PCBG. Finally, we found that a robust correlation between the specific microbiota and intestinal mucositis-related index. In summary, these findings revealed the beneficial effects of PCBG on the intestinal barrier and gut microbiota of irinotecan-induced intestinal mucositis, which may be one of the potential strategies to reduce the clinical side effects of irinotecan.
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Affiliation(s)
- Pei Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xiaoyi Xiao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jing Gong
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xingyuan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Kaiwei Cai
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Rongyao Liang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dawei Wang
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Yanlong Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hongying Chen
- Guangzhou Baiyunshan Mingxing Pharmaceutical Co., Ltd, Guangzhou, 510250, China
| | - Zhiyong Xie
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518106, China
| | - Qiongfeng Liao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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30
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Ji X, Wang E, Cui Q. Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. Brief Bioinform 2023; 24:6995381. [PMID: 36682004 DOI: 10.1093/bib/bbad017] [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: 07/27/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/23/2023] Open
Abstract
Somatic mutational signatures (MSs) identified by genome sequencing play important roles in exploring the cause and development of cancer. Thus far, many such signatures have been identified, and some of them do imply causes of cancer. However, a major bottleneck is that we do not know the potential meanings (i.e. carcinogenesis or biological functions) and contributing genes for most of them. Here, we presented a computational framework, Gene Somatic Genome Pattern (GSGP), which can decipher the molecular mechanisms of the MSs. More importantly, it is the first time that the GSGP is able to process MSs from ribonucleic acid (RNA) sequencing, which greatly extended the applications of both MS analysis and RNA sequencing (RNAseq). As a result, GSGP analyses match consistently with previous reports and identify the etiologies for a number of novel signatures. Notably, we applied GSGP to RNAseq data and revealed an RNA-derived MS involved in deficient deoxyribonucleic acid mismatch repair and microsatellite instability in colorectal cancer. Researchers can perform customized GSGP analysis using the web tools or scripts we provide.
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Affiliation(s)
- Xiangwen Ji
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
| | - Edwin Wang
- Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
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31
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Wilkinson B, Hill MA, Parsons JL. The Cellular Response to Complex DNA Damage Induced by Ionising Radiation. Int J Mol Sci 2023; 24:4920. [PMID: 36902352 PMCID: PMC10003081 DOI: 10.3390/ijms24054920] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Radiotherapy (ionising radiation; IR) is utilised in the treatment of ~50% of all human cancers, and where the therapeutic effect is largely achieved through DNA damage induction. In particular, complex DNA damage (CDD) containing two or more lesions within one to two helical turns of the DNA is a signature of IR and contributes significantly to the cell killing effects due to the difficult nature of its repair by the cellular DNA repair machinery. The levels and complexity of CDD increase with increasing ionisation density (linear energy transfer, LET) of the IR, such that photon (X-ray) radiotherapy is deemed low-LET whereas some particle ions (such as carbon ions) are high-LET radiotherapy. Despite this knowledge, there are challenges in the detection and quantitative measurement of IR-induced CDD in cells and tissues. Furthermore, there are biological uncertainties with the specific DNA repair proteins and pathways, including components of DNA single and double strand break mechanisms, that are engaged in CDD repair, which very much depends on the radiation type and associated LET. However, there are promising signs that advancements are being made in these areas and which will enhance our understanding of the cellular response to CDD induced by IR. There is also evidence that targeting CDD repair, particularly through inhibitors against selected DNA repair enzymes, can exacerbate the impact of higher LET, which could be explored further in a translational context.
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Affiliation(s)
- Beth Wilkinson
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Mark A. Hill
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jason L. Parsons
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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32
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Baljinnyam T, Conrad JW, Sowers ML, Chang-Gu B, Herring JL, Hackfeld LC, Zhang K, Sowers LC. Characterization of a Novel Thermostable DNA Lyase Used To Prepare DNA for Next-Generation Sequencing. Chem Res Toxicol 2023; 36:162-176. [PMID: 36647573 PMCID: PMC9945173 DOI: 10.1021/acs.chemrestox.2c00172] [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] [Indexed: 01/18/2023]
Abstract
Recently, we constructed a hybrid thymine DNA glycosylase (hyTDG) by linking a 29-amino acid sequence from the human thymine DNA glycosylase with the catalytic domain of DNA mismatch glycosylase (MIG) from M. thermoautotrophicum, increasing the overall activity of the glycosylase. Previously, it was shown that a tyrosine to lysine (Y126K) mutation in the catalytic site of MIG could convert the glycosylase activity to a lyase activity. We made the corresponding mutation to our hyTDG to create a hyTDG-lyase (Y163K). Here, we report that the hybrid mutant has robust lyase activity, has activity over a broad temperature range, and is active under multiple buffer conditions. The hyTDG-lyase cleaves an abasic site similar to endonuclease III (Endo III). In the presence of β-mercaptoethanol (β-ME), the abasic site unsaturated aldehyde forms a β-ME adduct. The hyTDG-lyase maintains its preference for cleaving opposite G, as with the hyTDG glycosylase, and the hyTDG-lyase and hyTDG glycosylase can function in tandem to cleave T:G mismatches. The hyTDG-lyase described here should be a valuable tool in studies examining DNA damage and repair. Future studies will utilize these enzymes to quantify T:G mispairs in cells, tissues, and genomic DNA using next-generation sequencing.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Bruce Chang-Gu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
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Wang X, Yu J, Wang J. Neural Tube Defects and Folate Deficiency: Is DNA Repair Defective? Int J Mol Sci 2023; 24:ijms24032220. [PMID: 36768542 PMCID: PMC9916799 DOI: 10.3390/ijms24032220] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Neural tube defects (NTDs) are complex congenital malformations resulting from failure of neural tube closure during embryogenesis, which is affected by the interaction of genetic and environmental factors. It is well known that folate deficiency increases the incidence of NTDs; however, the underlying mechanism remains unclear. Folate deficiency not only causes DNA hypomethylation, but also blocks the synthesis of 2'-deoxythymidine-5'-monophosphate (dTMP) and increases uracil misincorporation, resulting in genomic instabilities such as base mismatch, DNA breakage, and even chromosome aberration. DNA repair pathways are essential for ensuring normal DNA synthesis, genomic stability and integrity during embryonic neural development. Genomic instability or lack of DNA repair has been implicated in risk of development of NTDs. Here, we reviewed the relationship between folate deficiency, DNA repair pathways and NTDs so as to reveal the role and significance of DNA repair system in the pathogenesis of NTDs and better understand the pathogenesis of NTDs.
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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [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: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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35
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Li C, Xue Y, Ba X, Wang R. The Role of 8-oxoG Repair Systems in Tumorigenesis and Cancer Therapy. Cells 2022; 11:cells11233798. [PMID: 36497058 PMCID: PMC9735852 DOI: 10.3390/cells11233798] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Tumorigenesis is highly correlated with the accumulation of mutations. The abundant and extensive DNA oxidation product, 8-Oxoguanine (8-oxoG), can cause mutations if it is not repaired by 8-oxoG repair systems. Therefore, the accumulation of 8-oxoG plays an essential role in tumorigenesis. To avoid the accumulation of 8-oxoG in the genome, base excision repair (BER), initiated by 8-oxoguanine DNA glycosylase1 (OGG1), is responsible for the removal of genomic 8-oxoG. It has been proven that 8-oxoG levels are significantly elevated in cancer cells compared with cells of normal tissues, and the induction of DNA damage by some antitumor drugs involves direct or indirect interference with BER, especially through inducing the production and accumulation of reactive oxygen species (ROS), which can lead to tumor cell death. In addition, the absence of the core components of BER can result in embryonic or early post-natal lethality in mice. Therefore, targeting 8-oxoG repair systems with inhibitors is a promising avenue for tumor therapy. In this study, we summarize the impact of 8-oxoG accumulation on tumorigenesis and the current status of cancer therapy approaches exploiting 8-oxoG repair enzyme targeting, as well as possible synergistic lethality strategies involving exogenous ROS-inducing agents.
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Affiliation(s)
- Chunshuang Li
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
| | - Yaoyao Xue
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
- Correspondence: (X.B.); (R.W.)
| | - Ruoxi Wang
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Correspondence: (X.B.); (R.W.)
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36
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Venugopala KN. Targeting the DNA Damage Response Machinery for Lung Cancer Treatment. Pharmaceuticals (Basel) 2022; 15:ph15121475. [PMID: 36558926 PMCID: PMC9781725 DOI: 10.3390/ph15121475] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Lung cancer is considered the most commonly diagnosed cancer and one of the leading causes of death globally. Despite the responses from small-cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) patients to conventional chemo- and radiotherapies, the current outcomes are not satisfactory. Recently, novel advances in DNA sequencing technologies have started to take off which have provided promising tools for studying different tumors for systematic mutation discovery. To date, a limited number of DDR inhibition trials have been conducted for the treatment of SCLC and NSCLC patients. However, strategies to test different DDR inhibitor combinations or to target multiple pathways are yet to be explored. With the various biomarkers that have either been recently discovered or are the subject of ongoing investigations, it is hoped that future trials would be designed to allow for studying targeted treatments in a biomarker-enriched population, which is defensible for the improvement of prognosis for SCLC and NSCLC patients. This review article sheds light on the different DNA repair pathways and some of the inhibitors targeting the proteins involved in the DNA damage response (DDR) machinery, such as ataxia telangiectasia and Rad3-related protein (ATR), DNA-dependent protein kinase (DNA-PK), and poly-ADP-ribose polymerase (PARP). In addition, the current status of DDR inhibitors in clinical settings and future perspectives are discussed.
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Affiliation(s)
- Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa
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37
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Konis SMR, Hughes JR, Parsons JL. TRIM26 Maintains Cell Survival in Response to Oxidative Stress through Regulating DNA Glycosylase Stability. Int J Mol Sci 2022; 23:ijms231911613. [PMID: 36232914 PMCID: PMC9569934 DOI: 10.3390/ijms231911613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Oxidative DNA base lesions in DNA are repaired through the base excision repair (BER) pathway, which consequently plays a vital role in the maintenance of genome integrity and in suppressing mutagenesis. 8-oxoguanine DNA glycosylase (OGG1), endonuclease III-like protein 1 (NTH1), and the endonuclease VIII-like proteins 1-3 (NEIL1-3) are the key enzymes that initiate repair through the excision of the oxidized base. We have previously identified that the E3 ubiquitin ligase tripartite motif 26 (TRIM26) controls the cellular response to oxidative stress through regulating both NEIL1 and NTH1, although its potential, broader role in BER is unclear. We now show that TRIM26 is a central player in determining the response to different forms of oxidative stress. Using siRNA-mediated knockdowns, we demonstrate that the resistance of cells to X-ray radiation and hydrogen peroxide generated as a consequence of trim26 depletion can be reversed through suppression of selective DNA glycosylases. In particular, a knockdown of neil1 or ogg1 can enhance sensitivity and DNA repair rates in response to X-rays, whereas a knockdown of neil1 or neil3 can produce the same effect in response to hydrogen peroxide. Our study, therefore, highlights the importance of TRIM26 in balancing cellular DNA glycosylase levels required for an efficient BER response.
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Affiliation(s)
- Sifaddin M. R. Konis
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Jonathan R. Hughes
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Jason L. Parsons
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Bebington CH63 4JY, UK
- Correspondence: ; Tel.: +44-151-794-8848
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38
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Kumari S, Sharma S, Advani D, Khosla A, Kumar P, Ambasta RK. Unboxing the molecular modalities of mutagens in cancer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62111-62159. [PMID: 34611806 PMCID: PMC8492102 DOI: 10.1007/s11356-021-16726-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 04/16/2023]
Abstract
The etiology of the majority of human cancers is associated with a myriad of environmental causes, including physical, chemical, and biological factors. DNA damage induced by such mutagens is the initial step in the process of carcinogenesis resulting in the accumulation of mutations. Mutational events are considered the major triggers for introducing genetic and epigenetic insults such as DNA crosslinks, single- and double-strand DNA breaks, formation of DNA adducts, mismatched bases, modification in histones, DNA methylation, and microRNA alterations. However, DNA repair mechanisms are devoted to protect the DNA to ensure genetic stability, any aberrations in these calibrated mechanisms provoke cancer occurrence. Comprehensive knowledge of the type of mutagens and carcinogens and the influence of these agents in DNA damage and cancer induction is crucial to develop rational anticancer strategies. This review delineated the molecular mechanism of DNA damage and the repair pathways to provide a deep understanding of the molecular basis of mutagenicity and carcinogenicity. A relationship between DNA adduct formation and cancer incidence has also been summarized. The mechanistic basis of inflammatory response and oxidative damage triggered by mutagens in tumorigenesis has also been highlighted. We elucidated the interesting interplay between DNA damage response and immune system mechanisms. We addressed the current understanding of DNA repair targeted therapies and DNA damaging chemotherapeutic agents for cancer treatment and discussed how antiviral agents, anti-inflammatory drugs, and immunotherapeutic agents combined with traditional approaches lay the foundations for future cancer therapies.
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Affiliation(s)
- Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Dia Advani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Akanksha Khosla
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
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39
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Firnau MB, Brieger A. CK2 and the Hallmarks of Cancer. Biomedicines 2022; 10:1987. [PMID: 36009534 PMCID: PMC9405757 DOI: 10.3390/biomedicines10081987] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer is a leading cause of death worldwide. Casein kinase 2 (CK2) is commonly dysregulated in cancer, impacting diverse molecular pathways. CK2 is a highly conserved serine/threonine kinase, constitutively active and ubiquitously expressed in eukaryotes. With over 500 known substrates and being estimated to be responsible for up to 10% of the human phosphoproteome, it is of significant importance. A broad spectrum of diverse types of cancer cells has been already shown to rely on disturbed CK2 levels for their survival. The hallmarks of cancer provide a rationale for understanding cancer's common traits. They constitute the maintenance of proliferative signaling, evasion of growth suppressors, resisting cell death, enabling of replicative immortality, induction of angiogenesis, the activation of invasion and metastasis, as well as avoidance of immune destruction and dysregulation of cellular energetics. In this work, we have compiled evidence from the literature suggesting that CK2 modulates all hallmarks of cancer, thereby promoting oncogenesis and operating as a cancer driver by creating a cellular environment favorable to neoplasia.
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Affiliation(s)
| | - Angela Brieger
- Department of Internal Medicine I, Biomedical Research Laboratory, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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40
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Zhou C, Fabbrizi MR, Hughes JR, Grundy GJ, Parsons JL. Effectiveness of PARP inhibition in enhancing the radiosensitivity of 3D spheroids of head and neck squamous cell carcinoma. Front Oncol 2022; 12:940377. [PMID: 36052247 PMCID: PMC9424551 DOI: 10.3389/fonc.2022.940377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
A critical risk factor for head and neck squamous cell carcinoma (HNSCC), particularly of the oropharynx, and the response to radiotherapy is human papillomavirus (HPV) type-16/18 infection. Specifically, HPV-positive HNSCC display increased radiosensitivity and improved outcomes, which has been linked with defective signalling and repair of DNA double-strand breaks (DSBs). This differential response to radiotherapy has been recapitulated in vitro using cell lines, although studies utilising appropriate 3D models that are more reflective of the original tumour are scarce. Furthermore, strategies to enhance the sensitivity of relatively radioresistant HPV-negative HNSCC to radiotherapy are still required. We have analysed the comparative response of in vitro 3D spheroid models of oropharyngeal squamous cell carcinoma to x-ray (photon) irradiation and provide further evidence that HPV-positive cells, in this case now grown as spheroids, show greater inherent radiosensitivity compared to HPV-negative spheroids due to defective DSB repair. We subsequently analysed these and an expanded number of spheroid models, with a particular focus on relatively radioresistant HPV-negative HNSCC, for impact of poly(ADP-ribose) polymerase (PARP) inhibitors (olaparib and talazoparib) in significantly inhibiting spheroid growth in response to photons but also proton beam therapy. We demonstrate that in general, PARP inhibition can further radiosensitise particularly HPV-negative HNSCC spheroids to photons and protons leading to significant growth suppression. The degree of enhanced radiosensitivity was observed to be dependent on the model and on the tumour site (oropharynx, larynx, salivary gland, or hypopharynx) from which the cells were derived. We also provide evidence suggesting that PARP inhibitor effectiveness relates to homologous recombination repair proficiency. Interestingly though, we observed significantly enhanced effectiveness of talazoparib versus olaparib specifically in response to proton irradiation. Nevertheless, our data generally support that PARP inhibition in combination with radiotherapy (photons and protons) should be considered further as an effective treatment for HNSCC, particularly for relatively radioresistant HPV-negative tumours.
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Affiliation(s)
- Chumin Zhou
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Maria Rita Fabbrizi
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jonathan R. Hughes
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Gabrielle J. Grundy
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jason L. Parsons
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, United Kingdom
- *Correspondence: Jason L. Parsons,
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41
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Clarke TL, Mostoslavsky R. DNA repair as a shared hallmark in cancer and ageing. Mol Oncol 2022; 16:3352-3379. [PMID: 35834102 PMCID: PMC9490147 DOI: 10.1002/1878-0261.13285] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well‐orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing‐related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway‐targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.
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Affiliation(s)
- Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
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42
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Zhou W, Zhang W. A novel pyroptosis-related lncRNA prognostic signature associated with the immune microenvironment in lung squamous cell carcinoma. BMC Cancer 2022; 22:694. [PMID: 35739504 PMCID: PMC9229145 DOI: 10.1186/s12885-022-09790-z] [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: 04/26/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background A growing body of evidence suggests that pyroptosis-related lncRNAs (PRncRNAs) are associated with the prognoses of tumor patients and their tumor immune microenvironments. However, the function of PRlncRNAs in lung squamous cell carcinoma (LUSC) remains unclear. Methods We downloaded the transcriptome and clinical information of 551 LUSC samples from the The Cancer Genome Atlas (TCGA) database and randomly separated patients with complete information into two cohorts. Based on the training cohort, we developed a pyroptosis-related signature. We then examined the signature in the test cohort and all retained patients. We also clustered two risk groups in each cohort according to the signature and performed survival analysis, functional analysis, tumor immune microenvironment analysis and drug sensitivity analysis. Results A prognostic signature containing five PRlncRNAs (AP001189.1, PICART1, LINC02555, AC010422.4, and AL606469.1) was developed. A principal component analysis (PCA) indicated better differentiation between patients with different risk scores. Kaplan–Meier (K–M) analysis demonstrated poorer survival among patients with higher risk scores (P < 0.001). A receiver operating characteristic (ROC) curve analysis provided evidence confirming the accuracy of the signature, and univariate (p = 0.005) and multivariate (p = 0.008) Cox regression analyses confirmed the independent value of the risk score in prognoses. Clinical subgroup validation indicated that the signature was more suitable for patients with early-stage LUSC. We also created a nomogram to increase the accuracy of the prediction. Moreover, functional analysis revealed that pathways related to tumor development and pyroptosis were enriched in the high-risk group. Furthermore, the prognostic signature was proven to be a predictor of sensitivity to immunotherapy and chemotherapy. Conclusions We developed a novel pyroptosis-associated signature with independent value for the prognosis of LUSC patients. PRlncRNAs are closely associated with the tumor immune microenvironment in LUSC and might offer new directions for immunotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09790-z.
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Affiliation(s)
- Wei Zhou
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, 330006, Nanchang, China.,Jiangxi medical college, Nanchang University, 330006, Nanchang, China
| | - Wenxiong Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, 330006, Nanchang, China.
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43
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Westwood MN, Johnson CC, Oyler NA, Meints GA. Kinetics and thermodynamics of BI-BII interconversion altered by T:G mismatches in DNA. Biophys J 2022; 121:1691-1703. [PMID: 35367235 PMCID: PMC9117933 DOI: 10.1016/j.bpj.2022.03.031] [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: 08/30/2021] [Revised: 10/26/2021] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
T:G mismatches in DNA result in humans primarily from deamination of methylated CpG sites. They are repaired by redundant systems, such as thymine DNA glycosylase (TDG) and methyl-binding domain enzyme (MBD4), and maintenance of these sites has been implicated in epigenetic processes. The process by which these enzymes identify a canonical DNA base in the incorrect basepairing context remains a mystery. However, the conserved contacts of the repair enzymes with the DNA backbone suggests a role for protein-phosphate interaction in the recognition and repair processes. We have used 31P NMR to investigate the energetics of DNA backbone BI-BII interconversion, and for this work have focused on alterations to the activation barriers to interconversion and the effect of a mismatch compared with canonical DNA. We have found that alterations to the ΔG of interconversion for T:G basepairs are remarkably similar to U:G basepairs in the form of stepwise differences in ΔG of 1-2 kcal/mol greater than equivalent steps in unmodified DNA, suggesting a universality of this result for TDG substrates. Likewise, we see perturbations to the free energy (∼1 kcal/mol) and enthalpy (2-5 kcal/mol) of activation for the BI-BII interconversion localized to the phosphates flanking the mismatch. Overall our results strongly suggest that the perturbed backbone energetics in T:G basepairs play a significant role in the recognition process of DNA repair enzymes.
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Affiliation(s)
- M N Westwood
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri
| | - C C Johnson
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri
| | - Nathan A Oyler
- Department of Chemistry, University of Missouri-Kansas City, Kansas City, Missouri
| | - Gary A Meints
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri.
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44
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Malakoti F, Targhazeh N, Abadifard E, Zarezadeh R, Samemaleki S, Asemi Z, Younesi S, Mohammadnejad R, Hadi Hossini S, Karimian A, Alemi F, Yousefi B. DNA repair and damage pathways in mesothelioma development and therapy. Cancer Cell Int 2022; 22:176. [PMID: 35501851 PMCID: PMC9063177 DOI: 10.1186/s12935-022-02597-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/18/2022] [Indexed: 12/30/2022] Open
Abstract
Malignant mesothelioma (MMe) is an aggressive neoplasm that occurs through the transformation of mesothelial cells. Asbestos exposure is the main risk factor for MMe carcinogenesis. Other important etiologies for MMe development include DNA damage, over-activation of survival signaling pathways, and failure of DNA damage response (DDR). In this review article, first, we will describe the most important signaling pathways that contribute to MMe development and their interaction with DDR. Then, the contribution of DDR failure in MMe progression will be discussed. Finally, we will review the latest MMe therapeutic strategies that target the DDR pathway.
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Affiliation(s)
- Faezeh Malakoti
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Niloufar Targhazeh
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Erfan Abadifard
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Zarezadeh
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sahar Samemaleki
- Department of Immunology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Simin Younesi
- Schoole of Health and Biomedical Sciences, RMIT University, Melbourne, Vic, Australia
| | - Reza Mohammadnejad
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Hadi Hossini
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ansar Karimian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Bahman Yousefi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Alfarhan MW, Al-Hussaini H, Kilarkaje N. Role of PPAR-γ in diabetes-induced testicular dysfunction, oxidative DNA damage and repair in leptin receptor-deficient obese type 2 diabetic mice. Chem Biol Interact 2022; 361:109958. [PMID: 35472412 DOI: 10.1016/j.cbi.2022.109958] [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: 12/21/2021] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 11/03/2022]
Abstract
The testis expresses peroxisome proliferator-activated receptor-γ (PPAR-γ), but its involvement in regulating diabetes-induced testicular dysfunction and DNA damage repair is not known. Pioglitazone-induced activation of PPAR-γ for 12 weeks in db/db obese diabetic mice increases bodyweights and reduces blood glucose levels, but PPAR-γ inhibition by 2-chloro-5-nitro-N-phenylbenzamide does not alter these parameters; instead, improves testis and epididymis weights and sperm count. Neither activation nor inhibition of PPAR-γ normalizes the diabetes-induced seminiferous epithelial degeneration. The PPAR-γ activation normalizes testicular lipid peroxidation, but its inhibition reduces lipid peroxidation and oxidative DNA damage (8-oxo-dG) in diabetic mice. As a response to diabetes-induced oxidative DNA damage, the base-excision repair (BER) mechanism proteins- 8-oxoguanine DNA glycosylases (OGG1/2) and X-ray repair cross-complementing protein-1 (XRCC1) increase, whereas the redox-factor-1 (REF1), DNA polymerase (pol) δ and poly (ADP-ribose) polymerase-1 (PARP1) show a tendency to increase suggesting an attempt to repair the oxidative DNA damage. The PPAR-γ stimulation inhibits OGG2, DNA pol δ, and XRCC1 in diabetic mice testes, but PPAR-γ inhibition reduces oxidative DNA damage and normalizes BER protein levels. In conclusion, type 2 diabetes negatively affects testicular structure and function and increases oxidative DNA damage and BER protein levels due to increased DNA damage. The PPAR-γ modulation does not significantly affect the structural changes in the testis. The PPAR-γ stimulation aggravates diabetes-induced effects on testis, including oxidative DNA damage and BER proteins, but PPAR-γ inhibition marginally recovers these diabetic effects indicating the involvement of the receptor in the reproductive effects of diabetes.
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Affiliation(s)
| | - Heba Al-Hussaini
- Department of Anatomy, Faculty of Medicine, Kuwait University, Kuwait
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Choi W, Lee ES. Therapeutic Targeting of DNA Damage Response in Cancer. Int J Mol Sci 2022; 23:ijms23031701. [PMID: 35163621 PMCID: PMC8836062 DOI: 10.3390/ijms23031701] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 02/07/2023] Open
Abstract
DNA damage response (DDR) is critical to ensure genome stability, and defects in this signaling pathway are highly associated with carcinogenesis and tumor progression. Nevertheless, this also provides therapeutic opportunities, as cells with defective DDR signaling are directed to rely on compensatory survival pathways, and these vulnerabilities have been exploited for anticancer treatments. Following the impressive success of PARP inhibitors in the treatment of BRCA-mutated breast and ovarian cancers, extensive research has been conducted toward the development of pharmacologic inhibitors of the key components of the DDR signaling pathway. In this review, we discuss the key elements of the DDR pathway and how these molecular components may serve as anticancer treatment targets. We also summarize the recent promising developments in the field of DDR pathway inhibitors, focusing on novel agents beyond PARP inhibitors. Furthermore, we discuss biomarker studies to identify target patients expected to derive maximal clinical benefits as well as combination strategies with other classes of anticancer agents to synergize and optimize the clinical benefits.
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Affiliation(s)
- Wonyoung Choi
- Research Institute, National Cancer Center, Goyang 10408, Korea;
- Center for Clinical Trials, National Cancer Center, Goyang 10408, Korea
| | - Eun Sook Lee
- Research Institute, National Cancer Center, Goyang 10408, Korea;
- Center for Breast Cancer, National Cancer Center, Goyang 10408, Korea
- Correspondence: ; Tel.: +82-31-920-1633
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Particle radiotherapy and molecular therapies: mechanisms and strategies towards clinical applications. Expert Rev Mol Med 2022; 24:e8. [PMID: 35101155 DOI: 10.1017/erm.2022.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunotherapy and targeted therapy are now commonly used in clinical trials in combination with radiotherapy for several cancers. While results are promising and encouraging, the molecular mechanisms of the interaction between the drugs and radiation remain largely unknown. This is especially important when switching from conventional photon therapy to particle therapy using protons or heavier ions. Different dose deposition patterns and molecular radiobiology can in fact modify the interaction with drugs and their effectiveness. We will show here that whilst the main molecular players are the same after low and high linear energy transfer radiation exposure, significant differences are observed in post-exposure signalling pathways that may lead to different effects of the drugs. We will also emphasise that the problem of the timing between drug administration and radiation and the fractionation regime are critical issues that need to be addressed urgently to achieve optimal results in combined treatments with particle therapy.
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Liu T, Chen L, Gao G, Liang X, Peng J, Zheng M, Li J, Ye Y, Shao C. Development of a Gene Risk Signature for Patients of Pancreatic Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4136825. [PMID: 35035831 PMCID: PMC8759853 DOI: 10.1155/2022/4136825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Pancreatic cancer is a highly malignant solid tumor with a high lethality rate, but there is a lack of clinical biomarkers that can assess patient prognosis to optimize treatment. METHODS Gene-expression datasets of pancreatic cancer tissues and normal pancreatic tissues were obtained from the GEO database, and differentially expressed genes analysis and WGCNA analysis were performed after merging and normalizing the datasets. Univariate Cox regression analysis and Lasso Cox regression analysis were used to screen the prognosis-related genes in the modules with the strongest association with pancreatic cancer and construct risk signatures. The performance of the risk signature was subsequently validated by Kaplan-Meier curves, receiver operating characteristic (ROC), and univariate and multivariate Cox analyses. RESULT A three-gene risk signature containing CDKN2A, BRCA1, and UBL3 was established. Based on KM curves, ROC curves, and univariate and multivariate Cox regression analyses in the TRAIN cohort and TEST cohort, it was suggested that the three-gene risk signature had better performance in predicting overall survival. CONCLUSION This study identifies a three-gene risk signature, constructs a nomogram that can be used to predict pancreatic cancer prognosis, and identifies pathways that may be associated with pancreatic cancer prognosis.
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Affiliation(s)
- Tao Liu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
- Department of Hepatobiliary Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Long Chen
- Department of Gastrointestinal Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Guili Gao
- Department of Cardiology, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Xing Liang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Junfeng Peng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Minghui Zheng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Judong Li
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Yongqiang Ye
- Department of Hepatobiliary Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Chenghao Shao
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
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Qin L, Huiwen M, Wang J, Wang Y, Khan SA, Zhang Y, Qiu H, Jiang L, He L, Zhang Y, Jia S. A novel polymerase β inhibitor from phage displayed peptide library augments the anti-tumour effects of temozolomide on colorectal cancer. J Chemother 2021; 34:391-400. [PMID: 34870566 DOI: 10.1080/1120009x.2021.2009987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The therapeutic efficacy of TMZ, a common used drug for chemotherapy, is limited by the resistance from colorectal cancer cells. Base excision repair (BER) pathway has been identified as one of the reasons for drug resistance. By blocking Polβ-dependent BER (Base Excision Repair) pathway, the efficacy of TMZ treatment can be improved greatly. Several Polβ inhibitors that have been identified could not become approved drugs due to lack of potency or specificity. To find therapeutic candidates with exquisite specificity and high affinity to Polβ, phage display technology was used in the current research. We screened out a candidate Polβ inhibitor, 10 D, that can inhibit the activity of Polβand SP-BER (Short-Patch Base excision Repair) pathway. Co-treatment with 10 D enhanced the sensitivity of colorectal cancer (CRC) cells to TMZ both in vitro and in vivo. Our data suggested that the novel Polβ inhibitor we identified can improve TMZ efficacy and optimize CRC chemotherapy.
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Affiliation(s)
- Lihong Qin
- Changzhou No. 7 People's Hospital, Changzhou, China
| | - Mao Huiwen
- Shuyang Hospital of Traditional Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Shuyang, China
| | - Jianguo Wang
- Shuyang Hospital of Traditional Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Shuyang, China
| | - Yuanyaun Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Salman A Khan
- Shuyang Hospital of Traditional Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Shuyang, China
| | - Ying Zhang
- Qinhuai Medical District, Jinlin Hospital of Nanjing University, Nanjing, China
| | - Hong Qiu
- Qinhuai Medical District, Jinlin Hospital of Nanjing University, Nanjing, China
| | - Longwei Jiang
- Qinhuai Medical District, Jinlin Hospital of Nanjing University, Nanjing, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yan Zhang
- Qinhuai Medical District, Jinlin Hospital of Nanjing University, Nanjing, China
| | - Shaochang Jia
- Qinhuai Medical District, Jinlin Hospital of Nanjing University, Nanjing, China
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Impact of Chromatin Dynamics and DNA Repair on Genomic Stability and Treatment Resistance in Pediatric High-Grade Gliomas. Cancers (Basel) 2021; 13:cancers13225678. [PMID: 34830833 PMCID: PMC8616465 DOI: 10.3390/cancers13225678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Pediatric high-grade gliomas (pHGGs) are the leading cause of mortality in pediatric neuro-oncology, due in great part to treatment resistance driven by complex DNA repair mechanisms. pHGGs have recently been divided into molecular subtypes based on mutations affecting the N-terminal tail of the histone variant H3.3 and the ATRX/DAXX histone chaperone that deposits H3.3 at repetitive heterochromatin loci that are of paramount importance to the stability of our genome. This review addresses the functions of H3.3 and ATRX/DAXX in chromatin dynamics and DNA repair, as well as the impact of mutations affecting H3.3/ATRX/DAXX on treatment resistance and how the vulnerabilities they expose could foster novel therapeutic strategies. Abstract Despite their low incidence, pediatric high-grade gliomas (pHGGs), including diffuse intrinsic pontine gliomas (DIPGs), are the leading cause of mortality in pediatric neuro-oncology. Recurrent, mutually exclusive mutations affecting K27 (K27M) and G34 (G34R/V) in the N-terminal tail of histones H3.3 and H3.1 act as key biological drivers of pHGGs. Notably, mutations in H3.3 are frequently associated with mutations affecting ATRX and DAXX, which encode a chaperone complex that deposits H3.3 into heterochromatic regions, including telomeres. The K27M and G34R/V mutations lead to distinct epigenetic reprogramming, telomere maintenance mechanisms, and oncogenesis scenarios, resulting in distinct subgroups of patients characterized by differences in tumor localization, clinical outcome, as well as concurrent epigenetic and genetic alterations. Contrasting with our understanding of the molecular biology of pHGGs, there has been little improvement in the treatment of pHGGs, with the current mainstays of therapy—genotoxic chemotherapy and ionizing radiation (IR)—facing the development of tumor resistance driven by complex DNA repair pathways. Chromatin and nucleosome dynamics constitute important modulators of the DNA damage response (DDR). Here, we summarize the major DNA repair pathways that contribute to resistance to current DNA damaging agent-based therapeutic strategies and describe the telomere maintenance mechanisms encountered in pHGGs. We then review the functions of H3.3 and its chaperones in chromatin dynamics and DNA repair, as well as examining the impact of their mutation/alteration on these processes. Finally, we discuss potential strategies targeting DNA repair and epigenetic mechanisms as well as telomere maintenance mechanisms, to improve the treatment of pHGGs.
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