151
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Kim JH, Youn Y, Hwang JH. NCAPH Stabilizes GEN1 in Chromatin to Resolve Ultra-Fine DNA Bridges and Maintain Chromosome Stability. Mol Cells 2022; 45:792-805. [PMID: 36380731 PMCID: PMC9676985 DOI: 10.14348/molcells.2022.0048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/11/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Repairing damaged DNA and removing all physical connections between sister chromosomes is important to ensure proper chromosomal segregation by contributing to chromosomal stability. Here, we show that the depletion of non-SMC condensin I complex subunit H (NCAPH) exacerbates chromosome segregation errors and cytokinesis failure owing to sister-chromatid intertwinement, which is distinct from the ultra-fine DNA bridges induced by DNA inter-strand crosslinks (DNA-ICLs). Importantly, we identified an interaction between NCAPH and GEN1 in the chromatin involving binding at the N-terminus of NCAPH. DNA-ICL activation, using ICL-inducing agents, increased the expression and interaction between NCAPH and GEN1 in the soluble nuclear and chromatin, indicating that the NCAPH-GEN1 interaction participates in repairing DNA damage. Moreover, NCAPH stabilizes GEN1 within chromatin at the G2/M-phase and is associated with DNA-ICL-induced damage repair. Therefore, NCAPH resolves DNA-ICL-induced ultra-fine DNA bridges by stabilizing GEN1 and ensures proper chromosome separation and chromosome structural stability.
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Affiliation(s)
- Jae Hyeong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Yuna Youn
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Jin-Hyeok Hwang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
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152
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Saleem B, Farooq U, Rehman OU, Aqeel M, Farooq MS, Naeem MK, Inam S, Ajmal W, Rahim AA, Chen M, Kalsoom R, Uzair M, Fiaz S, Attia K, Alafari HA, Khan MR, Yu G. Genome-wide and molecular characterization of the DNA replication helicase 2 ( DNA2) gene family in rice under drought and salt stress. Front Genet 2022; 13:1039548. [PMID: 36506305 PMCID: PMC9728955 DOI: 10.3389/fgene.2022.1039548] [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: 09/08/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
Rice plants experience various biotic (such as insect and pest attack) and abiotic (such as drought, salt, heat, and cold etc.) stresses during the growing season, resulting in DNA damage and the subsequent losses in rice production. DNA Replication Helicase/Nuclease2 (DNA2) is known to be involved in DNA replication and repair. In animals and yeast DNA2 are well characterized because it has the abilities of both helicase and nuclease, it plays a crucial role in DNA replication in the nucleus and mitochondrial genomes. However; they are not fully examined in plants due to less focused on plants damage repair. To fill this research gap, the current study focused on the genome-wide identification and characterization of OsDNA2 genes, along with analyses of their transcriptional expression, duplication, and phylogeny in rice. Overall, 17 OsDNA2 members were reported to be found on eight different chromosomes (2, 3, 4, 6, 7, 9, 10, and 11). Among these chromosomes (Chr), Chr4 contained a maximum of six OsDNA2 genes. Based on phylogenetic analysis, the OsDNA2 gene members were clustered into three different groups. Furthermore, the conserved domains, gene structures, and cis-regulatory elements were systematically investigated. Gene duplication analysis revealed that OsDNA2_2 had an evolutionary relationship with OsDNA2_14, OsDNA2_5 with OsDNA2_6, and OsDNA2_1 with OsDNA2_8. Moreover, results showed that the conserved domain (AAA_11 superfamily) were present in the OsDNA2 genes, which belongs to the DEAD-like helicase superfamily. In addition, to understand the post-transcriptional modification of OsDNA2 genes, miRNAs were predicted, where 653 miRNAs were reported to target 17 OsDNA2 genes. The results indicated that at the maximum, OsDNA2_1 and OsDNA2_4 were targeted by 74 miRNAs each, and OsDNA2_9 was less targeted (20 miRNAs). The three-dimensional (3D) structures of 17 OsDNA2 proteins were also predicted. Expression of OsDNA2 members was also carried out under drought and salt stresses, and conclusively their induction indicated the possible involvement of OsDNA2 in DNA repair under stress when compared with the control. Further studies are recommended to confirm where this study will offer valuable basic data on the functioning of DNA2 genes in rice and other crop plants.
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Affiliation(s)
- Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Shahbaz Farooq
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Amna Abdul Rahim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rabia Kalsoom
- School of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Kotb Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hayat Ali Alafari
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| | - Guoping Yu
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China,China National Rice Research Institute, Hangzhou, China,Hainan Yazhou Bay Seed Lab, Sanya, China,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
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153
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A rapid multiplex cell-free assay on biochip to evaluate functional aspects of double-strand break repair. Sci Rep 2022; 12:20054. [PMID: 36414637 PMCID: PMC9681732 DOI: 10.1038/s41598-022-23819-0] [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: 02/23/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) involves interdependent molecular pathways, of which the choice is crucial for a cell's fate when facing a damage. Growing evidence points toward the fact that DSB repair capacities correlate with disease aggressiveness, treatment response and treatment-related toxicities in cancer. Scientific and medical communities need more easy-to-use and efficient tools to rapidly estimate DSB repair capacities from a tissue, enable routine-accessible treatment personalization, and hopefully, improve survival. Here, we propose a new functional biochip assay (NEXT-SPOT) that characterizes DSB repair-engaged cellular pathways and provides qualitative and quantitative information on the contribution of several pathways in less than 2 h, from 10 mg of cell lysates. We introduce the NEXT-SPOT technology, detail the molecular characterizations of different repair steps occurring on the biochip, and show examples of DSB repair profiling using three cancer cell lines treated or not with a DSB-inducer (doxorubicin) and/or a DNA repair inhibitor (RAD51 inhibitor; DNA-PK inhibitor; PARP inhibitor). Among others, we demonstrate that NEXT-SPOT can accurately detect decreased activities in strand invasion and end-joining mechanisms following DNA-PK or RAD51 inhibition in DNA-PK-proficient cell lines. This approach offers an all-in-one reliable strategy to consider DSB repair capacities as predictive biomarkers easily translatable to the clinic.
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154
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Fangaria N, Rani K, Singh P, Dey S, Kumar KA, Bhattacharyya S. DNA damage-induced nuclear import of HSP90α is promoted by Aha1. Mol Biol Cell 2022; 33:ar140. [PMID: 36260391 PMCID: PMC9727810 DOI: 10.1091/mbc.e21-11-0554] [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: 02/04/2023] Open
Abstract
The interplay between yHSP90α (Hsp82) and Rad51 has been implicated in the DNA double-strand break repair (DSB) pathway in yeast. Here we report that nuclear translocation of yHSP90α and its recruitment to the DSB end are essential for homologous recombination (HR)-mediated DNA repair in yeast. The HsHSP90α possesses an amino-terminal extension which is phosphorylated upon DNA damage. We find that the absence of the amino-terminal extension in yHSP90α does not compromise its nuclear import, and the nonphosphorylatable-mutant HsHSP90αT7A could be imported to the yeast nucleus upon DNA damage. Interestingly, the flexible charged-linker (CL) domains of both yHSP90α and HsHSP90α play a critical role during their nuclear translocation. The conformational restricted CL mutant yHSP90α∆(211-259), but not a shorter deletion version yHSP90α∆(211-242), fails to reach the nucleus. As the CL domain of yHSP90α is critical for its interaction with Aha1, we investigated whether Aha1 promotes the nuclear import of yHSP90α. We found that the nuclear import of yHSP90α is severely affected in ∆aha1 strain. Moreover, Aha1 is accumulated in the nucleus during DNA damage. Hence Aha1 may serve as a potential target for inhibiting nuclear function of yHSP90α. The increased sensitivity of ∆aha1 strain to genotoxic agents strengthens this notion.
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Affiliation(s)
- Nupur Fangaria
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Khushboo Rani
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Priyanka Singh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Sandeep Dey
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Kota Arun Kumar
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India,*Address correspondence to: Sunanda Bhattacharyya (; )
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155
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Wasim S, Lee SY, Kim J. Complexities of Prostate Cancer. Int J Mol Sci 2022; 23:14257. [PMID: 36430730 PMCID: PMC9696501 DOI: 10.3390/ijms232214257] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Prostate cancer has a long disease history and a wide variety and uncertainty in individual patients' clinical progress. In recent years, we have seen a revolutionary advance in both prostate cancer patient care and in the research field. The power of deep sequencing has provided cistromic and transcriptomic knowledge of prostate cancer that has not discovered before. Our understanding of prostate cancer biology, from bedside and molecular imaging techniques, has also been greatly advanced. It is important that our current theragnostic schemes, including our diagnostic modalities, therapeutic responses, and the drugs available to target non-AR signaling should be improved. This review article discusses the current progress in the understanding of prostate cancer biology and the recent advances in diagnostic and therapeutic strategies.
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Affiliation(s)
- Sobia Wasim
- Department of Neuroscience, College of Medicine, Gachon University, Incheon 21936, Republic of Korea
| | - Sang-Yoon Lee
- Department of Neuroscience, College of Medicine, Gachon University, Incheon 21936, Republic of Korea
| | - Jaehong Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
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156
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Cojocaru E, Napolitano A, Fisher C, Huang P, Jones RL, Thway K. What's the latest with investigational drugs for soft tissue sarcoma? Expert Opin Investig Drugs 2022; 31:1239-1253. [PMID: 36424693 DOI: 10.1080/13543784.2022.2152324] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Despite extensive research undertaken in the past 20-30 years, the treatment for soft tissue sarcoma (STS) has remained largely the same, with anthracycline-based chemotherapy remaining the first choice for treating advanced or metastatic STS. AREAS COVERED This review focuses on newly approved drugs for STS and current research directions, including recent results of late-phase trials in patients with STS. We cover several different histological subtypes, and we discuss the role of adoptive cell transfer (ACT) therapies for the treatment of synovial and myxoid/round cell (high-grade myxoid) liposarcoma, one of the most promising areas of treatment development to date. We searched clinicaltrials.gov and pubmed.ncbi.nih.gov, as well as recent year proceedings from the annual conferences of the American Society of Clinical Oncology (ASCO), European Society for Medical Oncology (ESMO), and Connective Tissue Oncology Society (CTOS). EXPERT OPINION Immune-oncology drugs (IOs) show promise in certain subtypes of STS, but it is recognized that PD-1/PD-L1 axis inhibition is not enough on its own. Better trial stratifications based on the molecular categorization of different subtypes of STS are needed, and more evidence suggests that 'one size fits all' treatment is no longer sustainable in this heterogeneous and aggressive group of tumors.
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Affiliation(s)
- Elena Cojocaru
- Cancer Genetic Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ, London, UK.,Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ, London, UK
| | - Andrea Napolitano
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ, London, UK
| | - Cyril Fisher
- Department of Pathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Paul Huang
- Protein Networks Team, Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, UK
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ, London, UK.,Protein Networks Team, Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, UK
| | - Khin Thway
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ, London, UK.,Protein Networks Team, Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, UK
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157
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Chen J, Wang X, Ma A, Wang QE, Liu B, Li L, Xu D, Ma Q. Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data. Nat Commun 2022; 13:6494. [PMID: 36310235 PMCID: PMC9618578 DOI: 10.1038/s41467-022-34277-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/19/2022] [Indexed: 12/25/2022] Open
Abstract
Drug screening data from massive bulk gene expression databases can be analyzed to determine the optimal clinical application of cancer drugs. The growing amount of single-cell RNA sequencing (scRNA-seq) data also provides insights into improving therapeutic effectiveness by helping to study the heterogeneity of drug responses for cancer cell subpopulations. Developing computational approaches to predict and interpret cancer drug response in single-cell data collected from clinical samples can be very useful. We propose scDEAL, a deep transfer learning framework for cancer drug response prediction at the single-cell level by integrating large-scale bulk cell-line data. The highlight in scDEAL involves harmonizing drug-related bulk RNA-seq data with scRNA-seq data and transferring the model trained on bulk RNA-seq data to predict drug responses in scRNA-seq. Another feature of scDEAL is the integrated gradient feature interpretation to infer the signature genes of drug resistance mechanisms. We benchmark scDEAL on six scRNA-seq datasets and demonstrate its model interpretability via three case studies focusing on drug response label prediction, gene signature identification, and pseudotime analysis. We believe that scDEAL could help study cell reprogramming, drug selection, and repurposing for improving therapeutic efficacy.
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Affiliation(s)
- Junyi Chen
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Xiaoying Wang
- Department of Mathematics, Shandong University, Shandong, 250100, China
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Qi-En Wang
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Bingqiang Liu
- Department of Mathematics, Shandong University, Shandong, 250100, China
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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158
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Meschichi A, Zhao L, Reeck S, White C, Da Ines O, Sicard A, Pontvianne F, Rosa S. The plant-specific DDR factor SOG1 increases chromatin mobility in response to DNA damage. EMBO Rep 2022; 23:e54736. [PMID: 36278395 PMCID: PMC9724665 DOI: 10.15252/embr.202254736] [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: 01/28/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measure chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, using lacO/LacI lines and two GFP-tagged HR reporters. We observe an increase in chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. This increase in mobility is lost in the sog1-1 mutant, a central transcription factor of the DNA damage response in plants. Also, DSB sites show particularly high mobility levels and their enhanced mobility requires the HR factor RAD54. Our data suggest that repair mechanisms promote chromatin mobility upon DNA damage, implying a role of this process in the early steps of the DNA damage response.
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Affiliation(s)
- Anis Meschichi
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Lihua Zhao
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Svenja Reeck
- John Innes Centre, Norwich Research ParkNorwichUK
| | - Charles White
- Institut Génétique Reproduction et Développement (iGReD)Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERMClermont‐FerrandFrance
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD)Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERMClermont‐FerrandFrance
| | - Adrien Sicard
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP)Université de Perpignan Via DomitiaPerpignanFrance
| | - Stefanie Rosa
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
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159
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PLK-1 Interacting Checkpoint Helicase, PICH, Mediates Cellular Oxidative Stress Response. EPIGENOMES 2022; 6:epigenomes6040036. [DOI: 10.3390/epigenomes6040036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Cells respond to oxidative stress by elevating the levels of antioxidants, signaling, and transcriptional regulation, often implemented by chromatin remodeling proteins. The study presented here shows that the expression of PICH, a Rad54-like helicase belonging to the ATP-dependent chromatin remodeling protein family, is upregulated during oxidative stress in HeLa cells. We also show that PICH regulates the expression of Nrf2, a transcription factor regulating antioxidant response in both the absence and presence of oxidative stress. The overexpression of PICH in PICH-depleted cells restored Nrf2 as well as antioxidant gene expression. In turn, Nrf2 regulated the expression of PICH in the presence of oxidative stress. ChIP experiments showed that PICH is present on the Nrf2 as well as antioxidant gene promoters, suggesting that the protein might be regulating the expression of these genes directly by binding to the DNA sequences. In addition, Nrf2 and histone acetylation (H3K27ac) also played a role in activating transcription in the presence of oxidative stress. Both Nrf2 and H3K27ac were found to be present on PICH and antioxidant promoters. Their occupancy was dependent on the PICH expression as fold enrichment was found to be decreased in PICH-depleted cells. PICH ablation led to the reduced expression of Nrf2 and impaired antioxidant response, leading to increased ROS content and thus showing PICH is essential for the cell to respond to oxidative stress.
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160
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Zhang Y, Yang L, Fang K, Li Q, Xu H, Ren Y, Zi J, Chen CD, Liu S. Dynamic Responses of Chromosome-Binding Protein Complexes to Meiotic Prophase I of Mouse Spermatocyte. J Proteome Res 2022; 21:2715-2726. [PMID: 36223561 DOI: 10.1021/acs.jproteome.2c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Meiotic prophase I (MPI) is the most important event in mammalian meiosis. The status of the chromosome-binding proteins (CBPs) and the corresponding complexes and their functions in MPI have not yet been well scrutinized. Quantitative proteomics focused on MPI-related CBPs was accomplished, in which mouse primary spermatocytes in four different subphases of MPI were collected, and chromosome-enriched proteins were extracted and quantitatively identified. According to a stringent criterion, 1136 CBPs in the MPI subphases were quantified. Looking at the dynamic patterns of CBP abundance in response to MPI progression, the patterns were broadly divided into two groups: high abundance in leptotene and zygotene or that in pachytene and diplotene. Furthermore, 152 such CBPs were regarded as 26 CBP complexes with strict filtration, in which some of these complexes were perceived to be MPI-dependent for the first time. These complexes basically belonged to four functional categories, while their dynamic abundance changes following MPI appeared; the functions of DNA replication decreased; and transcription and synapsis were activated in zygotene, pachytene, and diplotene; in contrast to the traditional prediction, condensin activity weakened in pachytene and diplotene. Profiling of protein complexes thus offered convincing evidence of the importance of CBP complexes in MPI.
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Affiliation(s)
- Yuxing Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,College of Life Sciences & Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049 China
| | | | - Kailun Fang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031 China
| | - Qidan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongkai Xu
- BGI-Shenzhen, Shenzhen 518083, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Ren
- BGI-Shenzhen, Shenzhen 518083, China.,Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen 518083, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China
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161
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Ravishankar K, Jiang X, Leddin EM, Morcos F, Cisneros GA. Computational compensatory mutation discovery approach: Predicting a PARP1 variant rescue mutation. Biophys J 2022; 121:3663-3673. [PMID: 35642254 PMCID: PMC9617126 DOI: 10.1016/j.bpj.2022.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/02/2022] Open
Abstract
The prediction of protein mutations that affect function may be exploited for multiple uses. In the context of disease variants, the prediction of compensatory mutations that reestablish functional phenotypes could aid in the development of genetic therapies. In this work, we present an integrated approach that combines coevolutionary analysis and molecular dynamics (MD) simulations to discover functional compensatory mutations. This approach is employed to investigate possible rescue mutations of a poly(ADP-ribose) polymerase 1 (PARP1) variant, PARP1 V762A, associated with lung cancer and follicular lymphoma. MD simulations show PARP1 V762A exhibits noticeable changes in structural and dynamical behavior compared with wild-type (WT) PARP1. Our integrated approach predicts A755E as a possible compensatory mutation based on coevolutionary information, and molecular simulations indicate that the PARP1 A755E/V762A double mutant exhibits similar structural and dynamical behavior to WT PARP1. Our methodology can be broadly applied to a large number of systems where single-nucleotide polymorphisms have been identified as connected to disease and can shed light on the biophysical effects of such changes as well as provide a way to discover potential mutants that could restore WT-like functionality. This can, in turn, be further utilized in the design of molecular therapeutics that aim to mimic such compensatory effect.
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Affiliation(s)
| | - Xianli Jiang
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas
| | - Faruck Morcos
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas; Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas; Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas.
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas; Department of Physics, The University of Texas at Dallas, Richardson, Texas; Department of Chemistry, The University of Texas at Dallas, Richardson, Texas.
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162
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Camero S, Cassandri M, Pomella S, Milazzo L, Vulcano F, Porrazzo A, Barillari G, Marchese C, Codenotti S, Tomaciello M, Rota R, Fanzani A, Megiorni F, Marampon F. Radioresistance in rhabdomyosarcomas: Much more than a question of dose. Front Oncol 2022; 12:1016894. [PMID: 36248991 PMCID: PMC9559533 DOI: 10.3389/fonc.2022.1016894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/15/2022] Open
Abstract
Management of rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children, frequently accounting the genitourinary tract is complex and requires a multimodal therapy. In particular, as a consequence of the advancement in dose conformity technology, radiation therapy (RT) has now become the standard therapeutic option for patients with RMS. In the clinical practice, dose and timing of RT are adjusted on the basis of patients' risk stratification to reduce late toxicity and side effects on normal tissues. However, despite the substantial improvement in cure rates, local failure and recurrence frequently occur. In this review, we summarize the general principles of the treatment of RMS, focusing on RT, and the main molecular pathways and specific proteins involved into radioresistance in RMS tumors. Specifically, we focused on DNA damage/repair, reactive oxygen species, cancer stem cells, and epigenetic modifications that have been reported in the context of RMS neoplasia in both in vitro and in vivo studies. The precise elucidation of the radioresistance-related molecular mechanisms is of pivotal importance to set up new more effective and tolerable combined therapeutic approaches that can radiosensitize cancer cells to finally ameliorate the overall survival of patients with RMS, especially for the most aggressive subtypes.
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Affiliation(s)
- Simona Camero
- Department of Maternal, Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Matteo Cassandri
- Department of Radiological Sciences, Oncology and Anatomical Pathology, Sapienza University of Rome, Rome, Italy
- Department of Oncohematology, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Silvia Pomella
- Department of Oncohematology, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Luisa Milazzo
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Vulcano
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Porrazzo
- Department of Radiological Sciences, Oncology and Anatomical Pathology, Sapienza University of Rome, Rome, Italy
- Units of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCSS), Rome, Italy
| | - Giovanni Barillari
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, “Sapienza” University of Rome, Rome, Italy
| | - Silvia Codenotti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Miriam Tomaciello
- Department of Radiological Sciences, Oncology and Anatomical Pathology, Sapienza University of Rome, Rome, Italy
| | - Rossella Rota
- Department of Oncohematology, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Alessandro Fanzani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesca Megiorni
- Department of Experimental Medicine, “Sapienza” University of Rome, Rome, Italy
| | - Francesco Marampon
- Department of Radiological Sciences, Oncology and Anatomical Pathology, Sapienza University of Rome, Rome, Italy
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163
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Groelly FJ, Dagg RA, Petropoulos M, Rossetti GG, Prasad B, Panagopoulos A, Paulsen T, Karamichali A, Jones SE, Ochs F, Dionellis VS, Puig Lombardi E, Miossec MJ, Lockstone H, Legube G, Blackford AN, Altmeyer M, Halazonetis TD, Tarsounas M. Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells. Mol Cell 2022; 82:3382-3397.e7. [PMID: 36002001 PMCID: PMC9631240 DOI: 10.1016/j.molcel.2022.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/31/2022] [Accepted: 07/16/2022] [Indexed: 12/24/2022]
Abstract
Aberrant replication causes cells lacking BRCA2 to enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS). Here, we identify genome-wide the sites where MiDAS reactions occur when BRCA2 is abrogated. High-resolution profiling revealed that these sites are different from MiDAS at aphidicolin-induced common fragile sites in that they map to genomic regions replicating in the early S-phase, which are close to early-firing replication origins, are highly transcribed, and display R-loop-forming potential. Both transcription inhibition in early S-phase and RNaseH1 overexpression reduced MiDAS in BRCA2-deficient cells, indicating that transcription-replication conflicts (TRCs) and R-loops are the source of MiDAS. Importantly, the MiDAS sites identified in BRCA2-deficient cells also represent hotspots for genomic rearrangements in BRCA2-mutated breast tumors. Thus, our work provides a mechanism for how tumor-predisposing BRCA2 inactivation links transcription-induced DNA damage with mitotic DNA repair to fuel the genomic instability characteristic of cancer cells.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Giacomo G Rossetti
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
| | - Birbal Prasad
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Andreas Panagopoulos
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Teressa Paulsen
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Fena Ochs
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Vasilis S Dionellis
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
| | - Emilia Puig Lombardi
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Matthieu J Miossec
- Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Helen Lockstone
- Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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164
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Mahmoud R, Dhakal S. Single-Molecule Analysis of DNA Branch Migration under Biomimetic Environments. J Phys Chem B 2022; 126:7252-7261. [DOI: 10.1021/acs.jpcb.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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165
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Gedminas JM, Laetsch TW. Targeting the DNA damage response in pediatric malignancies. Expert Rev Anticancer Ther 2022; 22:1099-1113. [PMID: 36099180 DOI: 10.1080/14737140.2022.2124970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION High levels of DNA damage and mutations in DNA damage response genes creates a high reliance on DNA damage repair in various tumors. This creates a vulnerability for new cancer therapies. Although there is extensive data for the use of these agents in adult tumors, the evaluation of these compounds in the pediatric population remains in the early stages. AREAS COVERED In this review, we discuss the role of the DNA damage response as a therapeutic vulnerability in pediatric malignancies, provide a summary of clinical data for the use of DNA damage response inhibitors in cancer, and review how these compounds can be extended to the pediatric population. EXPERT OPINION A number of pediatric cancers rely on robust DNA damage repair to maintain cell viability. This provides a therapeutic vulnerability in cancer cells resistant to other traditional therapies. Unfortunately, although clinical evaluation of inhibitors of various components of the DNA damage response has been done in adults, pediatric data remains limited. Further studies are needed to evaluate the efficacy of these compounds in the pediatric population.
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Affiliation(s)
- Jenna M Gedminas
- Children's Hospital of Philadelphia, Division of Oncology, Philadelphia, PA, USA
| | - Theodore W Laetsch
- Children's Hospital of Philadelphia, Division of Oncology, Philadelphia, PA, USA
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166
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Smc5/6 silences episomal transcription by a three-step function. Nat Struct Mol Biol 2022; 29:922-931. [PMID: 36097294 DOI: 10.1038/s41594-022-00829-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
In addition to its role in chromosome maintenance, the six-membered Smc5/6 complex functions as a restriction factor that binds to and transcriptionally silences viral and other episomal DNA. However, the underlying mechanism is unknown. Here, we show that transcriptional silencing by the human Smc5/6 complex is a three-step process. The first step is entrapment of the episomal DNA by a mechanism dependent on Smc5/6 ATPase activity and a function of its Nse4a subunit for which the Nse4b paralog cannot substitute. The second step results in Smc5/6 recruitment to promyelocytic leukemia nuclear bodies by SLF2 (the human ortholog of Nse6). The third step promotes silencing through a mechanism requiring Nse2 but not its SUMO ligase activity. By contrast, the related cohesin and condensin complexes fail to bind to or silence episomal DNA, indicating a property unique to Smc5/6.
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167
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The role of Platinum(IV)-based antitumor drugs and the anticancer immune response in medicinal inorganic chemistry. A systematic review from 2017 to 2022. Eur J Med Chem 2022; 243:114680. [PMID: 36152386 DOI: 10.1016/j.ejmech.2022.114680] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 11/20/2022]
Abstract
Platinum-based antitumor drugs have been used in many types of tumors due to its broad antitumor spectrum in clinic. Encouraged by the cisplatin's (CDDP) worldwide success in cancer chemotherapy, the research in platinum-based antitumor drugs has evolved from traditional platinum drug to multi-ligand and multifunctional platinum prodrugs over half a century. With the rapid development of metal drugs and the anticancer immune response, challenges and opportunities in platinum drug research have been shifted from traditional platinum-based drugs to platinum-based hybrids and the direction of development is tending toward photodynamic therapy, nano-delivery therapy, drug combination, targeted therapy, diagnostic therapy, immune-combination therapy and tumor stem cell therapy. In this review, we first exhaustively overviewed the role of platinum-based antitumor prodrugs and the anticancer immune response in medicinal inorganic chemistry based on the special nanomaterials, the modification of specific ligands, and the multiple functions obtained that are beneficial for tumor therapy in the last five years. We also categorized them according to drug potency and function. There hasn't been a comprehensive evaluation of precursor platinum drugs in prior articles. And a multifarious approach to distinguish and detail the variety of alterations of platinum-based precursors in various valence states also hasn't been summarized. In addition, this review points out the main problems at the interface of chemistry, biology, and medicine from their action mechanisms for current platinum drug development, and provides up-to-date potential strategies from drug design perspectives to circumvent those drawbacks. And a promising idea is also enlightened for researchers in the development and discovery of platinum prodrugs.
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168
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Domljanovic I, Ianiro A, Rüegg C, Mayer M, Taskova M. Natural and Modified Oligonucleotide Sequences Show Distinct Strand Displacement Kinetics and These Are Affected Further by Molecular Crowders. Biomolecules 2022; 12:biom12091249. [PMID: 36139087 PMCID: PMC9496266 DOI: 10.3390/biom12091249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/25/2022] Open
Abstract
DNA and RNA strand exchange is a process of fundamental importance in biology. Herein, we used a FRET-based assay to investigate, for the first time, the stand exchange kinetics of natural DNA, natural RNA, and locked nucleic acid (LNA)-modified DNA sequences in vitro in PBS in the absence or presence of molecular additives and macromolecular crowders such as diethylene glycol dimethyl ether (deg), polyethylene glycol (peg), and polyvinylpyrrolidone (pvp). The results show that the kinetics of strand exchange mediated by DNA, RNA, and LNA-DNA oligonucleotide sequences are different. Different molecular crowders further affect the strand displacement kinetics, highlighting the complexity of the process of nucleic acid strand exchange as it occurs in vivo. In a peg-containing buffer, the rate constant of displacement was slightly increased for the DNA displacement strand, while it was slightly decreased for the RNA and the LNA-DNA strands compared with displacement in pure PBS. When we used a deg-containing buffer, the rate constants of displacement for all three sequences were drastically increased compared with displacement in PBS. Overall, we show that interactions of the additives with the duplex strands have a significant effect on the strand displacement kinetics and this effect can exceed the one exerted by the chemical nature of the displacement strand itself.
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Affiliation(s)
- Ivana Domljanovic
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
| | - Alessandro Ianiro
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700 Fribourg, Switzerland
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
| | - Michael Mayer
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700 Fribourg, Switzerland
| | - Maria Taskova
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700 Fribourg, Switzerland
- Correspondence:
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169
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Khanal S, Cao D, Zhang J, Zhang Y, Schank M, Dang X, Nguyen LNT, Wu XY, Jiang Y, Ning S, Zhao J, Wang L, Gazzar ME, Moorman JP, Yao ZQ. Synthetic gRNA/Cas9 Ribonucleoprotein Inhibits HIV Reactivation and Replication. Viruses 2022; 14:1902. [PMID: 36146709 PMCID: PMC9500661 DOI: 10.3390/v14091902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
The current antiretroviral therapy (ART) for human immunodeficiency virus (HIV) can halt viral replication but cannot eradicate HIV infection because proviral DNA integrated into the host genome remains genetically silent in reservoir cells and is replication-competent upon interruption or cessation of ART. CRISPR/Cas9-based technology is widely used to edit target genes via mutagenesis (i.e., nucleotide insertion/deletion and/or substitution) and thus can inactivate integrated proviral DNA. However, CRISPR/Cas9 delivery systems often require viral vectors, which pose safety concerns for therapeutic applications in humans. In this study, we used synthetic guide RNA (gRNA)/Cas9-ribonucleoprotein (RNP) as a non-viral formulation to develop a novel HIV gene therapy. We designed a series of gRNAs targeting different HIV genes crucial for HIV replication and tested their antiviral efficacy and cellular cytotoxicity in lymphoid and monocytic latent HIV cell lines. Compared with the scramble gRNA control, HIV-gRNA/Cas9 RNP-treated cells exhibited efficient viral suppression with no apparent cytotoxicity, as evidenced by the significant inhibition of latent HIV DNA reactivation and RNA replication. Moreover, HIV-gRNA/Cas9 RNP inhibited p24 antigen expression, suppressed infectious viral particle production, and generated specific DNA cleavages in the targeted HIV genes that are confirmed by DNA sequencing. Because of its rapid DNA cleavage, low off-target effects, low risk of insertional mutagenesis, easy production, and readiness for use in clinical application, this study provides a proof-of-concept that synthetic gRNA/Cas9 RNP drugs can be utilized as a novel therapeutic approach for HIV eradication.
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Affiliation(s)
- Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
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170
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Du S, Liu Y, Yuan Y, Wang Y, Chen Y, Wang S, Chi Y. Advances in the study of HSP70 inhibitors to enhance the sensitivity of tumor cells to radiotherapy. Front Cell Dev Biol 2022; 10:942828. [PMID: 36036010 PMCID: PMC9399644 DOI: 10.3389/fcell.2022.942828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The 70 kDa heat shock protein (HSP70) is one of the most conserved proteins and a ubiquitous molecular chaperone that plays a role in the folding, remodeling, and degradation of various proteins to maintain proteostasis. It has been shown that HSP70 is abundantly expressed in cancer and enhances tumor resistance to radiotherapy by inhibiting multiple apoptotic pathways, such as interfering with the cellular senescence program, promoting angiogenesis, and supporting metastasis. Thus, HSP70 provides an effective target for enhancing the effects of radiation therapy in the clinical management of cancer patients. Inhibition of HSP70 enhances the radiation-induced tumor-killing effect and thus improves the efficacy of radiotherapy. This article reviews the sensitivity of Hsp70 and its related inhibitors to radiotherapy of tumor cells.
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Affiliation(s)
- Sihan Du
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, China
| | - Ying Liu
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, China
| | - Yuan Yuan
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yuran Wang
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yanfang Chen
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Shuai Wang
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
- *Correspondence: Shuai Wang, ; Yuhua Chi,
| | - Yuhua Chi
- Department of General Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
- *Correspondence: Shuai Wang, ; Yuhua Chi,
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171
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Protein Regulator of Cytokinesis 1 (PRC1) Upregulation Promotes Immune Suppression in Liver Hepatocellular Carcinoma. J Immunol Res 2022; 2022:7073472. [PMID: 35983074 PMCID: PMC9381293 DOI: 10.1155/2022/7073472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/23/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Liver hepatocellular carcinoma (LIHC) is a malignant cancer with widespread prevalence. The suppressive immune environment causes largely refractory to current treatment. The protein regulator of cytokinesis 1 (PRC1) is an essential gene for cytokinesis and is involved in cancer pathogenesis. However, the functions of PRC1 have been barely clarified, especially in LIHC. Here, we investigated the expression, prognostic value, and functions of PRC1 in LIHC. Pan-cancer analysis revealed the overexpression of PRC1 in the Cancer Genome Atlas (TCGA) database. Four LIHC datasets from the Gene Expression Omnibus (GEO) database confirmed the PRC1 overexpression in LIHC. The mRNA and protein levels of PRC1 in LIHC cells were higher than in normal liver cells. The overexpression of PRC1 predicted progressed clinical stage and poor prognosis of LIHC. We further investigated the functions of PRC1 by performing the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and Gene Set Enrichment Analysis (GSEA) of its coexpressing genes. High PRC1 expression was associated with increased genome instability of LIHC. Moreover, PRC1 was positively correlated with the infiltration of suppressive immune cells like T regulatory cells (Tregs) and polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) and was negatively correlated with the effector immune cells' infiltration, including B cells and CD8+ T cells. In addition, PRC1 was positively correlated with the expression of tumor immune checkpoint molecules. Taken together, PRC1 overexpression contributes to the genome instability and the suppressive immune microenvironment of LIHC. Thus, PRC1 has the potential to be a prognostic marker and therapeutic target of LIHC.
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172
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Song Q, Wu H, Zhang P, Tian K, Zhu H, Qiao J. LssR plays a positive regulatory role in acid and nisin tolerance response of Lactococcus lactis. J Dairy Sci 2022; 105:6483-6498. [PMID: 35840402 DOI: 10.3168/jds.2022-21842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/14/2022] [Indexed: 11/19/2022]
Abstract
In Lactococcus lactis, different regulation mechanisms can be activated to overcome the effects of adverse environmental stresses. Here, a TetR family regulator LssR was demonstrated as a positive regulator in the activation of the mechanisms involved in acid and nisin tolerance of L. lactis. The deletion of lssR led to the reduction of tolerance of L. lactis NZ9000 to nisin and acid stress, and the survival rates of NZ9000 under nisin and acid stress were roughly 20-fold, 10-fold (pH 3.0, hydrochloric acid), and 8.9-fold (pH 4.0, lactic acid) of the lssR mutant NZΔlssR, respectively. Moreover, the lssR mutant NZΔlssR also displayed a lower intracellular pH stability and a changed cell surface morphology. Subsequently, transcriptome analysis revealed that genes related to the arginine deiminase pathway, the surface polysaccharides biosynthesis, carbohydrates transport and metabolism, multidrug resistance, cell repair proteins and chaperones were predominantly down transcribed in NZΔlssR. The transcript levels of the arginine deiminase pathway and the surface polysaccharides biosynthesis-associated genes under acid and nisin stresses were compared between the wild type NZ9000 and NZΔlssR using real-time fluorescence quantitative PCR. It revealed that the arginine deiminase pathway genes (arcD1C1C2T) and the surface polysaccharides biosynthesis genes (cgT, gmhB, gmhA, hddA, tagH and tarS) were proposed to be the main regulatory mechanisms of LssR in response to the acid and nisin stresses. Overall, the important role of LssR in the acid and nisin stresses response was demonstrated and the putative regulation mechanism of LssR was revealed.
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Affiliation(s)
- Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Wu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Peng Zhang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Kairen Tian
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
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173
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Palamenghi M, De Luca M, De Rosa L. The steep uphill path leading to ex vivo gene therapy for genodermatoses. Am J Physiol Cell Physiol 2022; 323:C896-C906. [PMID: 35912986 DOI: 10.1152/ajpcell.00117.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell therapy, gene therapy and tissue engineering have the potential to revolutionize the field of regenerative medicine. In particular, gene therapy is understood as the therapeutical correction of mutated genes by addition of a correct copy of the gene or site-specific gene modifications. Gene correction of somatic stem cells sustaining renewing tissues is critical to ensure long-term clinical success of ex vivo gene therapy. To date, remarkable clinical outcomes arose from combined ex vivo cell and gene therapy of different genetic diseases, such as immunodeficiencies and genodermatoses. Despite the efforts of researchers around the world, only few of these advanced approaches has yet made it to routine therapy. In fact, gene therapy poses one of the greatest technical challenges in modern medicine, spanning safety and efficacy issues, regulatory constraints, registration and market access, all of which need to be addressed to make the therapy available to rare disease patients. In this review, we survey at some of the main challenges in the development of combined cell and gene therapy of genetic skin diseases.
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Affiliation(s)
- Michele Palamenghi
- Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
| | - Michele De Luca
- Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
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Gilbert S, Péant B, Mes-Masson AM, Saad F. IKKe Inhibitor Amlexanox Promotes Olaparib Sensitivity through the C/EBP-b-Mediated Transcription of Rad51 in Castrate-Resistant Prostate Cancer. Cancers (Basel) 2022; 14:cancers14153684. [PMID: 35954347 PMCID: PMC9367422 DOI: 10.3390/cancers14153684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Most men with advanced hormone-sensitive prostate cancer (HSPC) treated with androgen deprivation therapy will develop castrate resistant prostate cancer (CRPC), a lethal form of prostate cancer (PC). Our group has previously shown that IKKε expression is stronger in CRPC tumors and correlates with aggressive PC. Moreover, we have shown that IKKε depletion or inhibition (BX795, Amlexanox) decrease CRPC cell proliferation and tumor volume in an in vivo mouse model. We also demonstrate that IKKε inhibitors specifically target CRPC to induce a senescent phenotype as well as DNA damage and genomic instability. In this study, we demonstrated that IKKε depletion or inhibition block C/EBP-β recruitment on Rad51 promoter to decrease promoter activity. We have also shown that Amlexanox treatment sensitizes CRPC cells to Olaparib in vitro and in mouse models. Taken together, targeting IKKε with Amlexanox combined with Olaparib may lead to additional effective therapeutic strategies in the management of patients with CRPC. Abstract The progression of prostate cancer (PC) is often characterized by the development of castrate-resistant PC (CRPC). Patients with CRPC are treated with a variety of agents including new generation hormonal therapies or chemotherapy. However, as the cancer develops more resistance mechanisms, these drugs eventually become less effective and finding new therapeutic approaches is critical to improving patient outcomes. Previously, we have shown that IKKε depletion and IKKε inhibitors, BX795 and Amlexanox, decrease CRPC cell proliferation in vitro and in vivo and that IKKε inhibitors induce a senescence phenotype accompanied by increased DNA damage and genomic instability in CRPC cells. Here, we describe a new role for IKKε in DNA damage repair involving Rad51 and examine the therapeutic potential of Amlexanox combined with the PARP inhibitor Olaparib in CRPC cell lines. Combining Amlexanox with Olaparib decreased CRPC cell proliferation and enhanced DNA damage through the inhibition of Olaparib-induced Rad51 recruitment and expression in CRPC cells or IKKε-depleted PC-3 cells. We demonstrated that Rad51 promoter activity, measured by luciferase assay, was decreased with Amlexanox treatment or IKKε depletion and that Amlexanox treatment decreased the occupancy of transcription factor C/EBP-β on the Rad51 promoter. Our mouse model also showed that Amlexanox combined with Olaparib inhibited tumor growth of CRPC xenografts. Our study highlights a new role for IKKε in DNA damage repair through the regulation of Rad51 transcription and provides a rationale for the combination of Amlexanox and Olaparib in the treatment of patients with CRPC.
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Affiliation(s)
- Sophie Gilbert
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) et Institut du Cancer de Montréal, Montréal, QC H2X 0A9, Canada; (S.G.); (B.P.); (F.S.)
| | - Benjamin Péant
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) et Institut du Cancer de Montréal, Montréal, QC H2X 0A9, Canada; (S.G.); (B.P.); (F.S.)
| | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) et Institut du Cancer de Montréal, Montréal, QC H2X 0A9, Canada; (S.G.); (B.P.); (F.S.)
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: ; Tel.: +1-514-890-8000 (ext. 25496)
| | - Fred Saad
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) et Institut du Cancer de Montréal, Montréal, QC H2X 0A9, Canada; (S.G.); (B.P.); (F.S.)
- Department of Surgery, Université de Montréal, Montréal, QC H3C 3J7, Canada
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175
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ZSTK474 Sensitizes Glioblastoma to Temozolomide by Blocking Homologous Recombination Repair. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8568528. [PMID: 35872860 PMCID: PMC9300311 DOI: 10.1155/2022/8568528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/31/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Temozolomide (TMZ) is used as the standard chemotherapeutic agent for GBM but with limited success, and treatment failure is mainly due to tumor resistance. One of the leading causes of TMZ resistance is the upregulation of the DNA repair mechanism. Therefore, targeting the DNA damage response (DDR) is proposed to be an effective strategy to sensitize tumor cells to TMZ. In the present study, we demonstrated that the combined use of the PI3K inhibitor ZSTK474 and TMZ showed synergetic anticancer effects on human GBM cells in vitro and in vivo. The combination treatment led to significantly increased cell apoptosis and DNA double strand breaks (DSBs). In addition, a mechanistic study indicated that TMZ enhanced the homologous recombination (HR) repair efficiency in GBM cells, while ZSTK474 impaired HR repair by blocking the phosphorylation of ATM and the expression of BRCA1/2 and Rad51, thereby sensitizing GBM cells to TMZ. Moreover, TMZ activated the PI3K signaling pathway through upregulation of the PI3K catalytic subunits p110α and p110β and the phosphorylation of Akt. Meanwhile, ZSTK474 blocked the activity of the PI3K/Akt pathway. Taken together, our findings suggested that the combination of ZSTK474 and TMZ might be a potential therapeutic option for GBM.
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Scandolara TB, Valle SF, Esteves C, Scherer NDM, de Armas EM, Furtado C, Gomes R, Boroni M, Jaques HDS, Alves FM, Rech D, Panis C, Bonvicino CR. Somatic DNA Damage Response and Homologous Repair Gene Alterations and Its Association With Tumor Variant Burden in Breast Cancer Patients With Occupational Exposure to Pesticides. Front Oncol 2022; 12:904813. [PMID: 35875117 PMCID: PMC9305859 DOI: 10.3389/fonc.2022.904813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination is a crucial pathway that is specialized in repairing double-strand breaks; thus, alterations in genes of this pathway may lead to loss of genomic stability and cell growth suppression. Pesticide exposure potentially increases cancer risk through several mechanisms, such as the genotoxicity caused by chronic exposure, leading to gene alteration. To analyze this hypothesis, we investigated if breast cancer patients exposed to pesticides present a different mutational pattern in genes related to homologous recombination (BRCA1, BRCA2, PALB2, and RAD51D) and damage-response (TP53) concerning unexposed patients. We performed multiplex PCR-based assays and next-generation sequencing (NGS) of all coding regions and flanking splicing sites of BRCA1, BRCA2, PALB2, TP53, and RAD51D in 158 unpaired tumor samples from breast cancer patients on MiSeq (Illumina) platform. We found that exposed patients had tumors with more pathogenic and likely pathogenic variants than unexposed patients (p = 0.017). In general, tumors that harbored a pathogenic or likely pathogenic variant had a higher mutational burden (p < 0.001). We also observed that breast cancer patients exposed to pesticides had a higher mutational burden when diagnosed before 50 years old (p = 0.00978) and/or when carrying BRCA1 (p = 0.0138), BRCA2 (p = 0.0366), and/or PALB2 (p = 0.00058) variants, a result not found in the unexposed group. Our results show that pesticide exposure impacts the tumor mutational landscape and could be associated with the carcinogenesis process, therapy response, and disease progression. Further studies should increase the observation period in exposed patients to better evaluate the impact of these findings.
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Affiliation(s)
- Thalita Basso Scandolara
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Ferreira Valle
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Esteves
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Nicole de Miranda Scherer
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Elvismary Molina de Armas
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- Department of Informatics, Pontificia Universidade Católica (PUC)-Rio, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Renan Gomes
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | | | - Fernanda Mara Alves
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
| | - Daniel Rech
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
- Francisco Beltrão Cancer Hospital, Francisco Beltrão, Brazil
| | - Carolina Panis
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
| | - Cibele Rodrigues Bonvicino
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
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177
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Shah S, Cheung A, Kutka M, Sheriff M, Boussios S. Epithelial Ovarian Cancer: Providing Evidence of Predisposition Genes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19138113. [PMID: 35805770 PMCID: PMC9265838 DOI: 10.3390/ijerph19138113] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/19/2022]
Abstract
Epithelial ovarian cancer (EOC) is one of the cancers most influenced by hereditary factors. A fourth to a fifth of unselected EOC patients carry pathogenic variants (PVs) in a number of genes, the majority of which encode for proteins involved in DNA mismatch repair (MMR) pathways. PVs in BRCA1 and BRCA2 genes are responsible for a substantial fraction of hereditary EOC. In addition, PV genes involved in the MMR pathway account for 10–15% of hereditary EOC. The identification of women with homologous recombination (HR)-deficient EOCs has significant clinical implications, concerning chemotherapy regimen planning and development as well as the use of targeted therapies such as poly(ADP-ribose) polymerase (PARP) inhibitors. With several genes involved, the complexity of genetic testing increases. In this context, next-generation sequencing (NGS) allows testing for multiple genes simultaneously with a rapid turnaround time. In this review, we discuss the EOC risk assessment in the era of NGS.
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Affiliation(s)
- Sidrah Shah
- Department of Palliative Care, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK;
| | - Alison Cheung
- Department of Hematology/Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK; (A.C.); (M.K.)
| | - Mikolaj Kutka
- Department of Hematology/Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK; (A.C.); (M.K.)
| | - Matin Sheriff
- Department of Urology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK;
| | - Stergios Boussios
- Department of Palliative Care, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK;
- King’s College London, Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, London SE1 9RT, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
- Correspondence: or or
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Gupta V, Shekhawat SS, Kulshreshtha NM, Gupta AB. A systematic review on chlorine tolerance among bacteria and standardization of their assessment protocol in wastewater. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 86:261-291. [PMID: 35906907 DOI: 10.2166/wst.2022.206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Though chlorine is a cost-effective disinfectant for water and wastewaters, the bacteria surviving after chlorination pose serious public health and environmental problems. This review critically assesses the mechanism of chlorine disinfection as described by various researchers; factors affecting chlorination efficacy; and the re-growth potential of microbial contaminations in treated wastewater post chlorination to arrive at meaningful doses for ensuring health safety. Literature analysis shows procedural inconsistencies in the assessment of chlorine tolerant bacteria, making it extremely difficult to compare the tolerance characteristics of different reported tolerant bacteria. A comparison of logarithmic reduction after chlorination and the concentration-time values for prominent pathogens led to the generation of a standard protocol for the assessment of chlorine tolerance. The factors that need to be critically monitored include applied chlorine doses, contact time, determination of chlorine demands of the medium, and the consideration of bacterial counts immediately after chlorination and in post chlorinated samples (regrowth). The protocol devised here appropriately assesses the chlorine-tolerant bacteria and urges the scientific community to report the regrowth characteristics as well. This would increase the confidence in data interpretation that can provide a better understanding of chlorine tolerance in bacteria and aid in formulating strategies for effective chlorination.
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Affiliation(s)
- Vinayak Gupta
- Alumnus, Department of Civil and Environmental Engineering, National University of Singapore, Singapore; School of Environment and Society, Tokyo Institute of Technology, Tokyo, Japan
| | - Sandeep Singh Shekhawat
- Department of Civil Engineering, Malaviya National Institute of Technology, Jaipur, India E-mail: ; School of Life and Basic Sciences, SIILAS Campus, Jaipur National University Jaipur, India
| | - Niha Mohan Kulshreshtha
- Department of Civil Engineering, Malaviya National Institute of Technology, Jaipur, India E-mail:
| | - Akhilendra Bhushan Gupta
- Department of Civil Engineering, Malaviya National Institute of Technology, Jaipur, India E-mail:
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Dash HR, Arora M. CRISPR-CasB technology in forensic DNA analysis: challenges and solutions. Appl Microbiol Biotechnol 2022; 106:4367-4374. [PMID: 35704073 DOI: 10.1007/s00253-022-12016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 01/23/2023]
Abstract
CRISPR-Cas technology has revolutionized the field of biotechnology with its precise therapeutic use from genetic as well as infectious diseases point of view. This technology is rapidly evolving to single tool enabling site-directed cut in the genome and highly specific activation or inhibition of gene expression or the exchange of single bases. Besides clinical applications, CRISPR-Cas technology has also shown promising use in the field of forensic DNA analysis. Enrichment of targeted genetic marker for identification followed by sequencing and non-PCR-dependent technique ensures the use of CRISPR-Cas technology in challenging forensic biological samples. The use of this advanced technology is also deemed helpful in mixed profile attribution, mostly in LCN contributors and the generation of a useful DNA profile in degraded samples. Besides its useful applications in forensic DNA analysis, CRISPR-Cas technology poses a huge threat from the generation of ghost DNA profiles by modification/alteration of target genetic markers. Forensic DNA analysts should carry out analysis of additional markers such as non-CODIS markers, Y-, X-chromosome markers, and mitochondrial DNA sequencing in a suspected ghost DNA profile case. KEY POINTS: • CRISPR-Cas9 technique is useful in analyzing LCN, mixed and degraded samples • Alteration of DNA using this technique can lead to generation of ghost DNA profiles • Alternative genetic markers and methylation pattern may detect a ghost DNA profile.
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Affiliation(s)
- Hirak Ranjan Dash
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India.
| | - Mansi Arora
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India
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180
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The Homologous Recombination Deficiency Scar in Advanced Cancer: Agnostic Targeting of Damaged DNA Repair. Cancers (Basel) 2022; 14:cancers14122950. [PMID: 35740616 PMCID: PMC9221128 DOI: 10.3390/cancers14122950] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Tumor-suppressor genes are involved in DNA break repair through the homologous recombination system and are widely known for their role in hereditary cancer. Beyond breast and ovarian cancer, prostate and pancreatic cancer also have targetable homologous recombination deficiency (HRD) beyond the well-known BRCA1 and BRCA2 with relevance that exceeds diagnostic purposes. In this review, we aim to summarize the roles of HRD across tumor types and the treatment landscape to guide the targeting of damaged DNA repair based on the cancer’s genetic features. Abstract BRCA1 and BRCA2 are the most recognized tumor-suppressor genes involved in double-strand DNA break repair through the homologous recombination (HR) system. Widely known for its role in hereditary cancer, HR deficiency (HRD) has turned out to be critical beyond breast and ovarian cancer: for prostate and pancreatic cancer also. The relevance for the identification of these patients exceeds diagnostic purposes, since results published from clinical trials with poly-ADP ribose polymerase (PARP) inhibitors (PARPi) have shown how this type of targeted therapy can modify the long-term evolution of patients with HRD. Somatic aberrations in other HRD pathway genes, but also indirect genomic instability as a sign of this DNA repair impairment (known as HRD scar), have been reported to be relevant events that lead to more frequently than expected HR loss of function in several tumor types, and should therefore be included in the current diagnostic and therapeutic algorithm. However, the optimal strategy to identify HRD and potential PARPi responders in cancer remains undefined. In this review, we summarize the role and prevalence of HRD across tumor types and the current treatment landscape to guide the agnostic targeting of damaged DNA repair. We also discuss the challenge of testing patients and provide a special insight for new strategies to select patients who benefit from PARPi due to HRD scarring.
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181
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Chughtai AA, Pannhausen J, Dinger P, Wirtz J, Knüchel R, Gaisa NT, Eble MJ, Rose M. Effective Radiosensitization of Bladder Cancer Cells by Pharmacological Inhibition of DNA-PK and ATR. Biomedicines 2022; 10:biomedicines10061277. [PMID: 35740300 PMCID: PMC9220184 DOI: 10.3390/biomedicines10061277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/09/2022] Open
Abstract
This study aims at analyzing the impact of the pharmacological inhibition of DNA damage response (DDR) targets (DNA-PK and ATR) on radiosensitization of bladder cancer cell lines of different molecular/histological subtypes. Applying DNA-PK (AZD7648) and ATR (Ceralasertib) inhibitors on SCaBER, J82 and VMCUB-1 bladder cancer cell lines, we revealed sensitization upon ionizing radiation (IR), i.e., the IC50 for each drug shifted to a lower drug concentration with increased IR doses. In line with this, drug exposure retarded DNA repair after IR-induced DNA damage visualized by a neutral comet assay. Western blot analyses confirmed specific inhibition of targeted DDR pathways in the analyzed bladder cancer cell lines, i.e., drugs blocked DNA-PK phosphorylation at Ser2056 and the ATR downstream mediator CHK1 at Ser317. Interestingly, clonogenic survival assays indicated a cell-line-dependent synergism of combined DDR inhibition upon IR. Calculating combined index (CI) values, with and without IR, according to the Chou–Talalay method, confirmed drug- and IR-dose-specific synergistic CI values. Thus, we provide functional evidence that DNA-PK and ATR inhibitors specifically target corresponding DDR pathways retarding the DNA repair process at nano-molar concentrations. This, in turn, leads to a strong radiosensitizing effect and impairs the survival of bladder cancer cells.
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Affiliation(s)
- Ahmed Ali Chughtai
- Department of Radiation Oncology, RWTH Aachen University, 52074 Aachen, Germany;
- Correspondence: (A.A.C.); (M.R.); Tel.: +49-241-8036863 (A.A.C.); +49-241-8089715 (M.R.); Fax: +49-241-8082425 (A.A.C.); +49-241-8082439 (M.R.)
| | - Julia Pannhausen
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Pia Dinger
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Julia Wirtz
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Ruth Knüchel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Nadine T. Gaisa
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Michael J. Eble
- Department of Radiation Oncology, RWTH Aachen University, 52074 Aachen, Germany;
| | - Michael Rose
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
- Correspondence: (A.A.C.); (M.R.); Tel.: +49-241-8036863 (A.A.C.); +49-241-8089715 (M.R.); Fax: +49-241-8082425 (A.A.C.); +49-241-8082439 (M.R.)
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Leibowitz BD, Dougherty BV, Bell JSK, Kapilivsky J, Michuda J, Sedgewick AJ, Munson WA, Chandra TA, Dry JR, Beaubier N, Igartua C, Taxter T. Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort. BMC Cancer 2022; 22:587. [PMID: 35643464 PMCID: PMC9148513 DOI: 10.1186/s12885-022-09669-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types. Methods Genomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on their BRCA1, BRCA2 and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression. Results In a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively. Conclusions We predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09669-z.
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Shridharan RV, Kalakuntla N, Chirmule N, Tiwari B. The Happy Hopping of Transposons: The Origins of V(D)J Recombination in Adaptive Immunity. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.836066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nearly 50% of the human genome is derived from transposable elements (TEs). Though dysregulated transposons are deleterious to humans and can lead to diseases, co-opted transposons play an important role in generating alternative or new DNA sequence combinations to perform novel cellular functions. The appearance of an adaptive immune system in jawed vertebrates, wherein the somatic rearrangement of T and B cells generates a repertoire of antibodies and receptors, is underpinned by Class II TEs. This review follows the evolution of recombination activation genes (RAGs), components of adaptive immunity, from TEs, focusing on the structural and mechanistic similarities between RAG recombinases and DNA transposases. As evolution occurred from a transposon precursor, DNA transposases developed a more targeted and constrained mechanism of mobilization. As DNA repair is integral to transposition and recombination, we note key similarities and differences in the choice of DNA repair pathways following these processes. Understanding the regulation of V(D)J recombination from its evolutionary origins may help future research to specifically target RAG proteins to rectify diseases associated with immune dysregulation.
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184
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Peake JD, Noguchi E. Fanconi anemia: current insights regarding epidemiology, cancer, and DNA repair. Hum Genet 2022; 141:1811-1836. [PMID: 35596788 DOI: 10.1007/s00439-022-02462-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Fanconi anemia is a genetic disorder that is characterized by bone marrow failure, as well as a predisposition to malignancies including leukemia and squamous cell carcinoma (SCC). At least 22 genes are associated with Fanconi anemia, constituting the Fanconi anemia DNA repair pathway. This pathway coordinates multiple processes and proteins to facilitate the repair of DNA adducts including interstrand crosslinks (ICLs) that are generated by environmental carcinogens, chemotherapeutic crosslinkers, and metabolic products of alcohol. ICLs can interfere with DNA transactions, including replication and transcription. If not properly removed and repaired, ICLs cause DNA breaks and lead to genomic instability, a hallmark of cancer. In this review, we will discuss the genetic and phenotypic characteristics of Fanconi anemia, the epidemiology of the disease, and associated cancer risk. The sources of ICLs and the role of ICL-inducing chemotherapeutic agents will also be discussed. Finally, we will review the detailed mechanisms of ICL repair via the Fanconi anemia DNA repair pathway, highlighting critical regulatory processes. Together, the information in this review will underscore important contributions to Fanconi anemia research in the past two decades.
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Affiliation(s)
- Jasmine D Peake
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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Pal R, Paul N, Bhattacharya D, Rakshit S, Shanmugam G, Sarkar K. XPG in the Nucleotide Excision Repair and Beyond: a study on the different functional aspects of XPG and its associated diseases. Mol Biol Rep 2022; 49:7995-8006. [PMID: 35596054 DOI: 10.1007/s11033-022-07324-1] [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: 09/06/2021] [Revised: 12/17/2021] [Accepted: 03/02/2022] [Indexed: 11/26/2022]
Abstract
Several proteins are involved in DNA repair mechanisms attempting to repair damages to the DNA continuously. One such protein is Xeroderma Pigmentosum Complementation Group G (XPG), a significant component in the Nucleotide Excision Repair (NER) pathway. XPG is accountable for making the 3' incision in the NER, while XPF-ERCC4 joins ERCC1 to form the XPF-ERCC1 complex. This complex makes a 5' incision to eliminate bulky DNA lesions. XPG is also known to function as a cofactor in the Base Excision Repair (BER) pathway by increasing hNth1 activity, apart from its crucial involvement in the NER. Reports suggest that XPG also plays a non-catalytic role in the Homologous Recombination Repair (HRR) pathway by forming higher-order complexes with BRCA1, BRCA2, Rad51, and PALB2, further influencing the activity of these molecules. Studies show that, apart from its vital role in repairing DNA damages, XPG is also responsible for R-loop formation, which facilitates exhibiting phenotypes of Werner Syndrome. Though XPG has a role in several DNA repair pathways and molecular mechanisms, it is primarily a NER protein. Unrepaired and prolonged DNA damage leads to genomic instability and facilitates neurological disorders, aging, pigmentation, and cancer susceptibility. This review explores the vital role of XPG in different DNA repair mechanisms which are continuously involved in repairing these damaged sites and its failure leading to XP-G, XP-G/CS complex phenotypes, and cancer progression.
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Affiliation(s)
- Riasha Pal
- Department of Biotechnology, SRM Institute of Science and Technology, 603203, Kattankulathur, Tamil Nadu, India
| | - Nilanjan Paul
- Department of Biotechnology, SRM Institute of Science and Technology, 603203, Kattankulathur, Tamil Nadu, India
| | - Deep Bhattacharya
- Department of Biotechnology, SRM Institute of Science and Technology, 603203, Kattankulathur, Tamil Nadu, India
| | - Sudeshna Rakshit
- Department of Biotechnology, SRM Institute of Science and Technology, 603203, Kattankulathur, Tamil Nadu, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, 603203, Kattankulathur, Tamil Nadu, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, 603203, Kattankulathur, Tamil Nadu, India.
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The Role of DNA Repair in Genomic Instability of Multiple Myeloma. Int J Mol Sci 2022; 23:ijms23105688. [PMID: 35628498 PMCID: PMC9144728 DOI: 10.3390/ijms23105688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Multiple Myeloma (MM) is a B cell malignancy marked by genomic instability that arises both through pathogenesis and during disease progression. Despite recent advances in therapy, MM remains incurable. Recently, it has been reported that DNA repair can influence genomic changes and drug resistance in MM. The dysregulation of DNA repair function may provide an alternative explanation for genomic instability observed in MM cells and in cells derived from MM patients. This review provides an overview of DNA repair pathways with a special focus on their involvement in MM and discusses the role they play in MM progression and drug resistance. This review highlights how unrepaired DNA damage due to aberrant DNA repair response in MM exacerbates genomic instability and chromosomal abnormalities, enabling MM progression and drug resistance.
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187
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Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
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Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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188
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Ke F, Zhang QY. ADRV 12L: A Ranaviral Putative Rad2 Family Protein Involved in DNA Recombination and Repair. Viruses 2022; 14:v14050908. [PMID: 35632650 PMCID: PMC9146916 DOI: 10.3390/v14050908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
The Andrias davidianus ranavirus (ADRV) is a member of the family Iridoviridae and belongs to the nucleocytoplasmic large DNA viruses. Based on genomic analysis, an ADRV-encoding protein, ADRV 12L, and its homologs from other iridoviruses were predicted as Rad2 family proteins based on the conserved amino acids, domains, and secondary structures. Expression analysis showed that the transcription of ADRV 12L started at 4 h post infection, and its expression was not inhibited by a DNA-replication inhibitor. Meanwhile, immunofluorescence localization showed that ADRV 12L mainly localized in viral factories and colocalized with the viral nascent DNA, which hinted at a possible role in DNA replication. Furthermore, a mutant ADRV lacking 12L (ADRV-Δ12L) was constructed. In both luciferase assays based on homologous recombination (HR) and double-strand break repair (DSBR) that followed, ADRV-Δ12L induced less luciferase activity than the wild-type ADRV, indicating that HR and DSBR were impaired in ADRV-Δ12L infected cells. In addition, infection with ADRV-Δ12L resulted in smaller plaque sizes and lower viral titers than that with wild-type ADRV, indicating an important role for 12L in efficient virus infection. Therefore, the results suggest that Rad2 homologs encoded by iridovirus have important roles in HR- and DSBR-process of the viral DNA and, thus, affect virus replication and the production of progeny virions.
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Affiliation(s)
- Fei Ke
- Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China;
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-027-6878-0002
| | - Qi-Ya Zhang
- Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China;
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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189
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Dalmasso B, Puccini A, Catalano F, Borea R, Iaia ML, Bruno W, Fornarini G, Sciallero S, Rebuzzi SE, Ghiorzo P. Beyond BRCA: The Emerging Significance of DNA Damage Response and Personalized Treatment in Pancreatic and Prostate Cancer Patients. Int J Mol Sci 2022; 23:ijms23094709. [PMID: 35563100 PMCID: PMC9099822 DOI: 10.3390/ijms23094709] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/07/2022] Open
Abstract
The BRCA1/2 germline and/or somatic pathogenic variants (PVs) are key players in the hereditary predisposition and therapeutic response for breast, ovarian and, more recently, pancreatic and prostate cancers. Aberrations in other genes involved in homologous recombination and DNA damage response (DDR) pathways are being investigated as promising targets in ongoing clinical trials. However, DDR genes are not routinely tested worldwide. Due to heterogeneity in cohort selection and dissimilar sequencing approaches across studies, neither the burden of PVs in DDR genes nor the prevalence of PVs in genes in common among pancreatic and prostate cancer can be easily quantified. We aim to contextualize these genes, altered in both pancreatic and prostate cancers, in the DDR process, to summarize their hereditary and somatic burden in different studies and harness their deficiency for cancer treatments in the context of currently ongoing clinical trials. We conclude that the inclusion of DDR genes, other than BRCA1/2, shared by both cancers considerably increases the detection rate of potentially actionable variants, which are triplicated in pancreatic and almost doubled in prostate cancer. Thus, DDR alterations are suitable targets for drug development and to improve the outcome in both pancreatic and prostate cancer patients. Importantly, this will increase the detection of germline pathogenic variants, thereby patient referral to genetic counseling.
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Affiliation(s)
- Bruna Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
| | - Alberto Puccini
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Fabio Catalano
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Roberto Borea
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Maria Laura Iaia
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - William Bruno
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
| | - Giuseppe Fornarini
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Stefania Sciallero
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Sara Elena Rebuzzi
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Ospedale San Paolo, Medical Oncology, 17100 Savona, Italy
| | - Paola Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Correspondence:
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190
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Genome-wide CRISPR screen identified Rad18 as a determinant of doxorubicin sensitivity in osteosarcoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:154. [PMID: 35459258 PMCID: PMC9034549 DOI: 10.1186/s13046-022-02344-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/25/2022] [Indexed: 12/14/2022]
Abstract
Background Osteosarcoma (OS) is a malignant bone tumor mostly occurring in children and adolescents, while chemotherapy resistance often develops and the mechanisms involved remain challenging to be fully investigated. Methods Genome-wide CRISPR screening combined with transcriptomic sequencing were used to identify the critical genes of doxorubicin resistance. Analysis of clinical samples and datasets, and in vitro and in vivo experiments (including CCK-8, apoptosis, western blot, qRT-PCR and mouse models) were applied to confirm the function of these genes. The bioinformatics and IP-MS assays were utilized to further verify the downstream pathway. RGD peptide-directed and exosome-delivered siRNA were developed for the novel therapy strategy. Results We identified that E3 ubiquitin-protein ligase Rad18 (Rad18) contributed to doxorubicin-resistance in OS. Further exploration revealed that Rad18 interact with meiotic recombination 11 (MRE11) to promote the formation of the MRE11-RAD50-NBS1 (MRN) complex, facilitating the activation of the homologous recombination (HR) pathway, which ultimately mediated DNA damage tolerance and leaded to a poor prognosis and chemotherapy response in patients with OS. Rad18-knockout effectively restored the chemotherapy response in vitro and in vivo. Also, RGD-exosome loading chemically modified siRad18 combined with doxorubicin, where exosome and chemical modification guaranteed the stability of siRad18 and the RGD peptide provided prominent targetability, had significantly improved antitumor activity of doxorubicin. Conclusions Collectively, our study identifies Rad18 as a driver of OS doxorubicin resistance that promotes the HR pathway and indicates that targeting Rad18 is an effective approach to overcome chemotherapy resistance in OS. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02344-y.
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191
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Czajkowski D, Szmyd R, Gee HE. Impact of DNA damage response defects in cancer cells on response to immunotherapy and radiotherapy. J Med Imaging Radiat Oncol 2022; 66:546-559. [PMID: 35460184 PMCID: PMC9321602 DOI: 10.1111/1754-9485.13413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022]
Abstract
The DNA damage response (DDR) is a complex set of downstream pathways triggered in response to DNA damage to maintain genomic stability. Many tumours exhibit mutations which inactivate components of the DDR, making them prone to the accumulation of DNA defects. These can both facilitate the development of tumours and provide potential targets for novel therapeutic interventions. The inhibition of the DDR has been shown to induce radiosensitivity in certain cancers, rendering them susceptible to treatment with radiotherapy and improving the therapeutic window. Moreover, DDR defects are a strong predictor of patient response to immune checkpoint inhibition (ICI). The ability to target the DDR selectively has the potential to expand the tumour neoantigen repertoire, thus increasing tumour immunogenicity and facilitating a CD8+ T and NK cell response against cancer cells. Combinatorial approaches, which seek to integrate DDR inhibition with radiotherapy and immunotherapy, have shown promise in early trials. Further studies are necessary to understand these synergies and establish reliable biomarkers.
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Affiliation(s)
| | - Radosław Szmyd
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Sydney West Radiation Oncology Network, Crown Princess Mary Cancer Centre Westmead, Sydney, New South Wales, Australia
| | - Harriet E Gee
- University of Sydney, Sydney, New South Wales, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Sydney West Radiation Oncology Network, Crown Princess Mary Cancer Centre Westmead, Sydney, New South Wales, Australia
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192
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Tsampoula M, Tarampoulous I, Manolakou T, Ninou E, Politis PK. The neurodevelopmental disorders associated gene Rnf113a regulates survival and differentiation properties of neural stem cells. Stem Cells 2022; 40:678-690. [DOI: 10.1093/stmcls/sxac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/23/2022] [Indexed: 11/15/2022]
Abstract
Abstract
RNF113A (Ring Finger Protein 113A) is genetically associated with autism spectrum disorders and X-linked trichothiodystrophy (TTD) syndrome. Loss-of-function mutations in human RNF113A are causally linked to TTD, which is characterized by abnormal development of central nervous system (CNS) and mental retardation. How loss of RNF113A activity affects brain development is not known. Here we identify Rnf113a1 as a critical regulator of cell death and neurogenesis during mouse brain development. Rnf113a1 gene exhibits widespread expression in the embryonic CNS. Knockdown studies in embryonic cortical neural stem/progenitor cells (NSCs) and the mouse cortex suggest that Rnf113a1 controls survival, proliferation and differentiation properties of progenitor cells. Importantly, Rnf113a1 deficiency triggers cell apoptosis via a combined action on essential regulators of cell survival, including p53, Nupr1 and Rad51. Collectively, these observations establish Rnf113a1 as a regulatory factor in CNS development and provide insights for its role in neurodevelopmental defects associated with TTD and autism.
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Affiliation(s)
- Matina Tsampoula
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Isaak Tarampoulous
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Theodora Manolakou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Elpinickie Ninou
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Panagiotis K Politis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- School of Medicine, European University Cyprus, Nicosia, Cyprus
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193
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Verma P, Kumari P, Negi S, Yadav G, Gaur V. Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism. Nucleic Acids Res 2022; 50:4630-4646. [PMID: 35412622 PMCID: PMC9071465 DOI: 10.1093/nar/gkac239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022] Open
Abstract
Holliday junction is the key homologous recombination intermediate, resolved by structure-selective endonucleases (SSEs). SLX1 is the most promiscuous SSE of the GIY-YIG nuclease superfamily. In fungi and animals, SLX1 nuclease activity relies on a non-enzymatic partner, SLX4, but no SLX1-SLX4 like complex has ever been characterized in plants. Plants exhibit specialized DNA repair and recombination machinery. Based on sequence similarity with the GIY-YIG nuclease domain of SLX1 proteins from fungi and animals, At-HIGLE was identified to be a possible SLX1 like nuclease from plants. Here, we elucidated the crystal structure of the At-HIGLE nuclease domain from Arabidopsis thaliana, establishing it as a member of the SLX1-lineage of the GIY-YIG superfamily with structural changes in DNA interacting regions. We show that At-HIGLE can process branched-DNA molecules without an SLX4 like protein. Unlike fungal SLX1, At-HIGLE exists as a catalytically active homodimer capable of generating two coordinated nicks during HJ resolution. Truncating the extended C-terminal region of At-HIGLE increases its catalytic activity, changes the nicking pattern, and monomerizes At-HIGLE. Overall, we elucidated the first structure of a plant SLX1-lineage protein, showed its HJ resolving activity independent of any regulatory protein, and identified an in-built novel regulatory mechanism engaging its C-terminal region.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Poonam Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shreya Negi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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194
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Sherill-Rofe D, Raban O, Findlay S, Rahat D, Unterman I, Samiei A, Yasmeen A, Kaiser Z, Kuasne H, Park M, Foulkes WD, Bloch I, Zick A, Gotlieb WH, Tabach Y, Orthwein A. Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair. NAR Cancer 2022; 4:zcac013. [PMID: 35399185 PMCID: PMC8991968 DOI: 10.1093/narcan/zcac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/14/2022] Open
Abstract
DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).
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Affiliation(s)
- Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Oded Raban
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Irene Unterman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Arash Samiei
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Amber Yasmeen
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Zafir Kaiser
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hellen Kuasne
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - William D Foulkes
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Ein-Kerem, Jerusalem 91120, Israel
| | - Walter H Gotlieb
- Division of Gynecology Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
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195
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Dietlein F, Wang AB, Fagre C, Tang A, Besselink NJM, Cuppen E, Li C, Sunyaev SR, Neal JT, Van Allen EM. Genome-wide analysis of somatic noncoding mutation patterns in cancer. Science 2022; 376:eabg5601. [PMID: 35389777 PMCID: PMC9092060 DOI: 10.1126/science.abg5601] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We established a genome-wide compendium of somatic mutation events in 3949 whole cancer genomes representing 19 tumor types. Protein-coding events captured well-established drivers. Noncoding events near tissue-specific genes, such as ALB in the liver or KLK3 in the prostate, characterized localized passenger mutation patterns and may reflect tumor-cell-of-origin imprinting. Noncoding events in regulatory promoter and enhancer regions frequently involved cancer-relevant genes such as BCL6, FGFR2, RAD51B, SMC6, TERT, and XBP1 and represent possible drivers. Unlike most noncoding regulatory events, XBP1 mutations primarily accumulated outside the gene's promoter, and we validated their effect on gene expression using CRISPR-interference screening and luciferase reporter assays. Broadly, our study provides a blueprint for capturing mutation events across the entire genome to guide advances in biological discovery, therapies, and diagnostics.
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Affiliation(s)
- Felix Dietlein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.,Corresponding author. (E.M.V.A.); (F.D.)
| | - Alex B. Wang
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Christian Fagre
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anran Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Nicolle J. M. Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands.,Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - James T. Neal
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.,Corresponding author. (E.M.V.A.); (F.D.)
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196
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Huang CC, Tseng LM. ASO Author Reflections: Broaden the Targeted Population of Synthetic Lethality for Taiwanese Breast Cancer. Ann Surg Oncol 2022; 29:3591-3592. [PMID: 35391610 DOI: 10.1245/s10434-022-11407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors selectively cause the failure of DNA single-stranded break (SSB) repair but do not affect double-stranded break (DSB) repair. Furthermore, antitumor activities have been reported for breast cancer, with germline BRCA1/2 mutations. The prevalence of germline BRCA1/2 mutations never exceed one-tenth; beyond BRCA1/2, genes recurrently altered (more than 5%) in the homologous repair pathway are ARID1A, PALB2, and PTEN. Altered homologous recombination repair genes can total up to one-quarter based on different definitions, and the potential of PARP inhibitors will be elucidated when further studies unraveling the impact of individual homologous recombination genes are conducted.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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197
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BRCA2 C-Terminal RAD51-Binding Domain Confers Resistance to DNA-Damaging Agents. Int J Mol Sci 2022; 23:ijms23074060. [PMID: 35409418 PMCID: PMC9000072 DOI: 10.3390/ijms23074060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In this study, we investigated CTRBD expression in cells exposed to X-ray irradiation and mitomycin C treatment. Surprisingly, BRCA2 CTRBD expression in HeLa cells increased their resistance to X-ray irradiation and mitomycin C. Under endogenous BRCA2 depletion using shRNA, the sensitivities of the BRCA2-depleted cells with and without the CTRBD did not significantly differ. Thus, the resistance to X-ray irradiation conferred by an exogenous CTRBD required endogenous BRCA2 expression. BRCA2 CTRBD-expressing cells demonstrated effective RAD51 foci formation and increased homologous recombination efficiency, but not nonhomologous end-joining efficiency. To the best of our knowledge, our study is the first to report the ability of the BRCA2 functional domain to confer resistance to X-ray irradiation and mitomycin C treatment by increased homologous recombination efficiency. Thus, this peptide may be useful for protecting cells against X-ray irradiation or chemotherapeutic agents.
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198
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Kelm JM, Samarbakhsh A, Pillai A, VanderVere-Carozza PS, Aruri H, Pandey DS, Pawelczak KS, Turchi JJ, Gavande NS. Recent Advances in the Development of Non-PIKKs Targeting Small Molecule Inhibitors of DNA Double-Strand Break Repair. Front Oncol 2022; 12:850883. [PMID: 35463312 PMCID: PMC9020266 DOI: 10.3389/fonc.2022.850883] [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: 01/08/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
The vast majority of cancer patients receive DNA-damaging drugs or ionizing radiation (IR) during their course of treatment, yet the efficacy of these therapies is tempered by DNA repair and DNA damage response (DDR) pathways. Aberrations in DNA repair and the DDR are observed in many cancer subtypes and can promote de novo carcinogenesis, genomic instability, and ensuing resistance to current cancer therapy. Additionally, stalled or collapsed DNA replication forks present a unique challenge to the double-strand DNA break (DSB) repair system. Of the various inducible DNA lesions, DSBs are the most lethal and thus desirable in the setting of cancer treatment. In mammalian cells, DSBs are typically repaired by the error prone non-homologous end joining pathway (NHEJ) or the high-fidelity homology directed repair (HDR) pathway. Targeting DSB repair pathways using small molecular inhibitors offers a promising mechanism to synergize DNA-damaging drugs and IR while selective inhibition of the NHEJ pathway can induce synthetic lethality in HDR-deficient cancer subtypes. Selective inhibitors of the NHEJ pathway and alternative DSB-repair pathways may also see future use in precision genome editing to direct repair of resulting DSBs created by the HDR pathway. In this review, we highlight the recent advances in the development of inhibitors of the non-phosphatidylinositol 3-kinase-related kinases (non-PIKKs) members of the NHEJ, HDR and minor backup SSA and alt-NHEJ DSB-repair pathways. The inhibitors described within this review target the non-PIKKs mediators of DSB repair including Ku70/80, Artemis, DNA Ligase IV, XRCC4, MRN complex, RPA, RAD51, RAD52, ERCC1-XPF, helicases, and DNA polymerase θ. While the DDR PIKKs remain intensely pursued as therapeutic targets, small molecule inhibition of non-PIKKs represents an emerging opportunity in drug discovery that offers considerable potential to impact cancer treatment.
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Affiliation(s)
- Jeremy M. Kelm
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Amirreza Samarbakhsh
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Athira Pillai
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | | | - Hariprasad Aruri
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Deepti S. Pandey
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | | | - John J. Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,NERx Biosciences, Indianapolis, IN, United States,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Navnath S. Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States,*Correspondence: Navnath S. Gavande, ; orcid.org/0000-0002-2413-0235
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199
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Yang Y, Yu Q, Wang M, Zhao R, Liu H, Xun L, Xia Y. Escherichia coli BW25113 Competent Cells Prepared Using a Simple Chemical Method Have Unmatched Transformation and Cloning Efficiencies. Front Microbiol 2022; 13:838698. [PMID: 35401484 PMCID: PMC8989280 DOI: 10.3389/fmicb.2022.838698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Escherichia coli recA− strains are usually used for cloning to prevent insert instability via RecA-dependent recombination. Here, we report that E. coli BW25113 (recA+) competent cells prepared by using a previously reported transformation and storage solution (TSS) had 100-fold or higher transformation efficiency than the commonly used E. coli cloning strains, including XL1-Blue MRF’. The cloning success rates with E. coli BW25113 were 440 to 1,267-fold higher than those with E. coli XL1-Blue MRF’ when several inserts were assembled into four vectors by using a simple DNA assembly method. The difference was in part due to RecA, as the recA deletion in E. coli BW25113 reduced the transformation efficiency by 16 folds and cloning success rate by about 10 folds. However, the transformation efficiency and the cloning success rate of the recA deletion mutant of E. coli BW25113 are still 12- and >48-fold higher than those of E. coli XL1-Blue MRF’, which is a commonly used cloning strain. The cloned inserts with different lengths of homologous sequences were assembled into four vectors and transformed into E. coli BW25113, and they were stably maintained in BW25113. Thus, we recommend using E. coli BW25113 for efficient cloning and DNA assembly.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- *Correspondence: Luying Xun, Yongzhen Xia,
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Luying Xun, Yongzhen Xia,
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200
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Identify a DNA Damage Repair Gene Signature for Predicting Prognosis and Immunotherapy Response in Cervical Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:8736575. [PMID: 35368888 PMCID: PMC8967547 DOI: 10.1155/2022/8736575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022]
Abstract
The DNA damage repair (DDR) genes are increasingly gaining attention as potential therapeutic targets in cancers. In this study, we identified the DDR genes associated with the tumor mutation burden (TMB) and prognosis of cervical squamous cell carcinoma (CESC) based on The Cancer Genome Atlas (TCGA) database. Through LASSO Cox regression, the prognostic signature involving five DDR genes (ACTR2, TEX12, UBE2V1, HSF1, and FBXO6) was established, and the risk score was identified as an independent risk factor for CESC. The nomogram consisting of the five genes accurately predicted the overall survival (OS) and the immunotherapeutic response of CESC patients. Finally, the loss of the copies of the transcription factor (TF) SP140 in CESC patients may decrease the expression of FBXO6, improve DNA repair function, and reduce the diversity of neoantigens, thereby lowering the response to immunotherapies. Therefore, the DDR gene signature is a novel prognostic model and a biomarker for immunotherapies in CESC patients.
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