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Gonzáles-Córdova RA, Dos Santos TR, Gachet-Castro C, Andrade Vieira J, Trajano-Silva LAM, Sakamoto-Hojo ET, Baqui MMA. Trypanosoma cruzi infection induces DNA double-strand breaks and activates DNA damage response pathway in host epithelial cells. Sci Rep 2024; 14:5225. [PMID: 38433244 PMCID: PMC10909859 DOI: 10.1038/s41598-024-53589-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, invades many cell types affecting numerous host-signalling pathways. During the T. cruzi infection, we demonstrated modulations in the host RNA polymerase II activity with the downregulation of ribonucleoproteins affecting host transcription and splicing machinery. These alterations could be a result of the initial damage to the host DNA caused by the presence of the parasite, however, the mechanisms are not well understood. Herein, we examined whether infection by T. cruzi coincided with enhanced DNA damage in the host cell. We studied the engagement of the DNA damage response (DDR) pathways at the different time points (0-24 h post-infection, hpi) by T. cruzi in LLC-MK2 cells. In response to double-strand breaks (DSB), maximum phosphorylation of the histone variant H2AX is observed at 2hpi and promotes recruitment of the DDR p53-binding protein (53BP1). During T. cruzi infection, Ataxia-telangiectasia mutated protein (ATM) and DNA-PK protein kinases remained active in a time-dependent manner and played roles in regulating the host response to DSB. The host DNA lesions caused by the infection are likely orchestrated by the non-homologous end joining (NHEJ) pathway to maintain the host genome integrity.
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Affiliation(s)
- Raul Alexander Gonzáles-Córdova
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Thamires Rossi Dos Santos
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Camila Gachet-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Johnathan Andrade Vieira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Lays Adrianne Mendonça Trajano-Silva
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
| | - Elza Tiemi Sakamoto-Hojo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil
- Department of Biology, Faculty of Philosophy Sciences and Letters at Ribeirão Preto, University of São Paulo, São Paulo, 14040-901, Brazil
| | - Munira Muhammad Abdel Baqui
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo-USP, Ribeirão Preto, 14049-900, Brazil.
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2
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Ali U, Vungarala S, Tiriveedhi V. Genomic Features of Homologous Recombination Deficiency in Breast Cancer: Impact on Testing and Immunotherapy. Genes (Basel) 2024; 15:162. [PMID: 38397152 PMCID: PMC10887603 DOI: 10.3390/genes15020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Genomic instability is one of the well-established hallmarks of cancer. The homologous recombination repair (HRR) pathway plays a critical role in correcting the double-stranded breaks (DSB) due to DNA damage in human cells. Traditionally, the BRCA1/2 genes in the HRR pathway have been tested for their association with breast cancer. However, defects in the HRR pathway (HRD, also termed 'BRCAness'), which has up to 50 genes, have been shown to be involved in tumorigenesis and treatment susceptibility to poly-ADP ribose polymerase inhibitors (PARPis), platinum-based chemotherapy, and immune checkpoint inhibitors (ICIs). A reliable consensus on HRD scores is yet to be established. Emerging evidence suggests that only a subset of breast cancer patients benefit from ICI-based immunotherapy. Currently, albeit with limitations, the expression of programmed death-ligand 1 (PDL1) and tumor mutational burden (TMB) are utilized as biomarkers to predict the favorable outcomes of ICI therapy in breast cancer patients. Preclinical studies demonstrate an interplay between the HRR pathway and PDL1 expression. In this review, we outline the current understanding of the role of HRD in genomic instability leading to breast tumorigenesis and delineate outcomes from various clinical trials. Furthermore, we discuss potential strategies for combining HRD-targeted therapy with immunotherapy to achieve the best healthcare outcomes in breast cancer patients.
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Affiliation(s)
- Umer Ali
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
| | - Sunitha Vungarala
- Meharry-Vanderbilt Alliance, Vanderbilt University Medical Center, Nashville, TN 37209, USA;
| | - Venkataswarup Tiriveedhi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37209, USA
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3
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Conjunctive Analyses of BSA-Seq and BSR-Seq Unveil the Msβ-GAL and MsJMT as Key Candidate Genes for Cytoplasmic Male Sterility in Alfalfa (Medicago sativa L.). Int J Mol Sci 2022; 23:ijms23137172. [PMID: 35806189 PMCID: PMC9266382 DOI: 10.3390/ijms23137172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/21/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Knowing the molecular mechanism of male sterility in alfalfa is important to utilize the heterosis more effectively. However, the molecular mechanisms of male sterility in alfalfa are still unclear. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-seq (BSR) were performed with F2 separation progeny to study the molecular mechanism of male sterility in alfalfa. The BSA-seq analysis was located in a candidate region on chromosome 5 containing 626 candidate genes which were associated with male sterility in alfalfa, while the BSR-seq analysis filtered seven candidate DEGs related to male sterility, and these candidate genes including EF-Tu, β-GAL, CESA, PHGDH, and JMT. The conjunctive analyses of BSR and BSA methods revealed that the genes of Msβ-GAL and MsJMT are the common detected candidate genes involved in male sterility in alfalfa. Our research provides a theory basis for further study of the molecular mechanism of male sterility in alfalfa and significant information for the genetic breeding of Medicago sativa.
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4
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Genome Integrity and Neurological Disease. Int J Mol Sci 2022; 23:ijms23084142. [PMID: 35456958 PMCID: PMC9025063 DOI: 10.3390/ijms23084142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
Neurological complications directly impact the lives of hundreds of millions of people worldwide. While the precise molecular mechanisms that underlie neuronal cell loss remain under debate, evidence indicates that the accumulation of genomic DNA damage and consequent cellular responses can promote apoptosis and neurodegenerative disease. This idea is supported by the fact that individuals who harbor pathogenic mutations in DNA damage response genes experience profound neuropathological manifestations. The review article here provides a general overview of the nervous system, the threats to DNA stability, and the mechanisms that protect genomic integrity while highlighting the connections of DNA repair defects to neurological disease. The information presented should serve as a prelude to the Special Issue “Genome Stability and Neurological Disease”, where experts discuss the role of DNA repair in preserving central nervous system function in greater depth.
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5
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Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
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Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
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6
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Zhang X, Li T, Yang M, Du Q, Wang R, Fu B, Tan Y, Cao M, Chen Y, Wang Q, Hu R. Acquired temozolomide resistance in MGMT low gliomas is associated with regulation of homologous recombination repair by ROCK2. Cell Death Dis 2022; 13:138. [PMID: 35145081 PMCID: PMC8831658 DOI: 10.1038/s41419-022-04590-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/05/2022] [Accepted: 01/27/2022] [Indexed: 02/08/2023]
Abstract
It was reported that MGMTlow gliomas may still be resistant to TMZ, while the mechanisms remain poorly understood. In this study, we demonstrated that rho-associated kinase 2 (ROCK2), a cytoskeleton regulator, was highly expressed in MGMTlow recurrent gliomas, and its expression strongly correlated with poor overall survival (OS) time in a subset of MGMTlow recurrent gliomas patients with TMZ therapy. And we also found that overactive ROCK2 enhanced homologous recombination repair (HR) in TMZ-resistant (TMZ-R) glioma cell lines with low MGMT expression. Silencing ROCK2 impaired HR repair, and induced double-strand break (DSB) and eradicated TMZ-R glioma cells in culture. Notably, in MGMTlow TMZ-R models, as a key factor of HR, ataxia telangiectasia-mutated (ATM) expression was upregulated directly by hyper-activation of ROCK2 to improve HR efficiency. ROCK2 enhanced the binding of transcription factor zinc finger E-box binding homeobox 1 (ZEB1) to ATM promoter for increasing ATM expression. Moreover, ROCK2 transformed ZEB1 into a gene activator via Yes-associated protein 1 (YAP1). These results provide evidence for the use of ROCK inhibitors in the clinical therapy for MGMTlow TMZ-resistant glioma. Our study also offered novel insights for improving therapeutic management of MGMTlow gliomas.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Tao Li
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mengdi Yang
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qianming Du
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,General Clinical Research Center, Nanjing First Hospital, China Pharmaceutical University, Nanjing, China
| | - Rui Wang
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Bin Fu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yingying Tan
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mengran Cao
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yaxin Chen
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qing Wang
- Department of Neurosurgery, Wuxi Second Hospital Affiliated Nanjing Medical University, Wuxi, Jiangsu, China.
| | - Rong Hu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.
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7
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Katoueezadeh M, Pilehvari N, Fatemi A, Hassanshahi G, Torabizadeh SA. Inhibition of DNA damage response pathway using combination of DDR pathway inhibitors and radiation in treatment of acute lymphoblastic leukemia cells. Future Oncol 2021; 17:2803-2816. [PMID: 33960207 DOI: 10.2217/fon-2020-1072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
An alarming increase in acute lymphoblastic leukemia cases among children and adults has attracted the attention of researchers to discover new therapeutic strategies with a better prognosis. In cancer cells, the DNA damage response (DDR) pathway elements have been recognized to protect tumor cells from various stresses and cause tumor progression; targeting these DDR members is an attractive strategy for treatment of cancers. The inhibition of the DDR pathway in cancer cells for the treatment of cancers has recently been introduced. Hence, effective treatment strategies are needed for this purpose. Chemotherapy in combination with radiotherapy is considered a potential therapeutic strategy for acute leukemia. This review aims to assess the synergistic effects of these inhibitors with irradiation for the treatment of leukemia.
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Affiliation(s)
- Maryam Katoueezadeh
- Department of Hematology & Medical Laboratory Science, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, 7616911333, Iran
| | - Niloofar Pilehvari
- Department of Hematology & Medical Laboratory Science, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, 7616911333, Iran
| | - Ahmad Fatemi
- Department of Hematology & Medical Laboratory Science, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, 7616911333, Iran
| | - Gholamhossein Hassanshahi
- Molecular Medicine Research Center, Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, 7718796755, Iran
| | - Seyedeh Atekeh Torabizadeh
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, 7616911319, Iran
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8
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Hausmann M, Falk M, Neitzel C, Hofmann A, Biswas A, Gier T, Falkova I, Heermann DW, Hildenbrand G. Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach. Int J Mol Sci 2021; 22:3636. [PMID: 33807337 PMCID: PMC8037797 DOI: 10.3390/ijms22073636] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/20/2021] [Accepted: 03/26/2021] [Indexed: 02/06/2023] Open
Abstract
In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a "double-edged sword"-it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Martin Falk
- Institute of Biophysics, Czech Academy of Sciences, 612 65 Brno, Czech Republic;
| | - Charlotte Neitzel
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Andreas Hofmann
- Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany; (A.H.); (D.W.H.)
| | - Abin Biswas
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Theresa Gier
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Iva Falkova
- Institute of Biophysics, Czech Academy of Sciences, 612 65 Brno, Czech Republic;
| | - Dieter W. Heermann
- Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany; (A.H.); (D.W.H.)
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
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9
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Origin, Regulation, and Fitness Effect of Chromosomal Rearrangements in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22020786. [PMID: 33466757 PMCID: PMC7830279 DOI: 10.3390/ijms22020786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/02/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosomal rearrangements comprise unbalanced structural variations resulting in gain or loss of DNA copy numbers, as well as balanced events including translocation and inversion that are copy number neutral, both of which contribute to phenotypic evolution in organisms. The exquisite genetic assay and gene editing tools available for the model organism Saccharomyces cerevisiae facilitate deep exploration of the mechanisms underlying chromosomal rearrangements. We discuss here the pathways and influential factors of chromosomal rearrangements in S. cerevisiae. Several methods have been developed to generate on-demand chromosomal rearrangements and map the breakpoints of rearrangement events. Finally, we highlight the contributions of chromosomal rearrangements to drive phenotypic evolution in various S. cerevisiae strains. Given the evolutionary conservation of DNA replication and recombination in organisms, the knowledge gathered in the small genome of yeast can be extended to the genomes of higher eukaryotes.
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10
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Singh B, Yang S, Krishna A, Sridhar S. Nanoparticle Formulations of Poly (ADP-ribose) Polymerase Inhibitors for Cancer Therapy. Front Chem 2020; 8:594619. [PMID: 33330383 PMCID: PMC7719718 DOI: 10.3389/fchem.2020.594619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022] Open
Abstract
A number of poly(ADP-ribose) polymerase (PARP) inhibitors have been recently approved for clinical use in BRCA mutated and other cancers. However, off-target toxicity of PARP inhibitors and the emergence of drug resistance following prolonged administration of these inhibitors indicate the need for improved methods of drug delivery to the tumors. Nanomedicines based upon nanoparticle formulations of conventional small molecule drugs and inhibitors offer many advantages, such as increased solubility and bioavailability of drugs, reduced toxicity and drug resistance, and improved tissue selectivity and therapeutic efficacy. This review highlights the current trends in formulations of PARP inhibitors developed by nanotechnology approaches and provides an insight into the applications and limitations of these PARP inhibitor nanomedicines for cancer therapies.
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Affiliation(s)
- Bijay Singh
- Nanomedicine Innovation Center, Northeastern University, Boston, MA, United States.,Department of Physics, Northeastern University, Boston, MA, United States
| | - Shicheng Yang
- Nanomedicine Innovation Center, Northeastern University, Boston, MA, United States.,Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - Apurva Krishna
- Nanomedicine Innovation Center, Northeastern University, Boston, MA, United States.,Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Srinivas Sridhar
- Nanomedicine Innovation Center, Northeastern University, Boston, MA, United States.,Department of Physics, Northeastern University, Boston, MA, United States.,Department of Chemical Engineering, Northeastern University, Boston, MA, United States.,Department of Bioengineering, Northeastern University, Boston, MA, United States.,Department of Radiation Oncology, Harvard Medical School, Boston, MA, United States
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11
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Götting I, Jendrossek V, Matschke J. A New Twist in Protein Kinase B/Akt Signaling: Role of Altered Cancer Cell Metabolism in Akt-Mediated Therapy Resistance. Int J Mol Sci 2020; 21:ijms21228563. [PMID: 33202866 PMCID: PMC7697684 DOI: 10.3390/ijms21228563] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer resistance to chemotherapy, radiotherapy and molecular-targeted agents is a major obstacle to successful cancer therapy. Herein, aberrant activation of the phosphatidyl-inositol-3-kinase (PI3K)/protein kinase B (Akt) pathway is one of the most frequently deregulated pathways in cancer cells and has been associated with multiple aspects of therapy resistance. These include, for example, survival under stress conditions, apoptosis resistance, activation of the cellular response to DNA damage and repair of radiation-induced or chemotherapy-induced DNA damage, particularly DNA double strand breaks (DSB). One further important, yet not much investigated aspect of Akt-dependent signaling is the regulation of cell metabolism. In fact, many Akt target proteins are part of or involved in the regulation of metabolic pathways. Furthermore, recent studies revealed the importance of certain metabolites for protection against therapy-induced cell stress and the repair of therapy-induced DNA damage. Thus far, the likely interaction between deregulated activation of Akt, altered cancer metabolism and therapy resistance is not yet well understood. The present review describes the documented interactions between Akt, its target proteins and cancer cell metabolism, focusing on antioxidant defense and DSB repair. Furthermore, the review highlights potential connections between deregulated Akt, cancer cell metabolism and therapy resistance of cancer cells through altered DSB repair and discusses potential resulting therapeutic implications.
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12
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Wengner AM, Scholz A, Haendler B. Targeting DNA Damage Response in Prostate and Breast Cancer. Int J Mol Sci 2020; 21:E8273. [PMID: 33158305 PMCID: PMC7663807 DOI: 10.3390/ijms21218273] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Steroid hormone signaling induces vast gene expression programs which necessitate the local formation of transcription factories at regulatory regions and large-scale alterations of the genome architecture to allow communication among distantly related cis-acting regions. This involves major stress at the genomic DNA level. Transcriptionally active regions are generally instable and prone to breakage due to the torsional stress and local depletion of nucleosomes that make DNA more accessible to damaging agents. A dedicated DNA damage response (DDR) is therefore essential to maintain genome integrity at these exposed regions. The DDR is a complex network involving DNA damage sensor proteins, such as the poly(ADP-ribose) polymerase 1 (PARP-1), the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the ataxia-telangiectasia-mutated (ATM) kinase and the ATM and Rad3-related (ATR) kinase, as central regulators. The tight interplay between the DDR and steroid hormone receptors has been unraveled recently. Several DNA repair factors interact with the androgen and estrogen receptors and support their transcriptional functions. Conversely, both receptors directly control the expression of agents involved in the DDR. Impaired DDR is also exploited by tumors to acquire advantageous mutations. Cancer cells often harbor germline or somatic alterations in DDR genes, and their association with disease outcome and treatment response led to intensive efforts towards identifying selective inhibitors targeting the major players in this process. The PARP-1 inhibitors are now approved for ovarian, breast, and prostate cancer with specific genomic alterations. Additional DDR-targeting agents are being evaluated in clinical studies either as single agents or in combination with treatments eliciting DNA damage (e.g., radiation therapy, including targeted radiotherapy, and chemotherapy) or addressing targets involved in maintenance of genome integrity. Recent preclinical and clinical findings made in addressing DNA repair dysfunction in hormone-dependent and -independent prostate and breast tumors are presented. Importantly, the combination of anti-hormonal therapy with DDR inhibition or with radiation has the potential to enhance efficacy but still needs further investigation.
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Affiliation(s)
| | | | - Bernard Haendler
- Preclinical Research, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (A.M.W.); (A.S.)
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Zhao F, Kim W, Kloeber JA, Lou Z. DNA end resection and its role in DNA replication and DSB repair choice in mammalian cells. Exp Mol Med 2020; 52:1705-1714. [PMID: 33122806 PMCID: PMC8080561 DOI: 10.1038/s12276-020-00519-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/29/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022] Open
Abstract
DNA end resection has a key role in double-strand break repair and DNA replication. Defective DNA end resection can cause malfunctions in DNA repair and replication, leading to greater genomic instability. DNA end resection is initiated by MRN-CtIP generating short, 3′-single-stranded DNA (ssDNA). This newly generated ssDNA is further elongated by multiple nucleases and DNA helicases, such as EXO1, DNA2, and BLM. Effective DNA end resection is essential for error-free homologous recombination DNA repair, the degradation of incorrectly replicated DNA and double-strand break repair choice. Because of its importance in DNA repair, DNA end resection is strictly regulated. Numerous mechanisms have been reported to regulate the initiation, extension, and termination of DNA end resection. Here, we review the general process of DNA end resection and its role in DNA replication and repair pathway choice. Carefully regulated enzymatic processing of the ends of DNA strands is essential for efficient replication and damage repair while also minimizing the risk of genomic instability. Replication and repair depend on a mechanism known as DNA resection, in which enzymes trim back double-stranded DNA ends to leave single-stranded overhangs. Zhenkun Lou and colleagues at the Mayo Clinic in Rochester, USA, have reviewed the various steps involved in the initiation and control of DNA resection. There are multiple different DNA repair processes, and the manner in which resection occurs can determine which of these processes subsequently takes place. The authors note that cancer cells rely heavily on these repair pathways to survive radiotherapy and chemotherapy, and highlight research opportunities that might reveal therapeutically useful vulnerabilities in the resection mechanism.
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Affiliation(s)
- Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.,Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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Bröckelmann PJ, de Jong MRW, Jachimowicz RD. Targeting DNA Repair, Cell Cycle, and Tumor Microenvironment in B Cell Lymphoma. Cells 2020; 9:E2287. [PMID: 33066395 PMCID: PMC7602196 DOI: 10.3390/cells9102287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023] Open
Abstract
The DNA double-strand break (DSB) is the most cytotoxic lesion and compromises genome stability. In an attempt to efficiently repair DSBs, cells activate ATM kinase, which orchestrates the DNA damage response (DDR) by activating cell cycle checkpoints and initiating DSB repair pathways. In physiological B cell development, however, programmed DSBs are generated as intermediates for effective immune responses and the maintenance of genomic integrity. Disturbances of these pathways are at the heart of B cell lymphomagenesis. Here, we review the role of DNA repair and cell cycle control on B cell development and lymphomagenesis. In addition, we highlight the intricate relationship between the DDR and the tumor microenvironment (TME). Lastly, we provide a clinical perspective by highlighting treatment possibilities of defective DDR signaling and the TME in mantle cell lymphoma, which serves as a blueprint for B cell lymphomas.
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Affiliation(s)
- Paul J. Bröckelmann
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany;
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), University of Cologne, 50937 Cologne, Germany
| | - Mathilde R. W. de Jong
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ron D. Jachimowicz
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany;
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), University of Cologne, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
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15
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Lee EK, Matulonis UA. PARP Inhibitor Resistance Mechanisms and Implications for Post-Progression Combination Therapies. Cancers (Basel) 2020; 12:E2054. [PMID: 32722408 PMCID: PMC7465003 DOI: 10.3390/cancers12082054] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
The use of PARP inhibitors (PARPi) is growing widely as FDA approvals have shifted its use from the recurrence setting to the frontline setting. In parallel, the population developing PARPi resistance is increasing. Here we review the role of PARP, DNA damage repair, and synthetic lethality. We discuss mechanisms of resistance to PARP inhibition and how this informs on novel combinations to re-sensitize cancer cells to PARPi.
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Affiliation(s)
- Elizabeth K. Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA;
| | - Ursula A. Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA;
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
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16
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Streff HE, Gao Y, Nelson SW. Functional evaluation of the C-terminal region of bacteriophage T4 Rad50. Biochem Biophys Res Commun 2020; 526:485-490. [PMID: 32238267 DOI: 10.1016/j.bbrc.2020.02.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/27/2022]
Abstract
Bacteriophage T4 encodes orthologs of the proteins Rad50 (gp46) and Mre11 (gp47), which form a heterotetrameric complex (MR) that participates in the processing of DNA ends for recombination-dependent DNA repair. Crystal and high-resolution cryo-EM structures of Rad50 have revealed DNA binding sites near the dimer interface of Rad50 opposite of Mre11, and near the base of the coiled-coils that extend out from the globular head domain. An analysis of T4-Rad50 using sequenced-based algorithms to identify DNA binding residues predicts that a conserved region of positively charged residues near the C-terminus, distal to the observed binding sites, interacts with DNA. Mutant proteins were generated to test this prediction and their enzymatic and DNA binding activities were evaluated. Consistent with the predictions, the Rad50 C-terminal mutants had reduced affinity for DNA as measured by Rad50 equilibrium DNA binding assays and an increased Km-DNA as determined in MR complex nuclease assays. Moreover, the allosteric activation of ATP hydrolysis activity due to DNA binding was substantially reduced, suggesting that these residues may be involved in the communication between the DNA and ATP binding sites.
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Affiliation(s)
- Haley E Streff
- The Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA; Undergraduate Research Program at Iowa State University, Ames, IA, 50011, USA
| | - Yang Gao
- The Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Scott W Nelson
- The Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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17
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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18
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Kay J, Thadhani E, Samson L, Engelward B. Inflammation-induced DNA damage, mutations and cancer. DNA Repair (Amst) 2019; 83:102673. [PMID: 31387777 DOI: 10.1016/j.dnarep.2019.102673] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/15/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022]
Abstract
The relationships between inflammation and cancer are varied and complex. An important connection linking inflammation to cancer development is DNA damage. During inflammation reactive oxygen and nitrogen species (RONS) are created to combat pathogens and to stimulate tissue repair and regeneration, but these chemicals can also damage DNA, which in turn can promote mutations that initiate and promote cancer. DNA repair pathways are essential for preventing DNA damage from causing mutations and cytotoxicity, but RONS can interfere with repair mechanisms, reducing their efficacy. Further, cellular responses to DNA damage, such as damage signaling and cytotoxicity, can promote inflammation, creating a positive feedback loop. Despite coordination of DNA repair and oxidative stress responses, there are nevertheless examples whereby inflammation has been shown to promote mutagenesis, tissue damage, and ultimately carcinogenesis. Here, we discuss the DNA damage-mediated associations between inflammation, mutagenesis and cancer.
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Affiliation(s)
- Jennifer Kay
- Department of Biological Engineering, United States.
| | | | - Leona Samson
- Department of Biological Engineering, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
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