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Gene expression study to elucidate the anti-trypanosomal activity of quinapyramine methyl sulphate (QPS). Parasitol Int 2022; 91:102632. [PMID: 35870741 DOI: 10.1016/j.parint.2022.102632] [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: 04/11/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/22/2022]
Abstract
The kinetoplastid protozoan parasite, Trypanosoma evansi causes a fatal disease condition known as Surra in equines throughout the globe. Disease condition being acute in nature, entrust a huge economic and health impact on the equine industry. Till date, quinapyramine methyl sulphate (QPS) is the first line of treatment and a panacea for the T. evansi infection in equines. Still after the >70 years of its discovery, there is no clue about the mode of action of QPS in T. evansi. The establishment of in vitro cultivation of T. evansi in HMI-9 media has provided opportunity to study the alteration in mRNA expression of parasite on exposure to the drug. With this research gap, the present study aimed to investigate the relative mRNA expression of 13 important drug target genes to elucidate the anti-trypanosomal activity of QPS against T. evansi. The IC50 of QPS against a pony isolate of T. evansi was determined as 276.4 nM(147.21 ng/ mL) in the growth inhibitory assay. The in vitro cultured T. evansi population were further exposed to IC50 of QPS and their relative mRNA expression was studied at 12 h, 24 h and 48 h interval.The mRNA expression of several genes such as hexokinase, trypanothione reductase, aurora kinase, oligopeptidase B and ribonucleotide reductase II were found refractory (non-significant, p > 0.1234) to the exposure of QPS. Significant up-regulation of trans-sialidase (p < 0.0001), ESAG8 (p < 0.0021), ribonucleotide reductase I (p < 0.0001), ornithine decarboxylase (p < 0.0001), topoisomerase II (p < 0.0021) and casein kinase I (p < 0.0021) were recorded after exposure with QPS. The arginine kinase 1 and calcium ATPase I showed highly significant (p < 0.0001) down-regulation in the drug kinetics. Therefore, the arginine kinase 1 and calcium ATPase I can be explored further to elucidate the trypanocidal activity of QPS. The preliminary data generated provide the potential of arginine kinase 1 and calcium ATPase I mRNA mediated pathway of trypanocidal action of QPS. Further, transcriptomics approach is required to investigate the possible mechanism of action of drugs at molecular level against the targeted organism.
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152
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Yan S, Zeng M, Wang H, Zhang H. Micromonospora: A Prolific Source of Bioactive Secondary Metabolites with Therapeutic Potential. J Med Chem 2022; 65:8735-8771. [PMID: 35766919 DOI: 10.1021/acs.jmedchem.2c00626] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Micromonospora, one of the most important actinomycetes genera, is well-known as the treasure trove of bioactive secondary metabolites (SMs). Herein, together with an in-depth genomic analysis of the reported Micromonospora strains, all SMs from this genus are comprehensively summarized, containing structural features, bioactive properties, and mode of actions as well as their biosynthetic and chemical synthesis pathways. The perspective enables a detailed view of Micromonospora-derived SMs, which will enrich the chemical diversity of natural products and inspire new drug discovery in the pharmaceutical industry.
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Affiliation(s)
- Suqi Yan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Mingyuan Zeng
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
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153
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Khazeem MM, Casement JW, Schlossmacher G, Kenneth NS, Sumbung NK, Chan JYT, McGow JF, Cowell IG, Austin CA. TOP2B Is Required to Maintain the Adrenergic Neural Phenotype and for ATRA-Induced Differentiation of SH-SY5Y Neuroblastoma Cells. Mol Neurobiol 2022; 59:5987-6008. [PMID: 35831557 PMCID: PMC9463316 DOI: 10.1007/s12035-022-02949-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/23/2022] [Indexed: 12/13/2022]
Abstract
The neuroblastoma cell line SH-SY5Y is widely used to study retinoic acid (RA)-induced gene expression and differentiation and as a tool to study neurodegenerative disorders. SH-SY5Y cells predominantly exhibit adrenergic neuronal properties, but they can also exist in an epigenetically interconvertible alternative state with more mesenchymal characteristics; as a result, these cells can be used to study gene regulation circuitry controlling neuroblastoma phenotype. Using a combination of pharmacological inhibition and targeted gene inactivation, we have probed the requirement for DNA topoisomerase IIB (TOP2B) in RA-induced gene expression and differentiation and in the balance between adrenergic neuronal versus mesenchymal transcription programmes. We found that expression of many, but not all genes that are rapidly induced by ATRA in SH-SY5Y cells was significantly reduced in the TOP2B null cells; these genes include BCL2, CYP26A1, CRABP2, and NTRK2. Comparing gene expression profiles in wild-type versus TOP2B null cells, we found that long genes and genes expressed at a high level in WT SH-SY5Y cells were disproportionately dependent on TOP2B. Notably, TOP2B null SH-SY5Y cells upregulated mesenchymal markers vimentin (VIM) and fibronectin (FN1) and components of the NOTCH signalling pathway. Enrichment analysis and comparison with the transcription profiles of other neuroblastoma-derived cell lines supported the conclusion that TOP2B is required to fully maintain the adrenergic neural-like transcriptional signature of SH-SY5Y cells and to suppress the alternative mesenchymal epithelial-like epigenetic state.
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Affiliation(s)
- Mushtaq M Khazeem
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,National Center of Hematology, Mustansiriyah University, Baghdad, Iraq
| | - John W Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - George Schlossmacher
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Niall S Kenneth
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nielda K Sumbung
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Janice Yuen Tung Chan
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jade F McGow
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ian G Cowell
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Caroline A Austin
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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154
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Saha S, Yang X, Huang SYN, Agama K, Baechler SA, Sun Y, Zhang H, Saha LK, Su S, Jenkins LM, Wang W, Pommier Y. Resolution of R-loops by topoisomerase III-β (TOP3B) in coordination with the DEAD-box helicase DDX5. Cell Rep 2022; 40:111067. [PMID: 35830799 PMCID: PMC10575568 DOI: 10.1016/j.celrep.2022.111067] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/20/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
The present study demonstrates how TOP3B is involved in resolving R-loops. We observed elevated R-loops in TOP3B knockout cells (TOP3BKO), which are suppressed by TOP3B transfection. R-loop-inducing agents, the topoisomerase I inhibitor camptothecin, and the splicing inhibitor pladienolide-B also induce higher R-loops in TOP3BKO cells. Camptothecin- and pladienolide-B-induced R-loops are concurrent with the induction of TOP3B cleavage complexes (TOP3Bccs). RNA/DNA hybrid IP-western blotting show that TOP3B is physically associated with R-loops. Biochemical assays using recombinant TOP3B and oligonucleotides mimicking R-loops show that TOP3B cleaves the single-stranded DNA displaced by the R-loop RNA-DNA duplex. IP-mass spectrometry and IP-western experiments reveal that TOP3B interacts with the R-loop helicase DDX5 independently of TDRD3. Finally, we demonstrate that DDX5 and TOP3B are epistatic in resolving R-loops in a pathway parallel with senataxin. We propose a decatenation model for R-loop resolution by TOP3B-DDX5 protecting cells from R-loop-induced damage.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Keli Agama
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Simone Andrea Baechler
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Lisa M Jenkins
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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155
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Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading. Proc Natl Acad Sci U S A 2022; 119:e2001290119. [PMID: 35759655 PMCID: PMC9271158 DOI: 10.1073/pnas.2001290119] [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] [Indexed: 12/30/2022] Open
Abstract
The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.
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156
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Design, synthesis and biological evaluation of 3-arylisoquinoline derivatives as topoisomerase I and II dual inhibitors for the therapy of liver cancer. Eur J Med Chem 2022; 237:114376. [DOI: 10.1016/j.ejmech.2022.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022]
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157
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Wang H, Bai X, Huang Y, Chen Y, Dong G, Ou T, Wu S, Xu D, Sheng C. Discovery of novel triple targeting G‑quadruplex and topoisomerase 1/2 ligands from natural products evodiamine and rutaecarpine. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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158
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Ruan L, Chen J, Du C, Lu H, Zhang J, Cai X, Dou R, Lin W, Chai Z, Nie G, Hu Y. Mitochondrial temperature-responsive drug delivery reverses drug resistance in lung cancer. Bioact Mater 2022; 13:191-199. [PMID: 35224301 PMCID: PMC8844157 DOI: 10.1016/j.bioactmat.2021.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/12/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
Reversal of cancer drug resistance remains a critical challenge in chemotherapy. Mitochondria-targeted drug delivery has been suggested to mitigate drug resistance in cancer. To overcome the intrinsic limitations in conventional mitochondrial targeting strategies, we develop mitochondrial temperature-responsive drug delivery to reverse doxorubicin (DOX) resistance in lung cancer. Results demonstrate that the thermoresponsive nanocarrier can prevent DOX efflux and facilitate DOX accumulation and mitochondrial targeting in DOX-resistant tumors. As a consequence, thermoresponsive nanocarrier enhances the cytotoxicity of DOX and reverses the drug resistance in tumor-bearing mice. This work represents the first example of mitochondrial temperature-responsive drug delivery for reversing cancer drug resistance.
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Affiliation(s)
- Lifo Ruan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jun Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chuanchao Du
- Peking University Third Hospital, Beijing, 100191, PR China
| | - Huiru Lu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
| | - Jiayu Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
| | - Xiaomeng Cai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Rui Dou
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wenchu Lin
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, PR China
- University of Science and Technology of China, Hefei, 230026, Anhui, PR China
| | - Zhifang Chai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Guangjun Nie
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, PR China
| | - Yi Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multi-disciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
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159
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Elton TS, Hernandez VA, Carvajal-Moreno J, Wang X, Ipinmoroti D, Yalowich JC. Intronic Polyadenylation in Acquired Cancer Drug Resistance Circumvented by Utilizing CRISPR/Cas9 with Homology-Directed Repair: The Tale of Human DNA Topoisomerase IIα. Cancers (Basel) 2022; 14:cancers14133148. [PMID: 35804920 PMCID: PMC9265003 DOI: 10.3390/cancers14133148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA topoisomerase IIα (170 kDa, TOP2α/170) resolves nucleic acid topological entanglements by generating transient double-strand DNA breaks. TOP2α inhibitors/poisons stabilize TOP2α-DNA covalent complexes resulting in persistent DNA damage and are frequently utilized to treat a variety of cancers. Acquired resistance to these chemotherapeutic agents is often associated with decreased TOP2α/170 expression levels. Studies have demonstrated that a reduction in TOP2α/170 results from a type of alternative polyadenylation designated intronic polyadenylation (IPA). As a consequence of IPA, variant TOP2α mRNA transcripts have been characterized that have resulted in the translation of C-terminal truncated TOP2α isoforms with altered biological activities. In this paper, an example is discussed where circumvention of acquired TOP2α-mediated drug resistance was achieved by utilizing CRISPR/Cas9 specific gene editing of an exon/intron boundary through homology directed repair (HDR) to reduce TOP2α IPA. These results illustrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant IPA. Abstract Intronic polyadenylation (IPA) plays a critical role in malignant transformation, development, progression, and cancer chemoresistance by contributing to transcriptome/proteome alterations. DNA topoisomerase IIα (170 kDa, TOP2α/170) is an established clinical target for anticancer agents whose efficacy is compromised by drug resistance often associated with a reduction of nuclear TOP2α/170 levels. In leukemia cell lines with acquired resistance to TOP2α-targeted drugs and reduced TOP2α/170 expression, variant TOP2α mRNA transcripts have been reported due to IPA that resulted in the translation of C-terminal truncated isoforms with altered nuclear-cytoplasmic distribution or heterodimerization with wild-type TOP2α/170. This review provides an overview of the various mechanisms regulating pre-mRNA processing and alternative polyadenylation, as well as the utilization of CRISPR/Cas9 specific gene editing through homology directed repair (HDR) to decrease IPA when splice sites are intrinsically weak or potentially mutated. The specific case of TOP2α exon 19/intron 19 splice site editing is discussed in etoposide-resistant human leukemia K562 cells as a tractable strategy to circumvent acquired TOP2α-mediated drug resistance. This example supports the importance of aberrant IPA in acquired drug resistance to TOP2α-targeted drugs. In addition, these results demonstrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant splicing/polyadenylation.
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160
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Structural and Biochemical Basis of Etoposide-Resistant Mutations in Topoisomerase IIα. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Etoposide is a widely used anticancer drug that targets type II topoisomerases, including topoisomerase IIα (TOP2A). TOP2A is a nuclear enzyme involved in regulating DNA topology through a double-strand passage mechanism. TOP2A is a homodimeric enzyme with two symmetrical active sites formed by residues from either half of the dimer. Both active sites cleave DNA, forming an enzyme-bound, double-stranded DNA break. Etoposide acts by binding in the active site between the ends of cleaved DNA, preventing the enzyme from ligating the DNA. In the present study, biochemical and structural data are used to examine the mechanism of etoposide resistance found with specific point mutations in TOP2A. Mutations near the active site (D463A, G534R, R487K), along with some outside of the active site (ΔA429 and P716L), are examined. We hypothesize that changes in the coordination of DNA cleavage results from mutations that impact symmetrical relationships in the active site and surrounding regions. In some cases, we report the first data on purified versions of these enzymes. Based upon our results, both local and long-distance factors can impact etoposide action and may indicate interdependent relationships in structure and function.
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161
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Su S, Xue Y, Sharov A, Zhang Y, Lee SK, Martindale J, Li W, Ku WL, Zhao K, De S, Shen W, Sen P, Gorospe M, Xu D, Wang W. A dual-activity topoisomerase complex regulates mRNA translation and turnover. Nucleic Acids Res 2022; 50:7013-7033. [PMID: 35748872 PMCID: PMC9262614 DOI: 10.1093/nar/gkac538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/06/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA. Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover. First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation. Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation-enhancing for some mRNAs whereas reducing for others. Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is partly linked to its ability to change topology of mRNAs. Collectively, our data suggest that TOP3B-TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity.
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Affiliation(s)
- Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Wai Lim Ku
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Weidong Wang
- To whom correspondence should be addressed. Tel: +1 410 454 8418; Fax: +1 410 558 8331.
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162
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Yamamoto T, Schiessel H. Loop extrusion driven volume phase transition of entangled chromosomes. Biophys J 2022; 121:2742-2750. [PMID: 35706364 DOI: 10.1016/j.bpj.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/26/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Experiments on reconstituted chromosomes have revealed that mitotic chromosomes are assembled even without nucleosomes. When topoisomerase II (topo II) is depleted from such reconstituted chromosomes, these chromosomes are not disentangled and form "sparklers," where DNA and linker histone are condensed in the core and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels. The loop extrusion stiffens an entangled DNA network because DNA segments in the elastically effective chains are translocated to loops, which are elastically ineffective. Our theory predicts that the loop extrusion by condensin drives the volume phase transition that collapses a swollen entangled DNA gel because the stiffening of the network destabilizes the swollen phase. This may be an important piece to understand the mechanism of the assembly of mitotic chromosomes.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan.
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
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163
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [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: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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164
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Bhattacharjee S, Rehman I, Basu S, Nandy S, Richardson JM, Das BB. Interplay between symmetric arginine dimethylation and ubiquitylation regulates TDP1 proteostasis for the repair of topoisomerase I-DNA adducts. Cell Rep 2022; 39:110940. [PMID: 35705029 DOI: 10.1016/j.celrep.2022.110940] [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: 06/08/2021] [Revised: 04/05/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase (TDP1) hydrolyzes the phosphodiester bond between a DNA 3' end and a tyrosyl moiety and is implicated in the repair of trapped topoisomerase I (Top1)-DNA covalent complexes (Top1cc). Protein arginine methyltransferase 5 (PRMT5) catalyzes arginine methylation of TDP1 at the residues R361 and R586. Here, we establish mechanistic crosstalk between TDP1 arginine methylation and ubiquitylation, which is critical for TDP1 homeostasis and cellular responses to Top1 poisons. We show that R586 methylation promotes TDP1 ubiquitylation, which facilitates ubiquitin/proteasome-dependent TDP1 turnover by impeding the binding of UCHL3 (deubiquitylase enzyme) with TDP1. TDP1-R586 also promotes TDP1-XRCC1 binding and XRCC1 foci formation at Top1cc-damage sites. Intriguingly, R361 methylation enhances the 3'-phosphodiesterase activity of TDP1 in real-time fluorescence-based cleavage assays, and this was rationalized using structural modeling. Together, our findings establish arginine methylation as a co-regulator of TDP1 proteostasis and activity, which modulates the repair of trapped Top1cc.
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Affiliation(s)
- Sangheeta Bhattacharjee
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Rehman
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Saini Basu
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Souvik Nandy
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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165
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Szczepański J, Tuszewska H, Trotsko N. Anticancer Profile of Rhodanines: Structure-Activity Relationship (SAR) and Molecular Targets-A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123750. [PMID: 35744873 PMCID: PMC9231410 DOI: 10.3390/molecules27123750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
The rhodanine core is a well-known privileged heterocycle in medicinal chemistry. The rhodanines, as subtypes of thiazolidin-4-ones, show a broad spectrum of biological activity, including anticancer properties. This review aims to analyze the anticancer features of the rhodanines described over the last decade in the scientific literature. The structure–activity relationship of rhodanine derivatives, as well as some of the molecular targets, were discussed. The information contained in this review could be of benefit to the design of new, effective small molecules with anticancer potential among rhodanine derivatives or their related heterocycles.
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166
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Fila M, Jablkowska A, Pawlowska E, Blasiak J. DNA Damage and Repair in Migraine: Oxidative Stress and Beyond. Neuroscientist 2022; 29:277-286. [PMID: 35658694 DOI: 10.1177/10738584221090836] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Energy generation in the brain to ameliorate energy deficit in migraine leads to oxidative stress as it is associated with reactive oxygen species (ROS) that may damage DNA and show a pronociceptive action in meninges mediated by transient receptor potential cation channel subfamily A member 1 (TRPA1). Recent studies show high levels of single-strand breaks (SSBs) at specific sites in the genome of postmitotic neurons and point at SSB repair (SSBR) as an important element of homeostasis of the central nervous system. DNA topoisomerase 1 (TOP1) is stabilized in the DNA damage-inducing state by neuronal stimulation, including cortical spreading depression. Impairment in poly (ADP-ribose) polymerase 1 (PARP-1) and X-ray repair cross complementing 1 (XRCC1), key SSBR proteins, may be linked with migraine by transient receptor potential melastatin 2 (TRPM2). TRPM2 may also mediate the involvement of migraine-related neuroinflammation with PARP-1 activated by oxidative stress-related SSBs. In conclusion, aberrant activity of SSBR evoked by compromised PARP-1 and XRCC1 may contribute to pathological phenomena in the migraine brain. Such aberrant SSBR results in the lack of repair or misrepair of SSBs induced by ROS or resulting from impaired TOP1. Therefore, components of SSBR may be considered a prospective druggable target in migraine.
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Affiliation(s)
- Michal Fila
- Department of Developmental Neurology and Epileptology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | | | | | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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167
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Yang H, Wang FT, Wu M, Wang W, Agama K, Pommier Y, An LK. Synthesis of 11-aminoalkoxy substituted benzophenanthridine derivatives as tyrosyl-DNA phosphodiesterase 1 inhibitors and their anticancer activity. Bioorg Chem 2022; 123:105789. [PMID: 35429714 PMCID: PMC10557912 DOI: 10.1016/j.bioorg.2022.105789] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/19/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an enzyme that repairs DNA lesions caused by the trapping of DNA topoisomerase IB (TOP1)-DNA break-associated crosslinks. TDP1 inhibitors have synergistic effect with TOP1 inhibitors in cancer cells and can overcome cancer cell resistance to TOP1 inhibitors. Here, we report the synthesis of 11-aminoalkoxy substituted benzophenanthridine derivatives as selective TDP1 inhibitors and show that six compounds 14, 16, 18, 20, 25 and 27 exhibit high TDP1 inhibition potency. The most potent TDP1 inhibitor 14 (IC50 = 1.7 ± 0.24 μM) induces cellular TDP1cc formation and shows synergistic effect with topotecan in four human cancer cell lines MCF-7, A549, H460 and HepG2.
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Affiliation(s)
- Hao Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang-Ting Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenjie Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou 510006, China.
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168
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Bhandari N, Pfeiffer SC, Jaramillo-Lambert A. Characterization of N- and C-terminal endogenously tagged Tyrosyl-DNA phosphodiesterase 2 (TDPT-1) C. elegans strains. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000540. [PMID: 35622466 PMCID: PMC9010224 DOI: 10.17912/micropub.biology.000540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/09/2022]
Abstract
We have generated Tyrosyl-DNA phosphodiesterase 2 (TDPT-1) C. elegans strains where CRISPR/Cas9 was used to endogenously tag the protein at either the C- or N-terminus and validated the functionality of the resulting tagged TDPT-1 proteins. We have found that both the N-terminally tagged ( wrmScarlet::tdpt-1) and C-terminally tagged ( tdpt-1::3xflag ) worm TDPT-1 does not affect embryonic viability compared to wild type. Using the N-terminally tagged wrmScarlet::tdpt-1 strain we show, for the first time, that TDPT-1 is expressed in nuclei of the germ line and the soma. Moreover, we validate the expression of TDPT-1 at the protein level using the C-terminally tagged ( tdpt-1::3xflag ) strain.
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169
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The Profile of MicroRNA Expression and Potential Role in the Regulation of Drug-Resistant Genes in Doxorubicin and Topotecan Resistant Ovarian Cancer Cell Lines. Int J Mol Sci 2022; 23:ijms23105846. [PMID: 35628654 PMCID: PMC9144982 DOI: 10.3390/ijms23105846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/09/2022] Open
Abstract
Epithelial ovarian cancer has the highest mortality among all gynecological malignancies. The main reasons for high mortality are late diagnosis and development of resistance to chemotherapy. Resistance to chemotherapeutic drugs can result from altered expression of drug-resistance genes regulated by miRNA. The main goal of our study was to detect differences in miRNA expression levels in two doxorubicin (DOX)- and two topotecan (TOP)-resistant variants of the A2780 drug-sensitive ovarian cancer cell line by miRNA microarray. The next aim was to recognize miRNAs as factors responsible for the regulation of drug-resistance genes. We observed altered expression of 28 miRNA that may be related to drug resistance. The upregulation of miR-125b-5p and miR-935 and downregulation of miR-218-5p was observed in both DOX-resistant cell lines. In both TOP-resistant cell lines, we noted the overexpression of miR-99a-5p, miR-100-5p, miR-125b-5p, and miR-125b-2-3p and decreased expression of miR-551b-3p, miR-551b-5p, and miR-383-5p. Analysis of the targets suggested that expression of important drug-resistant genes such as the collagen type I alpha 2 chain (COL1A2), protein Tyrosine Phosphatase Receptor Type K (PTPRK), receptor tyrosine kinase—EPHA7, Roundabout Guidance Receptor 2 (ROBO2), myristoylated alanine-rich C-kinase substrate (MARCK), and the ATP-binding cassette subfamily G member 2 (ABCG2) can be regulated by miRNA.
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170
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Ozawa S, Miura T, Terashima J, Habano W. Cellular irinotecan resistance in colorectal cancer and overcoming irinotecan refractoriness through various combination trials including DNA methyltransferase inhibitors: a review. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 4:946-964. [PMID: 35582377 PMCID: PMC8992440 DOI: 10.20517/cdr.2021.82] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/27/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022]
Abstract
Treatment with pharmacological drugs for colorectal cancer (CRC) remains unsatisfactory. A major cause of failure in pharmacotherapy is the resistance of colon cancer cells to the drugs, creating an urgent issue. In this review, we summarize previous studies on the resistance of CRC cells to irinotecan and discuss possible reasons for refractoriness. Our review presents the following five major causes of irinotecan resistance in human CRC: (1) cellular irinotecan resistance is induced mainly through the increased expression of the drug efflux transporter, ABCG2; (2) cellular irinotecan resistance is also induced in association with a nuclear receptor, pregnane/steroid X receptor (PXR/SXR), which is enriched in the CYP3A4 gene enhancer region in CRC cells by exposing the cells to SN-38; (3) irinotecan-resistant cells possess either reduced DNA topoisomerase I (Top1) expression at both the mRNA and protein levels or Top1 missense mutations; (4) alterations in the tumor microenvironment lead to drug resistance through intercellular vesicle-mediated transmission of miRNAs; and (5) CRC stem cells are the most difficult targets to successfully treat CRC. In the clinical setting, CRC gradually develops resistance to initially effective irinotecan-based therapy. To solve this problem, several clinical trials, such as irinotecan plus cetuximab vs. cetuximab monotherapy, have been conducted. Another clinical trial on irinotecan plus guadecitabine, a DNA-methyltransferase inhibitor, has also been conducted.
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Affiliation(s)
- Shogo Ozawa
- Division of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Toshitaka Miura
- Division of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Jun Terashima
- Division of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Wataru Habano
- Division of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
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171
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Van Ravenstein SX, Mehta KP, Kavlashvili T, Byl JAW, Zhao R, Osheroff N, Cortez D, Dewar JM. Topoisomerase II poisons inhibit vertebrate DNA replication through distinct mechanisms. EMBO J 2022; 41:e110632. [PMID: 35578785 PMCID: PMC9194788 DOI: 10.15252/embj.2022110632] [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: 01/10/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Topoisomerase II (TOP2) unlinks chromosomes during vertebrate DNA replication. TOP2 "poisons" are widely used chemotherapeutics that stabilize TOP2 complexes on DNA, leading to cytotoxic DNA breaks. However, it is unclear how these drugs affect DNA replication, which is a major target of TOP2 poisons. Using Xenopus egg extracts, we show that the TOP2 poisons etoposide and doxorubicin both inhibit DNA replication through different mechanisms. Etoposide induces TOP2-dependent DNA breaks and TOP2-dependent fork stalling by trapping TOP2 behind replication forks. In contrast, doxorubicin does not lead to appreciable break formation and instead intercalates into parental DNA to stall replication forks independently of TOP2. In human cells, etoposide stalls forks in a TOP2-dependent manner, while doxorubicin stalls forks independently of TOP2. However, both drugs exhibit TOP2-dependent cytotoxicity. Thus, etoposide and doxorubicin inhibit DNA replication through distinct mechanisms despite shared genetic requirements for cytotoxicity.
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Affiliation(s)
| | - Kavi P Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Runxiang Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
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172
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Bosire R, Fadel L, Mocsár G, Nánási P, Sen P, Sharma AK, Naseem MU, Kovács A, Kugel J, Kroemer G, Vámosi G, Szabó G. Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor. Sci Rep 2022; 12:8087. [PMID: 35577872 PMCID: PMC9110345 DOI: 10.1038/s41598-022-11994-z] [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: 12/25/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Doxorubicin (Dox), a widely used anticancer DNA-binding drug, affects chromatin in multiple ways, and these effects contribute to both its efficacy and its dose-limiting side effects, especially cardiotoxicity. Here, we studied the effects of Dox on the chromatin binding of the architectural proteins high mobility group B1 (HMGB1) and the linker histone H1, and the transcription factor retinoic acid receptor (RARα) by fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS) in live cells. At lower doses, Dox increased the binding of HMGB1 to DNA while decreasing the binding of the linker histone H1. At higher doses that correspond to the peak plasma concentrations achieved during chemotherapy, Dox reduced the binding of HMGB1 as well. This biphasic effect is interpreted in terms of a hierarchy of competition between the ligands involved and Dox-induced local conformational changes of nucleosome-free DNA. Combined, FRAP and FCS mobility data suggest that Dox decreases the overall binding of RARα to DNA, an effect that was only partially overcome by agonist binding. The intertwined interactions described are likely to contribute to both the effects and side effects of Dox.
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Affiliation(s)
- Rosevalentine Bosire
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Lina Fadel
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Mocsár
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Pialy Sen
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Anshu Kumar Sharma
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Muhammad Umair Naseem
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Kovács
- Department of Radiation Therapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jennifer Kugel
- Department of Biochemistry, University of Colorado, Boulder, USA
| | - Guido Kroemer
- Centre de Recherche Des Cordeliers, Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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173
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Rao Z, Shen J, Wang J, Zhang Z, Zhou J, Zhu J, Chen J, Chen W, Wang H. The role of PICT1 in RPL11/Mdm2/p53 pathway-regulated inhibition of cell growth induced by topoisomerase IIα inhibitor against cervical cancer cell line. Biochem Pharmacol 2022; 201:115098. [DOI: 10.1016/j.bcp.2022.115098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/02/2022]
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174
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Sakasai R, Wakasugi M, Matsui T, Sunatani Y, Saijo M, Matsunaga T, Iwabuchi K. Camptothecin compromises transcription recovery and cell survival against cisplatin and ultraviolet irradiation regardless of transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2022; 113:103318. [PMID: 35325630 DOI: 10.1016/j.dnarep.2022.103318] [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: 09/10/2021] [Revised: 02/18/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022]
Abstract
DNA-damaging anti-cancer drugs are used clinically to induce cell death by causing DNA strand breaks or DNA replication stress. Camptothecin (CPT) and cisplatin are commonly used anti-cancer drugs, and their combined use enhances the anti-tumour effects. However, the mechanism underlying this enhanced effect has not been well studied. In this study, we analysed the combined effect of CPT and cisplatin or ultraviolet (UV) and found that CPT suppresses transcription recovery after UV damage and induces the disappearance of the Cockayne syndrome group B (CSB) protein, a transcription-coupled nucleotide excision repair (TC-NER) factor. This CPT-induced disappearance of CSB expression was suppressed by proteasome and transcription inhibitors. Moreover, CSB ubiquitination was detected after CPT treatment in a transcription-dependent manner, suggesting that the transcription stress caused by CPT induces CSB ubiquitination, resulting in CSB undetectability. However, Cockayne syndrome group A (CSA) and CUL4A were not involved in the CPT-induced CSB undetectability, suggesting that CSB ubiquitination caused by CPT is regulated differently from the UV response. However, cisplatin or UV sensitivity was enhanced by CPT even in CSB- or CSA-knockout cells. Furthermore, the excessive CSB expression, which suppressed CSB ubiquitination, did not cancel the combined effect of CPT. These results suggest that CPT blocks the repair of cisplatin or UV-induced DNA damage regardless of TC-NER status. CPT possibly compromised the alternative repair pathways other than TC-NER, leading to the suppression of transcription recovery and enhancement of cell killing.
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Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan.
| | - Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tsukasa Matsunaga
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan.
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175
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Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity. Curr Biol 2022; 32:2962-2971.e4. [DOI: 10.1016/j.cub.2022.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
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176
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Abstract
Significance: The small, multicopy mitochondrial genome (mitochondrial DNA [mtDNA]) is essential for efficient energy production, as alterations in its coding information or a decrease in its copy number disrupt mitochondrial ATP synthesis. However, the mitochondrial replication machinery encounters numerous challenges that may limit its ability to duplicate this important genome and that jeopardize mtDNA stability, including various lesions in the DNA template, topological stress, and an insufficient nucleotide supply. Recent Advances: An ever-growing array of DNA repair or maintenance factors are being reported to localize to the mitochondria. We review current knowledge regarding the mitochondrial factors that may contribute to the tolerance or repair of various types of changes in the mitochondrial genome, such as base damage, incorporated ribonucleotides, and strand breaks. We also discuss the newly discovered link between mtDNA instability and activation of the innate immune response. Critical Issues: By which mechanisms do mitochondria respond to challenges that threaten mtDNA maintenance? What types of mtDNA damage are repaired, and when are the affected molecules degraded instead? And, finally, which forms of mtDNA instability trigger an immune response, and how? Future Directions: Further work is required to understand the contribution of the DNA repair and damage-tolerance factors present in the mitochondrial compartment, as well as the balance between mtDNA repair and degradation. Finally, efforts to understand the events underlying mtDNA release into the cytosol are warranted. Pursuing these and many related avenues can improve our understanding of what goes wrong in mitochondrial disease. Antioxid. Redox Signal. 36, 885-905.
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Affiliation(s)
- Gustavo Carvalho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Bruno Marçal Repolês
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela Mendes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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177
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Sidarala V, Zhu J, Levi-D'Ancona E, Pearson GL, Reck EC, Walker EM, Kaufman BA, Soleimanpour SA. Mitofusin 1 and 2 regulation of mitochondrial DNA content is a critical determinant of glucose homeostasis. Nat Commun 2022; 13:2340. [PMID: 35487893 PMCID: PMC9055072 DOI: 10.1038/s41467-022-29945-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
The dynamin-like GTPases Mitofusin 1 and 2 (Mfn1 and Mfn2) are essential for mitochondrial function, which has been principally attributed to their regulation of fission/fusion dynamics. Here, we report that Mfn1 and 2 are critical for glucose-stimulated insulin secretion (GSIS) primarily through control of mitochondrial DNA (mtDNA) content. Whereas Mfn1 and Mfn2 individually were dispensable for glucose homeostasis, combined Mfn1/2 deletion in β-cells reduced mtDNA content, impaired mitochondrial morphology and networking, and decreased respiratory function, ultimately resulting in severe glucose intolerance. Importantly, gene dosage studies unexpectedly revealed that Mfn1/2 control of glucose homeostasis was dependent on maintenance of mtDNA content, rather than mitochondrial structure. Mfn1/2 maintain mtDNA content by regulating the expression of the crucial mitochondrial transcription factor Tfam, as Tfam overexpression ameliorated the reduction in mtDNA content and GSIS in Mfn1/2-deficient β-cells. Thus, the primary physiologic role of Mfn1 and 2 in β-cells is coupled to the preservation of mtDNA content rather than mitochondrial architecture, and Mfn1 and 2 may be promising targets to overcome mitochondrial dysfunction and restore glucose control in diabetes.
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Affiliation(s)
- Vaibhav Sidarala
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States
| | - Jie Zhu
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States
| | - Elena Levi-D'Ancona
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States
| | - Gemma L Pearson
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States
| | - Emma C Reck
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States
| | - Emily M Walker
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States
| | - Brett A Kaufman
- Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States
| | - Scott A Soleimanpour
- Division of Metabolism, Endocrinology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, United States.
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48105, United States.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, 48105, United States.
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178
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Sun Y, Nitiss JL, Pommier Y. SUMO: A Swiss Army Knife for Eukaryotic Topoisomerases. Front Mol Biosci 2022; 9:871161. [PMID: 35463961 PMCID: PMC9019546 DOI: 10.3389/fmolb.2022.871161] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 01/03/2023] Open
Abstract
Topoisomerases play crucial roles in DNA metabolism that include replication, transcription, recombination, and chromatin structure by manipulating DNA structures arising in double-stranded DNA. These proteins play key enzymatic roles in a variety of cellular processes and are also likely to play structural roles. Topoisomerases allow topological transformations by introducing transient breaks in DNA by a transesterification reaction between a tyrosine residue of the enzyme and DNA. The cleavage reaction leads to a unique enzyme intermediate that allows cutting DNA while minimizing the potential for damage-induced genetic changes. Nonetheless, topoisomerase-mediated cleavage has the potential for inducing genome instability if the enzyme-mediated DNA resealing is impaired. Regulation of topoisomerase functions is accomplished by post-translational modifications including phosphorylation, polyADP-ribosylation, ubiquitylation, and SUMOylation. These modifications modulate enzyme activity and likely play key roles in determining sites of enzyme action and enzyme stability. Topoisomerase-mediated DNA cleavage and rejoining are affected by a variety of conditions including the action of small molecules, topoisomerase mutations, and DNA structural forms which permit the conversion of the short-lived cleavage intermediate to persistent topoisomerase DNA-protein crosslink (TOP-DPC). Recognition and processing of TOP-DPCs utilizes many of the same post-translational modifications that regulate enzyme activity. This review focuses on SUMOylation of topoisomerases, which has been demonstrated to be a key modification of both type I and type II topoisomerases. Special emphasis is placed on recent studies that indicate how SUMOylation regulates topoisomerase function in unperturbed cells and the unique roles that SUMOylation plays in repairing damage arising from topoisomerase malfunction.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - John L. Nitiss
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, IL, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
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179
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Patel PS, Krishnan R, Hakem R. Emerging roles of DNA topoisomerases in the regulation of R-loops. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503450. [PMID: 35483781 DOI: 10.1016/j.mrgentox.2022.503450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/24/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
R-loops are comprised of a DNA:RNA hybrid and a displaced single-strand DNA (ssDNA) that reinvades the DNA duplex behind the moving RNA polymerase. Because they have several physiological functions within the cell, including gene expression, chromosomal segregation, and mitochondrial DNA replication, among others, R-loop homeostasis is tightly regulated to ensure normal functioning of cellular processes. Thus, several classes of enzymes including RNases, helicases, topoisomerases, as well as proteins involved in splicing and the biogenesis of messenger ribonucleoproteins, have been implicated in R-loop prevention, suppression, and resolution. There exist six topoisomerase enzymes encoded by the human genome that function to introduce transient DNA breaks to relax supercoiled DNA. In this mini-review, we discuss functions of DNA topoisomerases and their emerging role in transcription, replication, and regulation of R-loops, and we highlight how their role in maintaining genome stability can be exploited for cancer therapy.
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Affiliation(s)
- Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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180
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Li X, Baek G, Carreira S, Yuan W, Ma S, Hofstad M, Lee S, Gao Y, Bertan C, Fenor de la Maza MDLD, Alluri PG, Burma S, Chen BP, Raj GV, de Bono J, Pommier Y, Mani RS. Targeting radioresistance and replication fork stability in prostate cancer. JCI Insight 2022; 7:152955. [PMID: 35349486 PMCID: PMC9090241 DOI: 10.1172/jci.insight.152955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
The bromodomain and extraterminal (BET) family of chromatin reader proteins bind to acetylated histones and regulate gene expression. The development of BET inhibitors (BETi) has expanded our knowledge of BET protein function beyond transcriptional regulation and has ushered several prostate cancer (PCa) clinical trials. However, BETi as a single agent is not associated with antitumor activity in patients with castration-resistant prostate cancer (CRPC). We hypothesized novel combinatorial strategies are likely to enhance the efficacy of BETi. By using PCa patient-derived explants and xenograft models, we show that BETi treatment enhanced the efficacy of radiation therapy (RT) and overcame radioresistance. Mechanistically, BETi potentiated the activity of RT by blocking DNA repair. We also report a synergistic relationship between BETi and topoisomerase I (TOP1) inhibitors (TOP1i). We show that the BETi OTX015 synergized with the new class of synthetic noncamptothecin TOP1i, LMP400 (indotecan), to block tumor growth in aggressive CRPC xenograft models. Mechanistically, BETi potentiated the antitumor activity of TOP1i by disrupting replication fork stability. Longitudinal analysis of patient tumors indicated that TOP1 transcript abundance increased as patients progressed from hormone-sensitive prostate cancer to CRPC. TOP1 was highly expressed in metastatic CRPC, and its expression correlated with the expression of BET family genes. These studies open new avenues for the rational combinatorial treatment of aggressive PCa.
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Affiliation(s)
- Xiangyi Li
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - GuemHee Baek
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Suzanne Carreira
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Wei Yuan
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | | | | | - Sora Lee
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Yunpeng Gao
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Claudia Bertan
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Maria de los Dolores Fenor de la Maza
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Prasanna G. Alluri
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology and Department of Neurosurgery, UT Health Science Center, San Antonio, Texas, USA
| | - Benjamin P.C. Chen
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Johann de Bono
- Prostate Cancer Targeted Therapy and Cancer Biomarkers Group, The Institute of Cancer Research and The Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, United Kingdom
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ram S. Mani
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
- Department of Urology and
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
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181
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Chowdhury SR, Das SK, Banerjee B, Paul Chowdhuri S, Majumder HK, Das BB. TDP1 knockout Leishmania donovani accumulate topoisomerase 1-linked DNA damage and are hypersensitive to clinically used antileishmanial drugs. FASEB J 2022; 36:e22265. [PMID: 35319800 DOI: 10.1096/fj.202101668rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 11/11/2022]
Abstract
Leishmania donovani, a unicellular protozoan parasite, causes a wide range of human diseases including fatal visceral leishmaniasis. Tyrosyl DNA-phosphodiesterase 1 (TDP1) hydrolyzes the phosphodiester bond between DNA 3'-end and a tyrosyl moiety of trapped topoisomerase I-DNA covalent complexes (Top1cc). We have previously shown Leishmania harbors a TDP1 gene (LdTDP1), however, the biological role of TDP1 remains largely unknown. In the present study, we have generated TDP1 knockout L. donovani (LdTDP1-/- ) promastigotes and have shown that LdTDP1-/- parasites are deficient in 3'-phosphodiesterase activities and were hypersensitive to Top1-poison like camptothecin (CPT), DNA alkylation agent like methyl methanesulfonate, and oxidative DNA lesions generated by hydrogen peroxide but were not sensitive to etoposide. We also detected elevated levels of CPT-induced reactive oxygen species triggering cell cycle arrest and cell death in LdTDP1-/- promastigotes. LdTDP1-/- promastigotes accumulate a significant change in the membrane morphology with the accumulation of membrane pores, which is associated with oxidative stress and lipid peroxidation. To our surprise, we detected that LdTDP1-/- parasites were hypersensitive to antileishmanial drugs like amphotericin B and miltefosine, which could be rescued by complementation of wild-type TDP1 gene in the LdTDP1-/- parasites. Notably, multidrug-resistant L. donovani clinical isolates showed a marked reduction in TDP1 expression and were sensitive to Top1 poisons. Taken together, our study provides a new role of LdTDP1 in protecting L. donovani parasites from oxidative stress-induced DNA damage and resistance to amphotericin B and miltefosine.
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Affiliation(s)
- Somenath Roy Chowdhury
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhendu K Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Bijoylaxmi Banerjee
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Srijita Paul Chowdhuri
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Hemanta K Majumder
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India
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182
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Martín-Encinas E, Selas A, Palacios F, Alonso C. The design and discovery of topoisomerase I inhibitors as anticancer therapies. Expert Opin Drug Discov 2022; 17:581-601. [PMID: 35321631 DOI: 10.1080/17460441.2022.2055545] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Cancer has been identified as one of the leading causes of death worldwide. The biological target of some anticancer agents is topoisomerase I, an enzyme involved in the relaxation of supercoiled DNA. The synthesis of new compounds with antiproliferative effect and behaving as topoisomerase I inhibitors has become an active field of research. Depending on their mechanism of inhibition, they can be classified as catalytic inhibitors or poisons. AREAS COVERED This review article summarizes the state of the art for the development of selective topoisomerase I inhibitors. Collected compounds showed inhibition of the enzyme, highlighting those approved for clinical use, the combination therapies developed, as well as related drawbacks and future focus. EXPERT OPINION Research related to topoisomerase I inhibitors in cancer therapy started with camptothecin (CPT). This compound was first selected as a good anticancer agent and then topoisomerase I was identified as its therapeutic target. Derivatives of CPT irinotecan, topotecan, and belotecan are the only clinically approved inhibitors. Currently, their limitations are being addressed by different stretegies. Future studies should focus not only on developing other active molecules but also on improving the bioavailability and pharmacokinetics of potent synthetic derivatives.
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Affiliation(s)
- Endika Martín-Encinas
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
| | - Asier Selas
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
| | - Francisco Palacios
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
| | - Concepción Alonso
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
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183
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Mihajlovic M, Vinken M. Mitochondria as the Target of Hepatotoxicity and Drug-Induced Liver Injury: Molecular Mechanisms and Detection Methods. Int J Mol Sci 2022; 23:ijms23063315. [PMID: 35328737 PMCID: PMC8951158 DOI: 10.3390/ijms23063315] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
One of the major mechanisms of drug-induced liver injury includes mitochondrial perturbation and dysfunction. This is not a surprise, given that mitochondria are essential organelles in most cells, which are responsible for energy homeostasis and the regulation of cellular metabolism. Drug-induced mitochondrial dysfunction can be influenced by various factors and conditions, such as genetic predisposition, the presence of metabolic disorders and obesity, viral infections, as well as drugs. Despite the fact that many methods have been developed for studying mitochondrial function, there is still a need for advanced and integrative models and approaches more closely resembling liver physiology, which would take into account predisposing factors. This could reduce the costs of drug development by the early prediction of potential mitochondrial toxicity during pre-clinical tests and, especially, prevent serious complications observed in clinical settings.
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184
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Molinaro C, Wambang N, Bousquet T, Vercoutter-Edouart AS, Pélinski L, Cailliau K, Martoriati A. A Novel Copper(II) Indenoisoquinoline Complex Inhibits Topoisomerase I, Induces G2 Phase Arrest, and Autophagy in Three Adenocarcinomas. Front Oncol 2022; 12:837373. [PMID: 35280788 PMCID: PMC8908320 DOI: 10.3389/fonc.2022.837373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2022] [Indexed: 12/30/2022] Open
Abstract
Topoisomerases, targets of inhibitors used in chemotherapy, induce DNA breaks accumulation leading to cancer cell death. A newly synthesized copper(II) indenoisoquinoline complex WN197 exhibits a cytotoxic effect below 0.5 µM, on MDA-MB-231, HeLa, and HT-29 cells. At low doses, WN197 inhibits topoisomerase I. At higher doses, it inhibits topoisomerase IIα and IIβ, and displays DNA intercalation properties. DNA damage is detected by the presence of γH2AX. The activation of the DNA Damage Response (DDR) occurs through the phosphorylation of ATM/ATR, Chk1/2 kinases, and the increase of p21, a p53 target. WN197 induces a G2 phase arrest characterized by the unphosphorylated form of histone H3, the accumulation of phosphorylated Cdk1, and an association of Cdc25C with 14.3.3. Cancer cells die by autophagy with Beclin-1 accumulation, LC3-II formation, p62 degradation, and RAPTOR phosphorylation in the mTOR complex. Finally, WN197 by inhibiting topoisomerase I at low concentration with high efficiency is a promising agent for the development of future DNA damaging chemotherapies.
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Affiliation(s)
- Caroline Molinaro
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | | | - Till Bousquet
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, Lille, France
| | | | - Lydie Pélinski
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, Lille, France
| | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Alain Martoriati
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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185
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Alecki C, Vera M. Role of Nuclear Non-Canonical Nucleic Acid Structures in Organismal Development and Adaptation to Stress Conditions. Front Genet 2022; 13:823241. [PMID: 35281835 PMCID: PMC8906566 DOI: 10.3389/fgene.2022.823241] [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: 11/26/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Over the last decades, numerous examples have involved nuclear non-coding RNAs (ncRNAs) in the regulation of gene expression. ncRNAs can interact with the genome by forming non-canonical nucleic acid structures such as R-loops or DNA:RNA triplexes. They bind chromatin and DNA modifiers and transcription factors and favor or prevent their targeting to specific DNA sequences and regulate gene expression of diverse genes. We review the function of these non-canonical nucleic acid structures in regulating gene expression of multicellular organisms during development and in response to different stress conditions and DNA damage using examples described in several organisms, from plants to humans. We also overview recent techniques developed to study where R-loops or DNA:RNA triplexes are formed in the genome and their interaction with proteins.
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Affiliation(s)
- Célia Alecki
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, QC, Canada
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186
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Effect of ALDH1A1 Gene Knockout on Drug Resistance in Paclitaxel and Topotecan Resistant Human Ovarian Cancer Cell Lines in 2D and 3D Model. Int J Mol Sci 2022; 23:ijms23063036. [PMID: 35328460 PMCID: PMC8950618 DOI: 10.3390/ijms23063036] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
Ovarian cancer is the most common cause of gynecological cancer death. Cancer Stem Cells (CSCs) characterized by drug transporters and extracellular matrix (ECM) molecules expression are responsible for drug resistance development. The goal of our study was to examine the role of aldehyde dehydrogenase 1A1 (ALDH1A1) expression in paclitaxel (PAC) and topotecan (TOP) resistant ovarian cancer cell lines. In both cell lines, we knocked out the ALDH1A1 gene using the CRISPR/Cas9 technique. Additionally, we derived an ALDH1A1 positive TOP-resistant cell line with ALDH1A1 expression in all cells via clonal selection. The effect of ALDH1A1 gene knockout or clonal selection on the expression of ALDH1A1, drug transporters (P-gp and BCRP), and ECM (COL3A1) was determined by Q-PCR, Western blot and immunofluorescence. Using MTT assay, we compared drug resistance in two-dimensional (2D) and three-dimensional (3D) cell culture conditions. We did not observe any effect of ALDH1A1 gene knockout on MDR1/P-gp expression and drug resistance in the PAC-resistant cell line. The knockout of ALDH1A1 in the TOP-resistant cell line resulted in a moderate decrease of BCRP and COL3A1 expression and weakened TOP resistance. The clonal selection of ALDH1A1 cells resulted in very strong downregulation of BCPR and COL3A1 expression and overexpression of MDR1/P-gp. This finally resulted in decreased resistance to TOP but increased resistance to PAC. All spheroids were more resistant than cells growing as monolayers, but the resistance mechanism differs. The spheroids' resistance may result from the presence of cell zones with different proliferation paces, the density of the spheroid, ECM expression, and drug capacity to diffuse into the spheroid.
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187
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Budzyński MA, Teves SS. System reset: topoisomerase 1 clears mitotic DNA for transcriptional memory. Trends Biochem Sci 2022; 47:556-557. [DOI: 10.1016/j.tibs.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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188
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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189
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Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
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Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
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190
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Machine Learning analysis of high-grade serous ovarian cancer proteomic dataset reveals novel candidate biomarkers. Sci Rep 2022; 12:3041. [PMID: 35197484 PMCID: PMC8866540 DOI: 10.1038/s41598-022-06788-2] [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: 08/02/2021] [Accepted: 02/02/2022] [Indexed: 12/19/2022] Open
Abstract
Ovarian cancer is one of the most common gynecological malignancies, ranking third after cervical and uterine cancer. High-grade serous ovarian cancer (HGSOC) is one of the most aggressive subtype, and the late onset of its symptoms leads in most cases to an unfavourable prognosis. Current predictive algorithms used to estimate the risk of having Ovarian Cancer fail to provide sufficient sensitivity and specificity to be used widely in clinical practice. The use of additional biomarkers or parameters such as age or menopausal status to overcome these issues showed only weak improvements. It is necessary to identify novel molecular signatures and the development of new predictive algorithms able to support the diagnosis of HGSOC, and at the same time, deepen the understanding of this elusive disease, with the final goal of improving patient survival. Here, we apply a Machine Learning-based pipeline to an open-source HGSOC Proteomic dataset to develop a decision support system (DSS) that displayed high discerning ability on a dataset of HGSOC biopsies. The proposed DSS consists of a double-step feature selection and a decision tree, with the resulting output consisting of a combination of three highly discriminating proteins: TOP1, PDIA4, and OGN, that could be of interest for further clinical and experimental validation. Furthermore, we took advantage of the ranked list of proteins generated during the feature selection steps to perform a pathway analysis to provide a snapshot of the main deregulated pathways of HGSOC. The datasets used for this study are available in the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data portal (https://cptac-data-portal.georgetown.edu/).
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191
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Abstract
Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
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192
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Williams JS, Kunkel TA. Ribonucleotide Incorporation by Eukaryotic B-family Replicases and Its Implications for Genome Stability. Annu Rev Biochem 2022; 91:133-155. [PMID: 35287470 DOI: 10.1146/annurev-biochem-032620-110354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our current view of how DNA-based genomes are efficiently and accurately replicated continues to evolve as new details emerge on the presence of ribonucleotides in DNA. Ribonucleotides are incorporated during eukaryotic DNA replication at rates that make them the most common noncanonical nucleotide placed into the nuclear genome, they are efficiently repaired, and their removal impacts genome integrity. This review focuses on three aspects of this subject: the incorporation of ribonucleotides into the eukaryotic nuclear genome during replication by B-family DNA replicases, how these ribonucleotides are removed, and the consequences of their presence or removal for genome stability and disease. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
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193
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Moreira F, Arenas M, Videira A, Pereira F. Evolutionary History of TOPIIA Topoisomerases in Animals. J Mol Evol 2022; 90:149-165. [PMID: 35165762 DOI: 10.1007/s00239-022-10048-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/26/2022] [Indexed: 01/15/2023]
Abstract
TOPIIA topoisomerases are required for the regulation of DNA topology by DNA cleavage and re-ligation and are important targets of antibiotic and anticancer agents. Humans possess two TOPIIA paralogue genes (TOP2A and TOP2B) with high sequence and structural similarity but distinct cellular functions. Despite their functional and clinical relevance, the evolutionary history of TOPIIA is still poorly understood. Here we show that TOPIIA is highly conserved in Metazoa. We also found that TOPIIA paralogues from jawed and jawless vertebrates had different origins related with tetraploidization events. After duplication, TOP2B evolved under a stronger purifying selection than TOP2A, perhaps promoted by the more specialized role of TOP2B in postmitotic cells. We also detected genetic signatures of positive selection in the highly variable C-terminal domain (CTD), possibly associated with adaptation to cellular interactions. By comparing TOPIIA from modern and archaic humans, we found two amino acid substitutions in the TOP2A CTD, suggesting that TOP2A may have contributed to the evolution of present-day humans, as proposed for other cell cycle-related genes. Finally, we identified six residues conferring resistance to chemotherapy differing between TOP2A and TOP2B. These six residues could be targets for the development of TOP2A-specific inhibitors that would avoid the side effects caused by inhibiting TOP2B. Altogether, our findings clarify the origin, diversification and selection pressures governing the evolution of animal TOPIIA.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal.
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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194
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Menendez D, Anand JR, Murphy CC, Bell WJ, Fu J, Slepushkina N, Buehler E, Martin SE, Lal-Nag M, Nitiss JL, Resnick MA. Etoposide-induced DNA damage is increased in p53 mutants: identification of ATR and other genes that influence effects of p53 mutations on Top2-induced cytotoxicity. Oncotarget 2022; 13:332-346. [PMID: 35178190 PMCID: PMC8845119 DOI: 10.18632/oncotarget.28195] [Citation(s) in RCA: 8] [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: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 11/25/2022] Open
Abstract
The functional status of the tumor suppressor p53 is a critical component in determining the sensitivity of cancer cells to many chemotherapeutic agents. DNA topoisomerase II (Top2) plays essential roles in DNA metabolism and is the target of FDA approved chemotherapeutic agents. Topoisomerase targeting drugs convert the enzyme into a DNA damaging agent and p53 influences cellular responses to these agents. We assessed the impact of the loss of p53 function on the formation of DNA damage induced by the Top2 poison etoposide. Using human HCT116 cells, we found resistance to etoposide in cell growth assays upon the functional loss of p53. Nonetheless, cells lacking fully functional p53 were etoposide hypersensitive in clonogenic survival assays. This complex role of p53 led us to directly examine the effects of p53 status on topoisomerase-induced DNA damage. A deficiency in functional p53 resulted in elevated levels of the Top2 covalent complexes (Top2cc) in multiple cell lines. Employing genome-wide siRNA screens, we identified a set of genes for which reduced expression resulted in enhanced synthetic lethality upon etoposide treatment of p53 defective cells. We focused on one hit from this screen, ATR, and showed that decreased expression sensitized the p53-defective cells to etoposide in all assays and generated elevated levels of Top2cc in both p53 proficient and deficient cells. Our findings suggest that a combination of etoposide treatment with functional inactivation of DNA repair in p53 defective cells could be used to enhance the therapeutic efficacy of Top2 targeting agents.
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Affiliation(s)
- Daniel Menendez
- Chromosomal Stability Group, Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Durham, NC 27709, USA
- Environmental Cardiopulmonary Disease Group, Immunity, Inflammation and Disease Laboratory, NIEHS, NIH, Durham, NC 27709, USA
- These authors contributed equally to this work
| | - Jay R. Anand
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, IL 61107, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- These authors contributed equally to this work
| | - Carri C. Murphy
- Chromosomal Stability Group, Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Durham, NC 27709, USA
| | - Whitney J. Bell
- Chromosomal Stability Group, Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Durham, NC 27709, USA
| | - Jiaqi Fu
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20850, USA
| | - Nadia Slepushkina
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20850, USA
| | - Eugen Buehler
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20850, USA
| | - Scott E. Martin
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20850, USA
| | - Madhu Lal-Nag
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20850, USA
| | - John L. Nitiss
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, IL 61107, USA
| | - Michael A. Resnick
- Chromosomal Stability Group, Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Durham, NC 27709, USA
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195
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Tsirkas I, Dovrat D, Thangaraj M, Brouwer I, Cohen A, Paleiov Z, Meijler MM, Lenstra T, Aharoni A. Transcription-replication coordination revealed in single live cells. Nucleic Acids Res 2022; 50:2143-2156. [PMID: 35137218 PMCID: PMC8887460 DOI: 10.1093/nar/gkac069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/04/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
The coexistence of DNA replication and transcription during S-phase requires their tight coordination to prevent harmful conflicts. While extensive research revealed important mechanisms for minimizing these conflicts and their consequences, little is known regarding how the replication and transcription machinery are coordinated in real-time. Here, we developed a live-cell imaging approach for the real-time monitoring of replisome progression and transcription dynamics during a transcription-replication encounter. We found a wave of partial transcriptional repression ahead of the moving replication fork, which may contribute to efficient fork progression through the transcribed gene. Real-time detection of conflicts revealed their negative impact on both processes, leading to fork stalling or slowdown as well as lower transcription levels during gene replication, with different trade-offs observed in defined subpopulations of cells. Our real-time measurements of transcription-replication encounters demonstrate how these processes can proceed simultaneously while maintaining genomic stability, and how conflicts can arise when coordination is impaired.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Manikandan Thangaraj
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute,1066CX Amsterdam, The Netherlands
| | - Amit Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Zohar Paleiov
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Michael M Meijler
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Tineke Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute,1066CX Amsterdam, The Netherlands
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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196
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Design, Synthesis and Cytotoxicity of Thiazole-Based Stilbene Analogs as Novel DNA Topoisomerase IB Inhibitors. Molecules 2022; 27:molecules27031009. [PMID: 35164276 PMCID: PMC8838847 DOI: 10.3390/molecules27031009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 11/17/2022] Open
Abstract
A series of new thiazole-based stilbene analogs were designed, synthesized and evaluated for DNA topoisomerase IB (Top1) inhibitory activity. Top1-mediated relaxation assays showed that the synthesized compounds possessed variable Top1 inhibitory activity. Among them, (E)-2-(3-methylstyryl)-4-(4-fluorophenyl)thiazole (8) acted as a potent Top1 inhibitor with high Top1 inhibition of ++++ which is comparable to that of CPT. A possible binding mode of compound 8 with Top1–DNA complex was further provided by molecular docking. An MTT assay against human breast cancer (MCF-7) and human colon cancer (HCT116) cell lines revealed that the majority of these compounds showed high cytotoxicity, with IC50 values at micromolar concentrations. Compounds 8 and (E)-2-(4-tert-butylstyryl)-4-(4-fluorophenyl)thiazole (11) exhibited the most potent cytotoxicity with IC50 values of 0.78 and 0.62 μM against MCF-7 and HCT116, respectively. Moreover, the preliminary structure–activity relationships of thiazole-based stilbene analogs was also discussed.
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197
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Liu X, Lv L, Jiang C, Bai J, Gao Y, Ma Z, Jiang P. A natural product, (S)-10-Hydroxycamptothecin inhibits pseudorabies virus proliferation through DNA damage dependent antiviral innate immunity. Vet Microbiol 2022; 265:109313. [PMID: 34968801 DOI: 10.1016/j.vetmic.2021.109313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/11/2021] [Accepted: 12/19/2021] [Indexed: 11/19/2022]
Abstract
Pseudorabies virus (PRV), a member of the subfamily alphaherpesvirinae, is one of the most important pathogenes that cause acute death in infected pigs and leads to substantial economic losses in the global swine industry. Recently, China's emerging PRV mutant strains resulted in the traditionally commercial vaccines not providing complete protection. Some studies reported that PRV could infect humans and cause endophthalmitis and encephalitis under certain circumstances. It is necessary to develop alternative manners to control the virus infection. Here, by screening a library of natural products, (S)-10-Hydroxycamptothecin (10-HCPT) was revealed to inhibit PRV replication with a selective index of 270.04. And 10-HCPT inhibited PRV replication by blocking the viral genome replication but not inhibiting the viral attachment, internalization, and release. RNA interference assay showed that 10-HCPT inhibited PRV replication by targeting DNA topoisomerase 1 (TOP1). Meanwhile, 10-HCPT treatment induced DNA damage response and stimulated antiviral innate immunity. Animal challenge experiments showed that 10-HCPT effectively alleviated clinical signs and hispathology, and increased INF-β responses in lung and brain tissues of mice induced by PRV infection. The results demonstrate that 10-HCPT is a promising therapeutic agent to control PRV infection.
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Affiliation(s)
- Xing Liu
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lin Lv
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenlong Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanni Gao
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zicheng Ma
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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198
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Kadagathur M, Sujat Shaikh A, Panda B, George J, Phanindranath R, Kumar Sigalapalli D, Bhale NA, Godugu C, Nagesh N, Shankaraiah N, Tangellamudi ND. Synthesis of indolo/pyrroloazepinone-oxindoles as potential cytotoxic, DNA-intercalating and Topo I inhibitors. Bioorg Chem 2022; 122:105706. [DOI: 10.1016/j.bioorg.2022.105706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
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199
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Reijns MAM, Parry DA, Williams TC, Nadeu F, Hindshaw RL, Rios Szwed DO, Nicholson MD, Carroll P, Boyle S, Royo R, Cornish AJ, Xiang H, Ridout K, Schuh A, Aden K, Palles C, Campo E, Stankovic T, Taylor MS, Jackson AP. Signatures of TOP1 transcription-associated mutagenesis in cancer and germline. Nature 2022; 602:623-631. [PMID: 35140396 PMCID: PMC8866115 DOI: 10.1038/s41586-022-04403-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
Abstract
The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to be mutagenic2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes4. Here we show that ID4-a cancer insertion-deletion (indel) mutation signature of unknown aetiology5 characterized by short (2 to 5 base pair) deletions -is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress6, their activity may also be an important source of mutations in the human genome.
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Affiliation(s)
- Martin A M Reijns
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
| | - David A Parry
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Biomedical Genomics, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rebecca L Hindshaw
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Diana O Rios Szwed
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Michael D Nicholson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Paula Carroll
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shelagh Boyle
- Genome Regulation, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Hang Xiang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Kate Ridout
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Universitat de Barcelona, Barcelona, Spain
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin S Taylor
- Biomedical Genomics, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
| | - Andrew P Jackson
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
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200
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Jauregui‐Lozano J, Escobedo S, Easton A, Lanman N, Weake VM, Hall H. Proper control of R-loop homeostasis is required for maintenance of gene expression and neuronal function during aging. Aging Cell 2022; 21:e13554. [PMID: 35048512 PMCID: PMC8844117 DOI: 10.1111/acel.13554] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/03/2021] [Accepted: 01/03/2022] [Indexed: 01/25/2023] Open
Abstract
Age‐related loss of cellular function and increased cell death are characteristic hallmarks of aging. While defects in gene expression and RNA metabolism have been linked with age‐associated human neuropathies, it is not clear how the changes that occur in aging neurons contribute to loss of gene expression homeostasis. R‐loops are RNA–DNA hybrids that typically form co‐transcriptionally via annealing of the nascent RNA to the template DNA strand, displacing the non‐template DNA strand. Dysregulation of R‐loop homeostasis has been associated with both transcriptional impairment and genome instability. Importantly, a growing body of evidence links R‐loop accumulation with cellular dysfunction, increased cell death, and chronic disease onset. Here, we characterized the R‐loop landscape in aging Drosophila melanogaster photoreceptor neurons and showed that bulk R‐loop levels increased with age. Further, genome‐wide mapping of R‐loops revealed that transcribed genes accumulated R‐loops over gene bodies during aging, which correlated with decreased expression of long and highly expressed genes. Importantly, while photoreceptor‐specific down‐regulation of Top3β, a DNA/RNA topoisomerase associated with R‐loop resolution, lead to decreased visual function, over‐expression of Top3β or nuclear‐localized RNase H1, which resolves R‐loops, enhanced positive light response during aging. Together, our studies highlight the functional link between dysregulation of R‐loop homeostasis, gene expression, and visual function during aging.
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Affiliation(s)
| | - Spencer Escobedo
- Department of Biochemistry Purdue University West Lafayette Indiana USA
| | - Alyssa Easton
- Department of Agricultural and Biological Engineering Purdue University West Lafayette Indiana USA
| | - Nadia A. Lanman
- Department of Comparative Pathobiology College of Veterinary Medicine Purdue University West Lafayette Indiana USA
- Purdue University Center for Cancer Research Purdue University West Lafayette Indiana USA
| | - Vikki M. Weake
- Department of Biochemistry Purdue University West Lafayette Indiana USA
- Purdue University Center for Cancer Research Purdue University West Lafayette Indiana USA
| | - Hana Hall
- Department of Biochemistry Purdue University West Lafayette Indiana USA
- Purdue Institute for Integrative Neuroscience Purdue University West Lafayette Indiana USA
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