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Ye BJ, Li DF, Li XY, Hao JL, Liu DJ, Yu H, Zhang CD. Methylation synthetic lethality: Exploiting selective drug targets for cancer therapy. Cancer Lett 2024:217010. [PMID: 38849016 DOI: 10.1016/j.canlet.2024.217010] [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: 04/28/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024]
Abstract
In cancer, synthetic lethality refers to the drug-induced inactivation of one gene and the inhibition of another in cancer cells by a drug, resulting in the death of only cancer cells; however, this effect is not present in normal cells, leading to targeted killing of cancer cells. Recent intensive epigenetic research has revealed that aberrant epigenetic changes are more frequently observed than gene mutations in certain cancers. Recently, numerous studies have reported various methylation synthetic lethal combinations involving DNA damage repair genes, metabolic pathway genes, and paralogs with significant results in cellular models, some of which have already entered clinical trials with promising results. This review systematically introduces the advantages of methylation synthetic lethality and describes the lethal mechanisms of methylation synthetic lethal combinations that have recently demonstrated success in cellular models. Furthermore, we discuss the future opportunities and challenges of methylation synthetic lethality in targeted anticancer therapies.
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Affiliation(s)
- Bing-Jie Ye
- Clinical Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Di-Fei Li
- Clinical Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Xin-Yun Li
- Clinical Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Jia-Lin Hao
- Central Laboratory, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Di-Jie Liu
- Central Laboratory, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Hang Yu
- Department of Surgical Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Chun-Dong Zhang
- Central Laboratory, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China;; Department of Surgical Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China;.
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2
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Jiang T, Zhang Y, Yu S, Hu B. Discovering potential WRN inhibitors from natural product database through computational methods. J Mol Graph Model 2024; 129:108758. [PMID: 38507856 DOI: 10.1016/j.jmgm.2024.108758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Microsatellite instability (MSI) is a relatively common feature associated with multiple cancers, and Werner syndrome (WRN) ATP-dependent helicase has been recognized as a novel target for treating MSI cancers, such as colorectal cancer. A small-molecule inhibitor targeting WRN would be a promising strategy for treating colorectal cancer with high MSI expression. In this study, we employed a computer-assisted drug discovery strategy to screen over 30,000 natural product molecules. By using a combination of docking, ligand efficiency, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), and thermodynamic integration (TI) calculations, we identified MOL008980, MOL010740, MOL011832, T4743, TN1166, and TNP-002173 as potential WRN inhibitors. Subsequent molecular dynamics simulation revealed that these screened natural products possessed better binding dynamic characteristics than ATP substrate and were capable of inhibiting the dynamic process of WRN, making them potential strong ATP competitive inhibitors. In conclusion, our computational approach revealed potential WRN inhibitors from a natural product database, providing a theoretical basis for future research.
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Affiliation(s)
| | | | - Shuihong Yu
- College of Pharmacy, Anqing Medical College, Anqing, China
| | - Bingde Hu
- Navy Anqing Hospital, Anqing, China.
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3
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Yamamoto H, Watanabe Y, Arai H, Umemoto K, Tateishi K, Sunakawa Y. Microsatellite instability: A 2024 update. Cancer Sci 2024; 115:1738-1748. [PMID: 38528657 PMCID: PMC11145116 DOI: 10.1111/cas.16160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Deficient mismatch repair (dMMR) results in microsatellite instability (MSI), a pronounced mutator phenotype. High-frequency MSI (MSI-H)/dMMR is gaining increasing interest as a biomarker for advanced cancer patients to determine their eligibility for immune checkpoint inhibitors (ICIs). Various methods based on next-generation sequencing (NGS) have been developed to assess the MSI status. Comprehensive genomic profiling (CGP) testing can precisely ascertain the MSI status as well as genomic alterations in a single NGS test. The MSI status can be also ascertained through the liquid biopsy-based CGP assays. MSI-H has thus been identified in various classes of tumors, resulting in a greater adoption of immunotherapy, which is hypothesized to be effective against malignancies that possess a substantial number of mutations and/or neoantigens. NGS-based studies have also characterized MSI-driven carcinogenesis, including significant rates of fusion kinases in colorectal cancers (CRCs) with MSI-H that are targets for therapeutic kinase inhibitors, particularly in MLH1-methylated CRCs with wild-type KRAS/BRAF. NTRK fusion is linked to the colorectal serrated neoplasia pathway. Recent advances in investigations of MSI-H malignancies have resulted in the development of novel diagnostic or therapeutic techniques, such as a synthetic lethal therapy that targets the Werner gene. DNA sensing in cancer cells is required for antitumor immunity induced by dMMR, opening up novel avenues and biomarkers for immunotherapy. Therefore, clinical relevance exists for analyses of MSI and MSI-H-associated genomic alterations in malignancy. In this article, we provide an update on MSI-driven carcinogenesis, with an emphasis on unique landscapes of diagnostic and immunotherapeutic strategies.
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Affiliation(s)
- Hiroyuki Yamamoto
- Department of BioinformaticsSt. Marianna University Graduate School of MedicineKawasakiJapan
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yoshiyuki Watanabe
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
- Department of Internal MedicineKawasaki Rinko General HospitalKawasakiJapan
| | - Hiroyuki Arai
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Kumiko Umemoto
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Keisuke Tateishi
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yu Sunakawa
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
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4
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Gadgil RY, Rider SD, Shrestha R, Alhawach V, Hitch D, Leffak M. Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs. NAR Cancer 2024; 6:zcae027. [PMID: 38854437 PMCID: PMC11161834 DOI: 10.1093/narcan/zcae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. We used inverse PCR of non-B microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures integrated at a common ectopic chromosomal site to show that these non-B DNAs generate highly mutagenized eccDNAs by replication-dependent mechanisms. Mutagenesis occurs within the non-B DNAs and extends several kilobases bidirectionally into flanking and nonallelic DNA. Each non-B DNA exhibits a different pattern of mutagenesis, while sister clones containing the same non-B DNA also display distinct patterns of recombination, microhomology-mediated template switching and base substitutions. Mutations include mismatches, short duplications, long nontemplated insertions, large deletions and template switches to sister chromatids and nonallelic chromosomes. Drug-induced replication stress or the depletion of DNA repair factors Rad51, the COPS2 signalosome subunit or POLη change the pattern of template switching and alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA double strand breaks to account for the generation and circularization of mutagenized eccDNAs and the appearance of genomic homologous recombination deficiency (HRD) scars. These results may help to explain the appearance of tumor eccDNAS and their roles in neoantigen production, oncogenesis and resistance to chemotherapy.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Resha Shrestha
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Venicia Alhawach
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - David C Hitch
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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5
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Li S, Han T. Frequent loss of FAM126A expression in colorectal cancer results in selective FAM126B dependency. iScience 2024; 27:109646. [PMID: 38638566 PMCID: PMC11025007 DOI: 10.1016/j.isci.2024.109646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/01/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Most advanced colorectal cancer (CRC) patients cannot benefit from targeted therapy due to lack of actionable targets. By mining data from the DepMap, we identified FAM126B as a specific vulnerability in CRC cell lines exhibiting low FAM126A expression. Employing a combination of genetic perturbation and inducible protein degradation techniques, we demonstrate that FAM126A and FAM126B function in a redundant manner to facilitate the recruitment of PI4KIIIα to the plasma membrane for PI4P synthesis. Examination of data from TCGA and GTEx revealed that over 7% of CRC tumor samples exhibited loss of FAM126A expression, contrasting with uniform FAM126A expression in normal tissues. In both CRC cell lines and tumor samples, promoter hypermethylation correlated with the loss of FAM126A expression, which could be reversed by DNA methylation inhibitors. In conclusion, our study reveals that loss of FAM126A expression results in FAM126B dependency, thus proposing FAM126B as a therapeutic target for CRC treatment.
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Affiliation(s)
- Shuang Li
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ting Han
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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6
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Yuan H, Liu RD, Gao ZY, Zhong LT, Zhou YC, Tan JH, Huang ZS, Li Z, Chen SB. Targeting ATP-binding site of WRN Helicase: Identification of novel inhibitors through pocket analysis and Molecular Dynamics-Enhanced virtual screening. Bioorg Med Chem Lett 2024; 104:129711. [PMID: 38521175 DOI: 10.1016/j.bmcl.2024.129711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
WRN helicase is a critical protein involved in maintaining genomic stability, utilizing ATP hydrolysis to dissolve DNA secondary structures. It has been identified as a promising synthetic lethal target for microsatellite instable (MSI) cancers. However, few WRN helicase inhibitors have been discovered, and their potential binding sites remain unexplored. In this study, we analyzed potential binding sites for WRN inhibitors and focused on the ATP-binding site for screening new inhibitors. Through molecular dynamics-enhanced virtual screening, we identified two compounds, h6 and h15, which effectively inhibited WRN's helicase and ATPase activity in vitro. Importantly, these compounds selectively targeted WRN's ATPase activity, setting them apart from other non-homologous proteins with ATPase activity. In comparison to the homologous protein BLM, h6 exhibits some degree of selectivity towards WRN. We also investigated the binding mode of these compounds to WRN's ATP-binding sites. These findings offer a promising strategy for discovering new WRN inhibitors and present two novel scaffolds, which might be potential for the development of MSI cancer treatment.
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Affiliation(s)
- Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Run-Duo Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuo-Yu Gao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Li-Ting Zhong
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Ying-Chen Zhou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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7
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Li H, Yu J, Yu G, Cheng S, Wu H, Wei J, You C, Liu K, Wang M, Meng X, Xu G, Luo H, Xu B. Design and synthesis of N-aryl-2-trifluoromethyl-quinazoline-4-amine derivatives as potential Werner-dependent antiproliferative agents. Mol Divers 2024:10.1007/s11030-024-10844-6. [PMID: 38739229 DOI: 10.1007/s11030-024-10844-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/08/2024] [Indexed: 05/14/2024]
Abstract
To discover new Werner (WRN) helicase inhibitors, a series of N-aryl-2-trifluoromethyl-quinazoline-4-amine derivatives were designed and synthesized through a structural optimization strategy, and the anticancer activities of 25 new target compounds against PC3, K562, and HeLa cell lines were evaluated by the MTT assay. Some of these compounds exhibited excellent inhibitory activity against three different cancer cell lines. Compounds 6a, 8i, and 13a showed better antiproliferative activity against K562 cells, with IC50 values of 3871.5, 613.6 and 134.7 nM, respectively, than did paclitaxel (35.6 nM), doxorubicin (2689.0 nM), and NSC 617145 (20.3 nM). To further verify whether the antiproliferative activity of these compounds is dependent on WRN, PC3 cells overexpressing WRN (PC3-WRN) were constructed to further study their antiproliferative potency in vitro, and the inhibition ratio and IC20 values showed that compounds 6a, 8i, and 13a were more sensitive to PC3-WRN than were the control group cells (PC3-NC). The IC20 ratios of compounds 6a, 8i, and 13a to PC3-NC and PC3-WRN were 94.3, 153.4 and 505.5, respectively. According to the docking results, the compounds 6a, 8i, and 13a overlapped well with the binding pocket of 6YHR. Further study demonstrated that among the tested compounds, 13a was the most sensitive to PC3-WRN. In summary, our research identified a series of N-aryl-2-trifluoromethyl-quinazoline-4-amine derivatives as potential WRN-dependent anticancer agents.
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Affiliation(s)
- Huimin Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, China
| | - Jia Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Gang Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Sha Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Hui Wu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Jiaomei Wei
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Chang You
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Kun Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Menghan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Xueling Meng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China
| | - Guangcan Xu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China.
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China.
| | - Heng Luo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China.
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China.
| | - Bixue Xu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China.
- Natural Products Research Center of Guizhou Province, Guiyang, 550014, China.
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8
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Ferretti S, Hamon J, de Kanter R, Scheufler C, Andraos-Rey R, Barbe S, Bechter E, Blank J, Bordas V, Dammassa E, Decker A, Di Nanni N, Dourdoigne M, Gavioli E, Hattenberger M, Heuser A, Hemmerlin C, Hinrichs J, Kerr G, Laborde L, Jaco I, Núñez EJ, Martus HJ, Quadt C, Reschke M, Romanet V, Schaeffer F, Schoepfer J, Schrapp M, Strang R, Voshol H, Wartmann M, Welly S, Zécri F, Hofmann F, Möbitz H, Cortés-Cros M. Discovery of WRN inhibitor HRO761 with synthetic lethality in MSI cancers. Nature 2024; 629:443-449. [PMID: 38658754 PMCID: PMC11078746 DOI: 10.1038/s41586-024-07350-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
The Werner syndrome RecQ helicase WRN was identified as a synthetic lethal target in cancer cells with microsatellite instability (MSI) by several genetic screens1-6. Despite advances in treatment with immune checkpoint inhibitors7-10, there is an unmet need in the treatment of MSI cancers11-14. Here we report the structural, biochemical, cellular and pharmacological characterization of the clinical-stage WRN helicase inhibitor HRO761, which was identified through an innovative hit-finding and lead-optimization strategy. HRO761 is a potent, selective, allosteric WRN inhibitor that binds at the interface of the D1 and D2 helicase domains, locking WRN in an inactive conformation. Pharmacological inhibition by HRO761 recapitulated the phenotype observed by WRN genetic suppression, leading to DNA damage and inhibition of tumour cell growth selectively in MSI cells in a p53-independent manner. Moreover, HRO761 led to WRN degradation in MSI cells but not in microsatellite-stable cells. Oral treatment with HRO761 resulted in dose-dependent in vivo DNA damage induction and tumour growth inhibition in MSI cell- and patient-derived xenograft models. These findings represent preclinical pharmacological validation of WRN as a therapeutic target in MSI cancers. A clinical trial with HRO761 (NCT05838768) is ongoing to assess the safety, tolerability and preliminary anti-tumour activity in patients with MSI colorectal cancer and other MSI solid tumours.
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Affiliation(s)
| | | | | | | | | | | | | | - Jutta Blank
- Novartis BioMedical Research, Basel, Switzerland
| | | | | | | | | | | | - Elena Gavioli
- Novartis BioMedical Research, Basel, Switzerland
- Novartis Pharma AG, Basel, Switzerland
| | | | - Alisa Heuser
- Novartis BioMedical Research, Basel, Switzerland
| | | | | | - Grainne Kerr
- Novartis BioMedical Research, Basel, Switzerland
| | | | - Isabel Jaco
- Novartis BioMedical Research, Basel, Switzerland
| | - Eloísa Jiménez Núñez
- Novartis BioMedical Research, Basel, Switzerland
- Pierre Fabre Laboratories, Toulouse, France
| | | | | | | | | | | | | | | | - Ross Strang
- Novartis BioMedical Research, Basel, Switzerland
| | - Hans Voshol
- Novartis BioMedical Research, Basel, Switzerland
| | | | - Sarah Welly
- Novartis BioMedical Research, Basel, Switzerland
| | | | - Francesco Hofmann
- Novartis BioMedical Research, Basel, Switzerland
- Pierre Fabre Laboratories, Toulouse, France
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9
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Baltgalvis KA, Lamb KN, Symons KT, Wu CC, Hoffman MA, Snead AN, Song X, Glaza T, Kikuchi S, Green JC, Rogness DC, Lam B, Rodriguez-Aguirre ME, Woody DR, Eissler CL, Rodiles S, Negron SM, Bernard SM, Tran E, Pollock J, Tabatabaei A, Contreras V, Williams HN, Pastuszka MK, Sigler JJ, Pettazzoni P, Rudolph MG, Classen M, Brugger D, Claiborne C, Plancher JM, Cuartas I, Seoane J, Burgess LE, Abraham RT, Weinstein DS, Simon GM, Patricelli MP, Kinsella TM. Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase. Nature 2024; 629:435-442. [PMID: 38658751 DOI: 10.1038/s41586-024-07318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
WRN helicase is a promising target for treatment of cancers with microsatellite instability (MSI) due to its essential role in resolving deleterious non-canonical DNA structures that accumulate in cells with faulty mismatch repair mechanisms1-5. Currently there are no approved drugs directly targeting human DNA or RNA helicases, in part owing to the challenging nature of developing potent and selective compounds to this class of proteins. Here we describe the chemoproteomics-enabled discovery of a clinical-stage, covalent allosteric inhibitor of WRN, VVD-133214. This compound selectively engages a cysteine (C727) located in a region of the helicase domain subject to interdomain movement during DNA unwinding. VVD-133214 binds WRN protein cooperatively with nucleotide and stabilizes compact conformations lacking the dynamic flexibility necessary for proper helicase function, resulting in widespread double-stranded DNA breaks, nuclear swelling and cell death in MSI-high (MSI-H), but not in microsatellite-stable, cells. The compound was well tolerated in mice and led to robust tumour regression in multiple MSI-H colorectal cancer cell lines and patient-derived xenograft models. Our work shows an allosteric approach for inhibition of WRN function that circumvents competition from an endogenous ATP cofactor in cancer cells, and designates VVD-133214 as a promising drug candidate for patients with MSI-H cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Betty Lam
- Vividion Therapeutics, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Piergiorgio Pettazzoni
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Markus G Rudolph
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Moritz Classen
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Doris Brugger
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Christopher Claiborne
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Jean-Marc Plancher
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Isabel Cuartas
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | | | - Robert T Abraham
- Vividion Therapeutics, San Diego, CA, USA
- Odyssey Therapeutics, San Diego, CA, USA
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10
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Pytko KG, Dannenberg RL, Eckert KA, Hedglin M. Replication of [AT/TA] 25 Microsatellite Sequences by Human DNA Polymerase δ Holoenzymes Is Dependent on dNTP and RPA Levels. Biochemistry 2024; 63:969-983. [PMID: 38623046 DOI: 10.1021/acs.biochem.4c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Fragile sites are unstable genomic regions that are prone to breakage during stressed DNA replication. Several common fragile sites (CFS) contain A+T-rich regions including perfect [AT/TA] microsatellite repeats that may collapse into hairpins when in single-stranded DNA (ssDNA) form and coincide with chromosomal hotspots for breakage and rearrangements. While many factors contribute to CFS instability, evidence exists for replication stalling within [AT/TA] microsatellite repeats. Currently, it is unknown how stress causes replication stalling within [AT/TA] microsatellite repeats. To investigate this, we utilized FRET to characterize the structures of [AT/TA]25 sequences and also reconstituted lagging strand replication to characterize the progression of pol δ holoenzymes through A+T-rich sequences. The results indicate that [AT/TA]25 sequences adopt hairpins that are unwound by the major ssDNA-binding complex, RPA, and the progression of pol δ holoenzymes through A+T-rich sequences saturated with RPA is dependent on the template sequence and dNTP concentration. Importantly, the effects of RPA on the replication of [AT/TA]25 sequences are dependent on dNTP concentration, whereas the effects of RPA on the replication of A+T-rich, nonstructure-forming sequences are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how [AT/TA] microsatellite repeats contribute to genome instability.
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Affiliation(s)
- Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kristin A Eckert
- Department of Pathology and Laboratory Medicine, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, United States
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
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11
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Heuser A, Abdul Rahman W, Bechter E, Blank J, Buhr S, Erdmann D, Fontana P, Mermet-Meillon F, Meyerhofer M, Strang R, Schrapp M, Zimmermann C, Cortes-Cros M, Möbitz H, Hamon J. Challenges for the Discovery of Non-Covalent WRN Helicase Inhibitors. ChemMedChem 2024; 19:e202300613. [PMID: 38334957 DOI: 10.1002/cmdc.202300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
The Werner Syndrome RecQ helicase (WRN) is a synthetic lethal target of interest for the treatment of cancers with microsatellite instability (MSI). Different hit finding approaches were initially tested. The identification of WRN inhibitors proved challenging due to a high propensity for artefacts via protein interference, i. e., hits inhibiting WRN enzymatic activities through multiple, unspecific mechanisms. Previously published WRN Helicase inhibitors (ML216, NSC19630 or NSC617145) were characterized in an extensive set of biochemical and biophysical assays and could be ruled out as specific WRN helicase probes. More innovative screening strategies need to be developed for successful drug discovery of non-covalent WRN helicase inhibitors.
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Affiliation(s)
- Alisa Heuser
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | | | - Elisabeth Bechter
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Jutta Blank
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Sylvia Buhr
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Dirk Erdmann
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Patrizia Fontana
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | | | - Marco Meyerhofer
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Ross Strang
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Maxime Schrapp
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | | | - Marta Cortes-Cros
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Henrik Möbitz
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
| | - Jacques Hamon
- Novartis Biomedical Research, Novartis Campus, CH-4056, Basel, Switzerland
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12
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Ding XH, Xiao Y, Chen F, Liu CL, Fu T, Shao ZM, Jiang YZ. The HLA-I landscape confers prognosis and antitumor immunity in breast cancer. Brief Bioinform 2024; 25:bbae151. [PMID: 38602320 PMCID: PMC11007120 DOI: 10.1093/bib/bbae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Breast cancer is a highly heterogeneous disease with varied subtypes, prognoses and therapeutic responsiveness. Human leukocyte antigen class I (HLA-I) shapes the immunity and thereby influences the outcome of breast cancer. However, the implications of HLA-I variations in breast cancer remain poorly understood. In this study, we established a multiomics cohort of 1156 Chinese breast cancer patients for HLA-I investigation. We calculated four important HLA-I indicators in each individual, including HLA-I expression level, somatic HLA-I loss of heterozygosity (LOH), HLA-I evolutionary divergence (HED) and peptide-binding promiscuity (Pr). Then, we evaluated their distribution and prognostic significance in breast cancer subtypes. We found that the four breast cancer subtypes had distinct features of HLA-I indicators. Increased expression of HLA-I and LOH were enriched in triple-negative breast cancer (TNBC), while Pr was relatively higher in hot tumors within TNBCs. In particular, a higher Pr indicated a better prognosis in TNBCs by regulating the infiltration of immune cells and the expression of immune molecules. Using the matched genomic and transcriptomic data, we found that mismatch repair deficiency-related mutational signature and pathways were enriched in low-Pr TNBCs, suggesting that targeting mismatch repair deficiency for synthetic lethality might be promising therapy for these patients. In conclusion, we presented an overview of HLA-I indicators in breast cancer and provided hints for precision treatment for low-Pr TNBCs.
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Affiliation(s)
- Xiao-Hong Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Fenfang Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
| | - Cheng-Lin Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
| | - Tong Fu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
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13
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes. Nat Commun 2024; 15:2370. [PMID: 38499542 PMCID: PMC10948877 DOI: 10.1038/s41467-024-45909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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Affiliation(s)
- Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexandrea Becker
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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14
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Yang H, Kang M, Jang S, Baek SY, Kim J, Kim GU, Kim D, Ha J, Kim JS, Jung C, Kim NJ, Cho SY, Shin WH, Lee J, Ko J, Lee A, Keum G, Lee S, Kang T. Discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for treating cancers with microsatellite instability. Bioorg Med Chem 2024; 100:117588. [PMID: 38295487 DOI: 10.1016/j.bmc.2024.117588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/23/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
Microsatellite instability (MSI) is a hypermutable condition caused by DNA mismatch repair system defects, contributing to the development of various cancer types. Recent research has identified Werner syndrome ATP-dependent helicase (WRN) as a promising synthetic lethal target for MSI cancers. Herein, we report the first discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for MSI cancer therapy. Initial computational analysis and biological evaluation identified a new scaffold for a WRN inhibitor. Subsequent SAR study led to the discovery of a highly potent WRN inhibitor. Furthermore, we demonstrated that the optimal compound induced DNA damage and apoptotic cell death in MSI cancer cells by inhibiting WRN. This study provides a new pharmacophore for WRN inhibitors, emphasizing their therapeutic potential for MSI cancers.
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Affiliation(s)
- Hwasun Yang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Miso Kang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Fundamental Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Seonyeong Jang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Soo Yeon Baek
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jiwon Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Gyeong Un Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Dongwoo Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsu Ha
- Arontier Co., Ltd., Seoul 06735, Republic of Korea
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Nam-Jung Kim
- Department of Fundamental Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung-Yup Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
| | - Woong-Hee Shin
- Arontier Co., Ltd., Seoul 06735, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Juyong Lee
- Arontier Co., Ltd., Seoul 06735, Republic of Korea; Research Institute of Pharmaceutical Science, Seoul National University, Seoul 08826, Republic of Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsu Ko
- Arontier Co., Ltd., Seoul 06735, Republic of Korea
| | - Ansoo Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Gyochang Keum
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Sanghee Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department for HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea.
| | - Taek Kang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
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15
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Gadgil RY, Rider SD, Shrestha R, Alhawach V, Hitch DC, Leffak M. Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575055. [PMID: 38260482 PMCID: PMC10802558 DOI: 10.1101/2024.01.12.575055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. In tumors, highly transcribed eccDNAs have been implicated in oncogenesis, neoantigen production and resistance to chemotherapy. Here we show that unstable microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures generate eccDNAs when integrated at a common ectopic site in human cells. These non-B DNA prone microsatellites form eccDNAs by replication-dependent mechanisms. The microsatellite-based eccDNAs are highly mutagenized and display template switches to sister chromatids and to nonallelic chromosomal sites. High frequency mutagenesis occurs within the eccDNA microsatellites and extends bidirectionally for several kilobases into flanking DNA and nonallelic DNA. Mutations include mismatches, short duplications, longer nontemplated insertions and large deletions. Template switching leads to recurrent deletions and recombination domains within the eccDNAs. Template switching events are microhomology-mediated, but do not occur at all potential sites of complementarity. Each microsatellite exhibits a distinct pattern of recombination, microhomology choice and base substitution signature. Depletion of Rad51, the COPS2 signalosome subunit or POLη alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA breaks for the generation and circularization of mutagenized eccDNAs and genomic homologous recombination deficiency (HRD) scars.
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16
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Mackay HL, Stone HR, Ellis K, Ronson GE, Walker AK, Starowicz K, Garvin AJ, van Eijk P, Vaitsiankova A, Vijayendran S, Beesley JF, Petermann E, Brown EJ, Densham RM, Reed SH, Dobbs F, Saponaro M, Morris JR. USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574674. [PMID: 38260523 PMCID: PMC10802463 DOI: 10.1101/2024.01.10.574674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mammalian DNA replication employs several RecQ DNA helicases to orchestrate the faithful duplication of genetic information. Helicase function is often coupled to the activity of specific nucleases, but how helicase and nuclease activities are co-directed is unclear. Here we identify the inactive ubiquitin-specific protease, USP50, as a ubiquitin-binding and chromatin-associated protein required for ongoing replication, fork restart, telomere maintenance and cellular survival during replicative stress. USP50 supports WRN:FEN1 at stalled replication forks, suppresses MUS81-dependent fork collapse and restricts double-strand DNA breaks at GC-rich sequences. Surprisingly we find that cells depleted for USP50 and recovering from a replication block exhibit increased DNA2 and RECQL4 foci and that the defects in ongoing replication, poor fork restart and increased fork collapse seen in these cells are mediated by DNA2, RECQL4 and RECQL5. These data define a novel ubiquitin-dependent pathway that promotes the balance of helicase: nuclease use at ongoing and stalled replication forks.
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17
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Ramsey JR, Shelton PM, Heiss TK, Olinares PDB, Vostal LE, Soileau H, Grasso M, Casebeer SW, Adaniya S, Miller M, Sun S, Huggins DJ, Myers RW, Chait BT, Vinogradova EV, Kapoor TM. Using a Function-First "Scout Fragment"-Based Approach to Develop Allosteric Covalent Inhibitors of Conformationally Dynamic Helicase Mechanoenzymes. J Am Chem Soc 2024; 146:62-67. [PMID: 38134034 PMCID: PMC10958666 DOI: 10.1021/jacs.3c10581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Helicases, classified into six superfamilies, are mechanoenzymes that utilize energy derived from ATP hydrolysis to remodel DNA and RNA substrates. These enzymes have key roles in diverse cellular processes, such as translation, ribosome assembly, and genome maintenance. Helicases with essential functions in certain cancer cells have been identified, and helicases expressed by many viruses are required for their pathogenicity. Therefore, helicases are important targets for chemical probes and therapeutics. However, it has been very challenging to develop chemical inhibitors for helicases, enzymes with high conformational dynamics. We envisioned that electrophilic "scout fragments", which have been used in chemical proteomic studies, could be leveraged to develop covalent inhibitors of helicases. We adopted a function-first approach, combining enzymatic assays with enantiomeric probe pairs and mass spectrometry, to develop a covalent inhibitor that selectively targets an allosteric site in SARS-CoV-2 nsp13, a superfamily-1 helicase. Further, we demonstrate that scout fragments inhibit the activity of two human superfamily-2 helicases, BLM and WRN, involved in genome maintenance. Together, our findings suggest an approach to discover covalent inhibitor starting points and druggable allosteric sites in conformationally dynamic mechanoenzymes.
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Affiliation(s)
- Jared R. Ramsey
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, United States
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Patrick M.M Shelton
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Tyler K. Heiss
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Paul Dominic B. Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, United States
| | - Lauren E. Vostal
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, United States
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Heather Soileau
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, United States
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Michael Grasso
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Sara W. Casebeer
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
| | - Stephanie Adaniya
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY 10065, United States
| | - Michael Miller
- Sanders Tri-Institutional Therapeutics Discovery Institute, New York, NY 10065, United States
| | - Shan Sun
- Sanders Tri-Institutional Therapeutics Discovery Institute, New York, NY 10065, United States
| | - David J. Huggins
- Sanders Tri-Institutional Therapeutics Discovery Institute, New York, NY 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Robert W. Myers
- Sanders Tri-Institutional Therapeutics Discovery Institute, New York, NY 10065, United States
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, United States
| | - Ekaterina V. Vinogradova
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, United States
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY 10065, United States
| | - Tarun M. Kapoor
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, United States
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, United States
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18
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Liang Y, Yuan Q, Zheng Q, Mei Z, Song Y, Yan H, Yang J, Wu S, Yuan J, Wu W. DNA Damage Atlas: an atlas of DNA damage and repair. Nucleic Acids Res 2024; 52:D1218-D1226. [PMID: 37831087 PMCID: PMC10767978 DOI: 10.1093/nar/gkad845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/06/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
DNA damage and its improper repair are the major source of genomic alterations responsible for many human diseases, particularly cancer. To aid researchers in understanding the underlying mechanisms of genome instability, a number of genome-wide profiling approaches have been developed to monitor DNA damage and repair events. The rapid accumulation of published datasets underscores the critical necessity of a comprehensive database to curate sequencing data on DNA damage and repair intermediates. Here, we present DNA Damage Atlas (DDA, http://www.bioinformaticspa.com/DDA/), the first large-scale repository of DNA damage and repair information. Currently, DDA comprises 6,030 samples from 262 datasets by 59 technologies, covering 16 species, 10 types of damage and 135 treatments. Data collected in DDA was processed through a standardized workflow, including quality checks, hotspots identification and a series of feature characterization for the hotspots. Notably, DDA encompasses analyses of highly repetitive regions, ribosomal DNA and telomere. DDA offers a user-friendly interface that facilitates browsing, searching, genome browser visualization, hotspots comparison and data downloading, enabling convenient and thorough exploration for datasets of interest. In summary, DDA will stand as a valuable resource for research in genome instability and its association with diseases.
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Affiliation(s)
- Yu Liang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qingqing Yuan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qijie Zheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Zilv Mei
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Yawei Song
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Huan Yan
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Jiajie Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Shuheng Wu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Jiao Yuan
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Wei Wu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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19
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Muyas F, Rodriguez MJG, Cascão R, Afonso A, Sauer CM, Faria CC, Cortés-Ciriano I, Flores I. The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients. Nat Commun 2024; 15:82. [PMID: 38167290 PMCID: PMC10762111 DOI: 10.1038/s41467-023-44287-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Rita Cascão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Angela Afonso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Claudia C Faria
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisboa, Portugal
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
| | - Ignacio Flores
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, 28029, Spain.
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, 28049, Spain.
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20
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Irony-Tur Sinai M, Kerem B. Insights into common fragile site instability: DNA replication challenges at DNA repeat sequences. Emerg Top Life Sci 2023; 7:277-287. [PMID: 37876349 PMCID: PMC10754330 DOI: 10.1042/etls20230023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Common fragile sites (CFS) are specific genomic regions prone to chromosomal instability under conditions of DNA replication stress. CFSs manifest as breaks, gaps, and constrictions on metaphase chromosomes under mild replication stress. These replication-sensitive CFS regions are preferentially unstable during cancer development, as reflected by their association with copy number variants (CNVs) frequently arise in most tumor types. Over the years, it became clear that a combination of different characteristics underlies the enhanced sensitivity of CFSs to replication stress. As of today, there is a strong evidence that the core fragility regions along CFSs overlap with actively transcribed large genes with delayed replication timing upon replication stress. Recently, the mechanistic basis for CFS instability was further extended to regions which span topologically associated domain (TAD) boundaries, generating a fragility signature composed of replication, transcription and genome organization. The presence of difficult-to-replicate AT-rich repeats was one of the early features suggested to characterize a subgroup of CFSs. These long stretches of AT-dinucleotide have the potential to fold into stable secondary structures which may impede replication fork progression, leaving the region under-replicated. Here, we focus on the molecular mechanisms underlying repeat instability at CFSs and on the proteins involved in the resolution of secondary structure impediments arising along repetitive sequence elements which are essential for the maintenance of genome stability.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
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21
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Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
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22
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Pytko KG, Dannenberg RL, Eckert KA, Hedglin M. Replication of [AT/TA] 25 microsatellite sequences by human DNA polymerase δ holoenzymes is dependent on dNTP and RPA levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566133. [PMID: 37986888 PMCID: PMC10659299 DOI: 10.1101/2023.11.07.566133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Difficult-to-Replicate Sequences (DiToRS) are natural impediments in the human genome that inhibit DNA replication under endogenous replication. Some of the most widely-studied DiToRS are A+T-rich, high "flexibility regions," including long stretches of perfect [AT/TA] microsatellite repeats that have the potential to collapse into hairpin structures when in single-stranded DNA (ssDNA) form and are sites of recurrent structural variation and double-stranded DNA (dsDNA) breaks. Currently, it is unclear how these flexibility regions impact DNA replication, greatly limiting our fundamental understanding of human genome stability. To investigate replication through flexibility regions, we utilized FRET to characterize the effects of the major ssDNA-binding complex, RPA, on the structure of perfect [AT/TA]25 microsatellite repeats and also re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with A+T-rich DNA template sequences. The results indicate that [AT/TA]25 sequences adopt hairpin structures that are unwound by RPA and pol δ holoenzymes support dNTP incorporation through the [AT/TA]25 sequences as well as an A+T-rich, non-structure forming sequence. Furthermore, the extent of dNTP incorporation is dependent on the sequence of the DNA template and the concentration of dNTPs. Importantly, the effects of RPA on the replication of [AT/TA]25 sequences are dependent on the concentration of dNTPs, whereas the effects of RPA on the replication of an A+T-rich, non-structure forming sequence are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how flexibility regions contribute to genome instability.
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Affiliation(s)
- Kara G. Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Rachel L. Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Kristin A. Eckert
- Department of Pathology and Laboratory Medicine, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
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23
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Matos-Rodrigues G, Hisey JA, Nussenzweig A, Mirkin SM. Detection of alternative DNA structures and its implications for human disease. Mol Cell 2023; 83:3622-3641. [PMID: 37863029 DOI: 10.1016/j.molcel.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/22/2023]
Abstract
Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.
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Affiliation(s)
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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24
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Bhamidipati D, Subbiah V. Tumor-agnostic drug development in dMMR/MSI-H solid tumors. Trends Cancer 2023; 9:828-839. [PMID: 37517955 DOI: 10.1016/j.trecan.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Mismatch repair deficiency (dMMR) or microsatellite instability-high (MSI-H) represents a distinct phenotype among solid tumors characterized by frequent frameshift mutations resulting in the generation of neoantigens that are highly immunogenic. Seminal studies identified that dMMR/MSI-H tumors are exquisitely sensitive to immune checkpoint inhibitors, which has dramatically improved outcomes for patients harboring dMMR/MSI-H tumors. Nevertheless, many patients develop resistance to single-agent immune checkpoint blockade, prompting the need for improved therapeutic options for this patient population. In this review, we highlight key studies examining the efficacy of PD1 inhibitors in the metastatic and neoadjuvant setting for patients with dMMR/MSI-H tumors, describe resistance mechanisms to immune checkpoint blockade, and discuss novel treatment approaches that are currently under investigation for dMMR/MSI-H tumors.
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Affiliation(s)
- Deepak Bhamidipati
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, TN, USA.
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25
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Wang M, Ran X, Leung W, Kawale A, Saxena S, Ouyang J, Patel PS, Dong Y, Yin T, Shu J, Manguso RT, Lan L, Wang XF, Lawrence MS, Zou L. ATR inhibition induces synthetic lethality in mismatch repair-deficient cells and augments immunotherapy. Genes Dev 2023; 37:929-943. [PMID: 37932012 PMCID: PMC10691477 DOI: 10.1101/gad.351084.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
The mismatch repair (MMR) deficiency of cancer cells drives mutagenesis and offers a useful biomarker for immunotherapy. However, many MMR-deficient (MMR-d) tumors do not respond to immunotherapy, highlighting the need for alternative approaches to target MMR-d cancer cells. Here, we show that inhibition of the ATR kinase preferentially kills MMR-d cancer cells. Mechanistically, ATR inhibitor (ATRi) imposes synthetic lethality on MMR-d cells by inducing DNA damage in a replication- and MUS81 nuclease-dependent manner. The DNA damage induced by ATRi is colocalized with both MSH2 and PCNA, suggesting that it arises from DNA structures recognized by MMR proteins during replication. In syngeneic mouse models, ATRi effectively reduces the growth of MMR-d tumors. Interestingly, the antitumor effects of ATRi are partially due to CD8+ T cells. In MMR-d cells, ATRi stimulates the accumulation of nascent DNA fragments in the cytoplasm, activating the cGAS-mediated interferon response. The combination of ATRi and anti-PD-1 antibody reduces the growth of MMR-d tumors more efficiently than ATRi or anti-PD-1 alone, showing the ability of ATRi to augment the immunotherapy of MMR-d tumors. Thus, ATRi selectively targets MMR-d tumor cells by inducing synthetic lethality and enhancing antitumor immunity, providing a promising strategy to complement and augment MMR deficiency-guided immunotherapy.
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Affiliation(s)
- Mingchao Wang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Xiaojuan Ran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Wendy Leung
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Ajinkya Kawale
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Parasvi S Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Yuting Dong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Tao Yin
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Jian Shu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Robert T Manguso
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Xiao-Fan Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA;
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27708, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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26
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Zong D, Koussa NC, Cornwell JA, Pankajam AV, Kruhlak MJ, Wong N, Chari R, Cappell SD, Nussenzweig A. Comprehensive mapping of cell fates in microsatellite unstable cancer cells supports dual targeting of WRN and ATR. Genes Dev 2023; 37:913-928. [PMID: 37932011 PMCID: PMC10691471 DOI: 10.1101/gad.351085.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
Addiction to the WRN helicase is a unique vulnerability of human cancers with high levels of microsatellite instability (MSI-H). However, while prolonged loss of WRN ultimately leads to cell death, little is known about how MSI-H cancers initially respond to acute loss of WRN-knowledge that would be helpful for informing clinical development of WRN targeting therapy, predicting possible resistance mechanisms, and identifying useful biomarkers of successful WRN inhibition. Here, we report the construction of an inducible ligand-mediated degradation system in which the stability of endogenous WRN protein can be rapidly and specifically tuned, enabling us to track the complete sequence of cellular events elicited by acute loss of WRN function. We found that WRN degradation leads to immediate accrual of DNA damage in a replication-dependent manner that curiously did not robustly engage checkpoint mechanisms to halt DNA synthesis. As a result, WRN-degraded MSI-H cancer cells accumulate DNA damage across multiple replicative cycles and undergo successive rounds of increasingly aberrant mitoses, ultimately triggering cell death. Of potential therapeutic importance, we found no evidence of any generalized mechanism by which MSI-H cancers could adapt to near-complete loss of WRN. However, under conditions of partial WRN degradation, addition of low-dose ATR inhibitor significantly increased their combined efficacy to levels approaching full inactivation of WRN. Overall, our results provide the first comprehensive view of molecular events linking upstream inhibition of WRN to subsequent cell death and suggest that dual targeting of WRN and ATR might be a useful strategy for treating MSI-H cancers.
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Affiliation(s)
- Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Natasha C Koussa
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James A Cornwell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ajith V Pankajam
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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27
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Ramsey JR, Shelton PMM, Heiss TK, Olinares PDB, Vostal LE, Soileau H, Grasso M, Warrington S, Adaniya S, Miller M, Sun S, Huggins DJ, Myers RW, Chait BT, Vinogradova EV, Kapoor TM. Using a function-first 'scout fragment'-based approach to develop allosteric covalent inhibitors of conformationally dynamic helicase mechanoenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559391. [PMID: 37808863 PMCID: PMC10557574 DOI: 10.1101/2023.09.25.559391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Helicases, classified into six superfamilies, are mechanoenzymes that utilize energy derived from ATP hydrolysis to remodel DNA and RNA substrates. These enzymes have key roles in diverse cellular processes, such as genome replication and maintenance, ribosome assembly and translation. Helicases with essential functions only in certain cancer cells have been identified and helicases expressed by certain viruses are required for their pathogenicity. As a result, helicases are important targets for chemical probes and therapeutics. However, it has been very challenging to develop selective chemical inhibitors for helicases, enzymes with highly dynamic conformations. We envisioned that electrophilic 'scout fragments', which have been used for chemical proteomic based profiling, could be leveraged to develop covalent inhibitors of helicases. We adopted a function-first approach, combining enzymatic assays with enantiomeric probe pairs and mass spectrometry, to develop a covalent inhibitor that selectively targets an allosteric site in SARS-CoV-2 nsp13, a superfamily-1 helicase. Further, we demonstrate that scout fragments inhibit the activity of two human superfamily-2 helicases, BLM and WRN, involved in genome maintenance. Together, our findings suggest a covalent inhibitor discovery approach to target helicases and potentially other conformationally dynamic mechanoenzymes.
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28
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Li Q, Qian W, Zhang Y, Hu L, Chen S, Xia Y. A new wave of innovations within the DNA damage response. Signal Transduct Target Ther 2023; 8:338. [PMID: 37679326 PMCID: PMC10485079 DOI: 10.1038/s41392-023-01548-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 09/09/2023] Open
Abstract
Genome instability has been identified as one of the enabling hallmarks in cancer. DNA damage response (DDR) network is responsible for maintenance of genome integrity in cells. As cancer cells frequently carry DDR gene deficiencies or suffer from replicative stress, targeting DDR processes could induce excessive DNA damages (or unrepaired DNA) that eventually lead to cell death. Poly (ADP-ribose) polymerase (PARP) inhibitors have brought impressive benefit to patients with breast cancer gene (BRCA) mutation or homologous recombination deficiency (HRD), which proves the concept of synthetic lethality in cancer treatment. Moreover, the other two scenarios of DDR inhibitor application, replication stress and combination with chemo- or radio- therapy, are under active clinical exploration. In this review, we revisited the progress of DDR targeting therapy beyond the launched first-generation PARP inhibitors. Next generation PARP1 selective inhibitors, which could maintain the efficacy while mitigating side effects, may diversify the application scenarios of PARP inhibitor in clinic. Albeit with unavoidable on-mechanism toxicities, several small molecules targeting DNA damage checkpoints (gatekeepers) have shown great promise in preliminary clinical results, which may warrant further evaluations. In addition, inhibitors for other DNA repair pathways (caretakers) are also under active preclinical or clinical development. With these progresses and efforts, we envision that a new wave of innovations within DDR has come of age.
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Affiliation(s)
- Qi Li
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Wenyuan Qian
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Yang Zhang
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Lihong Hu
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Shuhui Chen
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Yuanfeng Xia
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China.
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29
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Guan J, Li GM. DNA mismatch repair in cancer immunotherapy. NAR Cancer 2023; 5:zcad031. [PMID: 37325548 PMCID: PMC10262306 DOI: 10.1093/narcan/zcad031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
Tumors defective in DNA mismatch repair (dMMR) exhibit microsatellite instability (MSI). Currently, patients with dMMR tumors are benefitted from anti-PD-1/PDL1-based immune checkpoint inhibitor (ICI) therapy. Over the past several years, great progress has been made in understanding the mechanisms by which dMMR tumors respond to ICI, including the identification of mutator phenotype-generated neoantigens, cytosolic DNA-mediated activation of the cGAS-STING pathway, type-I interferon signaling and high tumor-infiltration of lymphocytes in dMMR tumors. Although ICI therapy shows great clinical benefits, ∼50% of dMMR tumors are eventually not responsive. Here we review the discovery, development and molecular basis of dMMR-mediated immunotherapy, as well as tumor resistant problems and potential therapeutic interventions to overcome the resistance.
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Affiliation(s)
- Junhong Guan
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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30
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Zong D, Koussa NC, Cornwell JA, Pankajam AV, Kruhlak MJ, Wong N, Chari R, Cappell SD, Nussenzweig A. Comprehensive mapping of cell fates in microsatellite unstable cancer cells support dual targe6ng of WRN and ATR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550976. [PMID: 37662356 PMCID: PMC10473727 DOI: 10.1101/2023.07.28.550976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Addiction to the WRN helicase is a unique vulnerability of human cancers with high levels of microsatellite instability (MSI-H). However, while prolonged loss of WRN ultimately leads to cell death, little is known about how MSI-H cancers initially respond to acute loss of WRN, knowledge that would be helpful for informing clinical development of WRN-targeting therapy, predicting possible resistance mechanisms, and identifying useful biomarkers of successful WRN inhibition. Here, we report the construction of an inducible ligand-mediated degradation system wherein the stability of endogenous WRN protein can be rapidly and specifically tuned, enabling us to track the complete sequence of cellular events elicited by acute loss of WRN function. We find that WRN degradation leads to immediate accrual of DNA damage in a replication-dependent manner that curiously did not robustly engage checkpoint mechanisms to halt DNA synthesis. As a result, WRN-degraded MSI-H cancer cells accumulate DNA damage across multiple replicative cycles and undergo successive rounds of increasingly aberrant mitoses, ultimately triggering cell death. Of potential therapeutic importance, we find no evidence of any generalized mechanism by which MSI-H cancers could adapt to near-complete loss of WRN. However, under conditions of partial WRN degradation, addition of low dose ATR inhibitor significantly increased their combined efficacy to levels approaching full inactivation of WRN. Overall, our results provided the first comprehensive view of molecular events linking upstream inhibition of WRN to subsequent cell death and suggested a potential therapeutical rationale for dual targeting of WRN and ATR.
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Affiliation(s)
- Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Natasha C. Koussa
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A. Cornwell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ajith V. Pankajam
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael J. Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Steven D. Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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31
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Ye T, Lin A, Qiu Z, Hu S, Zhou C, Liu Z, Cheng Q, Zhang J, Luo P. Microsatellite instability states serve as predictive biomarkers for tumors chemotherapy sensitivity. iScience 2023; 26:107045. [PMID: 37448561 PMCID: PMC10336167 DOI: 10.1016/j.isci.2023.107045] [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: 09/24/2022] [Revised: 03/17/2023] [Accepted: 06/01/2023] [Indexed: 07/15/2023] Open
Abstract
There is an urgent need for markers to predict the efficacy of different chemotherapy drugs. Herein, we examined whether microsatellite instability (MSI) status can predict tumor multidrug sensitivity and explored the underlying mechanisms. We downloaded data from several public databases. Drug sensitivity was compared between the high microsatellite instability (MSI-H) and microsatellite-stable/low microsatellite instability (MSS/MSI-L) groups. In addition, we performed pathway enrichment analysis and cellular chemosensitivity assays to explore the mechanisms by which MSI status may affect drug sensitivity and assessed the differences between drug-treated and control cell lines. We found that multiple MSI-H tumors were more sensitive to a variety of chemotherapy drugs than MSS/MSI-L tumors, and especially for CRC, chemosensitivity is enhanced through the downregulation of DDR pathways such as NHEJ. Additional DNA damage caused by chemotherapeutic drugs results in further downregulation of DDR pathways and enhances drug sensitivity, forming a cycle of increasing drug sensitivity.
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Affiliation(s)
- Taojun Ye
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhengang Qiu
- The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Shulu Hu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Chaozheng Zhou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Zaoqu Liu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Quan Cheng
- Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- The First Clinical Medical School, Southern Medical University, Guangzhou, Guangdong, China
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32
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Sakurada-Aono M, Sakamoto T, Kobayashi M, Takiuchi Y, Iwai F, Tada K, Sasanuma H, Hirabayashi S, Murakawa Y, Shirakawa K, Sakamoto C, Shindo K, Yasunaga JI, Matsuoka M, Pommier Y, Takeda S, Takaori-Kondo A. HTLV-1 bZIP factor impairs DNA mismatch repair system. Biochem Biophys Res Commun 2023; 657:43-49. [PMID: 36972660 PMCID: PMC10115849 DOI: 10.1016/j.bbrc.2023.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Adult T-cell leukemia (ATL) is a peripheral T-cell malignancy caused by human T-cell leukemia virus type 1 (HTLV-1). Microsatellite instability (MSI) has been observed in ATL cells. Although MSI results from impaired mismatch repair (MMR) pathway, no null mutations in the genes encoding MMR factors are detectable in ATL cells. Thus, it is unclear whether or not impairment of MMR causes the MSI in ATL cells. HTLV-1 bZIP factor (HBZ) protein interacts with numerous host transcription factors and significantly contributes to disease pathogenesis and progression. Here we investigated the effect of HBZ on MMR in normal cells. The ectopic expression of HBZ in MMR-proficient cells induced MSI, and also suppressed the expression of several MMR factors. We then hypothesized that the HBZ compromises MMR by interfering with a transcription factor, nuclear respiratory factor 1 (NRF-1), and identified the consensus NRF-1 binding site at the promoter of the gene encoding MutS homologue 2 (MSH2), an essential MMR factor. The luciferase reporter assay revealed that NRF-1 overexpression enhanced MSH2 promoter activity, while co-expression of HBZ reversed this enhancement. These results supported the idea that HBZ suppresses the transcription of MSH2 by inhibiting NRF-1. Our data demonstrate that HBZ causes impaired MMR, and may imply a novel oncogenesis driven by HTLV-1.
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Affiliation(s)
- Maki Sakurada-Aono
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takashi Sakamoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yoko Takiuchi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Fumie Iwai
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Kohei Tada
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Shigeki Hirabayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; IFOM ETS-the AIRC Institute of Molecular Oncology, 20139, Milan, MI, Italy
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Chihiro Sakamoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Jun-Ichirou Yasunaga
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; Shenzhen University School of Medicine, 1066, Xueyuan BLV, Shenzhen, Guangdong, China
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
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33
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Wang JE, Zhou YC, Wu BH, Chen XC, Zhai J, Tan JH, Huang ZS, Chen SB. A rapid and highly sensitive immunosorbent assay to monitor helicases unwinding diverse nucleic acid structures. Analyst 2023; 148:2343-2351. [PMID: 37185609 DOI: 10.1039/d2an01989b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Helicases are crucial enzymes in DNA and RNA metabolism and function by unwinding particular nucleic acid structures. However, most convenient and high-throughput helicase assays are limited to the typical duplex DNA. Herein, we developed an immunosorbent assay to monitor the Werner syndrome (WRN) helicase unwinding a wide range of DNA structures, such as a replication fork, a bubble, Holliday junction, G-quadruplex and hairpin. This assay could sensitively detect the unwinding of DNA structures with detection limits around 0.1 nM, and accurately monitor the substrate-specificity of WRN with a comparatively less time-consuming and high throughput process. Remarkably, we have established that this new assay was compatible in evaluating helicase inhibitors and revealed that the inhibitory effect was substrate-dependent, suggesting that diverse substrate structures other than duplex structures should be considered in discovering new inhibitors. Our study provided a foundational example for using this new assay as a powerful tool to study helicase functions and discover potent inhibitors.
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Affiliation(s)
- Jia-En Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Ying-Chen Zhou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Bi-Han Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Xiu-Cai Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Junqiu Zhai
- Guangzhou University of Chinese Medicine, Guangzhou, Guangzhou 510330, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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34
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Maeda Y, Koshizaka M, Shoji M, Kaneko H, Kato H, Maezawa Y, Kawashima J, Yoshinaga K, Ishikawa M, Sekiguchi A, Motegi SI, Nakagami H, Yamada Y, Tsukamoto S, Taniguchi A, Sugimoto K, Takami Y, Shoda Y, Hashimoto K, Yoshimura T, Kogure A, Suzuki D, Okubo N, Yoshida T, Watanabe K, Kuzuya M, Takemoto M, Oshima J, Yokote K. Renal dysfunction, malignant neoplasms, atherosclerotic cardiovascular diseases, and sarcopenia as key outcomes observed in a three-year follow-up study using the Werner Syndrome Registry. Aging (Albany NY) 2023; 15:3273-3294. [PMID: 37130431 PMCID: PMC10449280 DOI: 10.18632/aging.204681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/15/2023] [Indexed: 05/04/2023]
Abstract
Werner syndrome is an adult-onset progeria syndrome that results in various complications. This study aimed to clarify the profile and secular variation of the disease. Fifty-one patients were enrolled and registered in the Werner Syndrome Registry. Their data were collected annually following registration. A cross-sectional analysis at registration and a longitudinal analysis between the baseline and each subsequent year was performed. Pearson's chi-squared and Wilcoxon signed-rank tests were used. Malignant neoplasms were observed from the fifth decade of life (mean onset: 49.7 years) and were observed in approximately 30% of patients during the 3-year survey period. Regarding renal function, the mean estimated glomerular filtration rate calculated from serum creatinine (eGFRcre) and eGFRcys, which were calculated from cystatin C in the first year, were 98.3 and 83.2 mL/min/1.73 m2, respectively, and differed depending on the index used. In longitudinal analysis, the average eGFRcre for the first and fourth years was 74.8 and 63.4 mL/min/1.73 m2, showing a rapid decline. Secular changes in Werner syndrome in multiple patients were identified. The prevalence of malignant neoplasms is high, and renal function may decline rapidly. It is, therefore, necessary to carry out active and detailed examinations and pay attention to the type and dose of the drugs used.
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Affiliation(s)
- Yukari Maeda
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Masaya Koshizaka
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Mayumi Shoji
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hiyori Kaneko
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hisaya Kato
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshiro Maezawa
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Junji Kawashima
- Department of Metabolic Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kayo Yoshinaga
- Department of Metabolic Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mai Ishikawa
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Akiko Sekiguchi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Sei-Ichiro Motegi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hironori Nakagami
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshihiko Yamada
- Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Atami Hospital, International University of Health and Welfare, Atami, Japan
| | - Shinji Tsukamoto
- Department of Orthopaedic Surgery, Nara Medical University, Nara, Japan
| | - Akira Taniguchi
- Department of Orthopaedic Surgery, Nara Medical University, Nara, Japan
| | - Ken Sugimoto
- General Geriatric Medicine, Kawasaki Medical School, Okayama, Japan
| | - Yoichi Takami
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yukiko Shoda
- Department of Dermatology, Sumitomo Hospital, Osaka, Japan
| | - Kunihiko Hashimoto
- Department of Endocrinology and Metabolic Medicine, Nippon Life Hospital, Osaka, Japan
| | - Toru Yoshimura
- Diabetes and Endocrinology, Saga-Ken Medical Centre Koseikan, Saga, Japan
| | - Asako Kogure
- Department of Dermatology, Showa General Hospital, Tokyo, Japan
| | - Daisuke Suzuki
- Department of Dermatology, Showa General Hospital, Tokyo, Japan
| | - Naoki Okubo
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takashi Yoshida
- Department of Orthopaedic Surgery, North Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhisa Watanabe
- Department of Community Healthcare and Geriatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Minoru Takemoto
- Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, International University of Health and Welfare, Narita, Japan
| | - Junko Oshima
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Koutaro Yokote
- Department of Endocrinology, Hematology, and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
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35
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Zhang Y, Shi D, Zhang X, Wu S, Liu W, Luo B. Downregulation of MUS81 expression inhibits cell migration and maintains EBV latent infection through miR-BART9-5p in EBV-associated gastric cancer. J Med Virol 2023; 95:e28725. [PMID: 37185865 DOI: 10.1002/jmv.28725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/15/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Epstein-Barr virus (EBV) infection is associated with the occurrence and development of gastric cancer (GC). Methyl methanesulfonate and ultraviolet-sensitive gene 81 (MUS81) is the catalytic component of a structure-specific endonuclease and plays an important role in chromosomal stability. However, the link between EBV infection and MUS81 remains unclear. In the present study, we found that MUS81 expression was much lower in EBV-associated GC cells than in EBV-negative GC. MUS81 acts as an oncogene in GC by inducing the cell migration and proliferation. Western blot and luciferase reporter assays revealed that miR-BART9-5p directly targeted MUS81 and downregulated its expression. Additionally, overexpression of MUS81 in EBV-positive GC cells inhibited the expression of EBV nuclear antigen 1 (EBNA1). EBNA1 is critical for the pathogenesis of EBV-associated tumors and the maintenance of a stable copy number of the viral genomes. Altogether, these results indicated that the lowering MUS81 expression might be a mechanism by EBV to maintain its latent infection.
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Affiliation(s)
- Yan Zhang
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao, China
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo, China
| | - Duo Shi
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao, China
| | - Xing Zhang
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao, China
| | - Shuo Wu
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao, China
- Laboratory Medicine Center of Qingdao, Qilu Hospital of Shandong University (Qingdao), Qingdao, China
| | - Wen Liu
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao, China
| | - Bing Luo
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao, China
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36
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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37
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Datta A, Sommers JA, Jhujh SS, Harel T, Stewart GS, Brosh RM. Discovery of a new hereditary RECQ helicase disorder RECON syndrome positions the replication stress response and genome homeostasis as centrally important processes in aging and age-related disease. Ageing Res Rev 2023; 86:101887. [PMID: 36805074 PMCID: PMC10018417 DOI: 10.1016/j.arr.2023.101887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
Characterizing the molecular deficiencies underlying human aging has been a formidable challenge as it is clear that a complex myriad of factors including genetic mutations, environmental influences, and lifestyle choices influence the deterioration responsible for human pathologies. In addition, the common denominators of human aging, exemplified by the newly updated hallmarks of aging (López-Otín et al., 2023), suggest multiple avenues and layers of crosstalk between pathways important for genome and cellular homeostasis, both of which are major determinants of both good health and lifespan. In this regard, we postulate that hereditary disorders characterized by chromosomal instability offer a unique window of insight into aging and age-related disease processes. Recently, we discovered a new RECQ helicase disorder, designated RECON syndrome attributed to bi-allelic mutations in the RECQL1 gene (Abu-Libdeh et al., 2022). Cells deficient in RECQL1 exhibit genomic instability and a compromised response to replication stress, providing further evidence for the significance of genome homeostasis to suppress disease phenotypes. Here we provide a perspective on the pathology of RECON syndrome to inform the reader as to how molecular defects in the RECQL1 gene contribute to underlying deficiencies in nucleic acid metabolism often seen in certain aging or age-related diseases.
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Affiliation(s)
- Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Satpal S Jhujh
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Grant S Stewart
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA.
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38
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Li JSZ, Abbasi A, Kim DH, Lippman SM, Alexandrov LB, Cleveland DW. Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats. Nature 2023; 616:504-509. [PMID: 37046091 PMCID: PMC10328181 DOI: 10.1038/s41586-023-05923-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/07/2023] [Indexed: 04/14/2023]
Abstract
Epstein-Barr virus (EBV) is an oncogenic herpesvirus associated with several cancers of lymphocytic and epithelial origin1-3. EBV encodes EBNA1, which binds to a cluster of 20 copies of an 18-base-pair palindromic sequence in the EBV genome4-6. EBNA1 also associates with host chromosomes at non-sequence-specific sites7, thereby enabling viral persistence. Here we show that the sequence-specific DNA-binding domain of EBNA1 binds to a cluster of tandemly repeated copies of an EBV-like, 18-base-pair imperfect palindromic sequence encompassing a region of about 21 kilobases at human chromosome 11q23. In situ visualization of the repetitive EBNA1-binding site reveals aberrant structures on mitotic chromosomes characteristic of inherently fragile DNA. We demonstrate that increasing levels of EBNA1 binding trigger dose-dependent breakage at 11q23, producing a fusogenic centromere-containing fragment and an acentric distal fragment, with both mis-segregated into micronuclei in the next cell cycles. In cells latently infected with EBV, elevating EBNA1 abundance by as little as twofold was sufficient to trigger breakage at 11q23. Examination of whole-genome sequencing of EBV-associated nasopharyngeal carcinomas revealed that structural variants are highly enriched on chromosome 11. Presence of EBV is also shown to be associated with an enrichment of chromosome 11 rearrangements across 2,439 tumours from 38 cancer types. Our results identify a previously unappreciated link between EBV and genomic instability, wherein EBNA1-induced breakage at 11q23 triggers acquisition of structural variations in chromosome 11.
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MESH Headings
- Humans
- Binding Sites
- DNA/chemistry
- DNA/metabolism
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/metabolism
- Herpesvirus 4, Human/pathogenicity
- Viral Proteins/genetics
- Viral Proteins/metabolism
- DNA Breaks, Double-Stranded
- Chromosomes, Human, Pair 11/chemistry
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 11/metabolism
- Genomic Instability
- Mitosis
- Chromosome Breakage
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Affiliation(s)
- Julia Su Zhou Li
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Oncology Research Unit, Pfizer Inc., San Diego, CA, USA
| | | | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA.
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39
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Qin X, Wang J, Wang X, Huang T, Fang Z, Yan L, Fan Y, Xu D. Widespread genomic/molecular alterations of DNA helicases and their clinical/therapeutic implications across human cancer. Biomed Pharmacother 2023; 158:114193. [PMID: 36586240 DOI: 10.1016/j.biopha.2022.114193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
DNA helicases are essential to genomic stability by regulating DNA metabolisms and their loss-of-function mutations lead to genomic instability and predisposition to cancer. Paradoxically, overexpression of DNA helicases is observed in several cancers. Here we analyzed genomic and molecular alterations in 12 important DNA helicases in TCGA pan-cancers to provide an overview of their aberrations. Significant expression heterogeneity of 12 DNA helicases was observed. We calculated DNA helicase score (DHS) based on their expression, and categorized tumors into high, low and intermediate subtypes. High DHS subtypes were robustly associated with stemness, proliferation, hyperactivated oncogenic signaling, longer telomeres, total mutation burden, copy number alterations (CNAs) and shorter survival. Importantly, tumors with high DHSs exhibited stronger expression of alternative end-join (alt-EJ) factors, indicative of sensitivity to chemo- and radio-therapies. High DHSs were also associated with homologous recombination deficiency (HRD), BRCA1/2 mutations and sensitivity to PARP inhibitors. Moreover, several drugs are identified to inhibit DNA helicases, with the Auror A kinase inhibitor Danusertib as the strongest candidate that was confirmed experimentally. The aberrant expression of DNA helicases was associated with CNAs, DNA methylation and m6A regulators. Our findings thus reveal widespread dysregulation of DNA helicases and their broad connection with featured oncogenic aberrations across human cancers. The close association of DHS with the alt-EJ pathway and HRD, and identification of Danusertib as a putative DNA helicase inhibitor have translational significance. Taken together, these findings will contribute to DNA helicase-based cancer therapy.
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Affiliation(s)
- Xin Qin
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jing Wang
- Department of Urologic Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Xing Wang
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Wannan Medical College, Wuhu 241000, China
| | - Tao Huang
- Department of Urologic Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Lei Yan
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm 171 76, Sweden.
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Mengoli V, Ceppi I, Sanchez A, Cannavo E, Halder S, Scaglione S, Gaillard P, McHugh PJ, Riesen N, Pettazzoni P, Cejka P. WRN helicase and mismatch repair complexes independently and synergistically disrupt cruciform DNA structures. EMBO J 2023; 42:e111998. [PMID: 36541070 PMCID: PMC9890227 DOI: 10.15252/embj.2022111998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The Werner Syndrome helicase, WRN, is a promising therapeutic target in cancers with microsatellite instability (MSI). Long-term MSI leads to the expansion of TA nucleotide repeats proposed to form cruciform DNA structures, which in turn cause DNA breaks and cell lethality upon WRN downregulation. Here we employed biochemical assays to show that WRN helicase can efficiently and directly unfold cruciform structures, thereby preventing their cleavage by the SLX1-SLX4 structure-specific endonuclease. TA repeats are particularly prone to form cruciform structures, explaining why these DNA sequences are preferentially broken in MSI cells upon WRN downregulation. We further demonstrate that the activity of the DNA mismatch repair (MMR) complexes MutSα (MSH2-MSH6), MutSβ (MSH2-MSH3), and MutLα (MLH1-PMS2) similarly decreases the level of DNA cruciforms, although the mechanism is different from that employed by WRN. When combined, WRN and MutLα exhibited higher than additive effects in in vitro cruciform processing, suggesting that WRN and the MMR proteins may cooperate. Our data explain how WRN and MMR defects cause genome instability in MSI cells with expanded TA repeats, and provide a mechanistic basis for their recently discovered synthetic-lethal interaction with promising applications in precision cancer therapy.
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Affiliation(s)
- Valentina Mengoli
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Ilaria Ceppi
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Aurore Sanchez
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Elda Cannavo
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Swagata Halder
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Sarah Scaglione
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Pierre‐Henri Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Nathalie Riesen
- Roche Pharma Research & Early Development pREDRoche Innovation CenterBaselSwitzerland
| | | | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
- Department of Biology, Institute of BiochemistryEidgenössische Technische Hochschule (ETH)ZürichSwitzerland
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Groelly FJ, Fawkes M, Dagg RA, Blackford AN, Tarsounas M. Targeting DNA damage response pathways in cancer. Nat Rev Cancer 2023; 23:78-94. [PMID: 36471053 DOI: 10.1038/s41568-022-00535-5] [Citation(s) in RCA: 154] [Impact Index Per Article: 154.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Cells have evolved a complex network of biochemical pathways, collectively known as the DNA damage response (DDR), to prevent detrimental mutations from being passed on to their progeny. The DDR coordinates DNA repair with cell-cycle checkpoint activation and other global cellular responses. Genes encoding DDR factors are frequently mutated in cancer, causing genomic instability, an intrinsic feature of many tumours that underlies their ability to grow, metastasize and respond to treatments that inflict DNA damage (such as radiotherapy). One instance where we have greater insight into how genetic DDR abrogation impacts on therapy responses is in tumours with mutated BRCA1 or BRCA2. Due to compromised homologous recombination DNA repair, these tumours rely on alternative repair mechanisms and are susceptible to chemical inhibitors of poly(ADP-ribose) polymerase (PARP), which specifically kill homologous recombination-deficient cancer cells, and have become a paradigm for targeted cancer therapy. It is now clear that many other synthetic-lethal relationships exist between DDR genes. Crucially, some of these interactions could be exploited in the clinic to target tumours that become resistant to PARP inhibition. In this Review, we discuss state-of-the-art strategies for DDR inactivation using small-molecule inhibitors and highlight those compounds currently being evaluated in the clinic.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
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WRN suppresses p53/PUMA-induced apoptosis in colorectal cancer with microsatellite instability/mismatch repair deficiency. Proc Natl Acad Sci U S A 2023; 120:e2219963120. [PMID: 36598947 PMCID: PMC9926267 DOI: 10.1073/pnas.2219963120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Chan EM, Foster KJ, Bass AJ. WRN Is a Promising Synthetic Lethal Target for Cancers with Microsatellite Instability (MSI). Cancer Treat Res 2023; 186:313-328. [PMID: 37978143 DOI: 10.1007/978-3-031-30065-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Microsatellite instability (MSI), a type of genetic hypermutability arising from impaired DNA mismatch repair (MMR), is observed in approximately 3% of all cancers. Preclinical work has identified the RecQ helicase WRN as a promising synthetic lethal target for patients with MSI cancers. WRN depletion substantially impairs the viability of MSI, but not microsatellite stable (MSS), cells. Experimental evidence suggests that this synthetic lethal phenotype is driven by numerous TA dinucleotide repeats that undergo expansion mutations in the setting of long-standing MMR deficiency. The lengthening of TA repeats increases their propensity to form secondary DNA structures that require WRN to resolve. In the absence of WRN helicase activity, these unresolved DNA secondary structures stall DNA replication forks and induce catastrophic DNA damage.
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Affiliation(s)
- Edmond M Chan
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, USA.
- Broad Institute of MIT and Harvard, Cambridge, USA.
- New York Genome Center, New York, USA.
| | | | - Adam J Bass
- Novartis Institutes for BioMedical Research, Cambridge, USA
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Recurrent repeat expansions in human cancer genomes. Nature 2023; 613:96-102. [PMID: 36517591 DOI: 10.1038/s41586-022-05515-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/02/2022] [Indexed: 12/16/2022]
Abstract
Expansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 50 diseases1,2. However, repeat expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts of TRs, a phenomenon termed microsatellite instability; however, larger repeat expansions have not been systematically analysed in cancer3-8. Here we identified TR expansions in 2,622 cancer genomes spanning 29 cancer types. In seven cancer types, we found 160 recurrent repeat expansions (rREs), most of which (155/160) were subtype specific. We found that rREs were non-uniformly distributed in the genome with enrichment near candidate cis-regulatory elements, suggesting a potential role in gene regulation. One rRE, a GAAA-repeat expansion, located near a regulatory element in the first intron of UGT2B7 was detected in 34% of renal cell carcinoma samples and was validated by long-read DNA sequencing. Moreover, in preliminary experiments, treating cells that harbour this rRE with a GAAA-targeting molecule led to a dose-dependent decrease in cell proliferation. Overall, our results suggest that rREs may be an important but unexplored source of genetic variation in human cancer, and we provide a comprehensive catalogue for further study.
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Hao S, Tong J, Jha A, Risnik D, Lizardo D, Lu X, Goel A, Opresko PL, Yu J, Zhang L. Synthetical lethality of Werner helicase and mismatch repair deficiency is mediated by p53 and PUMA in colon cancer. Proc Natl Acad Sci U S A 2022; 119:e2211775119. [PMID: 36508676 PMCID: PMC9907101 DOI: 10.1073/pnas.2211775119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/01/2022] [Indexed: 12/15/2022] Open
Abstract
Synthetic lethality is a powerful approach for targeting oncogenic drivers in cancer. Recent studies revealed that cancer cells with microsatellite instability (MSI) require Werner (WRN) helicase for survival; however, the underlying mechanism remains unclear. In this study, we found that WRN depletion strongly induced p53 and its downstream apoptotic target PUMA in MSI colorectal cancer (CRC) cells. p53 or PUMA deletion abolished apoptosis induced by WRN depletion in MSI CRC cells. Importantly, correction of MSI abrogated the activation of p53/PUMA and cell killing, while induction of MSI led to sensitivity in isogenic CRC cells. Rare p53-mutant MSI CRC cells are resistant to WRN depletion due to lack of PUMA induction, which could be restored by wildtype (WT) p53 knock in or reconstitution. WRN depletion or treatment with the RecQ helicase inhibitor ML216 suppressed in vitro and in vivo growth of MSI CRCs in a p53/PUMA-dependent manner. ML216 treatment was efficacious in MSI CRC patient-derived xenografts. Interestingly, p53 gene remains WT in the majority of MSI CRCs. These results indicate a critical role of p53/PUMA-mediated apoptosis in the vulnerability of MSI CRCs to WRN loss, and support WRN as a promising therapeutic target in p53-WT MSI CRCs.
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Affiliation(s)
- Suisui Hao
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Jingshan Tong
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Anupma Jha
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
| | - Denise Risnik
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Darleny Lizardo
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Xinyan Lu
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA91010
| | - Patricia L. Opresko
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA15213
| | - Jian Yu
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Lin Zhang
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Correspondence may also be addressed to Christine J. Cardin. Tel: +44 118 378 8215;
| | - David Monchaud
- To whom correspondence should be addressed. Tel: +33 380 399 043;
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Morales-Juarez DA, Jackson SP. Clinical prospects of WRN inhibition as a treatment for MSI tumours. NPJ Precis Oncol 2022; 6:85. [DOI: 10.1038/s41698-022-00319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractThe discovery of synthetic lethal interactions with genetic deficiencies in cancers has highlighted several candidate targets for drug development, with variable clinical success. Recent work has unveiled a promising synthetic lethal interaction between inactivation/inhibition of the WRN DNA helicase and tumours with microsatellite instability, a phenotype that arises from DNA mismatch repair deficiency. While these and further studies have highlighted the therapeutic potential of WRN inhibitors, compounds with properties suitable for clinical exploitation remain to be described. Furthermore, the complexities of MSI development and its relationship to cancer evolution pose challenges for clinical prospects. Here, we discuss possible paths of MSI tumour development, the viability of WRN inhibition as a strategy in different scenarios, and the necessary conditions to create a roadmap towards successful implementation of WRN inhibitors in the clinic.
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Baxter JS, Zatreanu D, Pettitt SJ, Lord CJ. Resistance to DNA repair inhibitors in cancer. Mol Oncol 2022; 16:3811-3827. [PMID: 35567571 PMCID: PMC9627783 DOI: 10.1002/1878-0261.13224] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
The DNA damage response (DDR) represents a complex network of proteins which detect and repair DNA damage, thereby maintaining the integrity of the genome and preventing the transmission of mutations and rearranged chromosomes to daughter cells. Faults in the DDR are a known driver and hallmark of cancer. Furthermore, inhibition of DDR enzymes can be used to treat the disease. This is exemplified by PARP inhibitors (PARPi) used to treat cancers with defects in the homologous recombination DDR pathway. A series of novel DDR targets are now also under pre-clinical or clinical investigation, including inhibitors of ATR kinase, WRN helicase or the DNA polymerase/helicase Polθ (Pol-Theta). Drug resistance is a common phenomenon that impairs the overall effectiveness of cancer treatments and there is already some understanding of how resistance to PARPi occurs. Here, we discuss how an understanding of PARPi resistance could inform how resistance to new drugs targeting the DDR emerges. We also discuss potential strategies that could limit the impact of these therapy resistance mechanisms in cancer.
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Affiliation(s)
- Joseph S. Baxter
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Diana Zatreanu
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
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Voutsadakis IA. Sensitivities and Dependencies of BRAF Mutant Colorectal Cancer Cell Lines with or without PIK3CA Mutations for Discovery of Vulnerabilities with Therapeutic Potential. Medicina (B Aires) 2022; 58:medicina58101498. [PMID: 36295658 PMCID: PMC9608248 DOI: 10.3390/medicina58101498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Colorectal cancer represents a common malignancy and remains incurable in the metastatic stage. Identification of molecular alterations that are present in colorectal cancer has led to the introduction of targeted therapies that improve outcomes. BRAF and PIK3CA mutations are observed in a subset of colorectal cancers. Colorectal cancers bearing BRAF mutations may be treated with specific BRAF inhibitors. These drugs benefit patients with BRAF mutant colorectal cancers but responses are rather brief, and progression is the rule. In contrast, no PI3K inhibitors have proven successful yet in the disease. Thus, new treatments to supplement the currently available drugs would be welcome to further improve survival. Methods: Profiled colorectal cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were examined for BRAF and PIK3CA mutations and were interrogated for molecular characteristics and concomitant alterations that mirror clinical sample alterations. The Genomics of Drug Sensitivity in Cancer (GDSC) project was used for determination of drug sensitivities of BRAF mutated colorectal cell lines with or without concomitant PIK3CA mutations. The Cancer Dependency Map project served as the basis for identification of molecular dependencies and vulnerabilities in these cell lines. Results: CCLE includes 84 colorectal cancer cell lines, which recapitulate the molecular landscape of colorectal cancer. Of these, 23 and 24 cell lines possess BRAF and PIK3CA mutations, respectively. Seven BRAF mutant cell lines have V600E mutations and 14 PIK3CA mutant cell lines have hotspot helical or kinase domain mutations. V600E BRAF mutant cell lines with or without hotspot PIK3CA mutations are heterogeneous in their MSI status and mimic colorectal cancer tissues in other prevalent abnormalities including APC and TP53 mutations. Essential genes for survival include CTNNB1, WRN, and pyrimidine metabolism enzyme CAD. Besides BRAF mutations, BRAF inhibitor sensitivity in colorectal cancer cell lines is conferred by SACS mutations and PRKN locus loss. Conclusions: Colorectal cancer cell lines bearing the frequent BRAF and PIK3CA mutations present many alterations of the parental cancer tissue. Described vulnerabilities represent leads for therapeutic exploration in colorectal cancers with the corresponding alterations.
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Affiliation(s)
- Ioannis A. Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, 750 Great Northern Road, Sault Ste. Marie, ON P6B 0A8, Canada; or
- Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada
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50
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Research on Werner Syndrome: Trends from Past to Present and Future Prospects. Genes (Basel) 2022; 13:genes13101802. [PMID: 36292687 PMCID: PMC9601476 DOI: 10.3390/genes13101802] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
A rare and autosomal recessive premature aging disorder, Werner syndrome (WS) is characterized by the early onset of aging-associated diseases, including shortening stature, alopecia, bilateral cataracts, skin ulcers, diabetes, osteoporosis, arteriosclerosis, and chromosomal instability, as well as cancer predisposition. WRN, the gene responsible for WS, encodes DNA helicase with a 3′ to 5′ exonuclease activity, and numerous studies have revealed that WRN helicase is involved in the maintenance of chromosome stability through actions in DNA, e.g., DNA replication, repair, recombination, and epigenetic regulation via interaction with DNA repair factors, telomere-binding proteins, histone modification enzymes, and other DNA metabolic factors. However, although these efforts have elucidated the cellular functions of the helicase in cell lines, they have not been linked to the treatment of the disease. Life expectancy has improved for WS patients over the past three decades, and it is hoped that a fundamental treatment for the disease will be developed. Disease-specific induced pluripotent stem (iPS) cells have been established, and these are expected to be used in drug discovery and regenerative medicine for WS patients. In this article, we review trends in research to date and present some perspectives on WS research with regard to the application of pluripotent stem cells. Furthermore, the elucidation of disease mechanisms and drug discovery utilizing the vast amount of scientific data accumulated to date will be discussed.
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