101
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Hayward SB, Ciccia A. Towards a CRISPeR understanding of homologous recombination with high-throughput functional genomics. Curr Opin Genet Dev 2021; 71:171-181. [PMID: 34583241 PMCID: PMC8671205 DOI: 10.1016/j.gde.2021.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-dependent genome editing enables the study of genes and mutations on a large scale. Here we review CRISPR-based functional genomics technologies that generate gene knockouts and single nucleotide variants (SNVs) and discuss how their use has provided new important insights into the function of homologous recombination (HR) genes. In particular, we highlight discoveries from CRISPR screens that have contributed to define the response to PARP inhibition in cells deficient for the HR genes BRCA1 and BRCA2, uncover genes whose loss causes synthetic lethality in combination with BRCA1/2 deficiency, and characterize the function of BRCA1/2 SNVs of uncertain clinical significance. Further use of these approaches, combined with next-generation CRISPR-based technologies, will aid to dissect the genetic network of the HR pathway, define the impact of HR mutations on cancer etiology and treatment, and develop novel targeted therapies for HR-deficient tumors.
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Affiliation(s)
- Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States.
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102
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Adeyemi RO, Willis NA, Elia AEH, Clairmont C, Li S, Wu X, D'Andrea AD, Scully R, Elledge SJ. The Protexin complex counters resection on stalled forks to promote homologous recombination and crosslink repair. Mol Cell 2021; 81:4440-4456.e7. [PMID: 34597596 PMCID: PMC8588999 DOI: 10.1016/j.molcel.2021.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/11/2021] [Accepted: 09/07/2021] [Indexed: 02/06/2023]
Abstract
Protection of stalled replication forks is critical to genomic stability. Using genetic and proteomic analyses, we discovered the Protexin complex containing the ssDNA binding protein SCAI and the DNA polymerase REV3. Protexin is required specifically for protecting forks stalled by nucleotide depletion, fork barriers, fragile sites, and DNA inter-strand crosslinks (ICLs), where it promotes homologous recombination and repair. Protexin loss leads to ssDNA accumulation and profound genomic instability in response to ICLs. Protexin interacts with RNA POL2, and both oppose EXO1's resection of DNA on forks remodeled by the FANCM translocase activity. This pathway acts independently of BRCA/RAD51-mediated fork stabilization, and cells with BRCA2 mutations were dependent on SCAI for survival. These data suggest that Protexin and its associated factors establish a new fork protection pathway that counteracts fork resection in part through a REV3 polymerase-dependent resynthesis mechanism of excised DNA, particularly at ICL stalled forks.
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Affiliation(s)
- Richard O Adeyemi
- Department of Genetics, Harvard Medical School, and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Nicholas A Willis
- Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew E H Elia
- Department of Genetics, Harvard Medical School, and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Connor Clairmont
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ralph Scully
- Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA.
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103
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Singh DD, Parveen A, Yadav DK. Role of PARP in TNBC: Mechanism of Inhibition, Clinical Applications, and Resistance. Biomedicines 2021; 9:biomedicines9111512. [PMID: 34829741 PMCID: PMC8614648 DOI: 10.3390/biomedicines9111512] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer is a combative cancer type with a highly inflated histological grade that leads to poor theragnostic value. Gene, protein, and receptor-specific targets have shown effective clinical outcomes in patients with TNBC. Cells are frequently exposed to DNA-damaging agents. DNA damage is repaired by multiple pathways; accumulations of mutations occur due to damage to one or more pathways and lead to alterations in normal cellular mechanisms, which lead to development of tumors. Advances in target-specific cancer therapies have shown significant momentum; most treatment options cause off-target toxicity and side effects on healthy tissues. PARP (poly(ADP-ribose) polymerase) is a major protein and is involved in DNA repair pathways, base excision repair (BER) mechanisms, homologous recombination (HR), and nonhomologous end-joining (NEJ) deficiency-based repair mechanisms. DNA damage repair deficits cause an increased risk of tumor formation. Inhibitors of PARP favorably kill cancer cells in BRCA-mutations. For a few years, PARPi has shown promising activity as a chemotherapeutic agent in BRCA1- or BRCA2-associated breast cancers, and in combination with chemotherapy in triple-negative breast cancer. This review covers the current results of clinical trials testing and future directions for the field of PARP inhibitor development.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India;
| | - Amna Parveen
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-gu, Incheon 21924, Korea
- Correspondence: (A.P.); (D.K.Y.); Tel.: +82-32-820-4948 (D.K.Y.)
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-gu, Incheon 21924, Korea
- Correspondence: (A.P.); (D.K.Y.); Tel.: +82-32-820-4948 (D.K.Y.)
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104
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Thongchot S, Jamjuntra P, Prasopsiri J, Thuwajit P, Sawasdee N, Poungvarin N, Warnnissorn M, Sa-Nguanraksa D, O-Charoenrat P, Yenchitsomanus PT, Thuwajit C. Establishment and characterization of novel highly aggressive HER2‑positive and triple‑negative breast cancer cell lines. Oncol Rep 2021; 46:254. [PMID: 34651665 PMCID: PMC8548790 DOI: 10.3892/or.2021.8205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/16/2021] [Indexed: 11/05/2022] Open
Abstract
Breast cancer cell lines are widely used as an in vitro system with which to study the mechanisms underlying biological and chemotherapeutic resistance. In the present study, two novel breast cancer cell lines designated as PC‑B‑142CA and PC‑B‑148CA were successfully established from HER2‑positive and triple‑negative (TN) breast cancer tissues. The cell lines were characterized by cytokeratin (CK), α‑smooth muscle actin (α‑SMA), fibroblast‑activation protein (FAP) and programmed death‑ligand 1 (PD‑L1). Cell proliferation was assessed using a colony formation assay, an MTS assay, 3‑dimensional (3‑D) spheroid and 3‑D organoid models. Wound healing and Transwell migration assays were used to explore the cell migration capability. The responses to doxorubicin (DOX) and paclitaxel (PTX) were evaluated by 3‑D spheroids. The results showed that the PC‑B‑142CA and PC‑B‑148CA cell lines were α‑SMA‑negative, FAP‑negative, CK‑positive and PD‑L1‑positive. Both cell lines were adherent with the ability of 3‑D‑multicellular spheroid and organoid formations; invadopodia were found in the spheroids/organoids of only PC‑B‑148CA. PC‑B‑142CA had a faster proliferative but lower metastatic rate compared to PC‑B‑148CA. Compared to MDA‑MB‑231, a commercial TN breast cancer cell line, PC‑B‑148CA had a similar CD44+/CD24‑ stemness property (96.90%), whereas only 8.75% were found in PC‑B‑142CA. The mutations of BRCA1/2, KIT, PIK3CA, SMAD4, and TP53 were found in PC‑B‑142CA cells related to the resistance of several drugs, whereas PC‑B‑148CA had mutated BRCA2, NRAS and TP53. In conclusion, PC‑B‑142CA can serve as a novel HER2‑positive breast cancer cell line for drug resistance studies; while PC‑B‑148CA is a novel TN breast cancer cell line suitable for metastatic and stemness‑related properties.
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Affiliation(s)
- Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pranisa Jamjuntra
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jaturawitt Prasopsiri
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nunghathai Sawasdee
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Malee Warnnissorn
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Doonyapat Sa-Nguanraksa
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | | | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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105
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Mullen J, Kato S, Sicklick JK, Kurzrock R. Targeting ARID1A mutations in cancer. Cancer Treat Rev 2021; 100:102287. [PMID: 34619527 DOI: 10.1016/j.ctrv.2021.102287] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/22/2022]
Abstract
Genes encoding SWI/SNF chromatin remodeling complex subunits are collectively mutated in approximately 20% of human cancers. ARID1A is a SWI/SNF subunit gene whose protein product binds DNA. ARID1A gene alterations result in loss of function. It is the most commonly mutated member of the SWI/SNF complex, being aberrant in ∼6% of cancers overall, including ovarian clear cell cancers (∼45% of patients) and uterine endometrioid cancers (∼37%). ARID1A has a crucial role in regulating gene expression that drives oncogenesis or tumor suppression. In particular, ARID1A participates in control of the PI3K/AKT/mTOR pathway, immune responsiveness to cancer, EZH2 methyltransferase activity, steroid receptor modulation, DNA damage checkpoints, and regulation of p53 targets and KRAS signaling. A variety of compounds may be of benefit in ARID1A-altered cancers: immune checkpoint blockade, and inhibitors of mTOR, EZH2, histone deacetylases, ATR and/or PARP. ARID1A alterations may also mediate resistance to platinum chemotherapy and estrogen receptor degraders/modulators.
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Affiliation(s)
- Jaren Mullen
- Center for Personalized Cancer Therapy, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| | - Jason K Sicklick
- Center for Personalized Cancer Therapy, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, USA; Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA, USA
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106
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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107
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Seplyarskiy VB, Sunyaev S. The origin of human mutation in light of genomic data. Nat Rev Genet 2021; 22:672-686. [PMID: 34163020 DOI: 10.1038/s41576-021-00376-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Despite years of active research into the role of DNA repair and replication in mutagenesis, surprisingly little is known about the origin of spontaneous human mutation in the germ line. With the advent of high-throughput sequencing, genome-scale data have revealed statistical properties of mutagenesis in humans. These properties include variation of the mutation rate and spectrum along the genome at different scales in relation to epigenomic features and dependency on parental age. Moreover, mutations originated in mothers are less frequent than mutations originated in fathers and have a distinct genomic distribution. Statistical analyses that interpret these patterns in the context of known biochemistry can provide mechanistic models of mutagenesis in humans.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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108
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A complex of BRCA2 and PP2A-B56 is required for DNA repair by homologous recombination. Nat Commun 2021; 12:5748. [PMID: 34593815 PMCID: PMC8484605 DOI: 10.1038/s41467-021-26079-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Mutations in the tumour suppressor gene BRCA2 are associated with predisposition to breast and ovarian cancers. BRCA2 has a central role in maintaining genome integrity by facilitating the repair of toxic DNA double-strand breaks (DSBs) by homologous recombination (HR). BRCA2 acts by controlling RAD51 nucleoprotein filament formation on resected single-stranded DNA, but how BRCA2 activity is regulated during HR is not fully understood. Here, we delineate a pathway where ATM and ATR kinases phosphorylate a highly conserved region in BRCA2 in response to DSBs. These phosphorylations stimulate the binding of the protein phosphatase PP2A-B56 to BRCA2 through a conserved binding motif. We show that the phosphorylation-dependent formation of the BRCA2-PP2A-B56 complex is required for efficient RAD51 filament formation at sites of DNA damage and HR-mediated DNA repair. Moreover, we find that several cancer-associated mutations in BRCA2 deregulate the BRCA2-PP2A-B56 interaction and sensitize cells to PARP inhibition. Collectively, our work uncovers PP2A-B56 as a positive regulator of BRCA2 function in HR with clinical implications for BRCA2 and PP2A-B56 mutated cancers.
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109
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Prado F. Non-Recombinogenic Functions of Rad51, BRCA2, and Rad52 in DNA Damage Tolerance. Genes (Basel) 2021; 12:genes12101550. [PMID: 34680945 PMCID: PMC8535942 DOI: 10.3390/genes12101550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
The DNA damage tolerance (DDT) response is aimed to timely and safely complete DNA replication by facilitating the advance of replication forks through blocking lesions. This process is associated with an accumulation of single-strand DNA (ssDNA), both at the fork and behind the fork. Lesion bypass and ssDNA filling can be performed by translation synthesis (TLS) and template switching mechanisms. TLS uses low-fidelity polymerases to incorporate a dNTP opposite the blocking lesion, whereas template switching uses a Rad51/ssDNA nucleofilament and the sister chromatid to bypass the lesion. Rad51 is loaded at this nucleofilament by two mediator proteins, BRCA2 and Rad52, and these three factors are critical for homologous recombination (HR). Here, we review recent advances showing that Rad51, BRCA2, and Rad52 perform some of these functions through mechanisms that do not require the strand exchange activity of Rad51: the formation and protection of reversed fork structures aimed to bypass blocking lesions, and the promotion of TLS. These findings point to the central HR proteins as potential molecular switches in the choice of the mechanism of DDT.
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Affiliation(s)
- Félix Prado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, 41092 Seville, Spain
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110
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Fanconi Anaemia, Childhood Cancer and the BRCA Genes. Genes (Basel) 2021; 12:genes12101520. [PMID: 34680915 PMCID: PMC8535386 DOI: 10.3390/genes12101520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/18/2022] Open
Abstract
Fanconi anaemia (FA) is an inherited chromosomal instability disorder characterised by congenital and developmental abnormalities and a strong cancer predisposition. In less than 5% of cases FA can be caused by bi-allelic pathogenic variants (PGVs) in BRCA2/FANCD1 and in very rare cases by bi-allelic PGVs in BRCA1/FANCS. The rarity of FA-like presentation due to PGVs in BRCA2 and even more due to PGVs in BRCA1 supports a fundamental role of the encoded proteins for normal development and prevention of malignant transformation. While FA caused by BRCA1/2 PGVs is strongly associated with distinct spectra of embryonal childhood cancers and AML with BRCA2-PGVs, and also early epithelial cancers with BRCA1 PGVs, germline variants in the BRCA1/2 genes have also been identified in non-FA childhood malignancies, and thereby implying the possibility of a role of BRCA PGVs also for non-syndromic cancer predisposition in children. We provide a concise review of aspects of the clinical and genetic features of BRCA1/2-associated FA with a focus on associated malignancies, and review novel aspects of the role of germline BRCA2 and BRCA1 PGVs occurring in non-FA childhood cancer and discuss aspects of clinical and biological implications.
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111
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Caron P, Pobega E, Polo SE. DNA Double-Strand Break Repair: All Roads Lead to HeterochROMAtin Marks. Front Genet 2021; 12:730696. [PMID: 34539757 PMCID: PMC8440905 DOI: 10.3389/fgene.2021.730696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), chromatin modifications orchestrate DNA repair pathways thus safeguarding genome integrity. Recent studies have uncovered a key role for heterochromatin marks and associated factors in shaping DSB repair within the nucleus. In this review, we present our current knowledge of the interplay between heterochromatin marks and DSB repair. We discuss the impact of heterochromatin features, either pre-existing in heterochromatin domains or de novo established in euchromatin, on DSB repair pathway choice. We emphasize how heterochromatin decompaction and mobility further support DSB repair, focusing on recent mechanistic insights into these processes. Finally, we speculate about potential molecular players involved in the maintenance or the erasure of heterochromatin marks following DSB repair, and their implications for restoring epigenome function and integrity.
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Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Enrico Pobega
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
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112
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Castells-Roca L, Gutiérrez-Enríquez S, Bonache S, Bogliolo M, Carrasco E, Aza-Carmona M, Montalban G, Muñoz-Subirana N, Pujol R, Cruz C, Llop-Guevara A, Ramírez MJ, Saura C, Lasa A, Serra V, Diez O, Balmaña J, Surrallés J. Clinical consequences of BRCA2 hypomorphism. NPJ Breast Cancer 2021; 7:117. [PMID: 34504103 PMCID: PMC8429460 DOI: 10.1038/s41523-021-00322-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/02/2021] [Indexed: 12/24/2022] Open
Abstract
The tumor suppressor FANCD1/BRCA2 is crucial for DNA homologous recombination repair (HRR). BRCA2 biallelic pathogenic variants result in a severe form of Fanconi anemia (FA) syndrome, whereas monoallelic pathogenic variants cause mainly hereditary breast and ovarian cancer predisposition. For decades, the co-occurrence in trans with a clearly pathogenic variant led to assume that the other allele was benign. However, here we show a patient with biallelic BRCA2 (c.1813dup and c.7796 A > G) diagnosed at age 33 with FA after a hypertoxic reaction to chemotherapy during breast cancer treatment. After DNA damage, patient cells displayed intermediate chromosome fragility, reduced survival, cell cycle defects, and significantly decreased RAD51 foci formation. With a newly developed cell-based flow cytometric assay, we measured single BRCA2 allele contributions to HRR, and found that expression of the missense allele in a BRCA2 KO cellular background partially recovered HRR activity. Our data suggest that a hypomorphic BRCA2 allele retaining 37–54% of normal HRR function can prevent FA clinical phenotype, but not the early onset of breast cancer and severe hypersensitivity to chemotherapy.
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Affiliation(s)
- Laia Castells-Roca
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Sara Gutiérrez-Enríquez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sandra Bonache
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Massimo Bogliolo
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER) U-745, Barcelona, Spain
| | - Estela Carrasco
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Miriam Aza-Carmona
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Gemma Montalban
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,CHU de Québec - Université Laval Research Center, Oncology division, 9 Rue McMahon, Québec city, G1R 3S3, Québec, Canada
| | - Núria Muñoz-Subirana
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Roser Pujol
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER) U-745, Barcelona, Spain
| | - Cristina Cruz
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - María J Ramírez
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER) U-745, Barcelona, Spain
| | - Cristina Saura
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Adriana Lasa
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER) U-705, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Orland Diez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
| | - Jordi Surrallés
- Genome Instability and DNA repair Syndromes Group and Join Unit UAB-IR Sant Pau on Genomic Medicine, Biomedical Research Institute IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain. .,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER) U-745, Barcelona, Spain.
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113
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Somyajit K, Spies J, Coscia F, Kirik U, Rask MB, Lee JH, Neelsen KJ, Mund A, Jensen LJ, Paull TT, Mann M, Lukas J. Homology-directed repair protects the replicating genome from metabolic assaults. Dev Cell 2021; 56:461-477.e7. [PMID: 33621493 DOI: 10.1016/j.devcel.2021.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/14/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Homology-directed repair (HDR) safeguards DNA integrity under various forms of stress, but how HDR protects replicating genomes under extensive metabolic alterations remains unclear. Here, we report that besides stalling replication forks, inhibition of ribonucleotide reductase (RNR) triggers metabolic imbalance manifested by the accumulation of increased reactive oxygen species (ROS) in cell nuclei. This leads to a redox-sensitive activation of the ATM kinase followed by phosphorylation of the MRE11 nuclease, which in HDR-deficient settings degrades stalled replication forks. Intriguingly, nascent DNA degradation by the ROS-ATM-MRE11 cascade is also triggered by hypoxia, which elevates signaling-competent ROS and attenuates functional HDR without arresting replication forks. Under these conditions, MRE11 degrades daughter-strand DNA gaps, which accumulate behind active replisomes and attract error-prone DNA polymerases to escalate mutation rates. Thus, HDR safeguards replicating genomes against metabolic assaults by restraining mutagenic repair at aberrantly processed nascent DNA. These findings have implications for cancer evolution and tumor therapy.
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Affiliation(s)
- Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
| | - Julian Spies
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Fabian Coscia
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ufuk Kirik
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein, Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ji-Hoon Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kai John Neelsen
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein, Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Matthias Mann
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
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114
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Zahn KE, Jensen RB. Polymerase θ Coordinates Multiple Intrinsic Enzymatic Activities during DNA Repair. Genes (Basel) 2021; 12:1310. [PMID: 34573292 PMCID: PMC8470613 DOI: 10.3390/genes12091310] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
The POLQ gene encodes DNA polymerase θ, a 2590 amino acid protein product harboring DNA-dependent ATPase, template-dependent DNA polymerase, dNTP-dependent endonuclease, and 5'-dRP lyase functions. Polymerase θ participates at an essential step of a DNA double-strand break repair pathway able to join 5'-resected substrates by locating and pairing microhomologies present in 3'-overhanging single-stranded tails, cleaving the extraneous 3'-DNA by dNTP-dependent end-processing, before extending the nascent 3' end from the microhomology annealing site. Metazoans require polymerase θ for full resistance to DNA double-strand break inducing agents but can survive knockout of the POLQ gene. Cancer cells with compromised homologous recombination, or other DNA repair defects, over-utilize end-joining by polymerase θ and often over-express the POLQ gene. This dependency points to polymerase θ as an ideal drug target candidate and multiple drug-development programs are now preparing to enter clinical trials with small-molecule inhibitors. Specific inhibitors of polymerase θ would not only be predicted to treat BRCA-mutant cancers, but could thwart accumulated resistance to current standard-of-care cancer therapies and overcome PARP-inhibitor resistance in patients. This article will discuss synthetic lethal strategies targeting polymerase θ in DNA damage-response-deficient cancers and summarize data, describing molecular structures and enzymatic functions.
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Affiliation(s)
- Karl E. Zahn
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Repare Therapeutics, 7210 Rue Frederick Banting, Montreal, QC H4S 2A1, Canada
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
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115
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Simoneau A, Xiong R, Zou L. The trans cell cycle effects of PARP inhibitors underlie their selectivity toward BRCA1/2-deficient cells. Genes Dev 2021; 35:1271-1289. [PMID: 34385259 PMCID: PMC8415318 DOI: 10.1101/gad.348479.121] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/30/2021] [Indexed: 11/25/2022]
Abstract
In this study, Simoneau et al. investigated why PARPi is more effective than other DNA-damaging drugs when used to treat BRCA1/2-deficient tumors. They show that PARPi induces DSBs progressively through trans-cell-cycle ssDNA gaps, and BRCA1/2-deficient cells fail to slow down and repair DSBs over multiple cell cycles, explaining the unique efficacy of PARPi in BRCA1/2-deficient cells. PARP inhibitor (PARPi) is widely used to treat BRCA1/2-deficient tumors, but why PARPi is more effective than other DNA-damaging drugs is unclear. Here, we show that PARPi generates DNA double-strand breaks (DSBs) predominantly in a trans cell cycle manner. During the first S phase after PARPi exposure, PARPi induces single-stranded DNA (ssDNA) gaps behind DNA replication forks. By trapping PARP on DNA, PARPi prevents the completion of gap repair until the next S phase, leading to collisions of replication forks with ssDNA gaps and a surge of DSBs. In the second S phase, BRCA1/2-deficient cells are unable to suppress origin firing through ATR, resulting in continuous DNA synthesis and more DSBs. Furthermore, BRCA1/2-deficient cells cannot recruit RAD51 to repair collapsed forks. Thus, PARPi induces DSBs progressively through trans cell cycle ssDNA gaps, and BRCA1/2-deficient cells fail to slow down and repair DSBs over multiple cell cycles, explaining the unique efficacy of PARPi in BRCA1/2-deficient cells.
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Affiliation(s)
- Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Rosalinda Xiong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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116
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Gondo N, Sakai Y, Zhang Z, Hato Y, Kuzushima K, Phimsen S, Kawashima Y, Kuroda M, Suzuki M, Okada S, Iwata H, Toyama T, Rezano A, Kuwahara K. Increased chemosensitivity via BRCA2-independent DNA damage in DSS1- and PCID2-depleted breast carcinomas. J Transl Med 2021; 101:1048-1059. [PMID: 34031538 DOI: 10.1038/s41374-021-00613-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 11/09/2022] Open
Abstract
Breast cancer, the most common malignancy among women, is closely associated with mutations in the tumor suppressor gene BRCA. DSS1, a component of the TRanscription-EXport-2 (TREX-2) complex involved in transcription and mRNA nuclear export, stabilizes BRCA2 expression. DSS1 is also related to poor prognosis in patients with breast cancer owing to the induction of chemoresistance. Recently, BRCA2 was shown to be associated with the TREX-2 component PCID2, which prevents DNA:RNA hybrid R-loop formation and transcription-coupled DNA damage. This study aimed to elucidate the involvement of these TREX-2 components and BRCA2 in the chemosensitivity of breast carcinomas. Our results showed that compared with that in normal breast tissues, DSS1 expression was upregulated in human breast carcinoma, whereas PCID2 expression was comparable between normal and malignant tissues. We then compared patient survival time among groups divided by high or low expressions of DSS1, BRCA2, and PCID2. Increased DSS1 expression was significantly correlated with poor prognosis in recurrence-free survival time, whereas no differences were detected in the high and low BRCA2 and PCID2 expression groups. We performed in vitro analyses, including propidium iodide nuclear staining, single-cell gel electrophoresis, and clonogenic survival assays, using breast carcinoma cell lines. The results confirmed that DSS1 depletion significantly increased chemosensitivity, whereas overexpression conferred chemoresistance to breast cancer cell lines; however, BRCA2 expression did not affect chemosensitivity. Similar to DSS1, PCID2 expression was also inversely correlated with chemosensitivity. These results strongly suggest that DSS1 and PCID2 depletion is closely associated with increased chemosensitivity via BRCA2-independent DNA damage. Together with the finding that DSS1 is not highly expressed in normal breast tissues, these results demonstrate that DSS1 depletion confers a druggable trait and may contribute to the development of novel chemotherapeutic strategies to treat DSS1-depleted breast carcinomas independent of BRCA2 mutations.
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Affiliation(s)
- Naomi Gondo
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasuhiro Sakai
- Department of Joint Research Laboratory of Clinical Medicine, Fujita Health University School of Medicine, Toyoake, Japan
| | - Zhenhuan Zhang
- Radiation Oncology Department, University of Florida, Gainesville, FL, USA
| | - Yukari Hato
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kiyotaka Kuzushima
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Suchada Phimsen
- Faculty of Medical Science, Department of Biochemistry, Naresuan University, Phitsanulok, Thailand
| | - Yoshiaki Kawashima
- Department of Pathology, Fujita Health University Hospital, Toyoake, Japan
| | - Makoto Kuroda
- Department of Pathology, Fujita Health University Okazaki Medical Center, Okazaki, Japan
| | - Motoshi Suzuki
- Department of Molecular Oncology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Retroviral Infection, Kumamoto University, Kumamoto, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Tatsuya Toyama
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Andri Rezano
- Division of Cell Biology, Faculty of Medicine, Department of Biomedical Sciences, Universitas Padjadjaran, West Java, Indonesia.
| | - Kazuhiko Kuwahara
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.
- Department of Diagnostic Pathology, Fujita Health University School of Medicine, Toyoake, Japan.
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117
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Ali R, Alabdullah M, Algethami M, Alblihy A, Miligy I, Shoqafi A, Mesquita KA, Abdel-Fatah T, Chan SYT, Chiang PW, Mongan NP, Rakha EA, Tomkinson AE, Madhusudan S. Ligase 1 is a predictor of platinum resistance and its blockade is synthetically lethal in XRCC1 deficient epithelial ovarian cancers. Theranostics 2021; 11:8350-8361. [PMID: 34373746 PMCID: PMC8344016 DOI: 10.7150/thno.51456] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Rationale: The human ligases (LIG1, LIG3 and LIG4) are essential for the maintenance of genomic integrity by catalysing the formation of phosphodiester bonds between adjacent 5'-phosphoryl and 3'-hydroxyl termini at single and double strand breaks in duplex DNA molecules generated either directly by DNA damage or during replication, recombination, and DNA repair. Whether LIG1, LIG3 and LIG4 can influence ovarian cancer pathogenesis and therapeutics is largely unknown. Methods: We investigated LIG1, LIG3 and LIG4 expression in clinical cohorts of epithelial ovarian cancers [protein level (n=525) and transcriptional level (n=1075)] and correlated to clinicopathological features and survival outcomes. Pre-clinically, platinum sensitivity was investigated in LIG1 depleted ovarian cancer cells. A small molecule inhibitor of LIG1 (L82) was tested for synthetic lethality application in XRCC1, BRCA2 or ATM deficient cancer cells. Results: LIG1 and LIG3 overexpression linked with aggressive phenotypes, platinum resistance and poor progression free survival (PFS). In contrast, LIG4 deficiency was associated with platinum resistance and worse PFS. In a multivariate analysis, LIG1 was independently associated with adverse outcome. In ovarian cancer cell lines, LIG1 depletion increased platinum cytotoxicity. L82 monotherapy was synthetically lethal in XRCC1 deficient ovarian cancer cells and 3D-spheroids. Increased cytotoxicity was linked with accumulation of DNA double strand breaks (DSBs), S-phase cell cycle arrest and increased apoptotic cells. L82 was also selectively toxic in BRCA2 deficient or ATM deficient cancer cells and 3D-spheroids. Conclusions: We provide evidence that LIG1 is an attractive target for personalization of ovarian cancer therapy.
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Affiliation(s)
- Reem Ali
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
| | - Muslim Alabdullah
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK
| | - Mashael Algethami
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
| | - Adel Alblihy
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
- Medical Center, King Fahad Security College (KFSC), Riyadh 11461, Saudi Arabia
| | - Islam Miligy
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK
| | - Ahmed Shoqafi
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
| | - Katia A. Mesquita
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
| | - Tarek Abdel-Fatah
- Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham NG5 1PB, UK
| | - Stephen YT Chan
- Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham NG5 1PB, UK
| | - Pei Wen Chiang
- Department of Obstetrics & Gynaecology, Queens Medical Centre, Nottingham University Hospitals, Nottingham NG7 2UH, UK
| | - Nigel P Mongan
- Faculty of Medicine and Health Sciences, Centre for Cancer Sciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK
| | - Alan E Tomkinson
- Department of Internal Medicine, Division of Molecular Medicine, Health Sciences Center, The University of New Mexico, Albuquerque, NM 87102, USA
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
- Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham NG5 1PB, UK
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118
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Foo TK, Vincelli G, Huselid E, Her J, Zheng H, Simhadri S, Wang M, Huo Y, Li T, Yu X, Li H, Zhao W, Bunting SF, Xia B. ATR/ATM-mediated phosphorylation of BRCA1 T1394 promotes homologous recombinational repair and G2/M checkpoint maintenance. Cancer Res 2021; 81:4676-4684. [PMID: 34301763 PMCID: PMC8448966 DOI: 10.1158/0008-5472.can-20-2723] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 06/22/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022]
Abstract
BRCA1 maintains genome integrity and suppresses tumorigenesis by promoting homologous recombination (HR)-mediated repair of DNA double strand breaks (DSB) and DNA damage-induced cell cycle checkpoints. Phosphorylation of BRCA1 by ATM, ATR, CHK2, CDK, and PLK1 kinases has been reported to regulate its functions. Here we show that ATR and ATM-mediated phosphorylation of BRCA1 on T1394, a highly conserved but functionally uncharacterized site, is a key modification for its function in the DNA damage response. Following DNA damage, T1394 phosphorylation ensured faithful repair of DSBs by promoting HR and preventing single strand annealing, a deletion-generating repair process. BRCA1 T1394 phosphorylation further safeguarded chromosomal integrity by maintaining the G2/M checkpoint. Moreover, multiple patient-derived BRCA1 variants of unknown significance were shown to affect T1394 phosphorylation. These results establish an important regulatory mechanism of BRCA1 function in the DNA damage response and may have implications in the development or prognosis of BRCA1-associated cancers.
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Affiliation(s)
- Tzeh K Foo
- Radiation Oncology, Rutgers Cancer Institute of New Jersey
| | | | - Eric Huselid
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey
| | - Joonyoung Her
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey
| | | | | | - Meiling Wang
- The University of Texas Health Science Center at San Antonio
| | - Yanying Huo
- Radiation Oncology, Rutgers Cancer Institute of New Jersey
| | - Tao Li
- Department of Medicine/Population Sciences, Rutgers Cancer Institute of New Jersey
| | | | - Hong Li
- Center for advanced proteomics, Rutgers, The State University of New Jersey
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio
| | - Samuel F Bunting
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey
| | - Bing Xia
- Radiation Oncology, Rutgers Cancer Institute of New Jersey
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119
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Muhseena N K, Mathukkada S, Das SP, Laha S. The repair gene BACH1 - a potential oncogene. Oncol Rev 2021; 15:519. [PMID: 34322202 PMCID: PMC8273628 DOI: 10.4081/oncol.2021.519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACH1 encodes for a protein that belongs to RecQ DEAH helicase family and interacts with the BRCT repeats of BRCA1. The N-terminus of BACH1 functions in DNA metabolism as DNA-dependent ATPase and helicase. The C-terminus consists of BRCT domain, which interacts with BRCA1 and this interaction is one of the major regulator of BACH1 function. BACH1 plays important roles both in phosphorylated as well as dephosphorylated state and functions in coordination with multiple signaling molecules. The active helicase property of BACH1 is maintained by its dephosphorylated state. Imbalance between these two states enhances the development and progression of the diseased condition. Currently BACH1 is known as a tumor suppressor gene based on the presence of its clinically relevant mutations in different cancers. Through this review we have justified it to be named as an oncogene. In this review, we have explained the mechanism of how BACH1 in collaboration with BRCA1 or independently regulates various pathways like cell cycle progression, DNA replication during both normal and stressed situation, recombination and repair of damaged DNA, chromatin remodeling and epigenetic modifications. Mutation and overexpression of BACH1 are significantly found in different cancer types. This review enlists the molecular players which interact with BACH1 to regulate DNA metabolic functions, thereby revealing its potential for cancer therapeutics. We have identified the most mutated functional domain of BACH1, the hot spot for tumorigenesis, justifying it as a target molecule in different cancer types for therapeutics. BACH1 has high potentials of transforming a normal cell into a tumor cell if compromised under certain circumstances. Thus, through this review, we justify BACH1 as an oncogene along with the existing role of being a tumor suppressant.
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Affiliation(s)
- Katheeja Muhseena N
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Sooraj Mathukkada
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Suparna Laha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
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120
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Brnich SE, Arteaga EC, Wang Y, Tan X, Berg JS. A Validated Functional Analysis of Partner and Localizer of BRCA2 Missense Variants for Use in Clinical Variant Interpretation. J Mol Diagn 2021; 23:847-864. [PMID: 33964450 PMCID: PMC8491091 DOI: 10.1016/j.jmoldx.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/06/2021] [Indexed: 12/29/2022] Open
Abstract
Clinical genetic testing readily detects germline genetic variants. Yet, the rarity of individual variants limits the evidence available for variant classification, leading to many variants of uncertain significance (VUS). VUS cannot guide clinical decisions, complicating counseling and management. In hereditary breast cancer gene PALB2, approximately 50% of clinically identified germline variants are VUS and approximately 90% of VUS are missense. Truncating PALB2 variants have homologous recombination (HR) defects and rely on error-prone nonhomologous end-joining for DNA damage repair (DDR). Recent reports show that some missense PALB2 variants may also be damaging, but most functional studies have lacked benchmarking controls required for sufficient predictive power for clinical use. Here, variant-level DDR capacity in hereditary breast cancer genes was assessed using the Traffic Light Reporter (TLR) to quantify cellular HR/nonhomologous end-joining with fluorescent markers. First, using BRCA2 missense variants of known significance as benchmarks, the TLR distinguished between normal/abnormal HR function. The TLR was then validated for PALB2 and used to test 37 PALB2 variants. Based on the TLR's ability to correctly classify PALB2 validation controls, these functional data where applied in subsequent germline variant interpretations at a moderate level of evidence toward a pathogenic interpretation (PS3_moderate) for 8 variants with abnormal DDR, or a supporting level of evidence toward a benign interpretation (BS3_supporting) for 13 variants with normal DDR.
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Affiliation(s)
- Sarah E Brnich
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eyla Cristina Arteaga
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yueting Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xianming Tan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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121
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Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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122
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Spiegel JO, Van Houten B, Durrant JD. PARP1: Structural insights and pharmacological targets for inhibition. DNA Repair (Amst) 2021; 103:103125. [PMID: 33940558 PMCID: PMC8206044 DOI: 10.1016/j.dnarep.2021.103125] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair pathways, including the base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR), and Okazaki-fragment processing pathways. In response to DNA strand breaks, PARP1 covalently attaches ADP-ribose moieties to arginine, glutamate, aspartate, cysteine, lysine, and serine acceptor sites on both itself and other proteins. This signal recruits DNA repair proteins to the site of DNA damage. PARP1 binding to these sites enhances ADP-ribosylation via allosteric communication between the distant DNA binding and catalytic domains. In this review, we provide a general overview of PARP1 and emphasize novel potential approaches for pharmacological inhibition. Clinical PARP1 inhibitors bind the catalytic pocket, where they directly interfere with ADP-ribosylation. Some inhibitors may further enhance potency by "trapping" PARP1 on DNA via an allosteric mechanism, though this proposed mode of action remains controversial. PARP1 inhibitors are used clinically to treat some cancers, but resistance is common, so novel pharmacological approaches are urgently needed. One approach may be to design novel small molecules that bind at inter-domain interfaces that are essential for PARP1 allostery. To illustrate these points, this review also includes instructive videos showing PARP1 structures and mechanisms.
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Affiliation(s)
- Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Ekstrom TL, Pathoulas NM, Huehls AM, Kanakkanthara A, Karnitz LM. VLX600 Disrupts Homologous Recombination and Synergizes with PARP Inhibitors and Cisplatin by Inhibiting Histone Lysine Demethylases. Mol Cancer Ther 2021; 20:1561-1571. [PMID: 34224364 DOI: 10.1158/1535-7163.mct-20-1099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022]
Abstract
Tumors with defective homologous recombination (HR) DNA repair are more sensitive to chemotherapies that induce lesions repaired by HR as well as PARP inhibitors (PARPis). However, these therapies have limited activity in HR-proficient cells. Accordingly, agents that disrupt HR may be a means to augment the activities of these therapies in HR-proficient tumors. Here we show that VLX600, a small molecule that has been in a phase I clinical trial, disrupts HR and synergizes with PARPis and platinum compounds in ovarian cancer cells. We further found that VLX600 and other iron chelators disrupt HR, in part, by inhibiting iron-dependent histone lysine demethylases (KDM) family members, thus blocking recruitment of HR repair proteins, including RAD51, to double-strand DNA breaks. Collectively, these findings suggest that pharmacologically targeting KDM family members with VLX600 may be a potential novel strategy to therapeutically induce HR defects in ovarian cancers and correspondingly sensitize them to platinum agents and PARPis, two standard-of-care therapies for ovarian cancer.
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Affiliation(s)
- Thomas L Ekstrom
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Nicholas M Pathoulas
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amelia M Huehls
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Arun Kanakkanthara
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Larry M Karnitz
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
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Zhou Q, Howard ME, Tu X, Zhu Q, Denbeigh JM, Remmes NB, Herman MG, Beltran CJ, Yuan J, Greipp PT, Boughey JC, Wang L, Johnson N, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. Inhibition of ATM Induces Hypersensitivity to Proton Irradiation by Upregulating Toxic End Joining. Cancer Res 2021; 81:3333-3346. [PMID: 33597272 PMCID: PMC8260463 DOI: 10.1158/0008-5472.can-20-2960] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/30/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022]
Abstract
Proton Bragg peak irradiation has a higher ionizing density than conventional photon irradiation or the entrance of the proton beam profile. Whether targeting the DNA damage response (DDR) could enhance vulnerability to the distinct pattern of damage induced by proton Bragg peak irradiation is currently unknown. Here, we performed genetic or pharmacologic manipulation of key DDR elements and evaluated DNA damage signaling, DNA repair, and tumor control in cell lines and xenografts treated with the same physical dose across a radiotherapy linear energy transfer spectrum. Radiotherapy consisted of 6 MV photons and the entrance beam or Bragg peak of a 76.8 MeV spot scanning proton beam. More complex DNA double-strand breaks (DSB) induced by Bragg peak proton irradiation preferentially underwent resection and engaged homologous recombination (HR) machinery. Unexpectedly, the ataxia-telangiectasia mutated (ATM) inhibitor, AZD0156, but not an inhibitor of ATM and Rad3-related, rendered cells hypersensitive to more densely ionizing proton Bragg peak irradiation. ATM inhibition blocked resection and shunted more DSBs to processing by toxic ligation through nonhomologous end-joining, whereas loss of DNA ligation via XRCC4 or Lig4 knockdown rescued resection and abolished the enhanced Bragg peak cell killing. Proton Bragg peak monotherapy selectively sensitized cell lines and tumor xenografts with inherent HR defects, and the repair defect induced by ATM inhibitor coadministration showed enhanced efficacy in HR-proficient models. In summary, inherent defects in HR or administration of an ATM inhibitor in HR-proficient tumors selectively enhances the relative biological effectiveness of proton Bragg peak irradiation. SIGNIFICANCE: Coadministration of an ATM inhibitor rewires DNA repair machinery to render cancer cells uniquely hypersensitive to DNA damage induced by the proton Bragg peak, which is characterized by higher density ionization.See related commentary by Nickoloff, p. 3156.
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Affiliation(s)
- Qin Zhou
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Janet M Denbeigh
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Michael G Herman
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Chris J Beltran
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jian Yuan
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Matthew P Goetz
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota.
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Analysis of chromatid-break-repair detects a homologous recombination to non-homologous end-joining switch with increasing load of DNA double-strand breaks. Mutat Res 2021; 867:503372. [PMID: 34266628 DOI: 10.1016/j.mrgentox.2021.503372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022]
Abstract
We recently reported that when low doses of ionizing radiation induce low numbers of DNA double-strand breaks (DSBs) in G2-phase cells, about 50 % of them are repaired by homologous recombination (HR) and the remaining by classical non-homologous end-joining (c-NHEJ). However, with increasing DSB-load, the contribution of HR drops to undetectable (at ∼10 Gy) as c-NHEJ dominates. It remains unknown whether the approximately equal shunting of DSBs between HR and c-NHEJ at low radiation doses and the predominant shunting to c-NHEJ at high doses, applies to every DSB, or whether the individual characteristics of each DSB generate processing preferences. When G2-phase cells are irradiated, only about 10 % of the induced DSBs break the chromatids. This breakage allows analysis of the processing of this specific subset of DSBs using cytogenetic methods. Notably, at low radiation doses, these DSBs are almost exclusively processed by HR, suggesting that chromatin characteristics awaiting characterization underpin chromatid breakage and determine the preferential engagement of HR. Strikingly, we also discovered that with increasing radiation dose, a pathway switch to c-NHEJ occurs in the processing of this subset of DSBs. Here, we confirm and substantially extend our initial observations using additional methodologies. Wild-type cells, as well as HR and c-NHEJ mutants, are exposed to a broad spectrum of radiation doses and their response analyzed specifically in G2 phase. Our results further consolidate the observation that at doses <2 Gy, HR is the main option in the processing of the subset of DSBs generating chromatid breaks and that a pathway switch at doses between 4-6 Gy allows the progressive engagement of c-NHEJ. PARP1 inhibition, irrespective of radiation dose, leaves chromatid break repair unaffected suggesting that the contribution of alternative end-joining is undetectable under these experimental conditions.
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126
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The epigenetic regulator LSH maintains fork protection and genomic stability via MacroH2A deposition and RAD51 filament formation. Nat Commun 2021; 12:3520. [PMID: 34112784 PMCID: PMC8192551 DOI: 10.1038/s41467-021-23809-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is caused by mutations in LSH/HELLS, a chromatin remodeler promoting incorporation of histone variant macroH2A. Here, we demonstrate that LSH depletion results in degradation of nascent DNA at stalled replication forks and the generation of genomic instability. The protection of stalled forks is mediated by macroH2A, whose knockdown mimics LSH depletion and whose overexpression rescues nascent DNA degradation. LSH or macroH2A deficiency leads to an impairment of RAD51 loading, a factor that prevents MRE11 and EXO1 mediated nascent DNA degradation. The defect in RAD51 loading is linked to a disbalance of BRCA1 and 53BP1 accumulation at stalled forks. This is associated with perturbed histone modifications, including abnormal H4K20 methylation that is critical for BRCA1 enrichment and 53BP1 exclusion. Altogether, our results illuminate the mechanism underlying a human syndrome and reveal a critical role of LSH mediated chromatin remodeling in genomic stability. LSH/HELLS is a chromatin remodeler promoting incorporation of histone variant macroH2A. Here the authors reveal a role for LSH in genome stability, in protecting nascent DNA at stalled forks mediated by macroH2A deposition and RAD51 filament formation.
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127
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Lyu X, Sang PB, Chai W. CST in maintaining genome stability: Beyond telomeres. DNA Repair (Amst) 2021; 102:103104. [PMID: 33780718 PMCID: PMC8081025 DOI: 10.1016/j.dnarep.2021.103104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
The human CST (CTC1-STN1-TEN1) complex is an RPA-like single-stranded DNA binding protein complex. While its telomeric functions have been well investigated, numerous studies have revealed that hCST also plays important roles in maintaining genome stability beyond telomeres. Here, we review and discuss recent discoveries on CST in various global genome maintenance pathways, including findings on the CST supercomplex structure, its functions in unperturbed DNA replication, stalled replication, double-strand break repair, and the ATR-CHK1 activation pathway. By summarizing these recent discoveries, we hope to offer new insights into genome maintenance mechanisms and the pathogenesis of CST mutation-associated diseases.
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Affiliation(s)
- Xinxing Lyu
- Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China; Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States.
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128
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Repar J, Zahradka D, Sović I, Zahradka K. Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Sci Rep 2021; 11:10939. [PMID: 34035321 PMCID: PMC8149714 DOI: 10.1038/s41598-021-89173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4-11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.
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Affiliation(s)
- Jelena Repar
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Davor Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Sović
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Ksenija Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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129
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Matos-Rodrigues G, Guirouilh-Barbat J, Martini E, Lopez BS. Homologous recombination, cancer and the 'RAD51 paradox'. NAR Cancer 2021; 3:zcab016. [PMID: 34316706 PMCID: PMC8209977 DOI: 10.1093/narcan/zcab016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
Genetic instability is a hallmark of cancer cells. Homologous recombination (HR) plays key roles in genome stability and variability due to its roles in DNA double-strand break and interstrand crosslink repair, and in the protection and resumption of arrested replication forks. HR deficiency leads to genetic instability, and, as expected, many HR genes are downregulated in cancer cells. The link between HR deficiency and cancer predisposition is exemplified by familial breast and ovarian cancers and by some subgroups of Fanconi anaemia syndromes. Surprisingly, although RAD51 plays a pivotal role in HR, i.e., homology search and in strand exchange with a homologous DNA partner, almost no inactivating mutations of RAD51 have been associated with cancer predisposition; on the contrary, overexpression of RAD51 is associated with a poor prognosis in different types of tumours. Taken together, these data highlight the fact that RAD51 differs from its HR partners with regard to cancer susceptibility and expose what we call the ‘RAD51 paradox’. Here, we catalogue the dysregulations of HR genes in human pathologies, including cancer and Fanconi anaemia or congenital mirror movement syndromes, and we discuss the RAD51 paradox.
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Affiliation(s)
- Gabriel Matos-Rodrigues
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
| | - Emmanuelle Martini
- Université de Paris and Université Paris-Saclay, Laboratory of Development of the Gonads, IRCM/IBFJ CEA, UMR Genetic Stability, Stem Cells and Radiation, F-92265 Fontenay aux Roses, France
| | - Bernard S Lopez
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
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130
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De Ravin SS, Brault J, Meis RJ, Liu S, Li L, Pavel-Dinu M, Lazzarotto CR, Liu T, Koontz SM, Choi U, Sweeney CL, Theobald N, Lee G, Clark AB, Burkett SS, Kleinstiver BP, Porteus MH, Tsai S, Kuhns DB, Dahl GA, Headey S, Wu X, Malech HL. Enhanced homology-directed repair for highly efficient gene editing in hematopoietic stem/progenitor cells. Blood 2021; 137:2598-2608. [PMID: 33623984 PMCID: PMC8120141 DOI: 10.1182/blood.2020008503] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/28/2021] [Indexed: 12/21/2022] Open
Abstract
Lentivector gene therapy for X-linked chronic granulomatous disease (X-CGD) has proven to be a viable approach, but random vector integration and subnormal protein production from exogenous promoters in transduced cells remain concerning for long-term safety and efficacy. A previous genome editing-based approach using Streptococcus pyogenes Cas9 mRNA and an oligodeoxynucleotide donor to repair genetic mutations showed the capability to restore physiological protein expression but lacked sufficient efficiency in quiescent CD34+ hematopoietic cells for clinical translation. Here, we report that transient inhibition of p53-binding protein 1 (53BP1) significantly increased (2.3-fold) long-term homology-directed repair to achieve highly efficient (80% gp91phox+ cells compared with healthy donor control subjects) long-term correction of X-CGD CD34+ cells.
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Affiliation(s)
- Suk See De Ravin
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Julie Brault
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Siyuan Liu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD
| | | | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, School of Medicine, Stanford, CA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Taylor Liu
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sherry M Koontz
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Uimook Choi
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Colin L Sweeney
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Narda Theobald
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - GaHyun Lee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Aaron B Clark
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD
| | - Sandra S Burkett
- Molecular Cytogenetic Core Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA; and
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, School of Medicine, Stanford, CA
| | - Shengdar Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Douglas B Kuhns
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Stephen Headey
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD
| | - Harry L Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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131
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Rosen MN, Goodwin RA, Vickers MM. BRCA mutated pancreatic cancer: A change is coming. World J Gastroenterol 2021; 27:1943-1958. [PMID: 34007132 PMCID: PMC8108028 DOI: 10.3748/wjg.v27.i17.1943] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/04/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer remains a leading cause of cancer-related death with few available therapies for advanced disease. Recently, patients with germline BRCA mutations have received increased attention due to advances in the management of BRCA mutated ovarian and breast tumors. Germline BRCA mutations significantly increase risk of developing pancreatic cancer and can be found in up to 8% of patients with sporadic pancreatic cancer. In patients with germline BRCA mutations, platinum-based chemotherapies and poly (ADP-ribose) polymerase inhibitors are effective treatment options which may offer survival benefits. This review will focus on the molecular biology, epidemiology, and management of BRCA-mutated pancreatic cancer. Furthermore, we will discuss future directions for this area of research and promising active areas of research.
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Affiliation(s)
- Michael N Rosen
- Faculty of Medicine, The University of Ottawa, Ottawa K1H 8L6, Ontario, Canada
| | - Rachel A Goodwin
- Faculty of Medicine, The University of Ottawa, Ottawa K1H 8L6, Ontario, Canada
| | - Michael M Vickers
- The Ottawa Hospital Cancer Center, The University of Ottawa, Ottawa K1H 8L6, Ontario, Canada
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132
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The Ubiquitin Ligase TRIP12 Limits PARP1 Trapping and Constrains PARP Inhibitor Efficiency. Cell Rep 2021; 32:107985. [PMID: 32755579 PMCID: PMC7408484 DOI: 10.1016/j.celrep.2020.107985] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/22/2020] [Accepted: 07/10/2020] [Indexed: 12/26/2022] Open
Abstract
PARP inhibitors (PARPi) cause synthetic lethality in BRCA-deficient tumors. Whether specific vulnerabilities to PARPi exist beyond BRCA mutations and related defects in homology-directed repair (HDR) is not well understood. Here, we identify the ubiquitin E3 ligase TRIP12 as negative regulator of PARPi sensitivity. We show that TRIP12 controls steady-state PARP1 levels and limits PARPi-induced cytotoxic PARP1 trapping. Upon loss of TRIP12, elevated PARPi-induced PARP1 trapping causes increased DNA replication stress, DNA damage, cell cycle arrest, and cell death. Mechanistically, we demonstrate that TRIP12 binds PARP1 via a central PAR-binding WWE domain and, using its carboxy-terminal HECT domain, catalyzes polyubiquitylation of PARP1, triggering proteasomal degradation and preventing supra-physiological PARP1 accumulation. Further, in cohorts of breast and ovarian cancer patients, PARP1 abundance is negatively correlated with TRIP12 expression. We thus propose TRIP12 as regulator of PARP1 stability and PARPi-induced PARP trapping, with potential implications for PARPi sensitivity and resistance.
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133
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Mouse Models for Deciphering the Impact of Homologous Recombination on Tumorigenesis. Cancers (Basel) 2021; 13:cancers13092083. [PMID: 33923105 PMCID: PMC8123484 DOI: 10.3390/cancers13092083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) is a fundamental evolutionarily conserved process that plays prime role(s) in genome stability maintenance through DNA repair and through the protection and resumption of arrested replication forks. Many HR genes are deregulated in cancer cells. Notably, the breast cancer genes BRCA1 and BRCA2, two important HR players, are the most frequently mutated genes in familial breast and ovarian cancer. Transgenic mice constitute powerful tools to unravel the intricate mechanisms controlling tumorigenesis in vivo. However, the genes central to HR are essential in mammals, and their knockout leads to early embryonic lethality in mice. Elaborated strategies have been developed to overcome this difficulty, enabling one to analyze the consequences of HR disruption in vivo. In this review, we first briefly present the molecular mechanisms of HR in mammalian cells to introduce each factor in the HR process. Then, we present the different mouse models of HR invalidation and the consequences of HR inactivation on tumorigenesis. Finally, we discuss the use of mouse models for the development of targeted cancer therapies as well as perspectives on the future potential for understanding the mechanisms of HR inactivation-driven tumorigenesis in vivo.
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134
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Tseng WC, Chen CY, Chern CY, Wang CA, Lee WC, Chi YC, Cheng SF, Kuo YT, Chiu YC, Tseng ST, Lin PY, Liou SJ, Li YC, Chen CC. Targeting HR Repair as a Synthetic Lethal Approach to Increase DNA Damage Sensitivity by a RAD52 Inhibitor in BRCA2-Deficient Cancer Cells. Int J Mol Sci 2021; 22:4422. [PMID: 33922657 PMCID: PMC8122931 DOI: 10.3390/ijms22094422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/01/2023] Open
Abstract
BRCA mutation, one of the most common types of mutations in breast and ovarian cancer, has been suggested to be synthetically lethal with depletion of RAD52. Pharmacologically inhibiting RAD52 specifically eradicates BRCA-deficient cancer cells. In this study, we demonstrated that curcumin, a plant polyphenol, sensitizes BRCA2-deficient cells to CPT-11 by impairing RAD52 recombinase in MCF7 cells. More specifically, in MCF7-siBRCA2 cells, curcumin reduced homologous recombination, resulting in tumor growth suppression. Furthermore, a BRCA2-deficient cell line, Capan1, became resistant to CPT-11 when BRCA2 was reintroduced. In vivo, xenograft model studies showed that curcumin combined with CPT-11 reduced the growth of BRCA2-knockout MCF7 tumors but not MCF7 tumors. In conclusion, our data indicate that curcumin, which has RAD52 inhibitor activity, is a promising candidate for sensitizing BRCA2-deficient cells to DNA damage-based cancer therapies.
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Affiliation(s)
- Wei-Che Tseng
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Chi-Yuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
- Graduate Institute of Health Industry Technology and Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
| | - Ching-Yuh Chern
- Department of Applied Chemistry, National Chiayi University, Chiayi 600, Taiwan; (C.-Y.C.); (Y.-C.L.)
| | - Chu-An Wang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Wen-Chih Lee
- Translational Research Program in Pediatric Orthopedics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Ying-Chih Chi
- Cryo-EM Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Shu-Fang Cheng
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Yi-Tsen Kuo
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Ya-Chen Chiu
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Shih-Ting Tseng
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Pei-Ya Lin
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Shou-Jhen Liou
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
| | - Yi-Chen Li
- Department of Applied Chemistry, National Chiayi University, Chiayi 600, Taiwan; (C.-Y.C.); (Y.-C.L.)
| | - Chin-Chuan Chen
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan; (W.-C.T.); (S.-F.C.); (Y.-T.K.); (Y.-C.C.); (S.-T.T.); (P.-Y.L.); (S.-J.L.)
- Tissue Bank, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
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135
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Huo Y, Selenica P, Mahdi AH, Pareja F, Kyker-Snowman K, Chen Y, Kumar R, Da Cruz Paula A, Basili T, Brown DN, Pei X, Riaz N, Tan Y, Huang YX, Li T, Barnard NJ, Reis-Filho JS, Weigelt B, Xia B. Genetic interactions among Brca1, Brca2, Palb2, and Trp53 in mammary tumor development. NPJ Breast Cancer 2021; 7:45. [PMID: 33893322 PMCID: PMC8065161 DOI: 10.1038/s41523-021-00253-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/24/2021] [Indexed: 02/08/2023] Open
Abstract
Inherited mutations in BRCA1, BRCA2, and PALB2 cause a high risk of breast cancer. Here, we conducted parallel conditional knockout (CKO) of Brca1, Palb2, and Brca2, individually and in combination, along with one copy of Trp53, in the mammary gland of nulliparous female mice. We observed a functional equivalence of the three genes in their basic tumor-suppressive activity, a linear epistasis of Palb2 and Brca2, but complementary roles of Brca1 and Palb2 in mammary tumor suppression, as combined ablation of either Palb2 or Brca2 with Brca1 led to delayed tumor formation. Whole-exome sequencing (WES) revealed both similarities and differences between Brca1 and Palb2 or Brca2 null tumors. Analyses of mouse mammary glands and cultured human cells showed that combined loss of BRCA1 and PALB2 led to high levels of reactive oxygen species (ROS) and increased apoptosis, implicating oxidative stress in the delayed tumor development in Brca1;Palb2 double CKO mice. The functional complementarity between BRCA1 and PALB2/BRCA2 and the role of ROS in tumorigenesis require further investigation.
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Affiliation(s)
- Yanying Huo
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amar H Mahdi
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Physiology, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly Kyker-Snowman
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Brain Research, Indian Institute of Science (IISc), Bangalore, India
| | - Arnaud Da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thais Basili
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xin Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yongmei Tan
- Stomatological Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu-Xiu Huang
- The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Tao Li
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Nicola J Barnard
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Bing Xia
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
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136
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Sullivan MR, Prakash R, Rawal Y, Wang W, Sung P, Radke MR, Kaufmann SH, Swisher EM, Bernstein KA, Jasin M. Long-term survival of an ovarian cancer patient harboring a RAD51C missense mutation. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006083. [PMID: 33832919 PMCID: PMC8040731 DOI: 10.1101/mcs.a006083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/28/2021] [Indexed: 11/30/2022] Open
Abstract
Mutations in homologous recombination (HR) genes predispose to cancer but also sensitize to chemotherapeutics. Although therapy can initially be effective, cancers frequently cease responding, leading to recurrence and poor prognosis. Here we identify a germline mutation in RAD51C, a critical HR factor and known tumor suppressor, in an ovarian cancer patient with exceptionally long, progression-free survival. The RAD51C–T132P mutation is in a highly conserved residue within the nucleotide-binding site and interferes with single-strand DNA binding of the RAD51 paralog complex RAD51B–RAD51C–RAD51D–XRCC2 and association with another RAD51 paralog XRCC3. These biochemical defects lead to highly defective HR and drug sensitivity in tumor cells, ascribing RAD51C–T132P as a deleterious mutation that was likely causal for tumor formation. Conversely, its position within a critical site suggests that it is refractory to secondary mutations that would restore RAD51C gene function and lead to therapy resistance. A need for a greater understanding of the relationship between mutation position and reversion potential of HR genes is underscored, as it may help predict the effectiveness of therapies in patients with HR-deficient cancers.
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Affiliation(s)
- Meghan R Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology, UT Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Weibin Wang
- Department of Radiation Medicine, Peking University Health Science Center, Beijing, 100191, China
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, UT Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Marc R Radke
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Elizabeth M Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Kara A Bernstein
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
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137
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Schwartzberg LS, Kiedrowski LA. Olaparib in hormone receptor-positive, HER2-negative metastatic breast cancer with a somatic BRCA2 mutation. Ther Adv Med Oncol 2021; 13:17588359211006962. [PMID: 33868464 PMCID: PMC8024449 DOI: 10.1177/17588359211006962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 11/19/2022] Open
Abstract
The oral poly(adenosine diphosphate-ribose) polymerase inhibitor olaparib is approved for the treatment of patients with human epidermal growth factor 2-negative (HER2-) metastatic breast cancer (mBC) and a germline breast cancer susceptibility gene (BRCA) mutation who have been treated with chemotherapy. This case report describes a 63-year-old postmenopausal woman with somatic BRCA2-mutated mBC who responded to olaparib treatment following multiple prior lines of therapy. The patient presented in January 2012 with locally advanced, hormone receptor-positive (HR+), HER2- BC which, despite initial response to neoadjuvant chemotherapy, recurred as bone disease in February 2014, and subsequently skin (June 2016) and liver (October 2016) metastases. A comprehensive 592-gene next-generation sequencing panel (Caris Life Sciences), performed on a skin biopsy, detected a pathogenic frameshift mutation in BRCA2 (H3154fs, c.9460delC), which was not identified in a 28-gene hereditary cancer germline analysis (Myriad Genetics, Inc.), and was therefore considered to be a somatic mutation. In January 2017, cell-free DNA (cfDNA) analysis (Guardant Health, Inc.) confirmed the BRCA2 H3154fs mutation in plasma. After several lines of chemotherapy and endocrine therapy, deriving clinical benefit from eribulin and capecitabine, the disease progressed by October 2017, and olaparib (300 mg orally twice daily) was initiated in January 2018. By April 2018, the liver lesions had shrunk by 80% and a >90% response in multiple skin lesions was noted. Clinical response was maintained for 8 months, followed by progression in the skin in September 2018. Biopsy of recurrent lesions revealed a novel BRCA2 mutation, E3152del (c.9455_9457delAGG), predicted to restore the open reading frame and presumably the mechanism of resistance to olaparib. Further likely resistance mutations were noted in subsequent cfDNA analyses. This case demonstrated a clinical response with olaparib as a later-line therapy for HR+, HER2- mBC with a somatic BRCA2 mutation.
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138
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Chilimoniuk J, Gosiewska A, Słowik J, Weiss R, Deckert PM, Rödiger S, Burdukiewicz M. countfitteR: efficient selection of count distributions to assess DNA damage. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:528. [PMID: 33987226 DOI: 10.21037/atm-20-6363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background DNA double-strand breaks can be counted as discrete foci by imaging techniques. In personalized medicine and pharmacology, the analysis of counting data is relevant for numerous applications, e.g., for cancer and aging research and the evaluation of drug efficacy. By default, it is assumed to follow the Poisson distribution. This assumption, however, may lead to biased results and faulty conclusions in datasets with excess zero values (zero-inflation), a variance larger than the mean (overdispersion), or both. In such cases, the assumption of a Poisson distribution would skew the estimation of mean and variance, and other models like the negative binomial (NB), zero-inflated Poisson or zero-inflated NB distributions should be employed. The model chosen has an influence on the parameter estimation (mean value and confidence interval). Yet the choice of the suitable distribution model is not trivial. Methods To support, simplify and objectify this process, we have developed the countfitteR software as an R package. We used a Bayesian approach for distribution model selection and the shiny web application framework for interactive data analysis. Results We show the application of our software based on examples of DNA double-strand break count data from phenotypic imaging by multiplex fluorescence microscopy. In analyzing numerous datasets of molecular pharmacological markers (phosphorylated histone H2AX and p53 binding protein), countfitteR demonstrated an equal or superior statistical performance compared to the usually employed two-step procedure, with an overall power of up to 98%. In addition, it still gave information in cases with no result at all from the two-step procedure. In our data sample we found that the NB distribution was the most frequent, with the Poisson distribution taking second place. Conclusions countfitteR can perform an automated distribution model selection and thus support the data analysis and lead to objective statistically verifiable estimated values. Originally designed for the analysis of foci in biomedical image data, countfitteR can be used in a variety of areas where non-Poisson distributed counting data is prevalent.
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Affiliation(s)
- Jarosław Chilimoniuk
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.,Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Alicja Gosiewska
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Jadwiga Słowik
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Romano Weiss
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - P Markus Deckert
- Faculty of Medicine and Psychology, Brandenburg Medical School Theodor Fontane, and Faculty of Health Sciences Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
| | - Stefan Rödiger
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany.,Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Michał Burdukiewicz
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany.,Medical University of Białystok, Białystok, Poland
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139
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Patel PS, Algouneh A, Hakem R. Exploiting synthetic lethality to target BRCA1/2-deficient tumors: where we stand. Oncogene 2021; 40:3001-3014. [PMID: 33716297 DOI: 10.1038/s41388-021-01744-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022]
Abstract
The principle of synthetic lethality, which refers to the loss of viability resulting from the disruption of two genes, which, individually, do not cause lethality, has become an attractive target approach due to the development and clinical success of Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi). In this review, we present the most recent findings on the use of PARPi in the clinic, which are currently approved for second-line therapy for advanced ovarian and breast cancer associated with mutations of BRCA1 or BRCA2 (BRCA1/2) genes. PARPi efficacy, however, appears to be limited by acquired and inherent resistance, highlighting the need for alternative and synergistic targets to eliminate these tumors. Here, we explore other identified synthetic lethal interactors of BRCA1/2, including DNA polymerase theta (POLQ), Fanconi anemia complementation group D2 (FANDC2), radiation sensitive 52 (RAD52), Flap structure-specific endonuclease 1 (FEN1), and apurinic/apyrimidinic endodeoxyribonuclease 2 (APE2), as well as other protein and nonprotein targets, for BRCA1/2-mutated cancers and their implications for future therapies. A wealth of information now exists for phenotypic and functional characterization of these novel synthetic lethal interactors of BRCA1/2, and leveraging these findings can pave the way for the development of new targeted therapies for patients suffering from these cancers.
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Affiliation(s)
- Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Arash Algouneh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Razq Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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140
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Yamaguchi H, Kitami K, Wu X, He L, Wang J, Wang B, Komatsu Y. Alteration of DNA Damage Response Causes Cleft Palate. Front Physiol 2021; 12:649492. [PMID: 33854442 PMCID: PMC8039291 DOI: 10.3389/fphys.2021.649492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Cleft palate is one of the most common craniofacial birth defects, however, little is known about how changes in the DNA damage response (DDR) cause cleft palate. To determine the role of DDR during palatogenesis, the DDR process was altered using a pharmacological intervention approach. A compromised DDR caused by a poly (ADP-ribose) polymerase (PARP) enzyme inhibitor resulted in cleft palate in wild-type mouse embryos, with increased DNA damage and apoptosis. In addition, a mouse genetic approach was employed to disrupt breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2), known as key players in DDR. An ectomesenchymal-specific deletion of Brca1 or Brca2 resulted in cleft palate due to attenuation of cell survival. This was supported by the phenotypes of the ectomesenchymal-specific Brca1/Brca2 double-knockout mice. The cleft palate phenotype was rescued by superimposing p53 null alleles, demonstrating that the BRCA1/2-p53 DDR pathway is critical for palatogenesis. Our study highlights the importance of DDR in palatogenesis.
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Affiliation(s)
- Hiroyuki Yamaguchi
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Kohei Kitami
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Xiao Wu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Li He
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Jianbo Wang
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Bin Wang
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Yoshihiro Komatsu
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States.,Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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141
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BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Nature 2021; 591:665-670. [PMID: 33536619 PMCID: PMC8245199 DOI: 10.1038/s41586-020-03150-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Strong connections exist between R-loops (three-stranded structures harbouring an RNA:DNA hybrid and a displaced single-strand DNA), genome instability and human disease1-5. Indeed, R-loops are favoured in relevant genomic regions as regulators of certain physiological processes through which homeostasis is typically maintained. For example, transcription termination pause sites regulated by R-loops can induce the synthesis of antisense transcripts that enable the formation of local, RNA interference (RNAi)-driven heterochromation6. Pause sites are also protected against endogenous single-stranded DNA breaks by BRCA17. Hypotheses about how DNA repair is enacted at pause sites include a role for RNA, which is emerging as a normal, albeit unexplained, regulator of genome integrity8. Here we report that a species of single-stranded, DNA-damage-associated small RNA (sdRNA) is generated by a BRCA1-RNAi protein complex. sdRNAs promote DNA repair driven by the PALB2-RAD52 complex at transcriptional termination pause sites that form R-loops and are rich in single-stranded DNA breaks. sdRNA repair operates in both quiescent (G0) and proliferating cells. Thus, sdRNA repair can occur in intact tissue and/or stem cells, and may contribute to tumour suppression mediated by BRCA1.
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142
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Arsenic hexoxide has differential effects on cell proliferation and genome-wide gene expression in human primary mammary epithelial and MCF7 cells. Sci Rep 2021; 11:3761. [PMID: 33580144 PMCID: PMC7881197 DOI: 10.1038/s41598-021-82551-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Arsenic is reportedly a biphasic inorganic compound for its toxicity and anticancer effects in humans. Recent studies have shown that certain arsenic compounds including arsenic hexoxide (AS4O6; hereafter, AS6) induce programmed cell death and cell cycle arrest in human cancer cells and murine cancer models. However, the mechanisms by which AS6 suppresses cancer cells are incompletely understood. In this study, we report the mechanisms of AS6 through transcriptome analyses. In particular, the cytotoxicity and global gene expression regulation by AS6 were compared in human normal and cancer breast epithelial cells. Using RNA-sequencing and bioinformatics analyses, differentially expressed genes in significantly affected biological pathways in these cell types were validated by real-time quantitative polymerase chain reaction and immunoblotting assays. Our data show markedly differential effects of AS6 on cytotoxicity and gene expression in human mammary epithelial normal cells (HUMEC) and Michigan Cancer Foundation 7 (MCF7), a human mammary epithelial cancer cell line. AS6 selectively arrests cell growth and induces cell death in MCF7 cells without affecting the growth of HUMEC in a dose-dependent manner. AS6 alters the transcription of a large number of genes in MCF7 cells, but much fewer genes in HUMEC. Importantly, we found that the cell proliferation, cell cycle, and DNA repair pathways are significantly suppressed whereas cellular stress response and apoptotic pathways increase in AS6-treated MCF7 cells. Together, we provide the first evidence of differential effects of AS6 on normal and cancerous breast epithelial cells, suggesting that AS6 at moderate concentrations induces cell cycle arrest and apoptosis through modulating genome-wide gene expression, leading to compromised DNA repair and increased genome instability selectively in human breast cancer cells.
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143
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Kim DS, Camacho CV, Kraus WL. Alternate therapeutic pathways for PARP inhibitors and potential mechanisms of resistance. Exp Mol Med 2021; 53:42-51. [PMID: 33487630 PMCID: PMC8080675 DOI: 10.1038/s12276-021-00557-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023] Open
Abstract
Homologous recombination (HR) repair deficiency impairs the proper maintenance of genomic stability, thus rendering cancer cells vulnerable to loss or inhibition of DNA repair proteins, such as poly(ADP-ribose) polymerase-1 (PARP-1). Inhibitors of nuclear PARPs are effective therapeutics for a number of different types of cancers. Here we review key concepts and current progress on the therapeutic use of PARP inhibitors (PARPi). PARPi selectively induce synthetic lethality in cancer cells with homologous recombination deficiencies (HRDs), the most notable being cancer cells harboring mutations in the BRCA1 and BRCA2 genes. Recent clinical evidence, however, shows that PARPi can be effective as cancer therapeutics regardless of BRCA1/2 or HRD status, suggesting that a broader population of patients might benefit from PARPi therapy. Currently, four PARPi have been approved by the Food and Drug Administration (FDA) for the treatment of advanced ovarian and breast cancer with deleterious BRCA mutations. Although PARPi have been shown to improve progression-free survival, cancer cells inevitably develop resistance, which poses a significant obstacle to the prolonged use of PARP inhibitors. For example, somatic BRCA1/2 reversion mutations are often identified in patients with BRCA1/2-mutated cancers after treatment with platinum-based therapy, causing restoration of HR capacity and thus conferring PARPi resistance. Accordingly, PARPi have been studied in combination with other targeted therapies to overcome PARPi resistance, enhance PARPi efficacy, and sensitize tumors to PARP inhibition. Moreover, multiple clinical trials are now actively underway to evaluate novel combinations of PARPi with other anticancer therapies for the treatment of PARPi-resistant cancer. In this review, we highlight the mechanisms of action of PARP inhibitors with or without BRCA1/2 defects and provide an overview of the ongoing clinical trials of PARPi. We also review the current progress on PARPi-based combination strategies and PARP inhibitor resistance.
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Affiliation(s)
- Dae-Seok Kim
- grid.267313.20000 0000 9482 7121Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Present Address: Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Cristel V. Camacho
- grid.267313.20000 0000 9482 7121Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - W. Lee Kraus
- grid.267313.20000 0000 9482 7121Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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144
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Zhou J, Zhou XA, Zhang N, Wang J. Evolving insights: how DNA repair pathways impact cancer evolution. Cancer Biol Med 2020; 17:805-827. [PMID: 33299637 PMCID: PMC7721097 DOI: 10.20892/j.issn.2095-3941.2020.0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
Viewing cancer as a large, evolving population of heterogeneous cells is a common perspective. Because genomic instability is one of the fundamental features of cancer, this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation, development, metastasis, and relapse. With the increased mutation rate and abundant diversity of the gene pool, this heterogeneity leads to cancer evolution, which is the major obstacle in the clinical treatment of cancer. Cells rely on the integrity of DNA repair machineries to maintain genomic stability, but these machineries often do not function properly in cancer cells. The deficiency of DNA repair could contribute to the generation of cancer genomic instability, and ultimately promote cancer evolution. With the rapid advance of new technologies, such as single-cell sequencing in recent years, we have the opportunity to better understand the specific processes and mechanisms of cancer evolution, and its relationship with DNA repair. Here, we review recent findings on how DNA repair affects cancer evolution, and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.
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Affiliation(s)
- Jiadong Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ning Zhang
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Biomedical Pioneering Innovation Center (BIOPIC) and Translational Cancer Research Center, School of Life Sciences, First Hospital, Peking University, Beijing 100871, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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145
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Rabl J. BRCA1-A and BRISC: Multifunctional Molecular Machines for Ubiquitin Signaling. Biomolecules 2020; 10:biom10111503. [PMID: 33142801 PMCID: PMC7692841 DOI: 10.3390/biom10111503] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The K63-linkage specific deubiquitinase BRCC36 forms the core of two multi-subunit deubiquitination complexes: BRCA1-A and BRISC. BRCA1-A is recruited to DNA repair foci, edits ubiquitin signals on chromatin, and sequesters BRCA1 away from the site of damage, suppressing homologous recombination by limiting resection. BRISC forms a complex with metabolic enzyme SHMT2 and regulates the immune response, mitosis, and hematopoiesis. Almost two decades of research have revealed how BRCA1-A and BRISC use the same core of subunits to perform very distinct biological tasks.
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Affiliation(s)
- Julius Rabl
- Cryo-EM Knowledge Hub, ETH Zürich, Otto-Stern-Weg 3, HPM C51, 8093 Zürich, Switzerland
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146
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O'Shaughnessy J, Brezden-Masley C, Cazzaniga M, Dalvi T, Walker G, Bennett J, Ohsumi S. Prevalence of germline BRCA mutations in HER2-negative metastatic breast cancer: global results from the real-world, observational BREAKOUT study. Breast Cancer Res 2020; 22:114. [PMID: 33109210 PMCID: PMC7590609 DOI: 10.1186/s13058-020-01349-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The global observational BREAKOUT study investigated germline BRCA mutation (gBRCAm) prevalence in a population of patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC). METHODS Eligible patients had initiated first-line cytotoxic chemotherapy for HER2-negative MBC within 90 days prior to enrollment. Hormone receptor (HR)-positive patients had experienced disease progression on or after prior endocrine therapy, or endocrine therapy was considered unsuitable. gBRCAm status was determined using baseline blood samples or prior germline test results. For patients with a negative gBRCAm test, archival tissue was tested for somatic BRCAm and homologous recombination repair mutations (HRRm). Details of first-line cytotoxic chemotherapy were also collected. RESULTS Between March 2017 and April 2018, 384 patients from 14 countries were screened and consented to study enrollment; 341 patients were included in the full analysis set (median [range] age at enrollment: 56 [25-89] years; 256 (75.3%) postmenopausal). Overall, 33 patients (9.7%) had a gBRCAm (16 [4.7%] in gBRCA1 only, 12 [3.5%] in gBRCA2 only, and 5 [1.5%] in both gBRCA1 and gBRCA2). gBRCAm prevalence was similar in HR-positive and HR-negative patients. gBRCAm prevalence was 9.0% in European patients and 10.6% in Asian patients and was higher in patients aged ≤ 50 years at initial breast cancer (BC) diagnosis (12.9%) than patients aged > 50 years (5.4%). In patients with any risk factor for having a gBRCAm (family history of BC and/or ovarian cancer, aged ≤ 50 years at initial BC diagnosis, or triple-negative BC), prevalence was 10.4%, versus 5.8% in patients without these risk factors. HRRm prevalence was 14.1% (n = 9/64) in patients with germline BRCA wildtype. CONCLUSIONS Patient demographic and disease characteristics supported the association of a gBRCAm with younger age at initial BC diagnosis and family history of BC and/or ovarian cancer. gBRCAm prevalence in this cohort, not selected on the basis of risk factors for gBRCAm, was slightly higher than previous results suggested. gBRCAm prevalence among patients without a traditional risk factor for harboring a gBRCAm (5.8%) supports current guideline recommendations of routine gBRCAm testing in HER2-negative MBC, as these patients may benefit from poly(ADP-ribose) polymerase (PARP) inhibitor therapy. TRIAL REGISTRATION NCT03078036 .
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Affiliation(s)
- Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology and US Oncology, Dallas, TX, USA.
| | | | | | - Tapashi Dalvi
- AstraZeneca Pharmaceuticals, LP, Gaithersburg, MD, USA
| | | | | | - Shozo Ohsumi
- NHO Shikoku Cancer Center, Matsuyama-shi, Ehime-Ken, Japan
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147
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Abstract
In this issue of Molecular Cell, Kim et al., 2020 report that PCAF is a fork-associated histone acetyltransferase (HAT) that regulates the stability of stalled forks and the response to PARP inhibition in BRCA1/2-deficient cells.
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148
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Tobalina L, Armenia J, Irving E, O'Connor MJ, Forment JV. A meta-analysis of reversion mutations in BRCA genes identifies signatures of DNA end-joining repair mechanisms driving therapy resistance. Ann Oncol 2020; 32:103-112. [PMID: 33091561 DOI: 10.1016/j.annonc.2020.10.470] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/27/2020] [Accepted: 10/04/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 or BRCA2 (BRCA) genes predispose to hereditary breast and ovarian cancer and, mostly in the case of BRCA2, are also prevalent in cases of pancreatic and prostate malignancies. Tumours from these patients tend to lose both copies of the wild-type BRCA gene, which makes them exquisitely sensitive to platinum drugs and poly(ADP-ribose) polymerase inhibitors (PARPi), treatments of choice in these disease settings. Reversion secondary mutations with the capacity of restoring BRCA protein expression have been documented in the literature as bona fide mechanisms of resistance to these treatments. PATIENTS AND METHODS We analysed published sequencing data of BRCA genes (from tumour or circulating tumour DNA) in 327 patients with tumours harbouring mutations in BRCA1 or BRCA2 (234 patients with ovarian cancer, 27 with breast cancer, 13 with pancreatic cancer, 11 with prostate cancer and 42 with a cancer of unknown origin) that progressed on platinum or PARPi treatment. RESULTS We describe 269 cases of reversion mutations in 86 patients in this cohort (26.0%). Detailed analyses of the reversion events highlight that most amino acid sequences encoded by exon 11 in BRCA1 and BRCA2 are dispensable to generate resistance to platinum or PARPi, whereas other regions are more refractory to sizeable amino acid losses. They also underline the key role of mutagenic end-joining DNA repair pathways in generating reversions, especially in those affecting BRCA2, as indicated by the significant accumulation of DNA sequence microhomologies surrounding deletions leading to reversion events. CONCLUSIONS Our analyses suggest that pharmacological inhibition of DNA end-joining repair pathways could improve durability of drug treatments by preventing the acquisition of reversion mutations in BRCA genes. They also highlight potential new therapeutic opportunities when reversions result in expression of hypomorphic versions of BRCA proteins, especially with agents targeting the response to DNA replication stress.
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Affiliation(s)
- L Tobalina
- Bioinformatics and Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - J Armenia
- Bioinformatics and Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - E Irving
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - M J O'Connor
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - J V Forment
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK.
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149
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Wang Y, Park JYP, Pacis A, Denroche RE, Jang GH, Zhang A, Cuggia A, Domecq C, Monlong J, Raitses-Gurevich M, Grant RC, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu IM, Bartlett JM, Wilson JM, Gao ZH, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher LM, Valenti D, Biagi J, Greenwood CM, Polak P, Foulkes WD, Golan T, O'Kane GM, Fischer SE, Knox JJ, Gallinger S, Zogopoulos G. A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination–deficient Pancreatic Cancer. Clin Cancer Res 2020; 26:5462-5476. [DOI: 10.1158/1078-0432.ccr-20-1439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 12/27/2022]
Abstract
Abstract
Purpose:
Pancreatic ductal adenocarcinoma (PDAC) arising in patients with a germline BRCA1 or BRCA2 (gBRCA) mutation may be sensitive to platinum and PARP inhibitors (PARPi). However, treatment stratification based on gBRCA mutational status alone is associated with heterogeneous responses.
Experimental Design:
We performed a seven-arm preclinical trial consisting of 471 mice, representing 12 unique PDAC patient-derived xenografts, of which nine were gBRCA mutated. From 179 patients whose PDAC was whole-genome and transcriptome sequenced, we identified 21 cases with homologous recombination deficiency (HRD), and investigated prognostic biomarkers.
Results:
We found that biallelic inactivation of BRCA1/BRCA2 is associated with genomic hallmarks of HRD and required for cisplatin and talazoparib (PARPi) sensitivity. However, HRD genomic hallmarks persisted in xenografts despite the emergence of therapy resistance, indicating the presence of a genomic scar. We identified tumor polyploidy and a low Ki67 index as predictors of poor cisplatin and talazoparib response. In patients with HRD PDAC, tumor polyploidy and a basal-like transcriptomic subtype were independent predictors of shorter survival. To facilitate clinical assignment of transcriptomic subtype, we developed a novel pragmatic two-marker assay (GATA6:KRT17).
Conclusions:
In summary, we propose a predictive and prognostic model of gBRCA-mutated PDAC on the basis of HRD genomic hallmarks, Ki67 index, tumor ploidy, and transcriptomic subtype.
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Affiliation(s)
- Yifan Wang
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jin Yong Patrick Park
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Alain Pacis
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 3Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | | | - Gun Ho Jang
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Adeline Cuggia
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Celine Domecq
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jean Monlong
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Maria Raitses-Gurevich
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Robert C. Grant
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ayelet Borgida
- 8Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- 8Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Chani Stossel
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- 9Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Simeng Bu
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Mehdi Masoomian
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ilinca M. Lungu
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M.S. Bartlett
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Julie M. Wilson
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Zu-Hua Gao
- 11Department of Pathology, McGill University, Montreal, Quebec, Canada
| | | | - Jamil Asselah
- 12Department of Oncology, McGill University, Montreal, Quebec, Canada
| | | | - Tatiana Cabrera
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - Louis-Martin Boucher
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - David Valenti
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - James Biagi
- 14Department of Oncology, Queen's University, Kingston, Ontario, Canada
| | - Celia M.T. Greenwood
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- 12Department of Oncology, McGill University, Montreal, Quebec, Canada
- 15Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
- 16Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Paz Polak
- 17Icahn School of Medicine at Mount Sinai Hospital, New York, New York
| | - William D. Foulkes
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Talia Golan
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- 9Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Grainne M. O'Kane
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Sandra E. Fischer
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer J. Knox
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - George Zogopoulos
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
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150
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p31 comet promotes homologous recombination by inactivating REV7 through the TRIP13 ATPase. Proc Natl Acad Sci U S A 2020; 117:26795-26803. [PMID: 33051298 PMCID: PMC7604461 DOI: 10.1073/pnas.2008830117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The repair of DNA double strand breaks (DSBs) that arise from external mutagenic agents and routine cellular processes is essential for life. DSBs are repaired by two major pathways, homologous recombination (HR) and classical nonhomologous end joining (C-NHEJ). DSB repair pathway choice is largely dictated at the step of 5'-3' DNA end resection, which is promoted during S phase, in part by BRCA1. Opposing end resection is the 53BP1 protein, which recruits the ssDNA-binding REV7-Shieldin complex to favor C-NHEJ repair. We recently identified TRIP13 as a proresection factor that remodels REV7, causing its dissociation from the Shieldin subunit SHLD3. Here, we identify p31comet, a negative regulator of MAD2 and the spindle assembly checkpoint, as an important mediator of the TRIP13-REV7 interaction. p31comet binds to the REV7-Shieldin complex in cells, promotes REV7 inactivation, and causes PARP inhibitor resistance. p31comet also participates in the extraction of REV7 from the chromatin. Furthermore, p31comet can counteract REV7 function in translesion synthesis (TLS) by releasing it from REV3 in the Pol ζ complex. Finally, p31comet, like TRIP13, is overexpressed in many cancers and this correlates with poor prognosis. Thus, we reveal a key player in the regulation of HR and TLS with significant clinical implications.
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