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Ma H, Kang Z, Foo TK, Shen Z, Xia B. Disrupted BRCA1-PALB2 interaction induces tumor immunosuppression and T-lymphocyte infiltration in HCC through cGAS-STING pathway. Hepatology 2023; 77:33-47. [PMID: 35006619 PMCID: PMC9271123 DOI: 10.1002/hep.32335] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND AIMS BRCA1 (BRCA1 DNA repair associated) and PALB2 (partner and localizer of BRCA2) interact with each other to promote homologous recombination and DNA double-strand breaks repair. The disruption of this interaction has been reported to play a role in tumorigenesis. However, its precise function in HCC remains poorly understood. APPROACH AND RESULTS We demonstrated that mice with disrupted BRCA1-PALB2 interaction were more susceptible to HCC than wild-type mice. HCC tumors arising from these mice showed plenty of T-lymphocyte infiltration and a better response to programmed cell death 1 (PD-1) antibody treatment. Mechanistically, disruption of the BRCA1-PALB2 interaction causes persistent high level of DNA damage in HCC cells, leading to activation of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway in both malignant hepatocytes and M1 macrophages in the tumor microenvironment. The activated cGAS-STING pathway induces programmed cell death 1 ligand 1 expression via the STING-interferon regulatory factor 3 (IRF3)-signal transducer and activator of transcription 1 pathway, causing immunosuppression to facilitate tumorigenesis and tumor progression. Meanwhile, M1 macrophages with an activated cGAS-STING pathway could recruit T lymphocytes through the STING-IRF3 pathway, leading to T-lymphocyte infiltration in tumors. After normalizing immune responses by PD-1 antibody treatment, the infiltrating T lymphocytes attack tumor cells rapidly and effectively. CONCLUSIONS This study reveals that persistent DNA damage caused by a defective BRCA pathway induces tumor immunosuppression and T-lymphocyte infiltration in HCC through the cGAS-STING pathway, providing insight into tumor immune microenvironment remodeling that may help improve HCC response to PD-1 antibody treatment.
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Affiliation(s)
- Hui Ma
- Liver Cancer Institute , Zhongshan Hospital , Fudan University , Shanghai , China
- Rutgers Cancer Institute of New Jersey , New Brunswick , New Jersey , USA
- Department of Radiation Oncology , Rutgers Robert Wood Johnson Medical School , New Brunswick , New Jersey , USA
| | - Zhihua Kang
- Rutgers Cancer Institute of New Jersey , New Brunswick , New Jersey , USA
- Department of Radiation Oncology , Rutgers Robert Wood Johnson Medical School , New Brunswick , New Jersey , USA
| | - Tzeh Keong Foo
- Rutgers Cancer Institute of New Jersey , New Brunswick , New Jersey , USA
- Department of Radiation Oncology , Rutgers Robert Wood Johnson Medical School , New Brunswick , New Jersey , USA
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey , New Brunswick , New Jersey , USA
- Department of Radiation Oncology , Rutgers Robert Wood Johnson Medical School , New Brunswick , New Jersey , USA
| | - Bing Xia
- Rutgers Cancer Institute of New Jersey , New Brunswick , New Jersey , USA
- Department of Radiation Oncology , Rutgers Robert Wood Johnson Medical School , New Brunswick , New Jersey , USA
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Valenzuela‐Palomo A, Bueno‐Martínez E, Sanoguera‐Miralles L, Lorca V, Fraile‐Bethencourt E, Esteban‐Sánchez A, Gómez‐Barrero S, Carvalho S, Allen J, García‐Álvarez A, Pérez‐Segura P, Dorling L, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Splicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants. J Pathol 2022; 256:321-334. [PMID: 34846068 PMCID: PMC9306493 DOI: 10.1002/path.5839] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022]
Abstract
PALB2 loss-of-function variants confer high risk of developing breast cancer. Here we present a systematic functional analysis of PALB2 splice-site variants detected in approximately 113,000 women in the large-scale sequencing project Breast Cancer After Diagnostic Gene Sequencing (BRIDGES; https://bridges-research.eu/). Eighty-two PALB2 variants at the intron-exon boundaries were analyzed with MaxEntScan. Forty-two variants were selected for the subsequent splicing functional assays. For this purpose, three splicing reporter minigenes comprising exons 1-12 were constructed. The 42 potential spliceogenic variants were introduced into the minigenes by site-directed mutagenesis and assayed in MCF-7/MDA-MB-231 cells. Splicing anomalies were observed in 35 variants, 23 of which showed no traces or minimal amounts of the expected full-length transcripts of each minigene. More than 30 different variant-induced transcripts were characterized, 23 of which were predicted to truncate the PALB2 protein. The pathogenicity of all variants was interpreted according to an in-house adaptation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) variant classification scheme. Up to 23 variants were classified as pathogenic/likely pathogenic. Remarkably, three ±1,2 variants (c.49-2A>T, c.108+2T>C, and c.211+1G>A) were classified as variants of unknown significance, as they produced significant amounts of either in-frame transcripts of unknown impact on the PALB2 protein function or the minigene full-length transcripts. In conclusion, we have significantly contributed to the ongoing effort of identifying spliceogenic variants in the clinically relevant PALB2 cancer susceptibility gene. Moreover, we suggest some approaches to classify the findings in accordance with the ACMG-AMP rationale. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Alberto Valenzuela‐Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Elena Bueno‐Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Lara Sanoguera‐Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Víctor Lorca
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eugenia Fraile‐Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
- Knight Cancer Research BuildingPortlandORUSA
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Alicia García‐Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Pedro Pérez‐Segura
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Peter Devilee
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
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Redington J, Deveryshetty J, Kanikkannan L, Miller I, Korolev S. Structural Insight into the Mechanism of PALB2 Interaction with MRG15. Genes (Basel) 2021; 12:genes12122002. [PMID: 34946951 PMCID: PMC8701324 DOI: 10.3390/genes12122002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/11/2021] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor protein partner and localizer of BRCA2 (PALB2) orchestrates the interactions between breast cancer susceptibility proteins 1 and 2 (BRCA1, -2) that are critical for genome stability, homologous recombination (HR) and DNA repair. PALB2 mutations predispose patients to a spectrum of cancers, including breast and ovarian cancers. PALB2 localizes HR machinery to chromatin and links it with transcription through multiple DNA and protein interactions. This includes its interaction with MRG15 (Morf-related gene on chromosome 15), which is part of many transcription complexes, including the HAT-associated and the HDAC-associated complexes. This interaction is critical for PALB2 localization in actively transcribed genes, where transcription/replication conflicts lead to frequent replication stress and DNA breaks. We solved the crystal structure of the MRG15 MRG domain bound to the PALB2 peptide and investigated the effect of several PALB2 mutations, including patient-derived variants. PALB2 interacts with an extended surface of the MRG that is known to interact with other proteins. This, together with a nanomolar affinity, suggests that the binding of MRG15 partners, including PALB2, to this region is mutually exclusive. Breast cancer-related mutations of PALB2 cause only minor attenuation of the binding affinity. New data reveal the mechanism of PALB2-MRG15 binding, advancing our understanding of PALB2 function in chromosome maintenance and tumorigenesis.
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Affiliation(s)
- Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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Beer A, Beck R, Schedel A, von Bonin M, Meinel J, Friedrich UA, Menzel M, Suttorp M, Brenner S, Fitze G, Lange B, Knöfler R, Hauer J, Auer F. A rare PALB2 germline variant causing G2/M cell cycle arrest is associated with isolated myelosarcoma in infancy. Mol Genet Genomic Med 2021; 9:e1746. [PMID: 34382369 PMCID: PMC8457705 DOI: 10.1002/mgg3.1746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/12/2021] [Accepted: 07/01/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Isolated myelosarcoma of infancy is a rare presentation of acute myelogenous leukaemia (AML). Because of its rarity and early onset in infancy underlying genetic predisposition is potentially relevant in disease initiation. METHODS AND RESULTS We report an oncologic emergency in an infant with thoracic and intraspinal aleukaemic myeloid sarcoma causing acute myelon compression and lower leg palsy. Whole-exome sequencing of the patient's germline DNA identified a rare PALB2 (OMIM 610355) variant (p.A1079S), which is located in a domain critical for the gene's proper function within the homology-directed repair pathway. In line with potential DNA damage repair defects mediated by the PALB2 deregulation, the patient's fibroblasts showed increased sensitivity towards radiation and DNA intercalating agents. CONCLUSION Therefore, we suggest PALB2 p.A1079S as a pathogenic variant potentially contributing to the here observed patient phenotype.
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Affiliation(s)
- Angelina Beer
- Neonatology and Pediatric Intensive CareDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Ricardo Beck
- Department of Pediatric SurgeryUniversity Hospital Carl Gustav CarusDresdenGermany
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Anne Schedel
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Malte von Bonin
- Medical Clinic IUniversity Hospital Carl Gustav CarusDresdenGermany
- German Cancer Consortium (DKTKDresdenGermany
- German Cancer Research Center (DKFZHeidelbergGermany
| | - Jörn Meinel
- Institute of PathologyUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Ulrike Anne Friedrich
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Maria Menzel
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Meinolf Suttorp
- Medical FacultyPediatric Hematology & OncologyTechnical UniversityDresdenGermany
| | - Sebastian Brenner
- Neonatology and Pediatric Intensive CareDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Guido Fitze
- Department of Pediatric SurgeryUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Björn Lange
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Ralf Knöfler
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
| | - Julia Hauer
- Pediatric Oncology and HematologyDepartment of PediatricsUniversity Hospital Carl Gustav CarusDresdenGermany
- National Center for Tumor Diseases (NCT)DresdenGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Franziska Auer
- National Center for Tumor Diseases (NCT)DresdenGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
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Han J, Yu M, Bai Y, Yu J, Jin F, Li C, Zeng R, Peng J, Li A, Song X, Li H, Wu D, Li L. Elevated CXorf67 Expression in PFA Ependymomas Suppresses DNA Repair and Sensitizes to PARP Inhibitors. Cancer Cell 2020; 38:844-856.e7. [PMID: 33186520 PMCID: PMC8455074 DOI: 10.1016/j.ccell.2020.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/12/2020] [Accepted: 10/07/2020] [Indexed: 01/01/2023]
Abstract
Ependymoma is the third most common pediatric tumor with posterior fossa group A (PFA) being its most aggressive subtype. Ependymomas are generally refractory to chemotherapies and thus lack any effective treatment. Here, we report that elevated expression of CXorf67 (chromosome X open reading frame 67), which frequently occurs in PFA ependymomas, suppresses homologous recombination (HR)-mediated DNA repair. Mechanistically, CXorf67 interacts with PALB2 and inhibits PALB2-BRCA2 interaction, thereby inhibiting HR repair. Concordantly, tumor cells with high CXorf67 expression levels show increased sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors, especially when combined with radiotherapy. Thus, our findings have revealed a role of CXorf67 in HR repair and suggest that combination of PARP inhibitors with radiotherapy could be an effective treatment option for PFA ependymomas.
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Affiliation(s)
- Jichang Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Meng Yu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiqin Bai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianzhong Yu
- Department of Neurosurgery, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Fei Jin
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Chen Li
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rong Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinghong Peng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ao Li
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 208089, USA
| | - Xiaomin Song
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Li
- Department of Neurosurgery, Children's Hospital of Fudan University, Shanghai 201102, China.
| | - Dianqing Wu
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 208089, USA.
| | - Lin Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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7
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Tsai L, Lopezcolorado F, Bhargava R, Mendez-Dorantes C, Jahanshir E, Stark J. RNF8 has both KU-dependent and independent roles in chromosomal break repair. Nucleic Acids Res 2020; 48:6032-6052. [PMID: 32427332 PMCID: PMC7293022 DOI: 10.1093/nar/gkaa380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/10/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
Chromosomal double strand breaks (DSBs) can initiate several signaling events, such as ubiquitination, however the precise influence of such signaling on DSB repair outcomes remains poorly understood. With an RNA interference screen, we found that the E3 ubiquitin ligase RNF8 suppresses a deletion rearrangement mediated by canonical non-homologous end joining (C-NHEJ). We also found that RNF8 suppresses EJ without insertion/deletion mutations, which is a hallmark of C-NHEJ. Conversely, RNF8 promotes alternative EJ (ALT-EJ) events involving microhomology that is embedded from the edge of the DSB. These ALT-EJ events likely require limited end resection, whereas RNF8 is not required for single-strand annealing repair involving extensive end resection. Thus, RNF8 appears to specifically facilitate repair events requiring limited end resection, which we find is dependent on the DSB end protection factor KU. However, we also find that RNF8 is important for homology-directed repair (HDR) independently of KU, which appears linked to promoting PALB2 function. Finally, the influence of RNF8 on EJ is distinct from 53BP1 and the ALT-EJ factor, POLQ. We suggest that RNF8 mediates both ALT-EJ and HDR, but via distinct mechanisms, since only the former is dependent on KU.
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Affiliation(s)
- Linda Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Eva Jahanshir
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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8
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Belotserkovskaya R, Raga Gil E, Lawrence N, Butler R, Clifford G, Wilson MD, Jackson SP. PALB2 chromatin recruitment restores homologous recombination in BRCA1-deficient cells depleted of 53BP1. Nat Commun 2020; 11:819. [PMID: 32041954 PMCID: PMC7010753 DOI: 10.1038/s41467-020-14563-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Loss of functional BRCA1 protein leads to defects in DNA double-strand break (DSB) repair by homologous recombination (HR) and renders cells hypersensitive to poly (ADP-ribose) polymerase (PARP) inhibitors used to treat BRCA1/2-deficient cancers. However, upon chronic treatment of BRCA1-mutant cells with PARP inhibitors, resistant clones can arise via several mechanisms, including loss of 53BP1 or its downstream co-factors. Defects in the 53BP1 axis partially restore the ability of a BRCA1-deficient cell to form RAD51 filaments at resected DSBs in a PALB2- and BRCA2-dependent manner, and thereby repair DSBs by HR. Here we show that depleting 53BP1 in BRCA1-null cells restores PALB2 accrual at resected DSBs. Moreover, we demonstrate that PALB2 DSB recruitment in BRCA1/53BP1-deficient cells is mediated by an interaction between PALB2's chromatin associated motif (ChAM) and the nucleosome acidic patch region, which in 53BP1-expressing cells is bound by 53BP1's ubiquitin-directed recruitment (UDR) domain.
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Affiliation(s)
- Rimma Belotserkovskaya
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Elisenda Raga Gil
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Nicola Lawrence
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Richard Butler
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Gillian Clifford
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK.
| | - Stephen P Jackson
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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9
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Nardi IK, Stark JM, Larsen A, Salgia R, Raz DJ. USP22 Interacts with PALB2 and Promotes Chemotherapy Resistance via Homologous Recombination of DNA Double-Strand Breaks. Mol Cancer Res 2019; 18:424-435. [PMID: 31685642 PMCID: PMC9285637 DOI: 10.1158/1541-7786.mcr-19-0053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/15/2019] [Accepted: 10/29/2019] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is a highly conserved pathway that can facilitate the repair of DNA double-strand breaks (DSB). Several Deubiquitinases (DUB) have been implicated as key players in DNA damage repair (DDR) through HR. Here, we report USP22, a DUB that is highly overexpressed in multiple cancer types, is necessary for HR through a direct interaction with PALB2 through its C-terminal WD40 domain. This interaction stimulates USP22 catalytic activity in vitro. Furthermore, we show USP22 is necessary for BRCA2, PALB2, and Rad51 recruitment to DSBs and this is, in part, through USP22 stabilizing BRCA2 and PALB2 levels. Taken together, our results describe a role for USP22 in DNA repair. IMPLICATIONS: This research provides new and exciting mechanistic insights into how USP22 overexpression promotes chemoresistance in lung cancer. We believe this study, and others, will help aid in developing targeted drugs toward USP22 and known binding partners for lung cancer treatment.
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Affiliation(s)
- Isaac K Nardi
- Division of Thoracic Surgery, Baum Family Thoracic Oncology Laboratory, City of Hope National Medical Center, Duarte, California.
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center, Duarte, California
| | - Adrien Larsen
- Department of Computational Therapeutics, City of Hope National Medical Center, Duarte, California
| | - Ravi Salgia
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Dan J Raz
- Division of Thoracic Surgery, Baum Family Thoracic Oncology Laboratory, City of Hope National Medical Center, Duarte, California
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California
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10
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Deveryshetty J, Peterlini T, Ryzhikov M, Brahiti N, Dellaire G, Masson JY, Korolev S. Novel RNA and DNA strand exchange activity of the PALB2 DNA binding domain and its critical role for DNA repair in cells. eLife 2019; 8:44063. [PMID: 31017574 PMCID: PMC6533086 DOI: 10.7554/elife.44063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
BReast Cancer Associated proteins 1 and 2 (BRCA1, -2) and Partner and Localizer of BRCA2 (PALB2) protein are tumour suppressors linked to a spectrum of malignancies, including breast cancer and Fanconi anemia. PALB2 coordinates functions of BRCA1 and BRCA2 during homology-directed repair (HDR) and interacts with several chromatin proteins. In addition to protein scaffold function, PALB2 binds DNA. The functional role of this interaction is poorly understood. We identified a major DNA-binding site of PALB2, mutations in which reduce RAD51 foci formation and the overall HDR efficiency in cells by 50%. PALB2 N-terminal DNA-binding domain (N-DBD) stimulates the function of RAD51 recombinase. Surprisingly, it possesses the strand exchange activity without RAD51. Moreover, N-DBD stimulates the inverse strand exchange and can use DNA and RNA substrates. Our data reveal a versatile DNA interaction property of PALB2 and demonstrate a critical role of PALB2 DNA binding for chromosome repair in cells.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Edward A Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSaint LouisUnited States
| | - Thibaut Peterlini
- Genome Stability LaboratoryCHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research CenterQuébec CityCanada
| | - Mikhail Ryzhikov
- Edward A Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSaint LouisUnited States
| | - Nadine Brahiti
- Genome Stability LaboratoryCHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research CenterQuébec CityCanada
| | | | - Jean-Yves Masson
- Genome Stability LaboratoryCHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research CenterQuébec CityCanada
| | - Sergey Korolev
- Edward A Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSaint LouisUnited States
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11
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Coggins NB, Stultz J, O'Geen H, Carvajal-Carmona LG, Segal DJ. Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance. Sci Rep 2017; 7:15044. [PMID: 29118424 PMCID: PMC5678142 DOI: 10.1038/s41598-017-15407-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/24/2017] [Indexed: 11/09/2022] Open
Abstract
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants. We also modeled a known functional risk SNP of colorectal cancer, rs6983267, in HCT-116 cells. Cells with extremely low levels of gene editing could still be identified and isolated using this approach. We also introduce a novel molecular assay, ChIPnQASO (Chromatin Immunoprecipitation and Quantitative Allele-Specific Occupation), which uses the same technology to reveal allele-specific function of these variants at the DNA-protein interaction level. We demonstrated preferential binding of the transcription factor TCF7L2 to the rs6983267 risk allele over the non-risk. Our pipeline provides a platform for functional variant discovery and validation that is accessible and broadly applicable for the progression of efforts towards precision medicine.
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Affiliation(s)
- Nicole B Coggins
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Jacob Stultz
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Luis G Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA.
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA.
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12
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Nepomuceno TC, De Gregoriis G, de Oliveira FMB, Suarez-Kurtz G, Monteiro AN, Carvalho MA. The Role of PALB2 in the DNA Damage Response and Cancer Predisposition. Int J Mol Sci 2017; 18:ijms18091886. [PMID: 28858227 PMCID: PMC5618535 DOI: 10.3390/ijms18091886] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/21/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
The deoxyribonucleic acid (DNA) damage response (DDR) is a major feature in the maintenance of genome integrity and in the suppression of tumorigenesis. PALB2 (Partner and Localizer of Breast Cancer 2 (BRCA2)) plays an important role in maintaining genome integrity through its role in the Fanconi anemia (FA) and homologous recombination (HR) DNA repair pathways. Since its identification as a BRCA2 interacting partner, PALB2 has emerged as a pivotal tumor suppressor protein associated to hereditary cancer susceptibility to breast and pancreatic cancers. In this review, we discuss how other DDR proteins (such as the kinases Ataxia Telangiectasia Mutated (ATM) and ATM- and Rad3-Related (ATR), mediators BRCA1 (Breast Cancer 1)/BRCA2 and effectors RAD51/DNA Polymerase η (Polη) interact with PALB2 to orchestrate DNA repair. We also examine the involvement of PALB2 mutations in the predisposition to cancer and the role of PALB2 in stimulating error-free DNA repair through the FA/HR pathway.
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Affiliation(s)
- Thales C Nepomuceno
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Giuliana De Gregoriis
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | | | - Guilherme Suarez-Kurtz
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
| | - Marcelo A Carvalho
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
- Instituto Federal do Rio de Janeiro-IFRJ, Rio de Janeiro 20270-021, Brazil.
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13
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Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F. MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress. Proc Natl Acad Sci U S A 2017; 114:7671-7676. [PMID: 28673974 PMCID: PMC5530651 DOI: 10.1073/pnas.1620208114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The partner and localiser of BRCA2 (PALB2) plays important roles in the maintenance of genome integrity and protection against cancer. Although PALB2 is commonly described as a repair factor recruited to sites of DNA breaks, recent studies provide evidence that PALB2 also associates with unperturbed chromatin. Here, we investigated the previously poorly described role of chromatin-associated PALB2 in undamaged cells. We found that PALB2 associates with active genes through its major binding partner, MRG15, which recognizes histone H3 trimethylated at lysine 36 (H3K36me3) by the SETD2 methyltransferase. Missense mutations that ablate PALB2 binding to MRG15 confer elevated sensitivity to the topoisomerase inhibitor camptothecin (CPT) and increased levels of aberrant metaphase chromosomes and DNA stress in gene bodies, which were suppressed by preventing DNA replication. Remarkably, the level of PALB2 at genic regions was frequently decreased, rather than increased, upon CPT treatment. We propose that the steady-state presence of PALB2 at active genes, mediated through the SETD2/H3K36me3/MRG15 axis, ensures an immediate response to DNA stress and therefore effective protection of these regions during DNA replication. This study provides a conceptual advance in demonstrating that the constitutive chromatin association of repair factors plays a key role in the maintenance of genome stability and furthers our understanding of why PALB2 defects lead to human genome instability syndromes.
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Affiliation(s)
- Jean-Yves Bleuyard
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Marjorie Fournier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Anthony M Couturier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Yuki Katou
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Christine Ralf
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Svenja S Hester
- Advanced Proteomics Facility, Department of Biochemisty, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Timothy C Humphrey
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom;
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