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Hu C, Nagaraj AB, Shimelis H, Montalban G, Lee KY, Huang H, Lumby CA, Na J, Susswein LR, Roberts ME, Marshall ML, Hiraki S, LaDuca H, Chao E, Yussuf A, Pesaran T, Neuhausen SL, Haiman CA, Kraft P, Lindstrom S, Palmer JR, Teras LR, Vachon CM, Yao S, Ong I, Nathanson KL, Weitzel JN, Boddicker N, Gnanaolivu R, Polley EC, Mer G, Cui G, Karam R, Richardson ME, Domchek SM, Yadav S, Hruska KS, Dolinsky J, Weroha SJ, Hart SN, Simard J, Masson JY, Pang YP, Couch FJ. Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C. Cancer Res 2023; 83:2557-2571. [PMID: 37253112 PMCID: PMC10390864 DOI: 10.1158/0008-5472.can-22-2319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/07/2022] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C-/- cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case-control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18-7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71-30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers. SIGNIFICANCE Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants.
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Affiliation(s)
| | | | | | - Gemma Montalban
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | | | | | | | - Jie Na
- Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | | | | | | | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lauren R. Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irene Ong
- University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques Simard
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Jean Yves Masson
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
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Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. Am J Hum Genet 2023; 110:940-949. [PMID: 37236177 PMCID: PMC10257006 DOI: 10.1016/j.ajhg.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
While pathogenic variants can significantly increase disease risk, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2, large cohort studies find no significant association between breast cancer and rare missense variants collectively. Here, we introduce REGatta, a method to estimate clinical risk from variants in smaller segments of individual genes. We first define these regions by using the density of pathogenic diagnostic reports and then calculate the relative risk in each region by using over 200,000 exome sequences in the UK Biobank. We apply this method in 13 genes with established roles across several monogenic disorders. In genes with no significant difference at the gene level, this approach significantly separates disease risk for individuals with rare missense variants at higher or lower risk (BRCA2 regional model OR = 1.46 [1.12, 1.79], p = 0.0036 vs. BRCA2 gene model OR = 0.96 [0.85, 1.07] p = 0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare our method with existing methods and the use of protein domains (Pfam) as regions and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors and are potentially useful for improving risk assessment for genes associated with monogenic diseases.
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Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
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3
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Cybulski C, Zamani N, Kluźniak W, Milano L, Wokołorczyk D, Stempa K, Rudnicka H, Zhang S, Zadeh M, Huzarski T, Jakubowska A, Dębniak T, Lener M, Szwiec M, Domagała P, Samani AA, Narod S, Gronwald J, Masson JY, Lubiński J, Akbari MR. Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank. Am J Hum Genet 2023; 110:648-662. [PMID: 36977412 PMCID: PMC10119148 DOI: 10.1016/j.ajhg.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023] Open
Abstract
Several breast cancer susceptibility genes have been discovered, but more are likely to exist. To identify additional breast cancer susceptibility genes, we used the founder population of Poland and performed whole-exome sequencing on 510 women with familial breast cancer and 308 control subjects. We identified a rare mutation in ATRIP (GenBank: NM_130384.3: c.1152_1155del [p.Gly385Ter]) in two women with breast cancer. At the validation phase, we found this variant in 42/16,085 unselected Polish breast cancer-affected individuals and in 11/9,285 control subjects (OR = 2.14, 95% CI = 1.13-4.28, p = 0.02). By analyzing the sequence data of the UK Biobank study participants (450,000 individuals), we identified ATRIP loss-of-function variants among 13/15,643 breast cancer-affected individuals versus 40/157,943 control subjects (OR = 3.28, 95% CI = 1.76-6.14, p < 0.001). Immunohistochemistry and functional studies showed the ATRIP c.1152_1155del variant allele is weakly expressed compared to the wild-type allele, and truncated ATRIP fails to perform its normal function to prevent replicative stress. We showed that tumors of women with breast cancer who have a germline ATRIP mutation have loss of heterozygosity at the site of ATRIP mutation and genomic homologous recombination deficiency. ATRIP is a critical partner of ATR that binds to RPA coating single-stranded DNA at sites of stalled DNA replication forks. Proper activation of ATR-ATRIP elicits a DNA damage checkpoint crucial in regulating cellular responses to DNA replication stress. Based on our observations, we conclude ATRIP is a breast cancer susceptibility gene candidate linking DNA replication stress to breast cancer.
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Affiliation(s)
- Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Neda Zamani
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Wojciech Kluźniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Larissa Milano
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Klaudia Stempa
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Helena Rudnicka
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Shiyu Zhang
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Maryam Zadeh
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tomasz Huzarski
- Department of Clinical Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Tadeusz Dębniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marcin Lener
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marek Szwiec
- Department of Surgery and Oncology, University of Zielona Góra, Zielona Góra, Poland
| | - Paweł Domagała
- Department of Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Amir Abbas Samani
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Humber River Hospital, University of Toronto, Toronto, ON, Canada
| | - Steven Narod
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Jan Lubiński
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.06.23284281. [PMID: 36711752 PMCID: PMC9882564 DOI: 10.1101/2023.01.06.23284281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
While pathogenic variants significantly increase disease risk in many genes, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2 , large cohort studies find no significant association between breast cancer and rare germline missense variants collectively. Here we introduce REGatta, a method to improve the estimation of clinical risk in gene segments. We define gene regions using the density of pathogenic diagnostic reports, and then calculate the relative risk in each of these regions using 109,581 exome sequences from women in the UK Biobank. We apply this method in seven established breast cancer genes, and identify regions in each gene with statistically significant differences in breast cancer incidence for rare missense carriers. Even in genes with no significant difference at the gene level, this approach significantly separates rare missense variant carriers at higher or lower risk ( BRCA2 regional model OR=1.46 [1.12, 1.79], p=0.0036 vs. BRCA2 gene model OR=0.96 [0.85,1.07] p=0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare with existing methods and the use of protein domains (Pfam) as regions, and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors which can potentially be used to improve risk assessment and clinical management.
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Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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5
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Muhammad N, Sadaqat R, Naeemi H, Masood I, Hassan U, Ijaz B, Hanif F, Syed AA, Yusuf MA, Rashid MU. Contribution of germline PALB2 variants to an unselected and prospectively registered pancreatic cancer patient cohort in Pakistan. HPB (Oxford) 2022; 24:2134-2144. [PMID: 36175305 DOI: 10.1016/j.hpb.2022.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/02/2022] [Accepted: 09/12/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND Partner and localizer of BRCA2 (PALB2) is a pancreatic cancer (PC) susceptibility gene reported in Caucasians. However, limited data are available among Asians. We investigated the contribution of PALB2 germline variants to Pakistani PC patients. METHODS 150 unselected and prospectively enrolled PC patients were comprehensively screened for PALB2 variants, using denaturing high-performance liquid chromatography and DNA sequencing. Novel variants were investigated for their pathogenic effect using in-silico tools. Potentially functional variants were screened in 200 controls. RESULTS Twenty-two different PALB2 variants were identified. A missense variant (p.Arg37His) was identified in a 48-years-old male patient with a family history of breast cancer. Another missense variant (p.Trp898Arg) was identified in a 48-years-old male patient with a family history of esophageal cancer. A novel 3' downstream variant (c.∗480A>G) was detected in a 34-years-old female patient with family history of lung cancer. Another novel 3' downstream variant (c.∗417A>C) was identified in a 41-years-old male patient. All these variants were absent in 200 controls. p.Arg37His and p.Trp898Arg were predicted as likely pathogenic. c.∗417A>C and c.∗480A>G were classified as variants of uncertain significance. CONCLUSION This is the first study that suggests a minimal contribution of PALB2 variants to PC risk in Pakistani population.
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Affiliation(s)
- Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Center (SKMCH&RC), Lahore, Pakistan
| | - Rida Sadaqat
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Center (SKMCH&RC), Lahore, Pakistan
| | - Humaira Naeemi
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Center (SKMCH&RC), Lahore, Pakistan
| | - Iqra Masood
- Clinical Research Office, SKMCH&RC, Lahore, Pakistan
| | - Usman Hassan
- Department of Pathology, SKMCH&RC, Lahore, Pakistan
| | - Bushra Ijaz
- Laboratory of Applied and Functional Genomics, National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Faisal Hanif
- Department of Surgical Oncology, SKMCH&RC, Lahore, Pakistan; Centre for Liver and Biliary Sciences, Bahria International Hospital, Lahore, Pakistan
| | - Aamir A Syed
- Department of Surgical Oncology, SKMCH&RC, Lahore, Pakistan
| | | | - Muhammad U Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Center (SKMCH&RC), Lahore, Pakistan.
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6
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Ping X, Stark JM. O-GlcNAc transferase is important for homology-directed repair. DNA Repair (Amst) 2022; 119:103394. [PMID: 36095925 PMCID: PMC9884008 DOI: 10.1016/j.dnarep.2022.103394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/11/2022] [Accepted: 09/01/2022] [Indexed: 01/31/2023]
Abstract
O-Linked β-N-acetylglucosamine glycosylation (O-GlcNAcylation) to serine or threonine residues is a reversible and dynamic post-translational modification. O-GlcNAc transferase (OGT) is the only enzyme for O-GlcNAcylation, and is a potential cancer therapeutic target in combination with clastogenic (i.e., chromosomal breaking) therapeutics. Thus, we sought to examine the influence of O-GlcNAcylation on chromosomal break repair. Using a set of DNA double strand break (DSB) reporter assays, we found that the depletion of OGT, and its inhibition with a small molecule each caused a reduction in repair pathways that involve use of homology: RAD51-dependent homology-directed repair (HDR), and single strand annealing. In contrast, such OGT disruption did not obviously affect chromosomal break end joining, and furthermore caused an increase in homology-directed gene targeting. Such disruption in OGT also caused a reduction in clonogenic survival, as well as modifications to cell cycle profiles, particularly an increase in G1-phase cells. We also examined intermediate steps of HDR, finding no obvious effects on an assay for DSB end resection, nor for RAD51 recruitment into ionizing radiation induced foci (IRIF) in proliferating cells. However, we also found that the influence of OGT on HDR and homology-directed gene targeting were dependent on RAD52, and that OGT is important for RAD52 IRIF in proliferating cells. Thus, we suggest that OGT is important for regulation of HDR that is partially linked to RAD52 function.
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Affiliation(s)
- Xiaoli Ping
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Jeremy M. Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA,Correspondence should be addressed to J.M.S:, Phone: 626-218-6346, Fax: 626-301-8892,
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7
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Fournier M, Rodrigue A, Milano L, Bleuyard JY, Couturier AM, Wall J, Ellins J, Hester S, Smerdon SJ, Tora L, Masson JY, Esashi F. KAT2-mediated acetylation switches the mode of PALB2 chromatin association to safeguard genome integrity. eLife 2022; 11:e57736. [PMID: 36269050 PMCID: PMC9671498 DOI: 10.7554/elife.57736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
The tumour suppressor PALB2 stimulates RAD51-mediated homologous recombination (HR) repair of DNA damage, whilst its steady-state association with active genes protects these loci from replication stress. Here, we report that the lysine acetyltransferases 2A and 2B (KAT2A/2B, also called GCN5/PCAF), two well-known transcriptional regulators, acetylate a cluster of seven lysine residues (7K-patch) within the PALB2 chromatin association motif (ChAM) and, in this way, regulate context-dependent PALB2 binding to chromatin. In unperturbed cells, the 7K-patch is targeted for KAT2A/2B-mediated acetylation, which in turn enhances the direct association of PALB2 with nucleosomes. Importantly, DNA damage triggers a rapid deacetylation of ChAM and increases the overall mobility of PALB2. Distinct missense mutations of the 7K-patch render the mode of PALB2 chromatin binding, making it either unstably chromatin-bound (7Q) or randomly bound with a reduced capacity for mobilisation (7R). Significantly, both of these mutations confer a deficiency in RAD51 foci formation and increase DNA damage in S phase, leading to the reduction of overall cell survival. Thus, our study reveals that acetylation of the ChAM 7K-patch acts as a molecular switch to enable dynamic PALB2 shuttling for HR repair while protecting active genes during DNA replication.
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Affiliation(s)
- Marjorie Fournier
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Amélie Rodrigue
- CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research CenterQuébecCanada
| | - Larissa Milano
- CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research CenterQuébecCanada
| | - Jean-Yves Bleuyard
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Anthony M Couturier
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Jacob Wall
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Jessica Ellins
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Svenja Hester
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
- Advanced Proteomics Facility, University of OxfordOxfordUnited Kingdom
| | | | - László Tora
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Jean-Yves Masson
- CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research CenterQuébecCanada
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
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8
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Xia B, Biswas K, Foo TK, Torres T, Riedel-Topper M, Southon E, Kang Z, Huo Y, Reid S, Stauffer S, Zhou W, Zhu B, Koka H, Yepes S, Brodie SA, Jones K, Vogt A, Zhu B, Cater B, Freedman ND, Hicks B, Yeager M, Chanock SJ, Couch F, Parry DM, Monteiro AN, Goldstein AM, Carvalho MA, Sharan SK, Yang XR. Rare germline variants in PALB2 and BRCA2 in familial and sporadic chordoma. Hum Mutat 2022; 43:1396-1407. [PMID: 35762214 PMCID: PMC9444938 DOI: 10.1002/humu.24427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/08/2022]
Abstract
Chordoma is a rare bone tumor with genetic risk factors largely unknown. We conducted a whole-exome sequencing (WES) analysis of germline DNA from 19 familial chordoma cases in five pedigrees and 137 sporadic chordoma patients and identified 17 rare germline variants in PALB2 and BRCA2, whose products play essential roles in homologous recombination (HR) and tumor suppression. One PALB2 variant showed disease cosegregation in a family with four affected people or obligate gene carrier. Chordoma cases had a significantly increased burden of rare variants in both genes when compared to population-based controls. Four of the six PALB2 variants identified from chordoma patients modestly affected HR function and three of the 11 BRCA2 variants caused loss of function in experimental assays. These results, together with previous reports of abnormal morphology and Brachyury expression of the notochord in Palb2 knockout mouse embryos and genomic signatures associated with HR defect and HR gene mutations in advanced chordomas, suggest that germline mutations in PALB2 and BRCA2 may increase chordoma susceptibility. Our data shed light on the etiology of chordoma and support the previous finding that PARP-1 inhibitors may be a potential therapy for some chordoma patients.
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Affiliation(s)
- Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Thiago Torres
- Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro 20230-130, Brazil
| | - Maximilian Riedel-Topper
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Zhihua Kang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Yanying Huo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Sally Yepes
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Seth A. Brodie
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Aurelie Vogt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Brian Cater
- American Cancer Society, Inc, Atlanta, GA 30303, USA
| | - Neal D. Freedman
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Fergus Couch
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dilys M. Parry
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Alvaro N. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Marcelo A. Carvalho
- Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro 20230-130, Brazil
- Instituto Federal do Rio de Janeiro - IFRJ, Rio de Janeiro 20270-021, Brazil
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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9
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Foo TK, Xia B. BRCA1-Dependent and Independent Recruitment of PALB2-BRCA2-RAD51 in the DNA Damage Response and Cancer. Cancer Res 2022; 82:3191-3197. [PMID: 35819255 PMCID: PMC9481714 DOI: 10.1158/0008-5472.can-22-1535] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
Abstract
The BRCA1-PALB2-BRCA2 axis plays essential roles in the cellular response to DNA double-strand breaks (DSB), maintenance of genome integrity, and suppression of cancer development. Upon DNA damage, BRCA1 is recruited to DSBs, where it facilitates end resection and recruits PALB2 and its associated BRCA2 to load the central recombination enzyme RAD51 to initiate homologous recombination (HR) repair. In recent years, several BRCA1-independent mechanisms of PALB2 recruitment have also been reported. Collectively, these available data illustrate a series of hierarchical, context-dependent, and cooperating mechanisms of PALB2 recruitment that is critical for HR and therapy response either in the presence or absence of BRCA1. Here, we review these BRCA1-dependent and independent mechanisms and their importance in DSB repair, cancer development, and therapy. As BRCA1-mutant cancer cells regain HR function, for which PALB2 is generally required, and become resistant to targeted therapies, such as PARP inhibitors, targeting BRCA1-independent mechanisms of PALB2 recruitment represents a potential new avenue to improve treatment of BRCA1-mutant tumors.
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Affiliation(s)
- Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
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10
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Functional assessment of missense variants of uncertain significance in the cancer susceptibility gene PALB2. NPJ Breast Cancer 2022; 8:86. [PMID: 35853885 PMCID: PMC9296472 DOI: 10.1038/s41523-022-00454-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
Germline PALB2 pathogenic variants are associated with an increased lifetime risk for breast, pancreatic, and ovarian cancer. However, the interpretation of the pathogenicity of numerous PALB2 missense variants of uncertain significance (VUSs) identified in germline genetic testing remains a challenge. Here we selected ten potentially pathogenic PALB2 VUSs identified in 2279 Chinese patients with breast cancer and evaluated their impacts on PALB2 function by systematic functional assays. We showed that three PALB2 VUSs p.K16M [c.47 A > T], p.L24F [c.72 G > C], and p.L35F [c.103 C > T] in the coiled-coil domain impaired PALB2-mediated homologous recombination. The p.L24F and p.L35F variants partially disrupted BRCA1-PALB2 interactions, reduced RAD51 foci formation in response to DNA damage, abrogated ionizing radiation-induced G2/M checkpoint maintenance, and conferred increased sensitivity to olaparib and cisplatin. The p.K16M variant presented mild effects on BRCA1-PALB2 interactions and RAD51 foci formation. Altogether, we identify two novel PALB2 VUSs, p.L24F and p.L35F, that compromise PALB2 function and may increase cancer risk. These two variants display marked olaparib and cisplatin sensitivity and may help predict response to targeted therapy in the clinical treatment of patients with these variants.
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11
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Cisneros-Aguirre M, Lopezcolorado FW, Tsai LJ, Bhargava R, Stark JM. The importance of DNAPKcs for blunt DNA end joining is magnified when XLF is weakened. Nat Commun 2022; 13:3662. [PMID: 35760797 PMCID: PMC9237100 DOI: 10.1038/s41467-022-31365-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
Canonical non-homologous end joining (C-NHEJ) factors can assemble into a long-range (LR) complex with DNA ends relatively far apart that contains DNAPKcs, XLF, XRCC4, LIG4, and the KU heterodimer and a short-range (SR) complex lacking DNAPKcs that has the ends positioned for ligation. Since the SR complex can form de novo, the role of the LR complex (i.e., DNAPKcs) for chromosomal EJ is unclear. We have examined EJ of chromosomal blunt DNA double-strand breaks (DSBs), and found that DNAPKcs is significantly less important than XLF for such EJ. However, weakening XLF via disrupting interaction interfaces causes a marked requirement for DNAPKcs, its kinase activity, and its ABCDE-cluster autophosphorylation sites for blunt DSB EJ. In contrast, other aspects of genome maintenance are sensitive to DNAPKcs kinase inhibition in a manner that is not further enhanced by XLF loss (i.e., suppression of homology-directed repair and structural variants, and IR-resistance). We suggest that DNAPKcs is required to position a weakened XLF in an LR complex that can transition into a functional SR complex for blunt DSB EJ, but also has distinct functions for other aspects of genome maintenance. DNAPKcs and its kinase activity are required for blunt DNA break end joining when the bridging factor XLF is weakened, but for homologous recombination and radiation resistance, the influence of DNAPKcs is not further enhanced with loss of XLF.
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Affiliation(s)
- Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Felicia Wednesday Lopezcolorado
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Linda Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA. .,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.
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12
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Dorling L, Carvalho S, Allen J, Parsons MT, Fortuno C, González-Neira A, Heijl SM, Adank MA, Ahearn TU, Andrulis IL, Auvinen P, Becher H, Beckmann MW, Behrens S, Bermisheva M, Bogdanova NV, Bojesen SE, Bolla MK, Bremer M, Briceno I, Camp NJ, Campbell A, Castelao JE, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Collée JM, Czene K, Dennis J, Dörk T, Eriksson M, Evans DG, Fasching PA, Figueroa J, Flyger H, Gabrielson M, Gago-Dominguez M, García-Closas M, Giles GG, Glendon G, Guénel P, Gündert M, Hadjisavvas A, Hahnen E, Hall P, Hamann U, Harkness EF, Hartman M, Hogervorst FBL, Hollestelle A, Hoppe R, Howell A, Jakubowska A, Jung A, Khusnutdinova E, Kim SW, Ko YD, Kristensen VN, Lakeman IMM, Li J, Lindblom A, Loizidou MA, Lophatananon A, Lubiński J, Luccarini C, Madsen MJ, Mannermaa A, Manoochehri M, Margolin S, Mavroudis D, Milne RL, Mohd Taib NA, Muir K, Nevanlinna H, Newman WG, Oosterwijk JC, Park SK, Peterlongo P, Radice P, Saloustros E, Sawyer EJ, Schmutzler RK, Shah M, Sim X, Southey MC, Surowy H, Suvanto M, Tomlinson I, Torres D, Truong T, van Asperen CJ, Waltes R, Wang Q, Yang XR, Pharoah PDP, Schmidt MK, Benitez J, Vroling B, Dunning AM, Teo SH, Kvist A, de la Hoya M, Devilee P, Spurdle AB, Vreeswijk MPG, Easton DF. Breast cancer risks associated with missense variants in breast cancer susceptibility genes. Genome Med 2022; 14:51. [PMID: 35585550 PMCID: PMC9116026 DOI: 10.1186/s13073-022-01052-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/04/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain. METHODS We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated. RESULTS The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47-2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set. CONCLUSIONS These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility.
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Affiliation(s)
- Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Cristina Fortuno
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, 70210, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, 70210, Kuopio, Finland
- Department of Oncology, Cancer Center, Kuopio University Hospital, 70210, Kuopio, Finland
| | - Heiko Becher
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael Bremer
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Ignacio Briceno
- Medical Faculty, Universidad de La Sabana, 140013, Bogota, Colombia
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, 36312, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- Nightingale & Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, M23 9LT, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, EH16 4UX, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, , 15706, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Pascal Guénel
- Team "Exposome and Heredity", CESP, Inserm, Gustave Roussy, University Paris-Saclay, UVSQ, Villejuif, France
| | - Melanie Gündert
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Andreas Hadjisavvas
- Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
- Department of Oncology, 118 83, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Elaine F Harkness
- Nightingale & Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, M23 9LT, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, UK
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
- Department of Surgery, National University Health System, Singapore, 119228, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, 3015 GD, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tübingen, 72074, Tübingen, Germany
| | - Anthony Howell
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- Division of Cancer Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450000, Russia
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary's Hospital, Seoul, 07442, Korea
| | - Yon-Dschun Ko
- Department of Internal Medicine, Johanniter GmbH Bonn, Johanniter Krankenhaus, 53113, Bonn, Germany
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0450, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0379, Oslo, Norway
| | - Inge M M Lakeman
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jingmei Li
- Department of Surgery, National University Health System, Singapore, 119228, Singapore
- Human Genetics Division, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Maria A Loizidou
- Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael J Madsen
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, 70210, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Sara Margolin
- Department of Oncology, 118 83, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 118 83, Stockholm, Sweden
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, 711 10, Heraklion, Greece
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Jan C Oosterwijk
- Department of Genetics, University Medical Center Groningen, University Groningen, Groningen, 9713 GZ, The Netherlands
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 03080, Korea
- Convergence Graduate Program in Innovative Medical Science, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University, Seoul, 03080, Korea
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), 20133, Milan, Italy
| | | | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Harald Surowy
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Maija Suvanto
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, 110231, Bogota, Colombia
| | - Thérèse Truong
- Team "Exposome and Heredity", CESP, Inserm, Gustave Roussy, University Paris-Saclay, UVSQ, Villejuif, France
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Regina Waltes
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Javier Benitez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
- Biomedical Network On Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Bas Vroling
- Bio-Prodict, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Soo Hwang Teo
- Breast Cancer Research Unit, Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, 47500, Selangor, Malaysia
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 22381, Lund, Sweden
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040, Madrid, Spain
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK.
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13
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Ng PS, Boonen RA, Wijaya E, Chong CE, Sharma M, Knaup S, Mariapun S, Ho WK, Lim J, Yoon SY, Mohd Taib NA, See MH, Li J, Lim SH, Tan EY, Tan BKT, Tan SM, Tan VKM, van Dam RM, Rahmat K, Yip CH, Carvalho S, Luccarini C, Baynes C, Dunning AM, Antoniou A, van Attikum H, Easton DF, Hartman M, Teo SH. Characterisation of protein-truncating and missense variants in PALB2 in 15 768 women from Malaysia and Singapore. J Med Genet 2022; 59:481-491. [PMID: 33811135 PMCID: PMC9046754 DOI: 10.1136/jmedgenet-2020-107471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Rare protein-truncating variants (PTVs) in partner and localiser of BRCA2 (PALB2) confer increased risk to breast cancer, but relatively few studies have reported the prevalence in South-East Asian populations. Here, we describe the prevalence of rare variants in PALB2 in a population-based study of 7840 breast cancer cases and 7928 healthy Chinese, Malay and Indian women from Malaysia and Singapore, and describe the functional impact of germline missense variants identified in this population. METHODS Mutation testing was performed on germline DNA (n=15 768) using targeted sequencing panels. The functional impact of missense variants was tested in mouse embryonic stem cell based functional assays. RESULTS PTVs in PALB2 were found in 0.73% of breast cancer patients and 0.14% of healthy individuals (OR=5.44; 95% CI 2.85 to 10.39, p<0.0001). In contrast, rare missense variants in PALB2 were not associated with increased risk of breast cancer. Whereas PTVs were associated with later stage of presentation and higher-grade tumours, no significant association was observed with missense variants in PALB2. However, two novel rare missense variants (p.L1027R and p.G1043V) produced unstable proteins and resulted in a decrease in homologous recombination-mediated repair of DNA double-strand breaks. CONCLUSION Despite genetic and lifestyle differences between Asian and other populations, the population prevalence of PALB2 PTVs and associated relative risk of breast cancer, are similar to those reported in European populations.
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Affiliation(s)
- Pei Sze Ng
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Rick Acm Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Chan Eng Chong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Milan Sharma
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Sabine Knaup
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Weang Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University of Nottingham - Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Sook-Yee Yoon
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Mee Hoong See
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Swee Ho Lim
- Breast Department, KK Women's and Children's Hospital, Singapore
- Duke-NUS Breast Centre, Singhealth, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Benita Kiat-Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore
| | - Su-Ming Tan
- Division of Breast Surgery, Changi General Hospital Department of General Surgery, Singapore
| | - Veronique Kiat-Mien Tan
- Singhealth Duke-NUS Breast Centre, Singhealth, Singapore
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Rob Martinus van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Nutrition, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Kartini Rahmat
- Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Antonis Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
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14
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Boonen RA, Vreeswijk MP, van Attikum H. CHEK2 variants: linking functional impact to cancer risk. Trends Cancer 2022; 8:759-770. [DOI: 10.1016/j.trecan.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/23/2022]
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15
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The Genetic and Molecular Analyses of RAD51C and RAD51D Identifies Rare Variants Implicated in Hereditary Ovarian Cancer from a Genetically Unique Population. Cancers (Basel) 2022; 14:cancers14092251. [PMID: 35565380 PMCID: PMC9104874 DOI: 10.3390/cancers14092251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/03/2022] Open
Abstract
To identify candidate variants in RAD51C and RAD51D ovarian cancer (OC) predisposing genes by investigating French Canadians (FC) exhibiting unique genetic architecture. Candidates were identified by whole exome sequencing analysis of 17 OC families and 53 early-onset OC cases. Carrier frequencies were determined by the genetic analysis of 100 OC or HBOC families, 438 sporadic OC cases and 1025 controls. Variants of unknown function were assayed for their biological impact and/or cellular sensitivity to olaparib. RAD51C c.414G>C;p.Leu138Phe and c.705G>T;p.Lys235Asn and RAD51D c.137C>G;p.Ser46Cys, c.620C>T;p.Ser207Leu and c.694C>T;p.Arg232Ter were identified in 17.6% of families and 11.3% of early-onset cases. The highest carrier frequency was observed in OC families (1/44, 2.3%) and sporadic cases (15/438, 3.4%) harbouring RAD51D c.620C>T versus controls (1/1025, 0.1%). Carriers of c.620C>T (n = 7), c.705G>T (n = 2) and c.137C>G (n = 1) were identified in another 538 FC OC cases. RAD51C c.705G>T affected splicing by skipping exon four, while RAD51D p.Ser46Cys affected protein stability and conferred olaparib sensitivity. Genetic and functional assays implicate RAD51C c.705G>T and RAD51D c.137C>G as likely pathogenic variants in OC. The high carrier frequency of RAD51D c.620C>T in FC OC cases validates previous findings. Our findings further support the role of RAD51C and RAD51D in hereditary OC.
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16
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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: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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17
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Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry. Sci Rep 2022; 12:802. [PMID: 35039564 PMCID: PMC8763903 DOI: 10.1038/s41598-022-04791-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/23/2021] [Indexed: 11/08/2022] Open
Abstract
Since the discovery of the breast cancer susceptibility genes, BRCA1 and BRCA2, various other genes conferring an increased risk for breast cancer have been identified. Studies to evaluate sequence variants in cancer predisposition genes among women of African ancestry are limited and mostly focused on BRCA1 and BRCA2. To characterize germline sequence variants in cancer susceptibility genes, we analysed a cohort of 165 South African women of self-identified African ancestry diagnosed with breast cancer, who were unselected for family history of cancer. With the exception of four cases, all others were previously investigated for BRCA1 and BRCA2 deleterious variants, and were negative for pathogenic variants. We utilized the Illumina TruSight cancer panel for targeted sequencing of 94 cancer susceptibility genes. A total of 3.6% of patients carried a pathogenic/likely pathogenic variant in a known breast cancer susceptibility gene: 1.2% in BRCA1, 0.6% in each of BRCA2, ATM, CHEK2 and PALB, none of whom had any family history of breast cancer. The mean age of patients who carried deleterious variant in BRCA1/BRCA2 was 39 years and 8 months compared to 47 years and 3 months among women who carried a deleterious variant in other breast cancer susceptibility genes.
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18
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Grosel TW, Karl M, Pilarski RT, Davidorf FH, Abdel-Rahman MH, Cebulla CM. Atypical choroidal nevus in a subject with a germline PALB2 pathogenic variant. Fam Cancer 2022; 21:1-5. [PMID: 33403473 PMCID: PMC8257753 DOI: 10.1007/s10689-020-00220-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/10/2020] [Indexed: 01/03/2023]
Abstract
Recent evidence suggests that PALB2 variants may increase risk for the development of uveal melanoma and uveal melanocytic neoplasms. Here we report a case of an atypical choroidal nevus in a patient with a personal history of cancer and pathogenic PALB2 germline variant. A 75-year-old white female presented with an elevated predominantly amelanotic choroidal lesion OS. On examination and ophthalmic imaging, the mass measured 8.8 mm × 6.5 mm × 1.5 mm. The mass showed predominantly medium to high reflectivity on diagnostic A-scan and acoustic hollowing on B-scan. OCT over the lesion showed no subretinal fluid. The patient has a personal history of breast cancer and gastric adenoma and a strong family history of cancer. The patient was found to have a pathogenic truncating variant in PALB2 (rs118203998 c.3549C > A, p.Y1183*). Together with our previous findings of pathogenic PALB2 variants in uveal melanoma patients, this new finding of an atypical choroidal nevus in a patient with a pathogenic PALB2 germline variant suggests that pathogenic PALB2 variants may be a risk factor for uveal melanocytic neoplasms. This finding warrants further assessment of the prevalence and progression of uveal melanocytic neoplasms in PALB2 pathogenic variant carriers.
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Affiliation(s)
- Timothy W Grosel
- Department of Ophthalmology and Visual Sciences, Havener Eye Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Matthew Karl
- Department of Ophthalmology and Visual Sciences, Havener Eye Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Robert T Pilarski
- Department of Internal Medicine Division of Human Genetics and James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Frederick H Davidorf
- Department of Ophthalmology and Visual Sciences, Havener Eye Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Mohamed H Abdel-Rahman
- Department of Ophthalmology and Visual Sciences, Havener Eye Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Department of Internal Medicine Division of Human Genetics and James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Colleen M Cebulla
- Department of Ophthalmology and Visual Sciences, Havener Eye Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
- Department of Ophthalmology and Visual Sciences, Havener Eye Institute, The Ohio State University Wexner Medical Center, 915 Olentangy River Road, Suite 5000, Columbus, OH, 43212, USA.
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19
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Fierheller CT, Guitton-Sert L, Alenezi WM, Revil T, Oros KK, Gao Y, Bedard K, Arcand SL, Serruya C, Behl S, Meunier L, Fleury H, Fewings E, Subramanian DN, Nadaf J, Bruce JP, Bell R, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Majewski J, Pugh TJ, Tischkowitz M, James PA, Campbell IG, Greenwood CMT, Ragoussis J, Masson JY, Tonin PN. A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. Genome Med 2021; 13:186. [PMID: 34861889 PMCID: PMC8642877 DOI: 10.1186/s13073-021-00998-5] [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: 09/02/2020] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes. Methods Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively. Results In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples. Conclusions This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00998-5.
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Affiliation(s)
- Caitlin T Fierheller
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Wejdan M Alenezi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Kathleen K Oros
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Suzanna L Arcand
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Supriya Behl
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rachel Bell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada. .,Department of Medicine, McGill University, Montreal, Quebec, Canada.
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20
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Sharma AB, Erasimus H, Pinto L, Caron MC, Gopaul D, Peterlini T, Neumann K, Nazarov PV, Fritah S, Klink B, Herold-Mende CC, Niclou SP, Pasero P, Calsou P, Masson JY, Britton S, Van Dyck E. XAB2 promotes Ku eviction from single-ended DNA double-strand breaks independently of the ATM kinase. Nucleic Acids Res 2021; 49:9906-9925. [PMID: 34500463 PMCID: PMC8464071 DOI: 10.1093/nar/gkab785] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022] Open
Abstract
Replication-associated single-ended DNA double-strand breaks (seDSBs) are repaired predominantly through RAD51-mediated homologous recombination (HR). Removal of the non-homologous end-joining (NHEJ) factor Ku from resected seDSB ends is crucial for HR. The coordinated actions of MRE11-CtIP nuclease activities orchestrated by ATM define one pathway for Ku eviction. Here, we identify the pre-mRNA splicing protein XAB2 as a factor required for resistance to seDSBs induced by the chemotherapeutic alkylator temozolomide. Moreover, we show that XAB2 prevents Ku retention and abortive HR at seDSBs induced by temozolomide and camptothecin, via a pathway that operates in parallel to the ATM-CtIP-MRE11 axis. Although XAB2 depletion preserved RAD51 focus formation, the resulting RAD51-ssDNA associations were unproductive, leading to increased NHEJ engagement in S/G2 and genetic instability. Overexpression of RAD51 or RAD52 rescued the XAB2 defects and XAB2 loss was synthetically lethal with RAD52 inhibition, providing potential perspectives in cancer therapy.
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Affiliation(s)
- Abhishek Bharadwaj Sharma
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Hélène Erasimus
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lia Pinto
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marie-Christine Caron
- CHU de Québec Research Center, Oncology Division, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Diyavarshini Gopaul
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Thibaut Peterlini
- CHU de Québec Research Center, Oncology Division, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Katrin Neumann
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Multiomics Data Science Group, LIH, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, LIH, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg.,Functional Tumour Genetics Group, Department of Oncology, LIH, Luxembourg
| | | | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, LIH, Luxembourg.,Department of Biomedicine, University of Bergen, Norway
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France, Equipe Labellisée Ligue Nationale Contre le Cancer 2018
| | - Jean-Yves Masson
- CHU de Québec Research Center, Oncology Division, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France, Equipe Labellisée Ligue Nationale Contre le Cancer 2018
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
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21
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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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22
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Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation (PERSPECTIVE I&I). J Pers Med 2021; 11:jpm11060511. [PMID: 34199804 PMCID: PMC8226444 DOI: 10.3390/jpm11060511] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
Early detection of breast cancer through screening reduces breast cancer mortality. The benefits of screening must also be considered within the context of potential harms (e.g., false positives, overdiagnosis). Furthermore, while breast cancer risk is highly variable within the population, most screening programs use age to determine eligibility. A risk-based approach is expected to improve the benefit-harm ratio of breast cancer screening programs. The PERSPECTIVE I&I (Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation) project seeks to improve personalized risk assessment to allow for a cost-effective, population-based approach to risk-based screening and determine best practices for implementation in Canada. This commentary describes the four inter-related activities that comprise the PERSPECTIVE I&I project. 1: Identification and validation of novel moderate to high-risk susceptibility genes. 2: Improvement, validation, and adaptation of a risk prediction web-tool for the Canadian context. 3: Development and piloting of a socio-ethical framework to support implementation of risk-based breast cancer screening. 4: Economic analysis to optimize the implementation of risk-based screening. Risk-based screening and prevention is expected to benefit all women, empowering them to work with their healthcare provider to make informed decisions about screening and prevention.
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23
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Tischkowitz M, Balmaña J, Foulkes WD, James P, Ngeow J, Schmutzler R, Voian N, Wick MJ, Stewart DR, Pal T. Management of individuals with germline variants in PALB2: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1416-1423. [PMID: 33976419 DOI: 10.1038/s41436-021-01151-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE PALB2 germline pathogenic variants are associated with increased breast cancer risk and smaller increased risk of pancreatic and likely ovarian cancer. Resources for health-care professionals managing PALB2 heterozygotes are currently limited. METHODS A workgroup of experts sought to outline management of PALB2 heterozygotes based on current evidence. Peer-reviewed publications from PubMed were identified to guide recommendations, which arose by consensus and the collective expertise of the authors. RESULTS PALB2 heterozygotes should be offered BRCA1/2-equivalent breast surveillance. Risk-reducing mastectomy can be considered guided by personalized risk estimates. Pancreatic cancer surveillance should be considered, but ideally as part of a clinical trial. Typically, ovarian cancer surveillance is not recommended, and risk-reducing salpingo-oophorectomy should only rarely be considered before the age of 50. Given the mechanistic similarities, PALB2 heterozygotes should be considered for therapeutic regimens and trials as those for BRCA1/2. CONCLUSION This guidance is similar to those for BRCA1/2. While the range of the cancer risk estimates overlap with BRCA1/2, point estimates are lower in PALB2 so individualized estimates are important for management decisions. Systematic prospective data collection is needed to determine as yet unanswered questions such as the risk of contralateral breast cancer and survival after cancer diagnosis.
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Affiliation(s)
- Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Rita Schmutzler
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,University Hospital of Cologne, Center of Integrated Oncology, CIO and Center of Familial Breast and Ovarian Cancer, Cologne, Germany
| | - Nicoleta Voian
- Genetic Risk Clinic, Providence Cancer Institute, Portland, OR, USA
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
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24
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Rare Germline Pathogenic Variants Identified by Multigene Panel Testing and the Risk of Aggressive Prostate Cancer. Cancers (Basel) 2021; 13:cancers13071495. [PMID: 33804961 PMCID: PMC8036662 DOI: 10.3390/cancers13071495] [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: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Identifying which men at the time of prostate cancer diagnosis have, or will progress to, an aggressive fatal disease will allow clinicians to assist men in making better informed treatment decisions. This will not only be important for those men whose disease is likely to remain indolent and who are currently undergoing unnecessary treatment procedures, but also for those who may need to be targeted with immediate and potentially life-saving therapy. Our case-control study confirms that men who carry BRCA1, BRCA2 and ATM germline pathogenic variants are at increased risk of aggressive disease and provides risk estimates that will be used by clinicians to improve counselling. Abstract While gene panel sequencing is becoming widely used for cancer risk prediction, its clinical utility with respect to predicting aggressive prostate cancer (PrCa) is limited by our current understanding of the genetic risk factors associated with predisposition to this potentially lethal disease phenotype. This study included 837 men diagnosed with aggressive PrCa and 7261 controls (unaffected men and men who did not meet criteria for aggressive PrCa). Rare germline pathogenic variants (including likely pathogenic variants) were identified by targeted sequencing of 26 known or putative cancer predisposition genes. We found that 85 (10%) men with aggressive PrCa and 265 (4%) controls carried a pathogenic variant (p < 0.0001). Aggressive PrCa odds ratios (ORs) were estimated using unconditional logistic regression. Increased risk of aggressive PrCa (OR (95% confidence interval)) was identified for pathogenic variants in BRCA2 (5.8 (2.7–12.4)), BRCA1 (5.5 (1.8–16.6)), and ATM (3.8 (1.6–9.1)). Our study provides further evidence that rare germline pathogenic variants in these genes are associated with increased risk of this aggressive, clinically relevant subset of PrCa. These rare genetic variants could be incorporated into risk prediction models to improve their precision to identify men at highest risk of aggressive prostate cancer and be used to identify men with newly diagnosed prostate cancer who require urgent treatment.
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25
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Zhang Y, Park JY, Zhang F, Olson SH, Orlow I, Li Y, Kurtz RC, Ladanyi M, Chen J, Toland AE, Zhang L, Andreassen PR. The p.Ser64Leu and p.Pro104Leu missense variants of PALB2 identified in familial pancreatic cancer patients compromise the DNA damage response. Hum Mutat 2020; 42:150-163. [PMID: 33169439 DOI: 10.1002/humu.24133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/17/2020] [Accepted: 11/01/2020] [Indexed: 11/12/2022]
Abstract
PALB2 has been identified as a breast and pancreatic cancer susceptibility gene. Utilizing a targeted sequencing approach, we discovered two novel germline missense PALB2 variants c.191C>T and c.311C>T, encoding p.Ser64Leu and p.Pro104Leu, respectively, in individuals in a pancreatic cancer registry. No missense PALB2 variants from familial pancreatic cancer patients, and few PALB2 variants overall, have been functionally characterized. Given the known role of PALB2, we tested the impact of p.Ser64Leu and p.Pro104Leu variants on DNA damage responses. Neither p.Ser64Leu nor p.Pro104Leu have clear effects on interactions with BRCA1 and KEAP1, which are mediated by adjacent motifs in PALB2. However, both variants are associated with defective recruitment of PALB2, and the RAD51 recombinase downstream, to DNA damage foci. Furthermore, p.Ser64Leu and p.Pro104Leu both largely compromise DNA double-strand break-initiated homologous recombination, and confer increased cellular sensitivity to ionizing radiation (IR) and the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib. Taken together, our results represent the first demonstration of functionally deleterious PALB2 missense variants associated with familial pancreatic cancer and of deleterious variants in the N-terminus outside of the coiled-coil domain. Furthermore, our results suggest the possibility of personalized treatments, using IR or PARP inhibitor, of pancreatic and other cancers that carry a deleterious PALB2 variant.
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Affiliation(s)
- Yue Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Jung-Young Park
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jie Chen
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.,Division of Human Genetics, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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26
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Nepomuceno TC, Carvalho MA, Rodrigue A, Simard J, Masson JY, Monteiro ANA. PALB2 Variants: Protein Domains and Cancer Susceptibility. Trends Cancer 2020; 7:188-197. [PMID: 33139182 DOI: 10.1016/j.trecan.2020.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 01/09/2023]
Abstract
Since its discovery, partner and localizer of breast cancer 2 (BRCA2) (PALB2) has emerged as a major tumor suppressor gene linked to breast cancer (BC), pancreatic cancer (PC), and ovarian cancer (OC) susceptibility. Its protein product plays a pivotal role in the maintenance of genome integrity. Here we discuss the first functional evaluation of a large set of PALB2 missense variants of uncertain significance (VUSs). Assessment of 136 VUSs interrogating a range of PALB2 biological functions resulted in the identification of 15 variants with consistent loss of function across different assays. All loss-of-function variants are located at the PALB2 coiled coil (CC) or at the WD40 domain, highlighting the importance of modular domains mechanistically involved in the DNA damage response (DDR) and pinpointing their roles in tumor suppression.
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Affiliation(s)
- Thales C Nepomuceno
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | - Marcelo A Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil; Instituto Federal do Rio de Janeiro (IFRJ), Rio de Janeiro 20270-021, Brazil
| | - Amélie Rodrigue
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Quebec City, QC G1R 3S3, Canada
| | - Jacques Simard
- Genomics Center, CHU de Quebec-Université Laval Research Center, Quebec City, QC, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Quebec City, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC G1V 0A6, Canada
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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27
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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28
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Yu Z, Mersaoui SY, Guitton-Sert L, Coulombe Y, Song J, Masson JY, Richard S. DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions. NAR Cancer 2020; 2:zcaa028. [PMID: 33015627 PMCID: PMC7520851 DOI: 10.1093/narcan/zcaa028] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
R-loops are three-stranded structures consisting of a DNA/RNA hybrid and a displaced DNA strand. The regulatory factors required to process this fundamental genetic structure near double-strand DNA breaks (DSBs) are not well understood. We previously reported that cellular depletion of the ATP-dependent DEAD box RNA helicase DDX5 increases R-loops genome-wide causing genomic instability. In this study, we define a pivotal role for DDX5 in clearing R-loops at or near DSBs enabling proper DNA repair to avoid aberrations such as chromosomal deletions. Remarkably, using the non-homologous end joining reporter gene (EJ5-GFP), we show that DDX5-deficient U2OS cells exhibited asymmetric end deletions on the side of the DSBs where there is overlap with a transcribed gene. Cross-linking and immunoprecipitation showed that DDX5 bound RNA transcripts near DSBs and required its helicase domain and the presence of DDX5 near DSBs was also shown by chromatin immunoprecipitation. DDX5 was excluded from DSBs in a transcription- and ATM activation-dependent manner. Using DNA/RNA immunoprecipitation, we show DDX5-deficient cells had increased R-loops near DSBs. Finally, DDX5 deficiency led to delayed exonuclease 1 and replication protein A recruitment to laser irradiation-induced DNA damage sites, resulting in homologous recombination repair defects. Our findings define a role for DDX5 in facilitating the clearance of RNA transcripts overlapping DSBs to ensure proper DNA repair.
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Affiliation(s)
- Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Sofiane Y Mersaoui
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Yan Coulombe
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Jingwen Song
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
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29
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Boonen RACM, Vreeswijk MPG, van Attikum H. Functional Characterization of PALB2 Variants of Uncertain Significance: Toward Cancer Risk and Therapy Response Prediction. Front Mol Biosci 2020; 7:169. [PMID: 33195396 PMCID: PMC7525363 DOI: 10.3389/fmolb.2020.00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years it has become clear that pathogenic variants in PALB2 are associated with a high risk for breast, ovarian and pancreatic cancer. However, the clinical relevance of variants of uncertain significance (VUS) in PALB2, which are increasingly identified through clinical genetic testing, is unclear. Here we review recent advances in the functional characterization of VUS in PALB2. A combination of assays has been used to assess the impact of PALB2 VUS on its function in DNA repair by homologous recombination, cell cycle regulation and the control of cellular levels of reactive oxygen species (ROS). We discuss the outcome of this comprehensive analysis of PALB2 VUS, which showed that VUS in PALB2’s Coiled-Coil (CC) domain can impair the interaction with BRCA1, whereas VUS in its WD40 domain affect PALB2 protein stability. Accordingly, the CC and WD40 domains of PALB2 represent hotspots for variants that impair PALB2 protein function. We also provide a future perspective on the high-throughput analysis of VUS in PALB2, as well as the functional characterization of variants that affect PALB2 RNA splicing. Finally, we discuss how results from these functional assays can be valuable for predicting cancer risk and responsiveness to cancer therapy, such as treatment with PARP inhibitor- or platinum-based chemotherapy.
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Affiliation(s)
- Rick A C M Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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Toh MR, Low CE, Chong ST, Chan SH, Ishak NDB, Courtney E, Kolinjivadi AM, Rodrigue A, Masson JY, Ngeow J. Missense PALB2 germline variant disrupts nuclear localization of PALB2 in a patient with breast cancer. Fam Cancer 2020; 19:123-131. [PMID: 32048105 DOI: 10.1007/s10689-020-00163-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The PALB2 protein is essential to RAD51-mediated homologous recombination (HR) repair. Germline monoallelic PALB2 pathogenic variants confer significant risks for breast cancer. However, the majority of PALB2 variants remain classified as variants of unknown significance (VUS). We aim to functionally and mechanistically evaluate three novel PALB2 VUS. Patient-derived lymphoblastoid cell lines containing the VUS were analyzed for nuclear localization and foci formation of RAD51 as a measure of HR efficiency. To understand the mechanism underlying the HR deficiency, PALB2 nuclear localization was assessed using immunofluorescence studies. Among these VUS, c.3251C>T (p.Ser1084Leu) occurred in a patient with metastatic breast cancer while c.1054G>C (p.Glu352Gln) and c.1057A>G (p.Lys353Glu) were seen in patients with squamous cell carcinoma of skin and renal cell carcinoma respectively. Variant c.3251C>T was located within the WD40 domain which normally masked the nuclear export signal sequence responsible for nuclear delocalization of PALB2. Correspondingly, c.3251C>T displayed aberrant cytoplasmic localization of PALB2 which led to an impaired RAD51 nuclear localization and foci formation. On the other hand, both c.1054G>C and c.1057A>G showed intact HR functions and nuclear localization of PALB2, consistent with their locations within domains of no known function. Additionally, the prevalence of c.1054G>C was similar among healthy controls and patients with breast cancer (as seen in other studies), suggestive of its non-pathogenicity. In conclusion, our studies provided the functional evidence showing the deleterious effect of c.3251C>T, and non-deleterious effects of c.1054G>C and c.1057A>G. Using the ClinGen Pathogenicity calculator, c.3251C>T remains a VUS while c.1054G>C and c.1057A>G may be classified as likely benign variants.
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Affiliation(s)
- Ming Ren Toh
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chen Ee Low
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Siao Ting Chong
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Nur Diana Binte Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Eliza Courtney
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Arun Mouli Kolinjivadi
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore
| | - Amélie Rodrigue
- CHU de Québec Research Center, Oncology Division, HDQ Pavilion, 9 McMahon, Québec City, QC, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, Oncology Division, HDQ Pavilion, 9 McMahon, Québec City, QC, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Joanne Ngeow
- Duke-NUS Medical School, Singapore, 169857, Singapore.
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore.
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673, Singapore.
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31
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Wu S, Zhou J, Zhang K, Chen H, Luo M, Lu Y, Sun Y, Chen Y. Molecular Mechanisms of PALB2 Function and Its Role in Breast Cancer Management. Front Oncol 2020; 10:301. [PMID: 32185139 PMCID: PMC7059202 DOI: 10.3389/fonc.2020.00301] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/20/2020] [Indexed: 12/31/2022] Open
Abstract
Partner and localizer of BRCA2 (PALB2) is vital for homologous recombination (HR) repair in response to DNA double-strand breaks (DSBs). PALB2 functions as a tumor suppressor and participates in the maintenance of genome integrity. In this review, we summarize the current knowledge of the biological roles of the multifaceted PALB2 protein and of its regulation. Moreover, we describe the link between PALB2 pathogenic variants (PVs) and breast cancer predisposition, aggressive clinicopathological features, and adverse clinical prognosis. We also refer to both the opportunities and challenges that the identification of PALB2 PVs provides in breast cancer genetic counseling and precision medicine.
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Affiliation(s)
- Shijie Wu
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaojiao Zhou
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Zhang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Huihui Chen
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Meng Luo
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuexin Lu
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuting Sun
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiding Chen
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
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32
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Southey MC, Rewse A, Nguyen-Dumont T. PALB2 Genetic Variants: Can Functional Assays Assist Translation? Trends Cancer 2020; 6:263-265. [PMID: 32209438 DOI: 10.1016/j.trecan.2020.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022]
Abstract
PALB2 loss-of-function variants are associated with increased risk of breast and other cancers, but the clinical relevance of missense variants (MVs) remains uncertain. Recent findings reported by Wiltshire et al., Rodrigue et al., and Boonen et al. demonstrate that some MVs disrupt PALB2 function. This new information will support the clinical management of families who carry these MVs and inform their treatment.
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Affiliation(s)
- Melissa C Southey
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, VIC 3168, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia.
| | - Amanda Rewse
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, VIC 3168, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, VIC 3168, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
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da Costa E Silva Carvalho S, Cury NM, Brotto DB, de Araujo LF, Rosa RCA, Texeira LA, Plaça JR, Marques AA, Peronni KC, Ruy PDC, Molfetta GA, Moriguti JC, Carraro DM, Palmero EI, Ashton-Prolla P, de Faria Ferraz VE, Silva WA. Germline variants in DNA repair genes associated with hereditary breast and ovarian cancer syndrome: analysis of a 21 gene panel in the Brazilian population. BMC Med Genomics 2020; 13:21. [PMID: 32039725 PMCID: PMC7011249 DOI: 10.1186/s12920-019-0652-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Hereditary Breast and Ovarian Cancer Syndrome (HBOC) occurs in families with a history of breast/ovarian cancer, presenting an autosomal dominant inheritance pattern. BRCA1 and BRCA2 are high penetrance genes associated with an increased risk of up to 20-fold for breast and ovarian cancer. However, only 20-30% of HBOC cases present pathogenic variants in those genes, and other DNA repair genes have emerged as increasing the risk for HBOC. In Brazil, variants in ATM, ATR, CHEK2, MLH1, MSH2, MSH6, POLQ, PTEN, and TP53 genes have been reported in up to 7.35% of the studied cases. Here we screened and characterized variants in 21 DNA repair genes in HBOC patients. METHODS We systematically analyzed 708 amplicons encompassing the coding and flanking regions of 21 genes related to DNA repair pathways (ABRAXAS1, ATM, ATR, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RAD50, RAD51, TP53 and UIMC1). A total of 95 individuals with HBOC syndrome clinical suspicion in Southeast Brazil were sequenced, and 25 samples were evaluated for insertions/deletions in BRCA1/BRCA2 genes. Identified variants were assessed in terms of population allele frequency and their functional effects were predicted through in silico algorithms. RESULTS We identified 80 variants in 19 genes. About 23.4% of the patients presented pathogenic variants in BRCA1, BRCA2 and TP53, a frequency higher than that identified among previous studies in Brazil. We identified a novel variant in ATR, which was predicted as pathogenic by in silico tools. The association analysis revealed 13 missense variants in ABRAXAS1, BARD1, BRCA2, CHEK2, CDH1, MLH1, PALB2, and PMS2 genes, as significantly associated with increased risk to HBOC, and the patients carrying those variants did not present large insertions or deletions in BRCA1/BRCA2 genes. CONCLUSIONS This study embodies the third report of a multi-gene analysis in the Brazilian population, and addresses the first report of many germline variants associated with HBOC in Brazil. Although further functional analyses are necessary to better characterize the contribution of those variants to the phenotype, these findings would improve the risk estimation and clinical follow-up of patients with HBOC clinical suspicion.
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Affiliation(s)
- Simone da Costa E Silva Carvalho
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathalia Moreno Cury
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Danielle Barbosa Brotto
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Luiza Ferreira de Araujo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Reginaldo Cruz Alves Rosa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Lorena Alves Texeira
- Division of Internal Medicine and Geriatrics, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Adriana Aparecida Marques
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Kamila Chagas Peronni
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Patricia de Cássia Ruy
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Greice Andreotti Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Julio Cesar Moriguti
- Division of Internal Medicine and Geriatrics, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Dirce Maria Carraro
- International Research, Center/CIPE, AC Camargo Cancer Center, Sao Paulo, SP, Brazil
| | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Victor Evangelista de Faria Ferraz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
- Department of Medical Genetics, University Hospital of the Ribeirão Preto Medical School, Ribeirão Preto, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil.
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil.
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34
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Abdel-Rahman MH, Sample KM, Pilarski R, Walsh T, Grosel T, Kinnamon D, Boru G, Massengill JB, Schoenfield L, Kelly B, Gordon D, Johansson P, DeBenedictis MJ, Singh A, Casadei S, Davidorf FH, White P, Stacey AW, Scarth J, Fewings E, Tischkowitz M, King MC, Hayward NK, Cebulla CM. Whole Exome Sequencing Identifies Candidate Genes Associated with Hereditary Predisposition to Uveal Melanoma. Ophthalmology 2019; 127:668-678. [PMID: 32081490 DOI: 10.1016/j.ophtha.2019.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/13/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE To identify susceptibility genes associated with hereditary predisposition to uveal melanoma (UM) in patients with no detectable germline BAP1 alterations. DESIGN Retrospective case series from academic referral centers. PARTICIPANTS Cohort of 154 UM patients with high risk of hereditary cancer defined as patients with 1 or more of the following: (1) familial UM, (2) young age (<35 years) at diagnosis, (3) personal history of other primary cancers, and (4) family history of 2 or more primary cancers with no detectable mutation or deletion in BAP1 gene. METHODS Whole exome sequencing, a cancer gene panel, or both were carried out. Probands included 27 patients with familial UM, 1 patient with bilateral UM, 1 patient with congenital UM, and 125 UM patients with strong personal or family histories, or both, of cancer. Functional validation of variants was carried out by immunohistochemistry, reverse-transcriptase polymerase chain reaction, and genotyping. MAIN OUTCOME MEASURES Clinical characterization of UM patients with germline alterations in known cancer genes. RESULTS We identified actionable pathogenic variants in 8 known hereditary cancer predisposition genes (PALB2, MLH1, MSH6, CHEK2, SMARCE1, ATM, BRCA1, and CTNNA1) in 9 patients, including 3 of 27 patients (11%) with familial UM and 6 of 127 patients (4.7%) with a high risk for cancer. Two patients showed pathogenic variants in CHEK2 and PALB2, whereas variants in the other genes each occurred in 1 patient. Biallelic inactivation of PALB2 and MLH1 was observed in tumors from the respective patients. The frequencies of pathogenic variants in PALB2, MLH1, and SMARCE1 in UM patients were significantly higher than the observed frequencies in noncancer controls (PALB2: P = 0.02; odds ratio, 8.9; 95% confidence interval, 1.5-30.6; MLH1: P = 0.04; odds ratio, 25.4; 95% confidence interval, 1.2-143; SMARCE1: P = 0.001; odds ratio, 2047; 95% confidence interval, 52-4.5e15, respectively). CONCLUSIONS The study provided moderate evidence of gene and disease association of germline mutations in PALB2 and MLH1 with hereditary predisposition to UM. It also identified several other candidate susceptibility genes. The results suggest locus heterogeneity in predisposition to UM. Genetic testing for hereditary predisposition to cancer is warranted in UM patients with strong personal or family history of cancers, or both.
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Affiliation(s)
- Mohamed H Abdel-Rahman
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio; Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
| | - Klarke M Sample
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Robert Pilarski
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Tomas Walsh
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Timothy Grosel
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Daniel Kinnamon
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Getachew Boru
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - James B Massengill
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Lynn Schoenfield
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Ben Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - David Gordon
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Peter Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Meghan J DeBenedictis
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Arun Singh
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Silvia Casadei
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Frederick H Davidorf
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Peter White
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Andrew W Stacey
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - James Scarth
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ellie Fewings
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Marc Tischkowitz
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom; East Anglian Medical Genetics Service, Cambridge University Hospitals, Cambridge, United Kingdom
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington
| | | | - Colleen M Cebulla
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
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