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Tuppurainen H, Laurila N, Nätynki M, Eshraghi L, Tervasmäki A, Erichsen L, Sørensen CS, Pylkäs K, Winqvist R, Peltoketo H. PALB2-mutated human mammary cells display a broad spectrum of morphological and functional abnormalities induced by increased TGFβ signaling. Cell Mol Life Sci 2024; 81:173. [PMID: 38597967 PMCID: PMC11006627 DOI: 10.1007/s00018-024-05183-6] [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: 06/02/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 04/11/2024]
Abstract
Heterozygous mutations in any of three major genes, BRCA1, BRCA2 and PALB2, are associated with high-risk hereditary breast cancer susceptibility frequently seen as familial disease clustering. PALB2 is a key interaction partner and regulator of several vital cellular activities of BRCA1 and BRCA2, and is thus required for DNA damage repair and alleviation of replicative and oxidative stress. Little is however known about how PALB2-deficiency affects cell function beyond that, especially in the three-dimensional setting, and also about its role during early steps of malignancy development. To answer these questions, we have generated biologically relevant MCF10A mammary epithelial cell lines with mutations that are comparable to certain clinically important PALB2 defects. We show in a non-cancerous background how both mono- and biallelically PALB2-mutated cells exhibit gross spontaneous DNA damage and mitotic aberrations. Furthermore, PALB2-deficiency disturbs three-dimensional spheroid morphology, increases the migrational capacity and invasiveness of the cells, and broadly alters their transcriptome profiles. TGFβ signaling and KRT14 expression are enhanced in PALB2-mutated cells and their inhibition and knock down, respectively, lead to partial restoration of cell functions. KRT14-positive cells are also more abundant with DNA damage than KRT14-negative cells. The obtained results indicate comprehensive cellular changes upon PALB2 mutations, even in the presence of half dosage of wild type PALB2 and demonstrate how PALB2 mutations may predispose their carriers to malignancy.
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Affiliation(s)
- Hanna Tuppurainen
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Niina Laurila
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Marjut Nätynki
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Leila Eshraghi
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Garvan Institute of Medical Research, Sydney, Australia
| | - Anna Tervasmäki
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Louisa Erichsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre, Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland.
| | - Hellevi Peltoketo
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland.
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Li N, Zethoven M, McInerny S, Healey E, DeSilva D, Devereux L, Scott RJ, James PA, Campbell IG. Contribution of large genomic rearrangements in PALB2 to familial breast cancer: implications for genetic testing. J Med Genet 2023; 60:112-118. [PMID: 35396271 DOI: 10.1136/jmedgenet-2021-108399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/08/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND PALB2 is the most important contributor to familial breast cancer after BRCA1 and BRCA2. Large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are routinely assessed in clinical testing and are a significant contributor to the yield of actionable findings. In contrast, the contribution of LGRs in PALB2 has not been systematically studied. METHODS We performed targeted sequencing and real-time qPCR validation to identify LGRs in PALB2 in 5770 unrelated patients with familial breast cancer and 5741 cancer-free control women from the same Australian population. RESULTS Seven large deletions ranging in size from 0.96 kbp to 18.07 kbp involving PALB2 were identified in seven cases, while no LGRs were identified in any of the controls. Six LGRs were considered pathogenic as they included one or more exons of PALB2 and disrupted the WD40 domain at the C terminal end of the PALB2 protein while one LGR only involved a partial region of intron 10 and was considered a variant of unknown significance. Altogether, pathogenic LGRs identified in this study accounted for 10.3% (6 of 58) of the pathogenic PALB2 variants detected among the 5770 families with familial breast cancer. CONCLUSIONS Our data show that a clinically important proportion of PALB2 pathogenic mutations in Australian patients with familial breast cancer are LGRs. Such observations have provided strong support for inclusion of PALB2 LGRs in routine clinical genetic testing.
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Affiliation(s)
- Na Li
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Eliza Healey
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Dilanka DeSilva
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Lifepool, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia.,Division of Molecular Medicine, Pathology North, Newcastle, New South Wales, Australia.,Discipline of Medical Genetics, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 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
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Lim BWX, Li N, Mahale S, McInerny S, Zethoven M, Rowley SM, Huynh J, Wang T, Lee JEA, Friedman M, Devereux L, Scott RJ, Sloan EK, James PA, Campbell IG. Somatic inactivation of breast cancer predisposition genes in tumors associated with pathogenic germline variants. J Natl Cancer Inst 2022; 115:181-189. [PMID: 36315097 PMCID: PMC9905963 DOI: 10.1093/jnci/djac196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Breast cancers (BCs) that arise in individuals heterozygous for a germline pathogenic variant in a susceptibility gene, such as BRCA1 and BRCA2, PALB2, and RAD51C, have been shown to exhibit biallelic loss in the respective genes and be associated with triple-negative breast cancer (TNBC) and distinctive somatic mutational signatures. Tumor sequencing thus presents an orthogonal approach to assess the role of candidate genes in BC development. METHODS Exome sequencing was performed on paired normal-breast tumor DNA from 124 carriers of germline loss-of-function (LoF) or missense variant carriers in 15 known and candidate BC predisposition genes identified in the BEACCON case-control study. Biallelic inactivation and association with tumor genome features including mutational signatures and homologous recombination deficiency (HRD) score were investigated. RESULTS BARD1-carrying TNBC (4 of 5) displayed biallelic loss and associated high HRD scores and mutational signature 3, as did a RAD51D-carrying TNBC and ovarian cancer. Biallelic loss was less frequent in BRIP1 BCs (4 of 13) and had low HRD scores. In contrast to other established BC genes, BCs from carriers of CHEK2 LoF (6 of 17) or missense (2 of 20) variant had low rates of biallelic loss. Exploratory analysis of BC from carriers of LoF variants in candidate genes such as BLM, FANCM, PARP2, and RAD50 found little evidence of biallelic inactivation. CONCLUSIONS BARD1 and RAD51D behave as classic BRCA-like predisposition genes with biallelic inactivation, but this was not observed for any of the candidate genes. However, as demonstrated for CHEK2, the absence of biallelic inactivation does not provide definitive evidence against the gene's involvement in BC predisposition.
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Affiliation(s)
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Sakshi Mahale
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Joanne Huynh
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Theresa Wang
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Jue Er Amanda Lee
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia,Molecular Genomics Core, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Mia Friedman
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia,Lifepool, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Rodney J Scott
- Discipline of Medical Genetics and The Centre for Cancer Detection and Therapy, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia,Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, New South Wales, Australia
| | - Erica K Sloan
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia,Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Ian G Campbell
- Correspondence to: Ian Campbell, PhD, Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia (e-mail: )
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Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study. NPJ Breast Cancer 2021; 7:76. [PMID: 34117267 PMCID: PMC8196173 DOI: 10.1038/s41523-021-00279-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/03/2021] [Indexed: 01/19/2023] Open
Abstract
Breast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. The coding regions and exon–intron boundaries of all candidate genes and 14 previously proposed BC genes were sequenced using custom designed sequencing panels. Pedigree and pathology data were analysed to identify genotype-specific associations. The contribution of ATM, PALB2 and CHEK2 to BC predisposition was confirmed, but not RAD50 and NBN. An overall excess of loss-of-function (LoF) (OR 1.27, p = 9.05 × 10−9) and missense (OR 1.27, p = 3.96 × 10−73) variants was observed in the cases for the 145 candidate genes. Leading candidates harbored LoF variants with observed ORs of 2–4 and individually accounted for no more than 0.79% of the cases. New genes proposed by this study include NTHL1, WRN, PARP2, CTH and CDK9. The new candidate BC predisposition genes identified in BEACCON indicate that much of the remaining genetic causes of high-risk BC families are due to genes in which pathogenic variants are both very rare and convey only low to moderate risk.
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5
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Li N, Zethoven M, McInerny S, Devereux L, Huang YK, Thio N, Cheasley D, Gutiérrez-Enríquez S, Moles-Fernández A, Diez O, Nguyen-Dumont T, Southey MC, Hopper JL, Simard J, Dumont M, Soucy P, Meindl A, Schmutzler R, Schmidt MK, Adank MA, Andrulis IL, Hahnen E, Engel C, Lesueur F, Girard E, Neuhausen SL, Ziv E, Allen J, Easton DF, Scott RJ, Gorringe KL, James PA, Campbell IG. Evaluation of the association of heterozygous germline variants in NTHL1 with breast cancer predisposition: an international multi-center study of 47,180 subjects. NPJ Breast Cancer 2021; 7:52. [PMID: 33980861 PMCID: PMC8115524 DOI: 10.1038/s41523-021-00255-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Bi-allelic loss-of-function (LoF) variants in the base excision repair (BER) gene NTHL1 cause a high-risk hereditary multi-tumor syndrome that includes breast cancer, but the contribution of heterozygous variants to hereditary breast cancer is unknown. An analysis of 4985 women with breast cancer, enriched for familial features, and 4786 cancer-free women revealed significant enrichment for NTHL1 LoF variants. Immunohistochemistry confirmed reduced NTHL1 expression in tumors from heterozygous carriers but the NTHL1 bi-allelic loss characteristic mutational signature (SBS 30) was not present. The analysis was extended to 27,421 breast cancer cases and 19,759 controls from 10 international studies revealing 138 cases and 93 controls with a heterozygous LoF variant (OR 1.06, 95% CI: 0.82-1.39) and 316 cases and 179 controls with a missense variant (OR 1.31, 95% CI: 1.09-1.57). Missense variants selected for deleterious features by a number of in silico bioinformatic prediction tools or located within the endonuclease III functional domain showed a stronger association with breast cancer. Somatic sequencing of breast cancers from carriers indicated that the risk associated with NTHL1 appears to operate through haploinsufficiency, consistent with other described low-penetrance breast cancer genes. Data from this very large international multicenter study suggests that heterozygous pathogenic germline coding variants in NTHL1 may be associated with low- to moderate- increased risk of breast cancer.
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Affiliation(s)
- Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Lisa Devereux
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Yu-Kuan Huang
- Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Melbourne, Vic, Australia
| | - Niko Thio
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Dane Cheasley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
| | - Sara Gutiérrez-Enríquez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alejandro Moles-Fernández
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Orland Diez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Area of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Quebec, Canada
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Quebec, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Quebec, Canada
| | - Alfons Meindl
- University of Munich, Campus Großhadern, Department of Gynecology and Obstetrics, Munich, Germany
| | - Rita Schmutzler
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology (CIO), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric Hahnen
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
| | - Christoph Engel
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Elodie Girard
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Discipline of Medical Genetics, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
- Division of Molecular Medicine, Pathology North, Newcastle, NSW, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia.
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia.
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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: 22] [Impact Index Per Article: 7.3] [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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7
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Ng PS, Pan JW, Ahmad Zabidi MM, Rajadurai P, Yip CH, Reuda OM, Dunning AM, Antoniou AC, Easton DF, Caldas C, Chin SF, Teo SH. Characterisation of PALB2 tumours through whole-exome and whole-transcriptomic analyses. NPJ Breast Cancer 2021; 7:46. [PMID: 33893315 PMCID: PMC8065101 DOI: 10.1038/s41523-021-00254-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/26/2021] [Indexed: 02/08/2023] Open
Abstract
Rare protein-truncating variants (PTVs) in PALB2 confer increased risk to breast cancer, but relatively few studies have reported the characteristics of tumours with PALB2 PTVs. In this study, we describe molecular characteristics of tumours with either germline or somatic alterations in PALB2. DNA from fresh frozen tumour tissues and matched peripheral blood lymphocytes for 560 breast cancer patients was subjected for whole-exome sequencing (WES), and RNA from tumour tissues was subjected to RNA sequencing (RNA-seq). We found six cases with germline and three with somatic protein-truncating variants in PALB2. The characteristics of tumours in patients with PALB2 PTVs were similar to those with BRCA1 and BRCA2 PTVs, having significantly more somatic alterations, and a high proportion of the mutational signature and genomic scar scores characteristic of deficiencies in homologous recombination (HR), compared to tumours arising in non-carriers. Unlike tumours arising in patients with BRCA1 and BRCA2 PTVs, PALB2 tumours did not have high prevalence of TP53 somatic alterations or an enriched immune microenvironment. In summary, PALB2 tumours show the homologous recombination deficiencies characteristic of BRCA1 and BRCA2 tumours, and highlight the potential clinical relevance of PALB2 mutational status in guiding therapeutic choices.
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Affiliation(s)
- Pei Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Oscar M Reuda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
- Cambridge Breast Cancer Research Unit, CRUK Cambridge Cancer Centre, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia.
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.
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8
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Whitworth J, Casey RT, Smith PS, Giger O, Martin JE, Clark G, Cook J, Fernando MS, Taniere P, Maher ER. Familial wild-type gastrointestinal stromal tumour in association with germline truncating variants in both SDHA and PALB2. Eur J Hum Genet 2021; 29:1139-1145. [PMID: 33854214 PMCID: PMC8298530 DOI: 10.1038/s41431-021-00862-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/04/2021] [Accepted: 03/04/2021] [Indexed: 11/11/2022] Open
Abstract
Gastrointestinal stromal tumour (GIST) is a mesenchymal neoplasm arising in the gastrointestinal tract. A rare subset of GISTs are classified as wild-type GIST (wtGIST) and these are frequently associated with germline variants that affect the function of cancer predisposition genes such as the succinate dehydrogenase subunit genes (SDHA, SDHB, SDHC, SDHD) or NF1. However, despite this high heritability, familial clustering of wtGIST is extremely rare. Here, we report a mother–son diad who developed wtGIST at age 66 and 34 years, respectively. Comprehensive genetic testing revealed germline truncating variants in both SDHA (c.1534C>T (p.Arg512*)) and PALB2 (c.3113G>A (p.Trp1038*)) in both affected individuals. The mother also developed breast ductal carcinoma in-situ at age 70 years. Immunohistochemistry and molecular analysis of the wtGISTs revealed loss of SDHB expression and loss of the wild-type SDHA allele in tumour material. No allele loss was detected at PALB2 suggesting that wtGIST tumourigenesis was principally driven by succinate dehydrogenase deficiency. However, we speculate that the presence of multilocus inherited neoplasia alleles syndrome (MINAS) in this family might have contributed to the highly unusual occurrence of familial wtGIST. Systematic reporting of tumour risks and phenotypes in individuals with MINAS will facilitate the clinical interpretation of the significance of this diagnosis, which is becoming more frequent as strategies for genetic testing for hereditary cancer becomes more comprehensive.
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Affiliation(s)
- James Whitworth
- University of Cambridge Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK.
| | - Ruth T Casey
- University of Cambridge Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Philip S Smith
- University of Cambridge Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Olivier Giger
- Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Jose Ezequiel Martin
- University of Cambridge Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Graeme Clark
- University of Cambridge Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Jaqueline Cook
- Department of Clinical Genetics, Northern General Hospital, Sheffield, UK
| | - Marlee S Fernando
- Department of Pathology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Phillipe Taniere
- Department of Pathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Eamonn R Maher
- University of Cambridge Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
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9
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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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10
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Huang X, Shao D, Wu H, Zhu C, Guo D, Zhou Y, Chen C, Lin Y, Lu T, Zhao B, Wang C, Sun Q. Genomic Profiling Comparison of Germline BRCA and Non- BRCA Carriers Reveals CCNE1 Amplification as a Risk Factor for Non- BRCA Carriers in Patients With Triple-Negative Breast Cancer. Front Oncol 2020; 10:583314. [PMID: 33194720 PMCID: PMC7662137 DOI: 10.3389/fonc.2020.583314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Differences in genomic profiling and immunity-associated parameters between germline BRCA and non-BRCA carriers in TNBC with high tumor burden remain unexplored. This study aimed to compare the differences and explore potential prognostic predictors and therapeutic targets. Methods: The study cohort included 21 consecutive TNBC cases with germline BRCA1/2 mutations and 54 non-BRCA carriers with a tumor size ≥ 2 cm and/or ≥1 affected lymph nodes. Differences in clinicopathological characteristics and genomic profiles were analyzed through next-generation sequencing. Univariate Kaplan-Meier analysis and Cox regression model were applied to survival analysis. Immunohistochemistry was used to confirm the consistency between CCNE1 amplification and cyclin E1 protein overexpression. Results: The cohort included 16 and five patients with germline BRCA1 and BRCA2 mutations, respectively. Patients with germline BRCA1/2 mutations were diagnosed at a significantly younger age and were more likely to have a family history of breast and/or ovarian cancer. Six non-BRCA carriers (11.11%) carried germline mutations in other cancer susceptibility genes, including five mutations in five homologous recombination repair (HRR) pathway genes (9.26%) and one mutation in MSH3 (1.85%). Somatic mutations in HRR pathway genes were found in 22.22 and 14.29% of the non-BRCA and BRCA carriers, respectively. PIK3CA missense mutation (p = 0.046) and CCNE1 amplification (p = 0.2) were found only in the non-BRCA carriers. The median tumor mutation burden (TMB) was 4.1 Muts/Mb, whereas none of the cases had high microsatellite instability (MSI). BRCA status did not affect disease-free survival (DFS, p = 0.15) or overall survival (OS, p = 0.52). CCNE1 amplification was an independent risk factor for DFS in non-BRCA carriers with TNBC (HR 13.07, 95% CI 2.47-69.24, p = 0.003). Consistency between CCNE1 amplification and cyclin E1 protein overexpression was confirmed with an AUC of 0.967 for cyclin E1 signal intensity. Conclusions: We found differences in genetic alterations between germline BRCA and non-BRCA carriers with TNBC and a high tumor burden. TMB and MSI may not be suitable predictors of TNBC for immune checkpoint inhibitors. Notably, CCNE1 amplification is a novel potential prognostic marker and therapeutic target for non-BRCA carriers with TNBC. Cyclin E1 may be used instead of CCNE1 to improve clinical applicability.
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Affiliation(s)
- Xin Huang
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Di Shao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | | | - Dan Guo
- Clinical Biobank, Medical Science Research Center, Peking Union Medical College Hospital, Beijing, China
| | - Yidong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Chang Chen
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Yan Lin
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Tao Lu
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Bin Zhao
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Changjun Wang
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Qiang Sun
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
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11
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Preobrazhenskaya EV, Shleykina AU, Gorustovich OA, Martianov AS, Bizin IV, Anisimova EI, Sokolova TN, Chuinyshena SA, Kuligina ES, Togo AV, Belyaev AM, Ivantsov AO, Sokolenko AP, Imyanitov EN. Frequency and molecular characteristics of PALB2-associated cancers in Russian patients. Int J Cancer 2020; 148:203-210. [PMID: 32997802 DOI: 10.1002/ijc.33317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/23/2022]
Abstract
PALB2 is а high-penetrance gene for hereditary breast cancer (BC). Our study aimed to investigate the spectrum of PALB2 mutations in Russian cancer patients. PALB2 sequencing revealed pathogenic variants in 3/190 (1.6%) young-onset and/or familial and/or bilateral BC cases but none in 96 ovarian cancer (OC) or 172 pancreatic cancer patients. Subsequently, seven recurrent PALB2 pathogenic alleles were selected from this and previous Slavic studies and tested in an extended patient series. PALB2 pathogenic variants were detected in 5/585 (0.9%) "high-risk" BC, 10/1508 (0.7%) consecutive BC and 5/1802 (0.3%) OC cases. Haplotyping suggested that subjects with Slavic alleles c.509-510delGA (n = 10) and c.172-175delTTGT (n = 4) as well as carriers of Finnish c.1592delT mutation (n = 4) originated from a single founder each, while PALB2 p.R414X allele (n = 4) had at least two independent founders. Somatic loss of heterozygosity (LOH) was revealed in 5/10 chemonaive BCs and in 0/2 BC samples obtained after neoadjuvant therapy. Multigene sequencing identified somatic PALB2 inactivating point mutation in one out of two tumors without PALB2 LOH but in none of four BCs with PALB2 LOH. Genomic instability, as determined by NGS, was observed in four out of five tumors with biallelic PALB2 inactivation but not in the BC sample with the preserved wild-type PALB2 allele. PALB2 germ-line mutations contribute to a small fraction of cancer cases in Russia. The majority although not all PALB2-driven BCs have somatic inactivation of the remaining PALB2 allele and therefore potential sensitivity to platinum compounds and PARP inhibitors.
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Affiliation(s)
- Elena V Preobrazhenskaya
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,St. Petersburg Pediatric Medical University, St. Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | | | | | | | - Ilya V Bizin
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | | | - Tatjana N Sokolova
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | | | - Ekatherina Sh Kuligina
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,St. Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Alexandr V Togo
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,St. Petersburg Pediatric Medical University, St. Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Alexey M Belyaev
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,I.I. Mechnikov North-Western Medical University, St. Petersburg, Russia
| | - Alexandr O Ivantsov
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,St. Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Anna P Sokolenko
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,St. Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Evgeny N Imyanitov
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia.,St. Petersburg Pediatric Medical University, St. Petersburg, Russia.,I.I. Mechnikov North-Western Medical University, St. Petersburg, Russia
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12
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von Ebner's glands intercalated duct adenocarcinoma with PALB2 gene mutation. Ann Diagn Pathol 2020; 49:151637. [PMID: 33069082 DOI: 10.1016/j.anndiagpath.2020.151637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/27/2020] [Indexed: 11/20/2022]
Abstract
Secretory carcinoma of the salivary glands is a distinct entity with distinct morphologic features, immunohistochemical profile and molecular alterations. It mainly affects middle aged individuals with slight male predominance and parotid gland is the most common site of involvement. Although ETV6-NTRK3 gene fusion is considered pathognomonic for secretory carcinoma, advances in molecular profiling of this tumor have led to the discovery of novel ETV6 fusion partners and gene mutations. Herein, we describe a case of an adenocarcinoma of intercalated duct origin favor secretory carcinoma, in a unique location of von Ebner's glands of mobile tongue in a 40-year-old Caucasian female. Aside from being in a unique location, the tumor showed somatic mutation for PALB2 gene which has not been described so far in secretory carcinoma. Discovery of novel fusions and mutations have therapeutic implications with respect to targeted therapy.
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13
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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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14
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Hu ZY, Liu L, Xie N, Lu J, Liu Z, Tang Y, Wang Y, Yang J, Ouyang Q. Germline PALB2 Mutations in Cancers and Its Distinction From Somatic PALB2 Mutations in Breast Cancers. Front Genet 2020; 11:829. [PMID: 33193564 PMCID: PMC7482549 DOI: 10.3389/fgene.2020.00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
PALB2 is an important BRCAx candidate for familial breast cancers (FBC). PALB2 pathogenic variants (PVs) may not to conform to "two hit" paradigm. However, a recent study demonstrates that in the majority PALB2 germline mutant breast cancers, the loss of heterozygosity (LOH) and somatic point mutations are the "second hit." This study aimed to investigate the second hits in germline PALB2 mutations in breast cancers. We screened out 28 germline PALB2-mutation carriers among 480 familial cancer patients (including 143 FBC patients) in Geneplus database pool. Of the 143 patients with FBC, 10 had mono-allelic PALB2 germline mutations. All these germline PALB2 mutations were high-risk stop-gain, frameshift, or splicing mutations that concentrated in EX5-EX9 and might led to truncated proteins, severe functional defects and malignant phenotype. The hotspots were c.1057A[3 > 2] and c.3114-1G > A. Other mutations included c.389delA, c.2068C > T, c.2167_2168delAT, c.2629delT and c.2968G > T. Only one FBC patient has PALB2 somatic mutation and two patients had LOH of PALB2. All germline PALB2 mutations were high-risk mutations, whereas the somatic PALB2 mutations were moderate-risk missense mutations. We also distinguished PALB2 "novel mutations" from "reported mutations." In conclusion, germline PALB2 mutation should be put into the context of future screening.
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Affiliation(s)
- Zhe-Yu Hu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Liping Liu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Ning Xie
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Jun Lu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | | | - Yu Tang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Yikai Wang
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Jianbo Yang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Fujian Medical University Union Hospital, Fuzhou, China.,Department of Otolaryngology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Quchang Ouyang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
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15
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Kaneyasu T, Mori S, Yamauchi H, Ohsumi S, Ohno S, Aoki D, Baba S, Kawano J, Miki Y, Matsumoto N, Nagasaki M, Yoshida R, Akashi-Tanaka S, Iwase T, Kitagawa D, Masuda K, Hirasawa A, Arai M, Takei J, Ide Y, Gotoh O, Yaguchi N, Nishi M, Kaneko K, Matsuyama Y, Okawa M, Suzuki M, Nezu A, Yokoyama S, Amino S, Inuzuka M, Noda T, Nakamura S. Prevalence of disease-causing genes in Japanese patients with BRCA1/2-wildtype hereditary breast and ovarian cancer syndrome. NPJ Breast Cancer 2020; 6:25. [PMID: 32566746 PMCID: PMC7293299 DOI: 10.1038/s41523-020-0163-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/30/2020] [Indexed: 12/30/2022] Open
Abstract
Panel sequencing of susceptibility genes for hereditary breast and ovarian cancer (HBOC) syndrome has uncovered numerous germline variants; however, their pathogenic relevance and ethnic diversity remain unclear. Here, we examined the prevalence of germline variants among 568 Japanese patients with BRCA1/2-wildtype HBOC syndrome and a strong family history. Pathogenic or likely pathogenic variants were identified on 12 causal genes for 37 cases (6.5%), with recurrence for 4 SNVs/indels and 1 CNV. Comparisons with non-cancer east-Asian populations and European familial breast cancer cohorts revealed significant enrichment of PALB2, BARD1, and BLM mutations. Younger onset was associated with but not predictive of these mutations. Significant somatic loss-of-function alterations were confirmed on the wildtype alleles of genes with germline mutations, including PALB2 additional somatic truncations. This study highlights Japanese-associated germline mutations among patients with BRCA1/2 wildtype HBOC syndrome and a strong family history, and provides evidence for the medical care of this high-risk population.
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Affiliation(s)
- Tomoko Kaneyasu
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Seiichi Mori
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Hideko Yamauchi
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Shozo Ohsumi
- National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto-machi, Matsuyama, Ehime Japan
| | - Shinji Ohno
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Daisuke Aoki
- Department of Obstetrics & Gynecology, Keio University School of Medicine, 35 Shinano-cho, Shinjuku-ku Tokyo, Japan
| | - Shinichi Baba
- Sagara Hospital, 3-31 Matsubara-cho, Kagoshima, Japan
| | - Junko Kawano
- Sagara Hospital, 3-31 Matsubara-cho, Kagoshima, Japan
| | - Yoshio Miki
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku Yokohama, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi Japan
| | - Reiko Yoshida
- Department of Clinical Genetic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Sadako Akashi-Tanaka
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Takuji Iwase
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Dai Kitagawa
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Kenta Masuda
- Department of Obstetrics & Gynecology, Keio University School of Medicine, 35 Shinano-cho, Shinjuku-ku Tokyo, Japan
| | - Akira Hirasawa
- Department of Obstetrics & Gynecology, Keio University School of Medicine, 35 Shinano-cho, Shinjuku-ku Tokyo, Japan
| | - Masami Arai
- Department of Clinical Genetic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Junko Takei
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Yoshimi Ide
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Osamu Gotoh
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Noriko Yaguchi
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Mitsuyo Nishi
- Sagara Hospital, 3-31 Matsubara-cho, Kagoshima, Japan
| | - Keika Kaneko
- National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto-machi, Matsuyama, Ehime Japan
| | - Yumi Matsuyama
- National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto-machi, Matsuyama, Ehime Japan
| | - Megumi Okawa
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Misato Suzuki
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Aya Nezu
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Shiro Yokoyama
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Sayuri Amino
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Mayuko Inuzuka
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Tetsuo Noda
- Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
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16
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Li N, McInerny S, Zethoven M, Cheasley D, Lim BWX, Rowley SM, Devereux L, Grewal N, Ahmadloo S, Byrne D, Lee JEA, Li J, Fox SB, John T, Antill Y, Gorringe KL, James PA, Campbell IG. Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer. J Natl Cancer Inst 2020; 111:1332-1338. [PMID: 30949688 DOI: 10.1093/jnci/djz045] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer. METHODS RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation. RESULTS A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) or triple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency. CONCLUSIONS This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.
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17
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Van Marcke C, Helaers R, De Leener A, Merhi A, Schoonjans CA, Ambroise J, Galant C, Delrée P, Rothé F, Bar I, Khoury E, Brouillard P, Canon JL, Vuylsteke P, Machiels JP, Berlière M, Limaye N, Vikkula M, Duhoux FP. Tumor sequencing is useful to refine the analysis of germline variants in unexplained high-risk breast cancer families. Breast Cancer Res 2020; 22:36. [PMID: 32295625 PMCID: PMC7161277 DOI: 10.1186/s13058-020-01273-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Background Multigene panels are routinely used to assess for predisposing germline mutations in families at high breast cancer risk. The number of variants of unknown significance thereby identified increases with the number of sequenced genes. We aimed to determine whether tumor sequencing can help refine the analysis of germline variants based on second somatic genetic events in the same gene. Methods Whole-exome sequencing (WES) was performed on whole blood DNA from 70 unrelated breast cancer patients referred for genetic testing and without a BRCA1, BRCA2, TP53, or CHEK2 mutation. Rare variants were retained in a list of 735 genes. WES was performed on matched tumor DNA to identify somatic second hits (copy number alterations (CNAs) or mutations) in the same genes. Distinct methods (among which immunohistochemistry, mutational signatures, homologous recombination deficiency, and tumor mutation burden analyses) were used to further study the role of the variants in tumor development, as appropriate. Results Sixty-eight patients (97%) carried at least one germline variant (4.7 ± 2.0 variants per patient). Of the 329 variants, 55 (17%) presented a second hit in paired tumor tissue. Of these, 53 were CNAs, resulting in tumor enrichment (28 variants) or depletion (25 variants) of the germline variant. Eleven patients received variant disclosure, with clinical measures for five of them. Seven variants in breast cancer-predisposing genes were considered not implicated in oncogenesis. One patient presented significant tumor enrichment of a germline variant in the oncogene ERBB2, in vitro expression of which caused downstream signaling pathway activation. Conclusion Tumor sequencing is a powerful approach to refine variant interpretation in cancer-predisposing genes in high-risk breast cancer patients. In this series, the strategy provided clinically relevant information for 11 out of 70 patients (16%), adapted to the considered gene and the familial clinical phenotype.
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Affiliation(s)
- Cédric Van Marcke
- Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc and Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium.,Human Molecular Genetics, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Raphaël Helaers
- Human Molecular Genetics, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Anne De Leener
- Center for Human Genetics, Cliniques universitaires Saint-Luc, Brussels, Belgium.,Breast Clinic, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Ahmad Merhi
- Laboratory of Translational Oncology and IPG BioBank, Institute of Pathology and Genetics, Gosselies, Belgium
| | | | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Christine Galant
- Breast Clinic, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Avenue Hippocrate 10, 1200, Brussels, Belgium.,Department of Pathology, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - Paul Delrée
- Department of Pathology, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabelle Bar
- Laboratory of Translational Oncology and IPG BioBank, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Elsa Khoury
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Pascal Brouillard
- Human Molecular Genetics, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Jean-Luc Canon
- Department of Oncology-Hematology, Grand Hôpital de Charleroi, Charleroi, Belgium
| | - Peter Vuylsteke
- Department of Medical Oncology, UCLouvain, CHU UCL Namur, site Sainte-Elisabeth, Namur, Belgium
| | - Jean-Pascal Machiels
- Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc and Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Martine Berlière
- Breast Clinic, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, UCLouvain, Brussels, Belgium
| | - François P Duhoux
- Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc and Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium. .,Center for Human Genetics, Cliniques universitaires Saint-Luc, Brussels, Belgium. .,Breast Clinic, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Avenue Hippocrate 10, 1200, Brussels, Belgium.
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18
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Kader T, Elder K, Zethoven M, Semple T, Hill P, Goode DL, Thio N, Cheasley D, Rowley SM, Byrne DJ, Pang JM, Miligy IM, Green AR, Rakha EA, Fox SB, Mann GB, Campbell IG, Gorringe KL. The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma. NPJ Breast Cancer 2020; 6:9. [PMID: 32195332 PMCID: PMC7067788 DOI: 10.1038/s41523-020-0150-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Intraductal papillomas (IDP) are challenging breast findings because of their variable risk of progression to malignancy. The molecular events driving IDP development and genomic features of malignant progression are poorly understood. In this study, genome-wide CNA and/or targeted mutation analysis was performed on 44 cases of IDP, of which 20 cases had coexisting ductal carcinoma in situ (DCIS), papillary DCIS or invasive ductal carcinoma (IDC). CNA were rare in pure IDP, but 69% carried an activating PIK3CA mutation. Among the synchronous IDP cases, 55% (11/20) were clonally related to the synchronous DCIS and/or IDC, only one of which had papillary histology. In contrast to pure IDP, PIK3CA mutations were absent from clonal cases. CNAs in any of chromosomes 1, 16 or 11 were significantly enriched in clonal IDP lesions compared to pure and non-clonal IDP. The observation that 55% of IDP are clonal to DCIS/IDC indicates that IDP can be a direct precursor for breast carcinoma, not limited to the papillary type. The absence of PIK3CA mutations and presence of CNAs in IDP could be used clinically to identify patients at high risk of progression to carcinoma.
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Affiliation(s)
- Tanjina Kader
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC Australia
| | - Kenneth Elder
- The Breast Service, The Royal Women’s Hospital, Fitzroy, VIC Australia
| | | | | | - Prue Hill
- Department of Anatomical Pathology, St Vincent’s Hospital, Fitzroy, VIC Australia
| | - David L. Goode
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Dane Cheasley
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | | | | | - Jia-Min Pang
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Islam M. Miligy
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Andrew R. Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Emad A. Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | | | - G. Bruce Mann
- The Breast Service, The Royal Women’s Hospital, Fitzroy, VIC Australia
| | - Ian G. Campbell
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC Australia
| | - Kylie L. Gorringe
- Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC Australia
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19
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Chen B, Zhang G, Li X, Ren C, Wang Y, Li K, Mok H, Cao L, Wen L, Jia M, Li C, Guo L, Wei G, Lin J, Li Y, Zhang Y, Han-Zhang H, Liu J, Lizaso A, Liao N. Comparison of BRCA versus non-BRCA germline mutations and associated somatic mutation profiles in patients with unselected breast cancer. Aging (Albany NY) 2020; 12:3140-3155. [PMID: 32091409 PMCID: PMC7066887 DOI: 10.18632/aging.102783] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022]
Abstract
The data on the phenotypes associated with some rare germline mutations in Chinese breast cancer patients are limited. The difference in somatic mutation profiles in breast cancer patients with germline BRCA and non-BRCA mutations remains unexplored. We interrogated the germline and somatic mutational profile of 524 Chinese breast cancer patients with various stages unselected for predisposing factors using a panel consisting of 520 cancer-related genes including 62 cancer susceptibility genes. We divided the patients into three groups according to germline mutations: Germline-BRCA1/2, Germline-others (non-BRCA) and Others (non-carriers). A total of 58 patients (11.1%) carried 76 likely pathogenic or pathogenic (LP/P) germline variants in 15 cancer predisposition genes. Germline BRCA1/2 mutations were detected from 29 (5.53%) patients; with 11 (2.10%) BRCA1 carriers and 18 (3.44%) BRCA2 carriers. In addition, LP/P germline mutations were detected in other genes including MUTYH (n=4), PALB2 (n=4), ATM (n=3), BRIP1 (n=3), CDH1 (n=3), RAD51C (n=3), CHEK2 (n=2), FANCA (n=2), PMS2 (n=2), TP53 (n=2), FANCI (n=1), FANCL (n=1) and PTEN (n=1). At least one variant of uncertain significance (VUS) was identified in 490 (93.5%) patients. Young age (P=0.011), premenopausal status (P=0.013), and breast/ovarian cancer family history (P=0.001) were correlated with germline mutations. Germline-BRCA1/2 group was detected with more missense (P=0.02) and less copy-number amplification (P=0.04) than Germline-others group. Meanwhile, Germline-others group and Others group are very similar (P>0.05). The mutation rates of AKT1, CCND1, FGFR1, and PIK3CA were different among the three groups. By investigating all breast and ovarian cancer-related genes listed in the US genetic guidelines, we identified 15 cancer susceptibility genes frequently mutated in the germline of our population and must be included in cancer predisposition screening. Our study contributed a better understanding of the tumor characteristics of patients with LP/P germline mutations.
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Affiliation(s)
- Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Guochun Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xuerui Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chongyang Ren
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yulei Wang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Kai Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hsiaopei Mok
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Li Cao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lingzhu Wen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Minghan Jia
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Cheukfai Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Liping Guo
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Guangnan Wei
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiali Lin
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yingzi Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yuchen Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | | | - Jing Liu
- Burning Rock Biotech, Guangzhou, China
| | | | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
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20
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Li A, Geyer FC, Blecua P, Lee JY, Selenica P, Brown DN, Pareja F, Lee SSK, Kumar R, Rivera B, Bi R, Piscuoglio S, Wen HY, Lozada JR, Gularte-Mérida R, Cavallone L, Rezoug Z, Nguyen-Dumont T, Peterlongo P, Tondini C, Terkelsen T, Rønlund K, Boonen SE, Mannerma A, Winqvist R, Janatova M, Rajadurai P, Xia B, Norton L, Robson ME, Ng PS, Looi LM, Southey MC, Weigelt B, Soo-Hwang T, Tischkowitz M, Foulkes WD, Reis-Filho JS. Homologous recombination DNA repair defects in PALB2-associated breast cancers. NPJ Breast Cancer 2019; 5:23. [PMID: 31428676 PMCID: PMC6687719 DOI: 10.1038/s41523-019-0115-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 01/02/2023] Open
Abstract
Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.
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Affiliation(s)
- Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Department of Pathology, Fudan University Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Felipe C. Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pedro Blecua
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - David N. Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Simon S. K. Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Barbara Rivera
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
| | - Rui Bi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Department of Pathology, Fudan University Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Hannah Y. Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - John R. Lozada
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | | | - Luca Cavallone
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
| | - Zoulikha Rezoug
- Cancer Prevention Center, Jewish General Hospital, Montreal, Quebec Canada
| | - Tu Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Paolo Peterlongo
- IFOM, The Italian Foundation for Cancer Research Institute of Molecular Oncology, Milan, Italy
| | | | - Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Karina Rønlund
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Susanne E. Boonen
- Clinical Genetics Unit, Department of Pediatrics, Zealand University Hospital, Roskilde, Denmark
| | - Arto Mannerma
- Biocenter Kuopio and Cancer Center of Easter Finland, University of Eastern Finland, Kuopio, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pei-Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Teo Soo-Hwang
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - William D. Foulkes
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
- Cancer Prevention Center, Jewish General Hospital, Montreal, Quebec Canada
- Cancer Program, Research Institute McGill University Health Centre, Montreal, Quebec Canada
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
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21
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Kader T, Hill P, Zethoven M, Goode DL, Elder K, Thio N, Doyle M, Semple T, Sufyan W, Byrne DJ, Pang JMB, Murugasu A, Miligy IM, Green AR, Rakha EA, Fox SB, Mann GB, Campbell IG, Gorringe KL. Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma. J Pathol 2019; 248:326-338. [PMID: 30843206 DOI: 10.1002/path.5262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 12/18/2022]
Abstract
The current model for breast cancer progression proposes independent 'low grade (LG)-like' and 'high grade (HG)-like' pathways but lacks a known precursor to HG cancer. We applied low-coverage whole-genome sequencing to atypical ductal hyperplasia (ADH) with and without carcinoma to shed light on breast cancer progression. Fourteen out of twenty isolated ADH cases harboured at least one copy number alteration (CNA), but had fewer aberrations than LG or HG ductal carcinoma in situ (DCIS). ADH carried more HG-like CNA than LG DCIS (e.g. 8q gain). Correspondingly, 64% (7/11) of ADH cases with synchronous HG carcinoma were clonally related, similar to LG carcinoma (67%, 6/9). This study represents a significant shift in our understanding of breast cancer progression, with ADH as a common precursor lesion to the independent 'low grade-like' and 'high grade-like' pathways. These data suggest that ADH can be a precursor of HG breast cancer and that LG and HG carcinomas can evolve from a similar ancestor lesion. We propose that although LG DCIS may be committed to a LG molecular pathway, ADH may remain multipotent, progressing to either LG or HG carcinoma. This multipotent nature suggests that some ADH cases could be more clinically significant than LG DCIS, requiring biomarkers for personalising management. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Tanjina Kader
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Prue Hill
- Department of Anatomical Pathology, St Vincent's Hospital, Fitzroy, Australia
| | | | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Kenneth Elder
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Maria Doyle
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Wajiha Sufyan
- Territory Pathology, Royal Darwin Hospital, Darwin, Australia
| | | | | | - Anand Murugasu
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Islam M Miligy
- Division of Cancer and Stem Cells, Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Andrew R Green
- Division of Cancer and Stem Cells, Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Emad A Rakha
- Division of Cancer and Stem Cells, Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | | | - G Bruce Mann
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Ian G Campbell
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
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22
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Cheasley D, Li N, Rowley SM, Elder K, Mann GB, Loi S, Savas P, Goode DL, Kader T, Zethoven M, Semple T, Fox SB, Pang JM, Byrne D, Devereux L, Nickson C, Procopio P, Lee G, Hughes S, Saunders H, Fujihara KM, Kuykhoven K, Connaughton J, James PA, Gorringe KL, Campbell IG. Molecular comparison of interval and screen-detected breast cancers. J Pathol 2019; 248:243-252. [PMID: 30746706 DOI: 10.1002/path.5251] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/15/2019] [Accepted: 01/30/2019] [Indexed: 01/22/2023]
Abstract
Breast cancer (BC) diagnosed after a negative mammogram but prior to the next screening episode is termed an 'interval BC' (IBC). Understanding the molecular differences between IBC and screen-detected BCs (SDBC) could improve mammographic screening and management options. Therefore, we assessed both germline and somatic genomic aberrations in a prospective cohort. Utilising the Lifepool cohort of >54 000 women attending mammographic screening programs, 930 BC cases with screening status were identified (726 SDBC and 204 IBC). Clinico-pathological and family history information were recorded. Germline and tumour DNA were collected where available and sequenced for BC predisposition and driver gene mutations. Compared to SDBC, IBCs were significantly associated with a younger age at diagnosis and tumour characteristics associated with worse prognosis. Germline DNA assessment of BC cases that developed post-enrolment (276 SDBCs and 77 IBCs) for pathogenic mutations in 12 hereditary BC predisposition genes identified 8 carriers (2.27%). The germline mutation frequency was higher in IBC versus SDBC, although not statistically significant (3.90% versus 1.81%, p = 0.174). Comparing somatic genetic features of IBC and SDBC matched for grade, histological subtype and hormone receptor revealed no significant differences, with the exception of higher homologous recombination deficiency scores in IBC, and copy number changes on chromosome Xq in triple negative SDBCs. Our data demonstrates that while IBCs are clinically more aggressive than SDBC, when matched for confounding clinico-pathological features they do not represent a unique molecular class of invasive BC, but could be a consequence of timing of tumour initiation and mammographic screening. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Dane Cheasley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kenneth Elder
- Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia.,The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia.,The Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - G Bruce Mann
- Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia.,The Royal Melbourne and Royal Women's Hospitals, Parkville, Victoria, Australia
| | - Sherene Loi
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Division of Clinical Medicine and Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Peter Savas
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Division of Clinical Medicine and Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David L Goode
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Tanjina Kader
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Bioinformatics Consulting Core, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Tim Semple
- Genomics Core, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne, Victoria, Australia
| | - Jia-Min Pang
- Department of Pathology, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne, Victoria, Australia
| | - David Byrne
- Department of Pathology, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne, Victoria, Australia
| | - Lisa Devereux
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Lifepool, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Carolyn Nickson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Pietro Procopio
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Grant Lee
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Siobhan Hughes
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Hugo Saunders
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kenji M Fujihara
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Keilly Kuykhoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jacquie Connaughton
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Cancer Genetics and Genomics Program, Peter MacCallum Cancer Centre, 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
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23
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Duran-Lozano L, Montalban G, Bonache S, Moles-Fernández A, Tenés A, Castroviejo-Bermejo M, Carrasco E, López-Fernández A, Torres-Esquius S, Gadea N, Stjepanovic N, Balmaña J, Gutiérrez-Enríquez S, Diez O. Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T. Breast Cancer Res Treat 2018; 174:543-550. [DOI: 10.1007/s10549-018-05094-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022]
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24
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Castroviejo-Bermejo M, Cruz C, Llop-Guevara A, Gutiérrez-Enríquez S, Ducy M, Ibrahim YH, Gris-Oliver A, Pellegrino B, Bruna A, Guzmán M, Rodríguez O, Grueso J, Bonache S, Moles-Fernández A, Villacampa G, Viaplana C, Gómez P, Vidal M, Peg V, Serres-Créixams X, Dellaire G, Simard J, Nuciforo P, Rubio IT, Dienstmann R, Barrett JC, Caldas C, Baselga J, Saura C, Cortés J, Déas O, Jonkers J, Masson JY, Cairo S, Judde JG, O'Connor MJ, Díez O, Balmaña J, Serra V. A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation. EMBO Mol Med 2018; 10:e9172. [PMID: 30377213 PMCID: PMC6284440 DOI: 10.15252/emmm.201809172] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are effective in cancers with defective homologous recombination DNA repair (HRR), including BRCA1/2-related cancers. A test to identify additional HRR-deficient tumors will help to extend their use in new indications. We evaluated the activity of the PARPi olaparib in patient-derived tumor xenografts (PDXs) from breast cancer (BC) patients and investigated mechanisms of sensitivity through exome sequencing, BRCA1 promoter methylation analysis, and immunostaining of HRR proteins, including RAD51 nuclear foci. In an independent BC PDX panel, the predictive capacity of the RAD51 score and the homologous recombination deficiency (HRD) score were compared. To examine the clinical feasibility of the RAD51 assay, we scored archival breast tumor samples, including PALB2-related hereditary cancers. The RAD51 score was highly discriminative of PARPi sensitivity versus PARPi resistance in BC PDXs and outperformed the genomic test. In clinical samples, all PALB2-related tumors were classified as HRR-deficient by the RAD51 score. The functional biomarker RAD51 enables the identification of PARPi-sensitive BC and broadens the population who may benefit from this therapy beyond BRCA1/2-related cancers.
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Affiliation(s)
| | - Cristina Cruz
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- High Risk and Familial Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Mandy Ducy
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
- CHU de Quebec - Université Laval Research Center, Genomics Center CHUL, Québec City, QC, Canada
| | - Yasir Hussein Ibrahim
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Albert Gris-Oliver
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Benedetta Pellegrino
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, University Hospital of Parma, Parma, Italy
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Marta Guzmán
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Olga Rodríguez
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judit Grueso
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Guillermo Villacampa
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Viaplana
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Patricia Gómez
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Maria Vidal
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Vicente Peg
- Pathology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Serres-Créixams
- Department of Radiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Jacques Simard
- CHU de Quebec - Université Laval Research Center, Genomics Center CHUL, Québec City, QC, Canada
| | - Paolo Nuciforo
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Isabel T Rubio
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Breast Surgical Unit, Breast Cancer Center, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Breast Cancer Programme, Cancer Research UK (CRUK) Cambridge Cancer Centre, Cambridge, UK
| | - José Baselga
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina Saura
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Javier Cortés
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Department of Oncology, Ramón y Cajal University Hospital, Madrid, Spain
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
| | | | | | - Mark J O'Connor
- Oncology Innovative Medicines and Early Clinical Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Clinical and Molecular Genetics Area, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Familial Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
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25
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Wu Y, Dong X, Wang Y, Wang Q, Gu H, Huang W. Association between rs120963, rs152451, rs249935, rs447529, rs8053188, and rs16940342 Polymorphisms in the PALB2 Gene and Breast Cancer Susceptibility: A Meta-Analysis. Oncol Res Treat 2018; 41:780-786. [PMID: 30458447 DOI: 10.1159/000492827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/10/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND The aim of this study was to explore the association between single nucleotide polymorphisms (SNPs) in the rs120963, rs152451, rs249935, rs447529, rs8053188, and rs16940342 loci in the PALB2 gene and breast cancer risk. METHODS Studies investigating the association between SNPs in the PALB2 gene and breast cancer susceptibility were retrieved from the PubMed, Embase, Web of Science, CNKI (Chinese National Knowledge Infrastructure), WanFang, and CBM (China Biology Medicine) databases. Eligible studies were screened according to inclusion/exclusion criteria and principles of quality evaluation. Meta-analysis was performed using Stata 14.0 software. Odds ratios with their corresponding 95% confidence intervals were pooled to assess the association between SNPs in the PALB2 gene loci rs249935, rs447529, rs8053188, rs16940342, rs152451, and rs120963 and breast cancer susceptibility. RESULTS A total of 9 case-control studies were eligible for this meta-analysis. SNPs in the PALB2 gene loci rs120963, rs249935, and rs447529 were significantly associated with an increased or decreased risk of breast cancer. No significant association was detected for rs152451, rs8053188, and rs16940342 under 4 genetic models. CONCLUSION The results of this study suggest that SNPs in the PALB2 loci rs120963/rs249935/rs447529, but not in the other 3 loci (rs152451/rs8053188/rs16940342), may contribute to breast cancer susceptibility.
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