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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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Yang W, Chen S, Cheng X, Xu B, Zeng H, Zou J, Su C, Chen Z. Characteristics of genomic mutations and signaling pathway alterations in thymic epithelial tumors. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1659. [PMID: 34988168 PMCID: PMC8667121 DOI: 10.21037/atm-21-5182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND To elucidate the mechanisms of thymic epithelial tumor (TET) canceration by characterizing genomic mutations and signaling pathway alterations. METHODS Primary tumor and blood samples were collected from 21 patients diagnosed with TETs (thymoma and thymic cancer), 15 of whom were screened by nucleic acid extraction and whole exon sequencing. Bioinformatics was used to comprehensively analyze the sequencing data for these samples, including gene mutation information and the difference of tumor mutation burden (TMB) between thymoma and thymic carcinoma groups. We performed signaling pathway and functional enrichment analysis using the WebGestalt 2017 toolkit. RESULTS ZNF429 (36%) was the gene with the highest mutation frequency in thymic carcinoma. Mutations in BAP1 (14%), ABI1 (7%), BCL9L (7%), and CHEK2 (7%) were exclusively detected in thymic carcinoma, whereas ZNF721 mutations (14%) and PABPC1 (14%) were found exclusively in thymoma. The mean TMB values for thymic carcinoma and thymoma were 0.722 and 0.663 mutations per megabase (Mb), respectively, and these differences were not statistically significant. The ErbB signaling pathway was enriched in the thymoma and intersection groups, and pathways of central carbon metabolism in cancer, longevity regulating and MAPK signaling were only found in the thymoma group, while pathways in cancer (hsa05200) was found in the thymoma and thymic carcinoma groups. CONCLUSIONS Multiple differences in somatic genes and pathways have been identified. Our findings provide insights into differences between thymoma and thymic carcinoma that could aid in designing personalized clinical therapeutic strategies.
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Affiliation(s)
- Weilin Yang
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sai Chen
- Center for Private Medical Service & Healthcare, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinxin Cheng
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bo Xu
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huilan Zeng
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianyong Zou
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunhua Su
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhenguang Chen
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Shahi RB, De Brakeleer S, Caljon B, Pauwels I, Bonduelle M, Joris S, Fontaine C, Vanhoeij M, Van Dooren S, Teugels E, De Grève J. Identification of candidate cancer predisposing variants by performing whole-exome sequencing on index patients from BRCA1 and BRCA2-negative breast cancer families. BMC Cancer 2019; 19:313. [PMID: 30947698 PMCID: PMC6449945 DOI: 10.1186/s12885-019-5494-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/20/2019] [Indexed: 12/30/2022] Open
Abstract
Background In the majority of familial breast cancer (BC) families, the etiology of the disease remains unresolved. To identify missing BC heritability resulting from relatively rare variants (minor allele frequency ≤ 1%), we have performed whole exome sequencing followed by variant analysis in a virtual panel of 492 cancer-associated genes on BC patients from BRCA1 and BRCA2 negative families with elevated BC risk. Methods BC patients from 54 BRCA1 and BRCA2-negative families with elevated BC risk and 120 matched controls were considered for germline DNA whole exome sequencing. Rare variants identified in the exome and in a virtual panel of cancer-associated genes [492 genes associated with different types of (hereditary) cancer] were compared between BC patients and controls. Nonsense, frame-shift indels and splice-site variants (strong protein-damaging variants, called PDAVs later on) observed in BC patients within the genes of the panel, which we estimated to possess the highest probability to predispose to BC, were further validated using an alternative sequencing procedure. Results Exome- and cancer-associated gene panel-wide variant analysis show that there is no significant difference in the average number of rare variants found in BC patients compared to controls. However, the genes in the cancer-associated gene panel with nonsense variants were more than two-fold over-represented in women with BC and commonly involved in the DNA double-strand break repair process. Approximately 44% (24 of 54) of BC patients harbored 31 PDAVs, of which 11 were novel. These variants were found in genes associated with known or suspected BC predisposition (PALB2, BARD1, CHEK2, RAD51C and FANCA) or in predisposing genes linked to other cancer types but not well-studied in the context of familial BC (EXO1, RECQL4, CCNH, MUS81, TDP1, DCLRE1A, DCLRE1C, PDE11A and RINT1) and genes associated with different hereditary syndromes but not yet clearly associated with familial cancer syndromes (ABCC11, BBS10, CD96, CYP1A1, DHCR7, DNAH11, ESCO2, FLT4, HPS6, MYH8, NME8 and TTC8). Exome-wide, only a few genes appeared to be enriched for PDAVs in the familial BC patients compared to controls. Conclusions We have identified a series of novel candidate BC predisposition variants/genes. These variants/genes should be further investigated in larger cohorts/case-control studies. Other studies including co-segregation analyses in affected families, locus-specific loss of heterozygosity and functional studies should shed further light on their relevance for BC risk. Electronic supplementary material The online version of this article (10.1186/s12885-019-5494-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rajendra Bahadur Shahi
- Laboratory of Medical and Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sylvia De Brakeleer
- Laboratory of Medical and Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Ben Caljon
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Universitair Ziekenhuis Brussel (UZ Brussel) / Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Ingrid Pauwels
- Familial Cancer Clinic, Oncologisch Centrum, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Maryse Bonduelle
- Centre for Medical Genetics, Reproduction and Genetics, Universitair Ziekenhuis Brussel (UZ Brussel) / Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sofie Joris
- Familial Cancer Clinic, Oncologisch Centrum, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Christel Fontaine
- Breast Cancer Clinic, Oncologisch Centrum, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Marian Vanhoeij
- Breast Cancer Clinic, Oncologisch Centrum, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Sonia Van Dooren
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Universitair Ziekenhuis Brussel (UZ Brussel) / Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Centre for Medical Genetics, Reproduction and Genetics, Universitair Ziekenhuis Brussel (UZ Brussel) / Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Erik Teugels
- Laboratory of Medical and Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium. .,Familial Cancer Clinic, Oncologisch Centrum, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.
| | - Jacques De Grève
- Laboratory of Medical and Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium. .,Familial Cancer Clinic, Oncologisch Centrum, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.
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Campos-Verdes LM, Costa-Silva DR, da Silva-Sampaio JP, Barros-Oliveira MDC, Escórcio-Dourado CS, Martins LM, Sampaio FA, Revoredo C, Alves-Ribeiro FA, da Silva BB. Review of Polymorphism of the Calcium-Sensing Receptor Gene and Breast Cancer Risk. Cancer Invest 2018; 36:1-7. [PMID: 29504802 DOI: 10.1080/07357907.2018.1430817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polymorphism of the calcium-sensing receptor gene (CaSR or CaR) has been associated with an increased risk for breast cancer. This receptor plays an important role in calcium homeostasis, and has also been detected in several tissues that are unrelated to calcium metabolism, such as the skin, brain, and breast. The calcium-sensing receptor on cellular level, it regulates cell differentiation, proliferation, cell death, and gene expression. In breast cancer cells, CaSR seems to stimulate secretion of the parathyroid hormone-related protein (PTHrP), which stimulates cellular proliferation. Likewise, some studies have supported not only an association between calcium receptor gene polymorphism and breast cancer risk, but also a higher aggressiveness and unfavorable outcomes in breast cancer, which led us to make a survey in Pubmed on the subject in the last 10 years. Thus, in the literature there is a paucity of studies on the subject and the aim of this review was to show the role of calcium-sensing receptor and its association with breast cancer risk.
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Affiliation(s)
- Larysse Maira Campos-Verdes
- a Postgraduate Program of Health in Sciences , Federal University of Piauí , 2280 Frei Serafim Avenue, Teresina , Piauí , Brazil
| | - Danylo Rafhael Costa-Silva
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - João Paulo da Silva-Sampaio
- a Postgraduate Program of Health in Sciences , Federal University of Piauí , 2280 Frei Serafim Avenue, Teresina , Piauí , Brazil
| | | | - Carla Solange Escórcio-Dourado
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Luana Mota Martins
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Fabiane Araújo Sampaio
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Camila Revoredo
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Francisco Adelton Alves-Ribeiro
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Benedito Borges da Silva
- a Postgraduate Program of Health in Sciences , Federal University of Piauí , 2280 Frei Serafim Avenue, Teresina , Piauí , Brazil.,b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
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