1
|
Andersen LVB, Larsen MJ, Davies H, Degasperi A, Nielsen HR, Jensen LA, Kroeldrup L, Gerdes AM, Lænkholm AV, Kruse TA, Nik-Zainal S, Thomassen M. Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness. Breast Cancer Res 2023; 25:69. [PMID: 37316882 DOI: 10.1186/s13058-023-01655-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Familial breast cancer is in most cases unexplained due to the lack of identifiable pathogenic variants in the BRCA1 and BRCA2 genes. The somatic mutational landscape and in particular the extent of BRCA-like tumour features (BRCAness) in these familial breast cancers where germline BRCA1 or BRCA2 mutations have not been identified is to a large extent unknown. METHODS We performed whole-genome sequencing on matched tumour and normal samples from high-risk non-BRCA1/BRCA2 breast cancer families to understand the germline and somatic mutational landscape and mutational signatures. We measured BRCAness using HRDetect. As a comparator, we also analysed samples from BRCA1 and BRCA2 germline mutation carriers. RESULTS We noted for non-BRCA1/BRCA2 tumours, only a small proportion displayed high HRDetect scores and were characterized by concomitant promoter hypermethylation or in one case a RAD51D splice variant previously reported as having unknown significance to potentially explain their BRCAness. Another small proportion showed no features of BRCAness but had mutationally active tumours. The remaining tumours lacked features of BRCAness and were mutationally quiescent. CONCLUSIONS A limited fraction of high-risk familial non-BRCA1/BRCA2 breast cancer patients is expected to benefit from treatment strategies against homologue repair deficient cancer cells.
Collapse
Affiliation(s)
- Lars V B Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Helen Davies
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Andrea Degasperi
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Louise A Jensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lone Kroeldrup
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne-Vibeke Lænkholm
- Department of Surgical Pathology, Zealand University Hospital, 4000, Roskilde, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Serena Nik-Zainal
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- European Sperm Bank, Copenhagen, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
2
|
Pipek O, Alpár D, Rusz O, Bödör C, Udvarnoki Z, Medgyes-Horváth A, Csabai I, Szállási Z, Madaras L, Kahán Z, Cserni G, Kővári B, Kulka J, Tőkés AM. Genomic Landscape of Normal and Breast Cancer Tissues in a Hungarian Pilot Cohort. Int J Mol Sci 2023; 24:ijms24108553. [PMID: 37239898 DOI: 10.3390/ijms24108553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
A limited number of studies have focused on the mutational landscape of breast cancer in different ethnic populations within Europe and compared the data with other ethnic groups and databases. We performed whole-genome sequencing of 63 samples from 29 Hungarian breast cancer patients. We validated a subset of the identified variants at the DNA level using the Illumina TruSight Oncology (TSO) 500 assay. Canonical breast-cancer-associated genes with pathogenic germline mutations were CHEK2 and ATM. Nearly all the observed germline mutations were as frequent in the Hungarian breast cancer cohort as in independent European populations. The majority of the detected somatic short variants were single-nucleotide polymorphisms (SNPs), and only 8% and 6% of them were deletions or insertions, respectively. The genes most frequently affected by somatic mutations were KMT2C (31%), MUC4 (34%), PIK3CA (18%), and TP53 (34%). Copy number alterations were most common in the NBN, RAD51C, BRIP1, and CDH1 genes. For many samples, the somatic mutational landscape was dominated by mutational processes associated with homologous recombination deficiency (HRD). Our study, as the first breast tumor/normal sequencing study in Hungary, revealed several aspects of the significantly mutated genes and mutational signatures, and some of the copy number variations and somatic fusion events. Multiple signs of HRD were detected, highlighting the value of the comprehensive genomic characterization of breast cancer patient populations.
Collapse
Affiliation(s)
- Orsolya Pipek
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Orsolya Rusz
- Department of Pathology, Forensic and Insurance Medicine, SE NAP, Brain Metastasis Research Group, Semmelweis University, 1091 Budapest, Hungary
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Zoltán Udvarnoki
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zoltán Szállási
- Department of Pathology, Forensic and Insurance Medicine, SE NAP, Brain Metastasis Research Group, Semmelweis University, 1091 Budapest, Hungary
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Lilla Madaras
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - Zsuzsanna Kahán
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary
| | - Gábor Cserni
- Department of Pathology, Albert Szent-Györgyi Medical Centre, University of Szeged, 6720 Szeged, Hungary
- Department of Pathology, Bács-Kiskun County Teaching Hospital, 6000 Kecskemét, Hungary
| | - Bence Kővári
- Department of Pathology, Albert Szent-Györgyi Medical Centre, University of Szeged, 6720 Szeged, Hungary
- Department of Pathology, Henry Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Janina Kulka
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - Anna Mária Tőkés
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| |
Collapse
|
3
|
Schwartz A, Manning DK, Koeller DR, Chittenden A, Isidro RA, Hayes CP, Abraamyan F, Manam MD, Dwan M, Barletta JA, Sholl LM, Yurgelun MB, Rana HQ, Garber JE, Ghazani AA. An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes. Front Oncol 2022; 12:942741. [PMID: 36091175 PMCID: PMC9453486 DOI: 10.3389/fonc.2022.942741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic profiles of tumors are often unique and represent characteristic mutational signatures defined by DNA damage or DNA repair response processes. The tumor-derived somatic information has been widely used in therapeutic applications, but it is grossly underutilized in the assessment of germline genetic variants. Here, we present a comprehensive approach for evaluating the pathogenicity of germline variants in cancer using an integrated interpretation of somatic and germline genomic data. We have previously demonstrated the utility of this integrated approach in the reassessment of pathogenic germline variants in selected cancer patients with unexpected or non-syndromic phenotypes. The application of this approach is presented in the assessment of rare variants of uncertain significance (VUS) in Lynch-related colon cancer, hereditary paraganglioma-pheochromocytoma syndrome, and Li-Fraumeni syndrome. Using this integrated method, germline VUS in PMS2, MSH6, SDHC, SHDA, and TP53 were assessed in 16 cancer patients after genetic evaluation. Comprehensive clinical criteria, somatic signature profiles, and tumor immunohistochemistry were used to re-classify VUS by upgrading or downgrading the variants to likely or unlikely actionable categories, respectively. Going forward, collation of such germline variants and creation of cross-institutional knowledgebase datasets that include integrated somatic and germline data will be crucial for the assessment of these variants in a larger cancer cohort.
Collapse
Affiliation(s)
- Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Connor P. Hayes
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Feruza Abraamyan
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Monica Devi Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Meaghan Dwan
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Matthew B. Yurgelun
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arezou A. Ghazani
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- *Correspondence: Arezou A. Ghazani,
| |
Collapse
|
4
|
Cyclin B2 (CCNB2) Stimulates the Proliferation of Triple-Negative Breast Cancer (TNBC) Cells In Vitro and In Vivo. DISEASE MARKERS 2021; 2021:5511041. [PMID: 34354775 PMCID: PMC8331305 DOI: 10.1155/2021/5511041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/10/2021] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive type of breast cancer. Currently, targeting therapy makes great advances for the treatment of TNBC, whereas more effective therapeutic targets are urgently needed. Cyclin B2 (CCNB2), which belongs to B-type cyclins, is known as a cell cycle regulator. CCNB2 is synthesized at G1 phase in cancer cells and downregulated at anaphase. The defects of CCNB2 led to the abnormal cell cycle and tumorigenesis. Though there are wide effects of CCNB2 on multiple types of tumors, the potential role of CCNB2 in TNBC progression is still unclear. Herein, we found that CCNB2 was highly expressed in human TNBC tissues and correlated with the prognosis and clinical pathological features including tumor size (p = 0.022∗) and pTNM stage (p = 0.021∗) of patients with TNBC. CCNB2 could promote the proliferation of TNBC cells in vitro and in mice. Our findings therefore confirmed the involvement of CCNB2 in TNBC progression and provided the evidence that CCNB2 could serve as a promising molecular target of TNBC.
Collapse
|
5
|
Application Areas of Traditional Molecular Genetic Methods and NGS in relation to Hereditary Urological Cancer Diagnosis. JOURNAL OF ONCOLOGY 2020; 2020:7363102. [PMID: 32612654 PMCID: PMC7317306 DOI: 10.1155/2020/7363102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/22/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
Next generation sequencing (NGS) is widely used for diagnosing hereditary cancer syndromes. Often, exome sequencing and extended gene panel approaches are the only means that can be used to detect a pathogenic germline mutation in the case of multiple primary tumors, early onset, a family history of cancer, or a lack of specific signs associated with a particular syndrome. Certain germline mutations of oncogenes and tumor suppressor genes that determine specific clinical phenotypes may occur in mutation hot spots. Diagnosis of such cases, which involve hereditary cancer, does not require NGS, but may be made using PCR and Sanger sequencing. Diagnostic criteria and professional community guidelines developed for hereditary cancers of particular organs should be followed when ordering molecular diagnostic tests for a patient. This review focuses on urological oncology associated with germline mutations. Clinical signs and genetic diagnostic laboratory tests for hereditary forms of renal cell cancer, prostate cancer, and bladder cancer are summarized. While exome sequencing, or, conversely, traditional molecular genetic methods are the procedure of choice in some cases, in most situations, sequencing of multigene panels that are specifically aimed at detecting germline mutations in early onset renal cancer, prostate cancer, and bladder cancer seems to be the basic solution for molecular genetic diagnosis of hereditary cancers.
Collapse
|