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Li H, Bartke R, Zhao L, Verma Y, Horacek A, Rechav Ben-Natan A, Pangilinan GR, Krishnappa N, Nielsen R, Hockemeyer D. Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells. Nat Biomed Eng 2024; 8:165-176. [PMID: 37488236 PMCID: PMC10878975 DOI: 10.1038/s41551-023-01065-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/15/2023] [Indexed: 07/26/2023]
Abstract
Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability and sensitize cancer cells to inhibition by the poly(ADP-ribose) polymerase (PARP). Here we show that human pluripotent stem cells (hPSCs) with one copy of BRCA2 deleted can be used to annotate variants of this gene and to test their sensitivities to PARP inhibition. By using Cas9 to edit the functional BRCA2 allele in the locally haploid hPSCs and in fibroblasts differentiated from them, we characterized essential regions in the gene to identify permissive and loss-of-function mutations. We also used Cas9 to directly test the function of individual amino acids, including amino acids encoded by clinical BRCA2 variants of uncertain significance, and identified alleles that are sensitive to PARP inhibitors used as a standard of care in BRCA2-deficient cancers. Locally haploid human pluripotent stem cells can facilitate detailed structure-function analyses of genes and the rapid functional evaluation of clinically observed mutations.
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Affiliation(s)
- Hanqin Li
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rebecca Bartke
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Lei Zhao
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yogendra Verma
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Anna Horacek
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Alma Rechav Ben-Natan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriella R Pangilinan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Rasmus Nielsen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Oosthuizen J, Van der Merwe NC, Kotze MJ. Navigating the genetic landscape of breast cancer in South Africa amidst a developing healthcare system. Front Genet 2024; 14:1330946. [PMID: 38259622 PMCID: PMC10800608 DOI: 10.3389/fgene.2023.1330946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a significant global health issue as it represents the leading cause of death in women worldwide. In 2021, the World Health Organization established the Global Breast Cancer Initiative framework with the aim to reduce the breast cancer mortality rate by the year 2040. In countries with developing healthcare systems, such as South Africa, the implementation of first-world technologies has been slow. We provide an overview of the strides taken to improve the cost-effectiveness of genetic service delivery for breast cancer patients in South Africa - from advances in the technology utilized for BRCA founder genotyping to variant screening in moderate-to high-penetrance genes. We furthermore reflect on research undertaken to improve accessibility by means of population-directed point-of-care genetic testing that is ideal for use in a primary healthcare setting. We also report on a pilot study utilizing exome sequencing at the intersection between research and service delivery. Finally, we discuss and conclude on the controversies, research gaps, and future prospects based on the most recent developments in first-world countries that are implementable in developing countries to improve early detection of breast cancer and overall disease management.
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Affiliation(s)
- Jaco Oosthuizen
- Division of Human Genetics, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Nerina C. Van der Merwe
- Division of Human Genetics, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Maritha J. Kotze
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Toncheva D, Marinova M, Borovska P, Serbezov D. Incidence of ancient variants associated with oncological diseases in modern populations. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2151376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Draga Toncheva
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
- Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Marinova
- Department of Computer Systems and Technologies, Faculty of Electronics and Automation, Technical University of Sofia, Sofia, Bulgaria
| | - Plamenka Borovska
- Department of Informatics, Faculty of Applied Mathematics and Informatics, Technical University of Sofia, Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
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Muhammad N, Azeem A, Arif S, Naeemi H, Masood I, Hassan U, Ijaz B, Hanif F, Syed AA, Yusuf MA, Rashid MU. Prevalence of BRCA1 and BRCA2 germline variants in an unselected pancreatic cancer patient cohort in Pakistan. Hered Cancer Clin Pract 2023; 21:22. [PMID: 37951914 PMCID: PMC10640758 DOI: 10.1186/s13053-023-00269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND BRCA1 and BRCA2 (BRCA1/2) are the most frequently investigated genes among Caucasian pancreatic cancer patients, whereas limited reports are available among Asians. We aimed to investigate the prevalence of BRCA1/2 germline variants in Pakistani pancreatic cancer patients. METHODS One hundred and fifty unselected and prospectively enrolled pancreatic cancer patients were comprehensively screened for BRCA1/2 germline variants using denaturing high-performance liquid chromatography and high-resolution melting analyses, followed by DNA sequencing of the variant fragments. The novel variants were analyzed for their pathogenic effect using in-silico tools. Potentially functional variants were further screened in 200 cancer-free controls. RESULTS Protein truncating variant was detected in BRCA2 only, with a prevalence of 0.7% (1/150). A frameshift BRCA2 variant (p.Asp946Ilefs*14) was identified in a 71-year-old male patient of Pathan ethnicity, with a family history of abdominal cancer. Additionally, we found a novel variant in BRCA2 (p.Glu2650Gln), two previously reported variants in BRCA1 (p.Thr293Ser) and BRCA2 (p.Ile2296Leu) and a recurrent nonsense variant in BRCA2 (p.Lys3326Ter). These variants were classified as variants of uncertain significance (VUS). It is noteworthy that none of these VUS carriers had a family history of pancreatic or other cancers. CONCLUSIONS In this first study, BRCA1/2 pathogenic variant is identified with a low frequency in pancreatic cancer patients from Pakistan. Comprehensive multigene panel testing is recommended in the Pakistani pancreatic cancer patients to enhance genetic understanding in this population.
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Affiliation(s)
- Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
- Laboratory of Applied and Functional Genomics, National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ayesha Azeem
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Shumaila Arif
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Humaira Naeemi
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Iqra Masood
- Clinical Research Office, SKMCH&RC, Lahore, Pakistan
| | - Usman Hassan
- Department of Pathology, SKMCH&RC, Lahore, Pakistan
| | - Bushra Ijaz
- Laboratory of Applied and Functional Genomics, National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Faisal Hanif
- Department of Surgical Oncology, SKMCH&RC, Lahore, Pakistan
- Centre for Liver and Biliary Sciences, Bahria International Hospital, Lahore, Pakistan
| | - Aamir Ali Syed
- Department of Surgical Oncology, SKMCH&RC, Lahore, Pakistan
| | | | - Muhammad Usman Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
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Yuan L, Liu G, Zhao D, Zhu H, Qi J, Lu K. Interaction of p53 with BRC analogs: A comparative design assisted by ZDOCK and CABS-Dock simulation. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Omole EB, Aijaz I, Ellegate J, Isenhart E, Desouki MM, Mastri M, Humphrey K, Dougherty EM, Rosario SR, Nastiuk KL, Ohm JE, Eng KH. Combined BRCA2 and MAGEC3 Expression Predict Outcome in Advanced Ovarian Cancers. Cancers (Basel) 2022; 14:cancers14194724. [PMID: 36230652 PMCID: PMC9562635 DOI: 10.3390/cancers14194724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 12/02/2022] Open
Abstract
Like BRCA2, MAGEC3 is an ovarian cancer predisposition gene that has been shown to have prognostic significance in ovarian cancer patients. Despite the clinical significance of each gene, no studies have been conducted to assess the clinical significance of their combined expression. We therefore sought to determine the relationship between MAGEC3 and BRCA2 expression in ovarian cancer and their association with patient characteristics and outcomes. Immunohistochemical staining was quantitated on tumor microarrays of human tumor samples obtained from 357 patients with epithelial ovarian cancer to ascertain BRCA2 expression levels. In conjunction with our previously published MAGEC3 expression data, we observed a weak inverse correlation of MAGEC3 with BRCA2 expression (r = −0.15; p < 0.05) in cases with full-length BRCA2. Patients with optimal cytoreduction, loss of MAGEC3, and detectable BRCA2 expression had better overall (median OS: 127.9 vs. 65.3 months, p = 0.035) and progression-free (median PFS: 85.3 vs. 18.8 months, p = 0.002) survival compared to patients that were BRCA2 expressors with MAGEC3 normal levels. Our results suggest that combined expression of MAGEC3 and BRCA2 serves as a better predictor of prognosis than each marker alone.
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Affiliation(s)
- Emmanuel B. Omole
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Iqbal Aijaz
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - James Ellegate
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Emily Isenhart
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Mohamed M. Desouki
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Michalis Mastri
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Kristen Humphrey
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Emily M. Dougherty
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Spencer R. Rosario
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Kent L. Nastiuk
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Joyce E. Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Correspondence:
| | - Kevin H. Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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The Genetic Analyses of French Canadians of Quebec Facilitate the Characterization of New Cancer Predisposing Genes Implicated in Hereditary Breast and/or Ovarian Cancer Syndrome Families. Cancers (Basel) 2021; 13:cancers13143406. [PMID: 34298626 PMCID: PMC8305212 DOI: 10.3390/cancers13143406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
The French Canadian population of the province of Quebec has been recognized for its contribution to research in medical genetics, especially in defining the role of heritable pathogenic variants in cancer predisposing genes. Multiple carriers of a limited number of pathogenic variants in BRCA1 and BRCA2, the major risk genes for hereditary breast and/or ovarian cancer syndrome families, have been identified in French Canadians, which is in stark contrast to the array of over 2000 different pathogenic variants reported in each of these genes in other populations. As not all such cancer syndrome families are explained by BRCA1 and BRCA2, newly proposed gene candidates identified in other populations have been investigated for their role in conferring risk in French Canadian cancer families. For example, multiple carriers of distinct variants were identified in PALB2 and RAD51D. The unique genetic architecture of French Canadians has been attributed to shared ancestry due to common ancestors of early settlers of this population with origins mainly from France. In this review, we discuss the merits of genetically characterizing cancer predisposing genes in French Canadians of Quebec. We focused on genes that have been implicated in hereditary breast and/or ovarian cancer syndrome families as they have been the most thoroughly characterized cancer syndromes in this population. We describe how genetic analyses of French Canadians have facilitated: (i) the classification of variants in BRCA1 and BRCA2; (ii) the identification and classification of variants in newly proposed breast and/or ovarian cancer predisposing genes; and (iii) the identification of a new breast cancer predisposing gene candidate, RECQL. The genetic architecture of French Canadians provides a unique opportunity to evaluate new candidate cancer predisposing genes regardless of the population in which they were identified.
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Butz H, Papp J, Bozsik A, Krokker L, Pócza T, Oláh E, Patócs A. Application of Multilayer Evidence for Annotation of C-Terminal BRCA2 Variants. Cancers (Basel) 2021; 13:cancers13040881. [PMID: 33672545 PMCID: PMC7923782 DOI: 10.3390/cancers13040881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The potential pathogenic role of germline BRCA2 c.9976A>T and c.10095delinsGAATTATATCT was evaluated in hereditary breast and ovarian cancer (HBOC) patients by investigating 2491 probands and verified in an independent cohort of 122,209 patients. Although the c.10095delinsGAATTATATCT variant was more prevalent among patients compared to control populations, no increased risk for cancer was found. No association between c.9976A>T and clinicopathological parameters or elevated risk for HBOC cases was detected. However, lung cancer was more prevalent in families carrying c.9976A>T compared to pathogenic BRCA1/BRCA2 carrier families. An increased frequency of pancreatic cancer was found in families where c.9976A>T occurred together with other pathogenic BRCA1 variants. The C-terminal stop codon variants showed no association with other pathogenic BRCA2 variants. No loss of heterozygosity (LOH) in tumor tissue and no allelic imbalance in RNA level were confirmed. The c.9976A>T variant may be considered as a potential risk for lung cancer, and a potential modifying factor in pancreatic cancer when it occurs along with the pathogenic BRCA1 variant, although this observation should be validated in a larger sample cohort. Abstract The clinical relevance of the BRCA2 C-terminal stop codon variants is controversial. The pathogenic role of the germline BRCA2 c.9976A>T and c.10095delinsGAATTATATCT variants in hereditary breast and ovarian cancer (HBOC) patients was evaluated. An association with clinicopathological parameters was performed in 2491 independent probands diagnosed with HBOC and in 122,209 cancer patients reported earlier. Loss-of-heterozygosity (LOH) in tumor samples and allelic imbalance in RNA extracted from peripheral blood cells were investigated. Neither c.10095delinsGAATTATATCT or c.9976A>T variants showed significant association with clinicopathological parameters or elevated risk for HBOC-associated tumors. Lung cancer was more prevalent in families carrying the c.9976A>T variant compared to pathogenic BRCA1 or BRCA2 carrier families. An increased prevalence of pancreatic cancer was found in families where c.9976A>T occurred together with other pathogenic BRCA1 variants. An increased risk for familial pancreatic, lung and upper aero-digestive tract cancers was confirmed in the validation set. Regarding BRCA2 C-terminal variants, no linkage with other pathogenic BRCA2 variants, no LOH in tumor tissue and no allelic imbalance in RNA level were confirmed. The c.9976A>T variant may be considered as a potential risk for lung cancer, and a potential modifying factor in pancreatic cancer when it occurs along with the pathogenic BRCA1 variant, although this observation should be validated in a larger sample cohort.
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Affiliation(s)
- Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
| | - Lilla Krokker
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
| | - Tímea Pócza
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
| | - Edit Oláh
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary; (H.B.); (J.P.); (A.B.); (T.P.); (E.O.)
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Correspondence:
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