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Elshwekh H, Alhudiri IM, Elzagheid A, Enattah N, Abbassi Y, Abou Assali L, Marino I, Stuani C, Buratti E, Romano M. Assessing the Impact of Novel BRCA1 Exon 11 Variants on Pre-mRNA Splicing. Cells 2024; 13:824. [PMID: 38786046 PMCID: PMC11119505 DOI: 10.3390/cells13100824] [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: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Our study focused on assessing the effects of three newly identified BRCA1 exon 11 variants (c.1019T>C, c.2363T>G, and c.3192T>C) on breast cancer susceptibility. Using computational predictions and experimental splicing assays, we evaluated their potential as pathogenic mutations. Our in silico analyses suggested that the c.2363T>G and c.3192T>C variants could impact both splicing and protein function, resulting in the V340A and V788G mutations, respectively. We further examined their splicing effects using minigene assays in MCF7 and SKBR3 breast cancer cell lines. Interestingly, we found that the c.2363T>G variant significantly altered splicing patterns in MCF7 cells but not in SKBR3 cells. This finding suggests a potential influence of cellular context on the variant's effects. While attempts to correlate in silico predictions with RNA binding factors were inconclusive, this observation underscores the complexity of splicing regulation. Splicing is governed by various factors, including cellular contexts and protein interactions, making it challenging to predict outcomes accurately. Further research is needed to fully understand the functional consequences of the c.2363T>G variant in breast cancer pathogenesis. Integrating computational predictions with experimental data will provide valuable insights into the role of alternative splicing regulation in different breast cancer types and stages.
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Affiliation(s)
- Halla Elshwekh
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Inas M. Alhudiri
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Nabil Enattah
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Yasmine Abbassi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Lubna Abou Assali
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Ilenia Marino
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio, 28, 34127 Trieste, Italy
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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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Christowitz C, Olivier DW, Schneider JW, Kotze MJ, Engelbrecht AM. Incorporating functional genomics into the pathology-supported genetic testing framework implemented in South Africa: A future view of precision medicine for breast carcinomas. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108492. [PMID: 38631437 DOI: 10.1016/j.mrrev.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation. We emphasize the distinct advantages of using in vitro, in vivo, and translational ex vivo models to improve the effectiveness of precision oncology. Moreover, we highlight the relevance of methodologies such as protein modelling and structural bioinformatics, multi-omics, metabolic activity assays, flow cytometry, cell migration and invasion assays, tube-formation assays, multiplex assays of variant effect, and database mining and machine learning models. The selection of the appropriate experimental approach largely depends on the molecular mechanism of the gene under investigation and the predicted functional effect of the VUS. However, before making final decisions regarding the pathogenicity of VUSs, it is essential to assess the functional evidence and clinical outcomes under current variant interpretation guidelines. The inclusion of a functional genomics infrastructure within the PSGT framework will significantly advance the reclassification of VUSs and enhance the precision medicine pipeline for patients with breast carcinomas in South Africa.
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Affiliation(s)
- Claudia Christowitz
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Daniel W Olivier
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Johann W Schneider
- Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Global Health, African Cancer Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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van der Merwe NC, Ntaita KS, Stofberg H, Combrink HM, Oosthuizen J, Kotze MJ. Implementation of multigene panel testing for breast and ovarian cancer in South Africa: A step towards excellence in oncology for the public sector. Front Oncol 2022; 12:938561. [PMID: 36568162 PMCID: PMC9768488 DOI: 10.3389/fonc.2022.938561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
Translation of genomic knowledge into public health benefits requires the implementation of evidence-based recommendations in clinical practice. In this study, we moved beyond BRCA1/2 susceptibility testing in breast and ovarian cancer patients to explore the application of pharmacogenetics across multiple genes participating in homologous recombination DNA damage repair. This involved the utilisation of next-generation sequencing (NGS) at the intersection of research and service delivery for development of a comprehensive genetic testing platform in South Africa. Lack of international consensus regarding risk categorization of established cancer susceptibility genes and the level of evidence required for prediction of drug response supported the development of a central database to facilitate clinical interpretation. Here we demonstrate the value of this approach using NGS to 1) determine the variant spectrum applicable to targeted therapy and implementation of prevention strategies using the 15-gene Oncomine™ BRCA Expanded Panel, and 2) searched for novel and known pathogenic variants in uninformative cases using whole exome sequencing (WES). Targeted NGS performed as a routine clinical service in 414 South African breast and/or ovarian cancer patients resulted in the detection of 48 actionable variants among 319 (15%) cases. BRCA1/2-associated cancers were identified in 70.8% of patients (34/48, including two double-heterozygotes), with the majority (35.3%, 12/34) representing known South African founder variants. Detection of actionable variants in established non-BRCA1/2 risk genes contributed 29% to the total percentage (14/48), distributed amongst ATM, CHEK2, BARD1, BRIP1, PALB2 and TP53. Experimental WES using a virtually constructed multi-cancer NGS panel in 16 genetically unresolved cases (and four controls) revealed novel protein truncating variants in the basal cell carcinoma gene PTCH1 (c.4187delG) and the signal transmission and transduction gene KIT (c.930delA) involved in crucial cellular processes. Based on these findings, the most cost-effective approach would be to perform BRCA1/2 founder variant testing at referral, followed by targeted multigene panel testing if clinically indicated and addition of WES in unresolved cases. This inventive step provides a constant flow of new knowledge into the diagnostic platform via a uniquely South African pathology-supported genetic approach implemented for the first time in this context to integrate research with service delivery.
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Affiliation(s)
- Nerina C. van der Merwe
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa,*Correspondence: Nerina C. van der Merwe,
| | - Kholiwe S. Ntaita
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Hanri Stofberg
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Herkulaas MvE. Combrink
- Office of the Dean, Economic and Management Sciences, University of the Free State, Bloemfontein, South Africa,Interdisciplinary Centre for Digital Futures, University of the Free State, Bloemfontein, South Africa
| | - Jaco Oosthuizen
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, 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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Milambo JPM, Ndirangu J, Nyasulu PS, Akudugu JM. Feasibility of point of care testing for prevention and management of breast cancer therapy associated comorbidities in 6 African countries: short communication. BMC Res Notes 2022; 15:328. [PMID: 36273209 PMCID: PMC9588212 DOI: 10.1186/s13104-022-06204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
Objective: Obesity and mediators of inflammation have been identified as the most important risk and predictive factors in postmenopausal breast cancer (BC) survivors using aromatase inhibitors (AIs). This study was conducted to assess the impact of point of care technology (PCOT) as part of pathology supported genetic testing (PSGT) to prevent BC therapy-associated comorbidities in African settings. Results The study revealed that high sensitivity C-reactive protein (hs-CRP) and body mass index (BMI) are predictors of cardiovascular (CVD) related adverse events in obese postmenopausal patients subjected to AIs. There were statistically significant variations in total body fat (TBF), weight, hs-CRP, body mass index (BMI), homocysteine, ferritin, and calcium between baseline and after 24 months of follow-up. The above inflammatory markers can be incorporated in pathology supported genetic testing (PSGT) using HyBeacon® probe technology at POC for prediction and management of AI-associated adverse events among postmenopausal breast cancer survivors and associated comorbidities. The barriers for implementation of POCT application among six African countries for diagnosis of breast cancer were documented as insufficient of BC diagnosis and management capacity at different levels of health system.
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Affiliation(s)
- Jean Paul Muambngu Milambo
- Department of Public health, Faculty of Medicine and Health Sciences, University of Free State, Florence Street, 7530, Bellville, Cape Town, South Africa.
| | - James Ndirangu
- Department of Public health, Faculty of Medicine and Health Sciences, University of Free State, Florence Street, 7530, Bellville, Cape Town, South Africa
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El-Attar EA, Helmy Elkaffas RM, Aglan SA, Naga IS, Nabil A, Abdallah HY. Genomics in Egypt: Current Status and Future Aspects. Front Genet 2022; 13:797465. [PMID: 35664315 PMCID: PMC9157251 DOI: 10.3389/fgene.2022.797465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from “one-size-fits all” to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.
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Affiliation(s)
- Eman Ahmed El-Attar
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
- *Correspondence: Eman Ahmed El-Attar,
| | | | - Sarah Ahmed Aglan
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Iman S. Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hoda Y. Abdallah
- Medical Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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Van der Merwe NC, Combrink HM, Ntaita KS, Oosthuizen J. Prevalence of Clinically Relevant Germline BRCA Variants in a Large Unselected South African Breast and Ovarian Cancer Cohort: A Public Sector Experience. Front Genet 2022; 13:834265. [PMID: 35464868 PMCID: PMC9024354 DOI: 10.3389/fgene.2022.834265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/23/2022] [Indexed: 01/14/2023] Open
Abstract
Breast cancer is a multifaceted disease that currently represents a leading cause of death in women worldwide. Over the past two decades (1998–2020), the National Health Laboratory Service’s Human Genetics Laboratory in central South Africa screened more than 2,974 breast and/or ovarian cancer patients for abnormalities characteristic of the widely known familial breast cancer genes, Breast Cancer gene 1 (BRCA1) and Breast Cancer gene 2 (BRCA2). Patients were stratified according to the presence of family history, age at onset, stage of the disease, ethnicity and mutation status relative to BRCA1/2. Collectively, 481 actionable (likely-to pathogenic) variants were detected in this cohort among the different ethnic/racial groups. A combination of old (pre-2014) and new (post-2014) laboratory techniques was used to identify these variants. Additionally, targeted genotyping was performed as translational research revealed the first three recurrent South African pathogenic variants, namely BRCA1 c.1374del (legacy name 1493delC), BRCA1 c.2641G>T (legacy name E881X) and BRCA2 c.7934del (legacy name 8162delG). This initial flagship study resulted in a cost-effective diagnostic test that enabled screening of a particular ethnic group for these variants. Since then, various non-Afrikaner frequent variants were identified that were proven to represent recurrent variants. These include BRCA2 c.5771_5774del (legacy name 5999del4) and BRCA2 c.582G>A, both Black African founder mutations. By performing innovative translational research, medical science in South Africa can adopt first-world technologies into its healthcare context as a developing country. Over the past two decades, the progress made in the public sector enabled a pivotal shift away from population-directed genetic testing to the screening of potentially all breast and ovarian cancer patients, irrespective of ethnicity, family history or immunohistochemical status. The modifications over the years complied with international standards and guidelines aimed at universal healthcare for all. This article shares all the cohort stratifications and the likely-to pathogenic variants detected.
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Affiliation(s)
- 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
- *Correspondence: Nerina C. Van der Merwe,
| | - Herkulaas MvE Combrink
- Economic and Management Sciences, University of the Free State, Bloemfontein, South Africa
- Interdisciplinary Centre for Digital Futures, University of the Free State, Bloemfontein, South Africa
| | - Kholiwe S. Ntaita
- 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
| | - 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
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