1
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van der Merwe NC, Buccimazza I, Rossouw B, Araujo M, Ntaita KS, Schoeman M, Vorster K, Napo K, Kotze MJ, Oosthuizen J. Clinical relevance of double heterozygosity revealed by next-generation sequencing of homologous recombination repair pathway genes in South African breast cancer patients. Breast Cancer Res Treat 2024; 207:331-342. [PMID: 38814507 PMCID: PMC11297091 DOI: 10.1007/s10549-024-07362-2] [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: 03/22/2024] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
PURPOSE Genetically predisposed breast cancer (BC) patients represent a minor but clinically meaningful subgroup of the disease, with 25% of all cases associated with actionable variants in BRCA1/2. Diagnostic implementation of next-generation sequencing (NGS) resulted in the rare identification of BC patients with double heterozygosity for deleterious variants in genes partaking in homologous recombination repair of DNA. As clinical heterogeneity poses challenges for genetic counseling, this study focused on the occurrence and clinical relevance of double heterozygous BC in South Africa. METHODS DNA samples were diagnostically screened using the NGS-based Oncomine™ BRCA Expanded Research Assay. Data was generated on the Ion GeneStudio S5 system and analyzed using the Torrent Suite™ and reporter software. The clinical significance of the variants detected was determined using international variant classification guidelines and treatment implications. RESULTS Six of 1600 BC patients (0.375%) tested were identified as being bi-allelic for two germline likely pathogenic or pathogenic variants. Most of the variants were present in BRCA1/2, including two founder-related small deletions in three cases, with family-specific variants detected in ATM, BARD1, FANCD2, NBN, and TP53. The scientific interpretation and clinical relevance were based on the clinical and tumor characteristics of each case. CONCLUSION This study increased current knowledge of the risk implications associated with the co-occurrence of more than one pathogenic variant in the BC susceptibility genes, confirmed to be a rare condition in South Africa. Further molecular pathology-based studies are warranted to determine whether clinical decision-making is affected by the detection of a second pathogenic variant in BRCA1/2 and TP53 carriers.
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Affiliation(s)
- Nerina C van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa.
| | - Ines Buccimazza
- Genetics Unit, Inkosi Albert Luthuli General Hospital, Durban, South Africa
- Department of Surgery, Nelson R Mandela School of Medicine, Inkosi Albert Luthuli General Hospital, Durban, South Africa
| | - Bianca Rossouw
- Division of Human Genetics, National Health Laboratory Service, Braamfontein, Johannesburg, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Monica Araujo
- Division of Human Genetics, National Health Laboratory Service, Braamfontein, Johannesburg, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kholiwe S Ntaita
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Mardelle Schoeman
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karin Vorster
- Department of Oncology, Free State Department of Health, Universitas Annex Hospital, Bloemfontein, South Africa
- Department of Oncology, Faculty of Health Science, University of the Free State, Bloemfontein, South Africa
| | - Kgabo Napo
- Department of Oncology, Free State Department of Health, Universitas Annex Hospital, Bloemfontein, South Africa
- Department of Oncology, Faculty of Health Science, 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
| | - Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
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Hosseini TM, Park SJ, Guo T. The Mutational and Microenvironmental Landscape of Cutaneous Squamous Cell Carcinoma: A Review. Cancers (Basel) 2024; 16:2904. [PMID: 39199674 DOI: 10.3390/cancers16162904] [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: 07/16/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) manifests through the complex interactions of UV-induced DNA damage, genetic mutations, and alterations in the tumor microenvironment. A high mutational burden is present in cSCC, as well as both cSCC precursors and normal skin, making driver genes difficult to differentiate. Despite this, several key driver genes have been identified, including TP53, the NOTCH family, CDKN2A, PIK3CA, and EGFR. In addition to mutations, the tumor microenvironment and the manipulation and evasion of the immune system play a critical role in cSCC progression. Novel therapeutic approaches, such as immunotherapy and EGFR inhibitors, have been used to target these dysregulations, and have shown promise in treating advanced cSCC cases, emphasizing the need for targeted interventions considering both genetic and microenvironmental factors for improved patient outcomes.
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Affiliation(s)
- Tara M Hosseini
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Soo J Park
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Theresa Guo
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Otolaryngology-Head & Neck Surgery, University of California San Diego, La Jolla, CA 92093, USA
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3
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Chahat, Nainwal N, Murti Y, Yadav S, Rawat P, Dhiman S, Kumar B. Advancements in targeting tumor suppressor genes (p53 and BRCA 1/2) in breast cancer therapy. Mol Divers 2024:10.1007/s11030-024-10964-z. [PMID: 39152355 DOI: 10.1007/s11030-024-10964-z] [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: 06/07/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024]
Abstract
Globally, among numerous cancer subtypes, breast cancer (BC) is one of the most prevalent forms of cancer affecting the female population. A female's family history significantly increases her risk of developing breast cancer. BC is caused by aberrant breast cells that proliferate and develop into tumors. It is estimated that 5-10% of breast carcinomas are inherited and involve genetic mutations that ensure the survival and prognosis of breast cancer cells. The most common genetic variations are responsible for hereditary breast cancer but are not limited to p53, BRCA1, and BRCA2. BRCA1 and BRCA2 are involved in genomic recombination, cell cycle monitoring, programmed cell death, and transcriptional regulation. When BRCA1 and 2 genetic variations are present in breast carcinoma, p53 irregularities become more prevalent. Both BRCA1/2 and p53 genes are involved in cell cycle monitoring. The present article discusses the current status of breast cancer research, spotlighting the tumor suppressor genes (BRCA1/2 and p53) along with structural activity relationship studies, FDA-approved drugs, and several therapy modalities for treating BC. Breast cancer drugs, accessible today in the market, have different side effects including anemia, pneumonitis, nausea, lethargy, and vomiting. Thus, the development of novel p53 and BRCA1/2 inhibitors with minimal possible side effects is crucial. We have covered compounds that have been examined subsequently (2020 onwards) in this overview which may be utilized as lead compounds. Further, we have covered mechanistic pathways to showcase the critical druggable targets and clinical and post-clinical drugs targeting them for their utility in BC.
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Affiliation(s)
- Chahat
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar, 246174, Uttarakhand, India
| | - Nidhi Nainwal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premanagar, Dehradun, 248007, Uttarakhand, India
| | - Yogesh Murti
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, India
| | - Savita Yadav
- IES Institute of Technology and Management, IES University, Bhopal, 462044, Madhya Pradesh, India
| | - Pramod Rawat
- Graphic Era (Deemed to Be University), Clement Town, Dehradun, 248002, India
- Graphic Era Hill University Clement Town, Dehradun, 248002, India
| | - Sonia Dhiman
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India
| | - Bhupinder Kumar
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar, 246174, Uttarakhand, India.
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Hall R, Bancroft E, Pashayan N, Kote-Jarai Z, Eeles RA. Genetics of prostate cancer: a review of latest evidence. J Med Genet 2024:jmg-2024-109845. [PMID: 39137963 DOI: 10.1136/jmg-2024-109845] [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: 01/02/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
Prostate cancer (PrCa) is a largely heritable and polygenic disease. It is the most common cancer in people with prostates (PwPs) in Europe and the USA, including in PwPs of African descent. In the UK in 2020, 52% of all cancers were diagnosed at stage I or II. The National Health Service (NHS) long-term plan is to increase this to 75% by 2028, to reduce absolute incidence of late-stage disease. In the absence of a UK PrCa screening programme, we should explore how to identify those at increased risk of clinically significant PrCa.Incorporating genomics into the PrCa screening, diagnostic and treatment pathway has huge potential for transforming patient care. Genomics can increase efficiency of PrCa screening by focusing on those with genetic predisposition to cancer-which when combined with risk factors such as age and ethnicity, can be used for risk stratification in risk-based screening (RBS) programmes. The goal of RBS is to facilitate early diagnosis of clinically significant PrCa and reduce overdiagnosis/overtreatment in those unlikely to experience PrCa-related symptoms in their lifetime. Genetic testing can guide PrCa management, by identifying those at risk of lethal PrCa and enabling access to novel targeted therapies.PrCa is curable if diagnosed below stage III when most people do not experience symptoms. RBS using genetic profiling could be key here if we could show better survival outcomes (or reduction in cancer-specific mortality accounting for lead-time bias), in addition to more cost efficiency than age-based screening alone. Furthermore, PrCa outcomes in underserved communities could be optimised if genetic testing was accessible, minimising health disparities.
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Affiliation(s)
- Rose Hall
- The Royal Marsden NHS Foundation Trust, London, UK
- Institute for Cancer Research, London, UK
| | | | | | | | - Rosalind A Eeles
- The Royal Marsden NHS Foundation Trust, London, UK
- Institute for Cancer Research, London, UK
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5
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Stella S, Vitale SR, Massimino M, Martorana F, Tornabene I, Tomarchio C, Drago M, Pavone G, Gorgone C, Barone C, Bianca S, Manzella L. In Silico Prediction of BRCA1 and BRCA2 Variants with Conflicting Clinical Interpretation in a Cohort of Breast Cancer Patients. Genes (Basel) 2024; 15:943. [PMID: 39062721 PMCID: PMC11276437 DOI: 10.3390/genes15070943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Germline BRCA1/2 alteration has been linked to an increased risk of hereditary breast and ovarian cancer syndromes. As a result, genetic testing, based on NGS, allows us to identify a high number of variants of uncertain significance (VUS) or conflicting interpretation of pathogenicity (CIP) variants. The identification of CIP/VUS is often considered inconclusive and clinically not actionable for the patients' and unaffected carriers' management. In this context, their assessment and classification remain a significant challenge. The aim of the study was to investigate whether the in silico prediction tools (PolyPhen-2, SIFT, Mutation Taster and PROVEAN) could predict the potential clinical impact and significance of BRCA1/2 CIP/VUS alterations, eventually impacting the clinical management of Breast Cancer subjects. In a cohort of 860 BC patients, 10.6% harbored BRCA1 or BRCA2 CIP/VUS alterations, mostly observed in BRCA2 sequences (85%). Among them, forty-two out of fifty-five alterations were predicted as damaging, with at least one in silico that used tools. Prediction agreement of the four tools was achieved in 45.5% of patients. Moreover, the highest consensus was obtained in twelve out of forty-two (28.6%) mutations by considering three out of four in silico algorithms. The use of prediction tools may help to identify variants with a potentially damaging effect. The lack of substantial agreement between the different algorithms suggests that the bioinformatic approaches should be combined with the personal and family history of the cancer patients.
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Affiliation(s)
- Stefania Stella
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Silvia Rita Vitale
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Michele Massimino
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy
| | - Federica Martorana
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
| | - Irene Tornabene
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Division of Pathology, Humanitas Istituto Clinico Catanese, 95045 Catania, Italy
| | - Cristina Tomarchio
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Melissa Drago
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
| | - Giuliana Pavone
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Medical Oncology Unit, Humanitas Istituto Clinico Catanese, 95045 Catania, Italy
| | | | | | | | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (F.M.); (I.T.); (C.T.); (M.D.); (G.P.); (L.M.)
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (S.R.V.); (M.M.)
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MacDonald N, Raven N, Diep W, Evans S, Pannipitiya S, Bramwell G, Vanbeek C, Thomas F, Russell T, Dujon AM, Telonis-Scott M, Ujvari B. The molecular evolution of cancer associated genes in mammals. Sci Rep 2024; 14:11650. [PMID: 38773187 PMCID: PMC11109183 DOI: 10.1038/s41598-024-62425-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Cancer is a disease that many multicellular organisms have faced for millions of years, and species have evolved various tumour suppression mechanisms to control oncogenesis. Although cancer occurs across the tree of life, cancer related mortality risks vary across mammalian orders, with Carnivorans particularly affected. Evolutionary theory predicts different selection pressures on genes associated with cancer progression and suppression, including oncogenes, tumour suppressor genes and immune genes. Therefore, we investigated the evolutionary history of cancer associated gene sequences across 384 mammalian taxa, to detect signatures of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and B2M). This approach allowed us to conduct a fine scale analysis of gene wide and site-specific signatures of selection across mammalian lineages under the lens of cancer susceptibility. Phylogenetic analyses revealed that for most species the evolution of cancer associated genes follows the species' evolution. The gene wide selection analyses revealed oncogenes being the most conserved, tumour suppressor and immune genes having similar amounts of episodic diversifying selection. Despite BRCA2's status as a key caretaker gene, episodic diversifying selection was detected across mammals. The site-specific selection analyses revealed that the two apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are under opposing forces of selection (positive and negative respectively), highlighting the importance of site-specific selection analyses to understand the evolution of highly complex gene families. Our results highlighted the need to critically assess different types of selection pressure on cancer associated genes when investigating evolutionary adaptations to cancer across the tree of life. This study provides an extensive assessment of cancer associated genes in mammals with highly representative, and substantially large sample size for a comparative genomic analysis in the field and identifies various avenues for future research into the mechanisms of cancer resistance and susceptibility in mammals.
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Affiliation(s)
- Nick MacDonald
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Nynke Raven
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Wendy Diep
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Samantha Evans
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Senuri Pannipitiya
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Georgina Bramwell
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Caitlin Vanbeek
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France
| | - Tracey Russell
- Faculty of Science, School of Life and Environmental Sciences, Sydney, NSW, Australia
| | - Antoine M Dujon
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Burwood, Burwood, VIC, 3125, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia.
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Ahmad H, Ali A, Ali R, Khalil AT, Khan I, Khan MM, Alorini M. Preliminary insights on the mutational spectrum of BRCA1 and BRCA2 genes in Pakhtun ethnicity breast cancer patients from Khyber Pakhtunkhwa (KP), Pakistan. Neoplasia 2024; 51:100989. [PMID: 38537553 PMCID: PMC11026844 DOI: 10.1016/j.neo.2024.100989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/11/2024] [Indexed: 04/17/2024]
Abstract
Gene mutations are a source of genetic instability which fuels the progression of cancer. Mutations in BRCA1 and BRCA2 are considered as major drivers in the progression of breast cancer and their detection indispensable for devising therapeutic and management approaches. The current study aims to identify novel pathogenic and recurrent mutations in BRCA1 and BRCA2 in Pakhtun population from the Khyber Pakhtunkhwa. To determine the BRCA1 and BRCA2 pathogenic mutation prevalence in Pakhtun population from KP, whole exome sequencing of 19 patients along with 6 normal FFPE embedded blocks were performed. The pathogenicity of the mutations were determined and they were further correlated with different hormonal, sociogenetic and clinicopathological features. We obtained a total of 10 mutations (5 somatic and 5 germline) in BRCA1 while 27 mutations (24 somatic and 3 germline) for BRCA2. Five and seventeen pathogenic or deleterious mutations were identified in BRCA1 and BRCA2 respectively by examining the mutational spectrum through SIFT, PolyPhen-2 and Mutation Taster. Among the SNVs, BRCA1 p.P824L, BRCA2 p. P153Q, p.I180F, p.D559Y, p.G1529R, p.L1576F, p.E2229K were identified as mutations of the interaction sites as predicted by the deep algorithm based ISPRED-SEQ prediction tool. SAAFEQ-SEQ web-based algorithm was used to calculate the changes in free energy and effect of SNVs on protein stability. All SNVs were found to have a destabilizing effect on the protein. ConSurf database was used to determine the evolutionary conservation scores and nature of the mutated residues. Gromacs 4.5 was used for the molecular simulations. Ramachandran plots were generated using procheck server. STRING and GeneMania was used for prediction of the gene interactions. The highest number of mutations (BRCA1 7/10, 70 %) were on exon 9 and (BRCA2, 11/27; 40 %) were on exon 11. 40 % and 60 % of the BRCA2 mutations were associated Grade 2 and Grade 3 tumors respectively. The present study reveals unique BRCA1 and BRCA2 mutations in Pakhtun population. We further suggest sequencing of the large cohorts for further characterizing the pathogenic mutations.
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Affiliation(s)
- Hilal Ahmad
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, Pakistan
| | - Asif Ali
- Institute of Pathology and Diagnostic Medicine (IPDM), Khyber Medical University, Peshawar, KP, Pakistan; College of Medicine, Gulf Medical University, Ajman, United Arab Emirates; School of Medicine, University of Glasgow, UK.
| | - Roshan Ali
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, Pakistan
| | - Ali Talha Khalil
- Department of Pathology, Lady Reading Hospital Medical Teaching Institution, Peshawar, KP, Pakistan.
| | - Ishaq Khan
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, Pakistan
| | - Mah Muneer Khan
- Department of Surgery, Khyber Teaching Hospital, Medical Teaching Institution, Peshawar, KP, Pakistan
| | - Mohammed Alorini
- Department of Basic Medical Sciences, Unaizah College of Medicine and Medical Sciences, Qassim University, Unaizah, Saudi Arabia
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Zawadzka A, Brzozowska B, Matyjanka A, Mikula M, Reszczyńska J, Tartas A, Fornalski KW. The Risk Function of Breast and Ovarian Cancers in the Avrami-Dobrzyński Cellular Phase-Transition Model. Int J Mol Sci 2024; 25:1352. [PMID: 38279352 PMCID: PMC10816518 DOI: 10.3390/ijms25021352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Specifying the role of genetic mutations in cancer development is crucial for effective screening or targeted treatments for people with hereditary cancer predispositions. Our goal here is to find the relationship between a number of cancerogenic mutations and the probability of cancer induction over the lifetime of cancer patients. We believe that the Avrami-Dobrzyński biophysical model can be used to describe this mechanism. Therefore, clinical data from breast and ovarian cancer patients were used to validate this model of cancer induction, which is based on a purely physical concept of the phase-transition process with an analogy to the neoplastic transformation. The obtained values of model parameters established using clinical data confirm the hypothesis that the carcinogenic process strongly follows fractal dynamics. We found that the model's theoretical prediction and population clinical data slightly differed for patients with the age below 30 years old, and that might point to the existence of an ancillary protection mechanism against cancer development. Additionally, we reveal that the existing clinical data predict breast or ovarian cancers onset two years earlier for patients with BRCA1/2 mutations.
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Affiliation(s)
- Anna Zawadzka
- Maria Skłodowska-Curie National Research Institute of Oncology (NIO-MSCI), 02-781 Warsaw, Poland; (A.Z.)
| | - Beata Brzozowska
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (B.B.)
| | - Anna Matyjanka
- Faculty of Physics, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Michał Mikula
- Maria Skłodowska-Curie National Research Institute of Oncology (NIO-MSCI), 02-781 Warsaw, Poland; (A.Z.)
| | - Joanna Reszczyńska
- Mossakowski Medical Research Institute, Polish Academy of Sciences (IMDiK PAN), 02-106 Warsaw, Poland;
| | - Adrianna Tartas
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (B.B.)
| | - Krzysztof W. Fornalski
- Faculty of Physics, Warsaw University of Technology, 00-662 Warsaw, Poland
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock-Świerk, Poland
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9
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Dias Nunes J, Demeestere I, Devos M. BRCA Mutations and Fertility Preservation. Int J Mol Sci 2023; 25:204. [PMID: 38203374 PMCID: PMC10778779 DOI: 10.3390/ijms25010204] [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: 11/28/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Hereditary cancers mostly affect the adolescent and young adult population (AYA) at reproductive age. Mutations in BReast CAncer (BRCA) genes are responsible for the majority of cases of hereditary breast and ovarian cancer. BRCA1 and BRCA2 act as tumor suppressor genes as they are key regulators of DNA repair through homologous recombination. Evidence of the accumulation of DNA double-strand break has been reported in aging oocytes, while BRCA expression decreases, leading to the hypothesis that BRCA mutation may impact fertility. Moreover, patients exposed to anticancer treatments are at higher risk of fertility-related issues, and BRCA mutations could exacerbate the treatment-induced depletion of the ovarian reserve. In this review, we summarized the functions of both genes and reported the current knowledge on the impact of BRCA mutations on ovarian ageing, premature ovarian insufficiency, female fertility preservation strategies and insights about male infertility. Altogether, this review provides relevant up-to-date information on the impact of BRCA1/2 mutations on fertility. Notably, BRCA-mutated patients should be adequately counselled for fertility preservation strategies, considering their higher sensitivity to chemotherapy gonadotoxic effects.
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Affiliation(s)
- Joana Dias Nunes
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.D.N.); (M.D.)
| | - Isabelle Demeestere
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.D.N.); (M.D.)
- Fertility Clinic, HUB-Erasme Hospital, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Melody Devos
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.D.N.); (M.D.)
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10
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Guo Q, Ji S, Takeuchi K, Urasaki W, Suzuki A, Iwasaki Y, Saito H, Xu Z, Arai M, Nakamura S, Momozawa Y, Chiba N, Miki Y, Matsuura M, Sunada S. Functional evaluation of BRCA1/2 variants of unknown significance with homologous recombination assay and integrative in silico prediction model. J Hum Genet 2023; 68:849-857. [PMID: 37731132 DOI: 10.1038/s10038-023-01194-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023]
Abstract
Numerous variants of unknown significance (VUSs) exist in hereditary breast and ovarian cancers. Although multiple methods have been developed to assess the significance of BRCA1/2 variants, functional discrepancies among these approaches remain. Therefore, a comprehensive functional evaluation system for these variants should be established. We performed conventional homologous recombination (HR) assays for 50 BRCA1 and 108 BRCA2 VUSs and complementarily predicted VUSs using a statistical logistic regression prediction model that integrated six in silico functional prediction tools. BRCA1/2 VUSs were classified according to the results of the integrative in vitro and in silico analyses. Using HR assays, we identified 10 BRCA1 and 4 BRCA2 VUSs as low-functional pathogenic variants. For in silico prediction, the statistical prediction model showed high accuracy for both BRCA1 and BRCA2 compared with each in silico prediction tool individually and predicted nine BRCA1 and seven BRCA2 variants to be pathogenic. Integrative functional evaluation in this study and the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines strongly suggested that seven BRCA1 variants (p.Glu272Gly, p.Lys1095Glu, p.Val1653Leu, p.Thr1681Pro, p.Phe1761Val, p.Thr1773Ile, and p.Gly1803Ser) and four BRCA2 variants (p.Trp31Gly, p.Ser2616Phe, p.Tyr2660Cys, and p.Leu2792Arg) were pathogenic. This study demonstrates that integrative evaluation using conventional HR assays and optimized in silico prediction comprehensively classified the significance of BRCA VUSs for future clinical applications.
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Affiliation(s)
- Qianqian Guo
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Shuting Ji
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kazuma Takeuchi
- Graduate School of Public Health, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Wataru Urasaki
- Department of Information Sciences, Tokyo University of Science, 2641 Yamazaki, Noda City, Chiba, 278-8510, Japan
| | - Asuka Suzuki
- Graduate School of Public Health, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Hiroko Saito
- Department of Genetic Diagnosis, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Zeyu Xu
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Masami Arai
- Department of Clinical Genetics, Juntendo University, Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Natsuko Chiba
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai, 980-8575, Japan
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Department of Genetic Diagnosis, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.
| | - Masaaki Matsuura
- Graduate School of Public Health, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
| | - Shigeaki Sunada
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Juntendo Advanced Research Institute for Health Science, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
- Department of Oncology, School of Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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11
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Chute JP. After DNA damage, AREG-ular niche it's not. Blood 2023; 142:1502-1504. [PMID: 37917083 PMCID: PMC10656713 DOI: 10.1182/blood.2023022173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
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12
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Skrivergaard S, Young JF, Sahebekhtiari N, Semper C, Venkatesan M, Savchenko A, Stogios PJ, Therkildsen M, Rasmussen MK. A simple and robust serum-free media for the proliferation of muscle cells. Food Res Int 2023; 172:113194. [PMID: 37689947 DOI: 10.1016/j.foodres.2023.113194] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 09/11/2023]
Abstract
Cultivated meat production requires an efficient, robust and highly optimized serum-free cell culture media for the needed upscaling of muscle cell expansion. Existing formulations of serum-free media are complex, expensive and have not been optimized for muscle cells. Thus, we undertook this work to develop a simple and robust serum-free media for the proliferation of bovine satellite cells (SCs) through Design of Experiment (DOE) and Response Surface Methodology (RSM) using precise and high-throughput image-based cytometry. Proliferative attributes were investigated with transcriptomics and long-term performance was validated using multiple live assays. Here we formulated a media based on three highly optimized components; FGF2 (2 ng/mL), fetuin (600 µg/mL) and BSA (75 µg/mL) which together with an insulin-transferrin-selenium (1x) supplement, sustained the proliferation of bovine SCs, porcine SCs and murine C2C12 muscle cells. Remarkably, cells cultured in our media named Tri-basal 2.0+ performed better than cell cultured in 10% FBS, with respect to proliferation. Hence, the optimized Tri-basal 2.0+ enhanced serum-free cell attachment and long-term proliferation, providing an alternative solution to the use of FBS in the production of cultivated meat.
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Affiliation(s)
| | | | | | - Cameron Semper
- Department of Microbiology, Immunology, and Infectious Disease. University of Calgary, Calgary, Canada
| | - Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology, and Infectious Disease. University of Calgary, Calgary, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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13
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Del Giglio A, da Costa Aguiar Alves B, Murad AM, Fonseca FLA. Metastatic lung adenocarcinoma with BRCA2 mutation and longstanding disease control on olaparib, developing triple negative breast adenocarcinoma with additional BRCA2 reversion mutation: a case report. J Med Case Rep 2023; 17:407. [PMID: 37743480 PMCID: PMC10519093 DOI: 10.1186/s13256-023-04139-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND The BRCA2 gene is a well-known tumor suppressor gene implicated in breast and ovarian cancers. BRCA1/2 mutations can be sensitive to poly ADP-ribose polymerase (PARP) inhibitors such as olaparib. However, some of these patients develop resistance to this treatment and an essential factor contributing to acquired insensitivity is the occurrence of reversion mutations in the BRCA1/2 genes. CASE PRESENTATION We report the case of a 65-year-old Brazilian female patient who had previously been diagnosed with metastatic lung carcinoma carrying a BRCA2 mutation that had extended to the central nervous system. Following disease progression, olaparib was administered, resulting in a stabilizing effect on her condition for ~ 30 months. During a routine follow-up, a new triple-negative breast tumor was found. Genetic testing revealed the presence of two distinct BRCA2 gene mutations in the breast tumor. The original mutation (p.Val220Ilefs4) led to a frameshift, culminating in the production of a truncated and non-functional BRCA2 protein; the second mutation, K437fs22, rectified the reading frame of exon 11. Consequently, Rad51 could properly bind to BRCA2-an essential protein crucial for DNA repair. This restoration resulted in a functional BRCA2 protein, effectively elucidating the clinical resistance observed in the new breast tumor in this case. CONCLUSIONS This case report highlights the clinical significance of comprehensive next-generation sequencing analyses for lung adenocarcinomas, both at diagnosis and upon progression. Such analyses enable informed decisions regarding targeted therapies and facilitate a deeper comprehension of resistance mechanisms.
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Affiliation(s)
- Auro Del Giglio
- Departamento de Oncologia e Hematologia, Centro Universitário FMABC, Av. Príncipe de Gales, 821, Santo André, SP, 09060-650, Brazil.
| | - Beatriz da Costa Aguiar Alves
- Laboratório de Análises Clínicas, Centro Universitário FMABC, Av. Príncipe de Gales, 821, Santo André, SP, 09060-650, Brazil
| | - André Márcio Murad
- CENANTRON-PERSONAL-Precision Oncology, R. Padre Rolim, 120, Belo Horizonte, Minas Gerais, 30130-090, Brazil
| | - Fernando Luiz Affonso Fonseca
- Laboratório de Análises Clínicas, Centro Universitário FMABC, Av. Príncipe de Gales, 821, Santo André, SP, 09060-650, Brazil
- Instituto de Ciências Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), Rua Professor Artur Riedel, 275, 09972-270, Diadema, SP, Brazil
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14
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Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. A general method for quantitative fractionation of mammalian cells. J Cell Biol 2023; 222:213941. [PMID: 36920247 PMCID: PMC10040634 DOI: 10.1083/jcb.202209062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
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Affiliation(s)
- Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University , New York, NY, USA
| | - Hilda A Pasolli
- Electron Microscopy Resource Center, The Rockefeller University , New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
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15
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Kodada D, Hyblova M, Krumpolec P, Janostiakova N, Barath P, Grendar M, Blandova G, Petrovic O, Janega P, Repiska V, Minarik G. The Potential of Liquid Biopsy in Detection of Endometrial Cancer Biomarkers: A Pilot Study. Int J Mol Sci 2023; 24:ijms24097811. [PMID: 37175518 PMCID: PMC10178554 DOI: 10.3390/ijms24097811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Endometrial cancer belongs to the most common gynecologic cancer types globally, with increasing incidence. There are numerous ways of classifying different cases. The most recent decade has brought advances in molecular classification, which show more accurate prognostic factors and the possibility of personalised adjuvant treatment. In addition, diagnostic approaches lag behind these advances, with methods causing patients discomfort while lacking the reproducibility of tissue sampling for biopsy. Minimally invasive liquid biopsies could therefore represent an alternative screening and diagnostic approach in patients with endometrial cancer. The method could potentially detect molecular changes in this cancer type and identify patients at early stages. In this pilot study, we tested such a detection method based on circulating tumour DNA isolated from the peripheral blood plasma of 21 Slovak endometrial cancer patients. We successfully detected oncomutations in the circulating DNA of every single patient, although the prognostic value of the detected mutations failed to offer certainty. Furthermore, we detected changes associated with clonal hematopoiesis, including DNMT3A mutations, which were present in the majority of circulating tumour DNA samples.
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Affiliation(s)
- Dominik Kodada
- Medirex Group Academy, 94905 Nitra, Slovakia
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | | | | | - Nikola Janostiakova
- Medirex Group Academy, 94905 Nitra, Slovakia
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | | | - Marian Grendar
- Medirex Group Academy, 94905 Nitra, Slovakia
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Gabriela Blandova
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | | | - Pavol Janega
- Medirex Group Academy, 94905 Nitra, Slovakia
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Vanda Repiska
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
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16
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Nguyen TT, Hamdan D, Angeli E, Feugeas JP, Le QV, Pamoukdjian F, Bousquet G. Genomics of Breast Cancer Brain Metastases: A Meta-Analysis and Therapeutic Implications. Cancers (Basel) 2023; 15:cancers15061728. [PMID: 36980614 PMCID: PMC10046845 DOI: 10.3390/cancers15061728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/05/2023] [Accepted: 03/05/2023] [Indexed: 03/14/2023] Open
Abstract
Breast cancer brain metastases are a challenging daily practice, and the biological link between gene mutations and metastatic spread to the brain remains to be determined. Here, we performed a meta-analysis on genomic data obtained from primary tumors, extracerebral metastases and brain metastases, to identify gene alterations associated with metastatic processes in the brain. Articles with relevant findings were selected using Medline via PubMed, from January 1999 up to February 2022. A critical review was conducted according to the Preferred Reporting Items for Systematic Review and Meta-analysis statement (PRISMA). Fifty-seven publications were selected for this meta-analysis, including 37,218 patients in all, 11,906 primary tumor samples, 5541 extracerebral metastasis samples, and 1485 brain metastasis samples. We report the overall and sub-group prevalence of gene mutations, including comparisons between primary tumors, extracerebral metastases and brain metastases. In particular, we identified six genes with a higher mutation prevalence in brain metastases than in extracerebral metastases, with a potential role in metastatic processes in the brain: ESR1, ERBB2, EGFR, PTEN, BRCA2 and NOTCH1. We discuss here the therapeutic implications. Our results underline the added value of obtaining biopsies from brain metastases to fully explore their biology, in order to develop personalized treatments.
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Affiliation(s)
- Thuy Thi Nguyen
- National Cancer Hospital, Ha Noi 100000, Vietnam
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Department of Pediatrics, Hanoi Medical University, Ha Noi 100000, Vietnam
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
| | - Diaddin Hamdan
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Hôpital La Porte Verte, 78000 Versailles, France
| | - Eurydice Angeli
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
- Service d’Oncologie Médicale, Hôpital Avicenne, Assistance Publique Hôpitaux de Paris, 93000 Bobigny, France
| | - Jean-Paul Feugeas
- INSERM U1098, 25030 Besançon, France
- Laboratoire de Biochimie Hôpital Jean Minjoz, Université de Franche-Comté, 25000 Besançon, France
- Correspondence: (J.-P.F.); (G.B.)
| | - Quang Van Le
- National Cancer Hospital, Ha Noi 100000, Vietnam
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
| | - Frédéric Pamoukdjian
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
- Service de Médecine Gériatrique, Hôpital Avicenne, Assistance Publique Hôpitaux de Paris, 93000 Bobigny, France
| | - Guilhem Bousquet
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
- Service d’Oncologie Médicale, Hôpital Avicenne, Assistance Publique Hôpitaux de Paris, 93000 Bobigny, France
- Correspondence: (J.-P.F.); (G.B.)
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17
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Hidalgo Mayoral I, Almeida Santiago A, Sánchez-Zapardiel JM, Hidalgo Calero B, de la Hoya M, Gómez-Sanz A, de Miguel Reyes M, Robles L. Unexpected Findings in Hereditary Breast and Ovarian Cancer Syndrome: Low-Level Constitutional Mosaicism in BRCA2. Genes (Basel) 2023; 14:502. [PMID: 36833429 PMCID: PMC9957471 DOI: 10.3390/genes14020502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome (HBOC) is a clinical entity characterized by an increased risk of developing breast and ovarian cancer. The genetic diagnosis is based on the identification of heterozygous germinal variants in HBOC susceptibility genes. However, it has recently been described that constitutional mosaic variants can contribute to the aetiology of HBOC. In constitutional mosaicism, individuals have at least two genotypically distinct populations of cells that arise from an early post-zygote event. The mutational event occurs early enough in development to affect several tissues. It is detected in germinal genetic studies as low variant allele frequency (VAF) variants (<30%) that are generally overlooked during the prioritization process. Constitutional mosaic variants can affect both somatic and germinal cells, and thus can be passed to the offspring and have important consequences for genetic counselling. In this work, we report the c.9648+1G>A mosaic variant in the BRCA2 gene and propose a diagnostic algorithm to deal with potential mosaic findings identified by Next Generation Sequencing (NGS).
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Affiliation(s)
- Irene Hidalgo Mayoral
- Hereditary Cancer Laboratory, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Ainhoa Almeida Santiago
- Hereditary Cancer Laboratory, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | | | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain
| | - Alicia Gómez-Sanz
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain
| | | | - Luis Robles
- Medical Oncology Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
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18
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Caleca L, Radice P. Refinement of the assignment to the ACMG/AMP BS3 and PS3 criteria of eight BRCA1 variants of uncertain significance by integrating available functional data with protein interaction assays. Front Oncol 2023; 13:1146604. [PMID: 37168384 PMCID: PMC10164951 DOI: 10.3389/fonc.2023.1146604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
The clinical screening of cancer predisposition genes has led to the identification of a large number of variants of uncertain significance (VUS). Multifactorial likelihood models that predict the odds ratio for VUS in favor or against cancer causality, have been developed, but their use is limited by the amount of necessary data, which are difficult to obtain for rare variants. The guidelines for variant interpretation of the American College of Medical Genetics and Genomics along with the Association for Molecular Pathology (ACMG/AMP) state that "well-established" functional studies provide strong support of a pathogenic or benign impact (criteria PS3 and BS3, respectively) and can be used as evidence type to reach a final classification. Moreover, the Clinical Genome Resource Sequence Variant Interpretation Working Group developed rule specifications to refine the PS3/BS3 criteria. Recently, Lira PC et al. developed the "Hi Set" approach that generated PS3/BS3 codes for over two-thousands BRCA1 VUS. While highly successful, this approach did not discriminate a group of variants with conflicting evidences. Here, we aimed to implement the outcomes of the "Hi-set" approach applying Green Fluorescent Protein (GFP)-reassembly assays, assessing the effect of variants in the RING and BRCT domains of BRCA1 on the binding of these domains with the UbcH5a or ABRAXAS proteins, respectively. The analyses of 26 clinically classified variants, including 13 tested in our previous study, showed 100% sensitivity and specificity in identifying pathogenic and benign variants for both the RING/UbcH5a and the BRCTs/ABRAXAS interactions. We derived the strength of evidences generated by the GFP-reassembly assays corresponding to moderate for both PS3 and BS3 criteria assessment. The GFP-reassembly assays were applied to the functional characterization of 8 discordant variants from the study by Lyra et al. The outcomes of these analyses, combined with those reported in the "Hi Set" study, allowed the assignment of ACMG/AMP criteria in favor or against pathogenicity for all 8 examined variants. The above findings were validated with a semi-quantitative Mammalian Two-Hybrid approach, and totally concordant results were observed. Our data contributes in shedding light on the functional significance of BRCA1 VUS and on their clinical interpretation within the ACMG/AMP framework.
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19
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Bosse KR, Giudice AM, Lane MV, McIntyre B, Schürch PM, Pascual-Pasto G, Buongervino SN, Suresh S, Fitzsimmons A, Hyman A, Gemino-Borromeo M, Saggio J, Berko ER, Daniels AA, Stundon J, Friedrichsen M, Liu X, Margolis ML, Li MM, Tierno MB, Oxnard GR, Maris JM, Mossé YP. Serial Profiling of Circulating Tumor DNA Identifies Dynamic Evolution of Clinically Actionable Genomic Alterations in High-Risk Neuroblastoma. Cancer Discov 2022; 12:2800-2819. [PMID: 36108156 PMCID: PMC9722579 DOI: 10.1158/2159-8290.cd-22-0287] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/21/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
Neuroblastoma evolution, heterogeneity, and resistance remain inadequately defined, suggesting a role for circulating tumor DNA (ctDNA) sequencing. To define the utility of ctDNA profiling in neuroblastoma, 167 blood samples from 48 high-risk patients were evaluated for ctDNA using comprehensive genomic profiling. At least one pathogenic genomic alteration was identified in 56% of samples and 73% of evaluable patients, including clinically actionable ALK and RAS-MAPK pathway variants. Fifteen patients received ALK inhibition (ALKi), and ctDNA data revealed dynamic genomic evolution under ALKi therapeutic pressure. Serial ctDNA profiling detected disease evolution in 15 of 16 patients with a recurrently identified variant-in some cases confirming disease progression prior to standard surveillance methods. Finally, ctDNA-defined ERRFI1 loss-of-function variants were validated in neuroblastoma cellular models, with the mutant proteins exhibiting loss of wild-type ERRFI1's tumor-suppressive functions. Taken together, ctDNA is prevalent in children with high-risk neuroblastoma and should be followed throughout neuroblastoma treatment. SIGNIFICANCE ctDNA is prevalent in children with neuroblastoma. Serial ctDNA profiling in patients with neuroblastoma improves the detection of potentially clinically actionable and functionally relevant variants in cancer driver genes and delineates dynamic tumor evolution and disease progression beyond that of standard tumor sequencing and clinical surveillance practices. See related commentary by Deubzer et al., p. 2727. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Anna Maria Giudice
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria V. Lane
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Brendan McIntyre
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Patrick M. Schürch
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Guillem Pascual-Pasto
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Samantha N. Buongervino
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Sriyaa Suresh
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alana Fitzsimmons
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Adam Hyman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria Gemino-Borromeo
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Saggio
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Esther R. Berko
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alexander A. Daniels
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Stundon
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | - Xin Liu
- Foundation Medicine, Inc. Cambridge, MA 02141; USA
| | | | - Marilyn M. Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and the Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | | | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Yael P. Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
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Yoshikawa Y, Kimura S, Soga A, Sugiyama M, Ueno A, Kondo H, Zhu Z, Ochiai K, Nakayama K, Hakozaki J, Kusakisako K, Haraguchi A, Kitano T, Orino K, Fukumoto S, Ikadai H. Plasmodium berghei Brca2 is required for normal development and differentiation in mice and mosquitoes. Parasit Vectors 2022; 15:244. [PMID: 35804459 PMCID: PMC9270840 DOI: 10.1186/s13071-022-05357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria is a major global parasitic disease caused by species of the genus Plasmodium. Zygotes of Plasmodium spp. undergo meiosis and develop into tetraploid ookinetes, which differentiate into oocysts that undergo sporogony. Homologous recombination (HR) occurs during meiosis and introduces genetic variation. However, the mechanisms of HR in Plasmodium are unclear. In humans, the recombinases DNA repair protein Rad51 homolog 1 (Rad51) and DNA meiotic recombinase 1 (Dmc1) are required for HR and are regulated by breast cancer susceptibility protein 2 (BRCA2). Most eukaryotes harbor BRCA2 homologs. Nevertheless, these have not been reported for Plasmodium. METHODS A Brca2 candidate was salvaged from a database to identify Brca2 homologs in Plasmodium. To confirm that the candidate protein was Brca2, interaction activity between Plasmodium berghei (Pb) Brca2 (PbBrca2) and Rad51 (PbRad51) was investigated using a mammalian two-hybrid assay. To elucidate the functions of PbBrca2, PbBrca2 was knocked out and parasite proliferation and differentiation were assessed in mice and mosquitoes. Transmission electron microscopy was used to identify sporogony. RESULTS The candidate protein was conserved among Plasmodium species, and it was indicated that it harbors critical BRCA2 domains including BRC repeats, tower, and oligonucleotide/oligosaccharide-binding-fold domains. The P. berghei BRC repeats interacted with PbRad51. Hence, the candidate was considered a Brca2 homolog. PbBrca2 knockout parasites were associated with reduced parasitemia with increased ring stage and decreased trophozoite stage counts, gametocytemia, female gametocyte ratio, oocyst number, and ookinete development in both mice and mosquitoes. Nevertheless, the morphology of the blood stages in mice and the ookinete stage was comparable to those of the wild type parasites. Transmission electron microscopy results showed that sporogony never progressed in Brca2-knockout parasites. CONCLUSIONS Brca2 is implicated in nearly all Plasmodium life cycle stages, and especially in sporogony. PbBrca2 contributes to HR during meiosis.
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Affiliation(s)
- Yasunaga Yoshikawa
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan.
| | - Shunta Kimura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Akira Soga
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
| | - Makoto Sugiyama
- Laboratory of Veterinary Anatomy, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Aki Ueno
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Hiroki Kondo
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Zida Zhu
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Kazuhiko Ochiai
- Laboratory of Veterinary Hygiene, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan
| | - Kazuhiko Nakayama
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Jun Hakozaki
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Kodai Kusakisako
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Asako Haraguchi
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Taisuke Kitano
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Koichi Orino
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Shinya Fukumoto
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
| | - Hiromi Ikadai
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
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21
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BRCA2 C-Terminal RAD51-Binding Domain Confers Resistance to DNA-Damaging Agents. Int J Mol Sci 2022; 23:ijms23074060. [PMID: 35409418 PMCID: PMC9000072 DOI: 10.3390/ijms23074060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In this study, we investigated CTRBD expression in cells exposed to X-ray irradiation and mitomycin C treatment. Surprisingly, BRCA2 CTRBD expression in HeLa cells increased their resistance to X-ray irradiation and mitomycin C. Under endogenous BRCA2 depletion using shRNA, the sensitivities of the BRCA2-depleted cells with and without the CTRBD did not significantly differ. Thus, the resistance to X-ray irradiation conferred by an exogenous CTRBD required endogenous BRCA2 expression. BRCA2 CTRBD-expressing cells demonstrated effective RAD51 foci formation and increased homologous recombination efficiency, but not nonhomologous end-joining efficiency. To the best of our knowledge, our study is the first to report the ability of the BRCA2 functional domain to confer resistance to X-ray irradiation and mitomycin C treatment by increased homologous recombination efficiency. Thus, this peptide may be useful for protecting cells against X-ray irradiation or chemotherapeutic agents.
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