1
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Repo PE, Backlund MP, Kivelä TT, Turunen JA. Functional assay for assessment of pathogenicity of BAP1 variants. Hum Mol Genet 2024; 33:426-434. [PMID: 37956408 PMCID: PMC10877462 DOI: 10.1093/hmg/ddad193] [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: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Pathogenic germline variants in BRCA1-Associated Protein 1 (BAP1) cause BAP1 tumor predisposition syndrome (BAP1-TPDS). Carriers run especially a risk of uveal (UM) and cutaneous melanoma, malignant mesothelioma, and clear cell renal carcinoma. Approximately half of increasingly reported BAP1 variants lack accurate classification. Correct interpretation of pathogenicity can improve prognosis of the patients through tumor screening with better understanding of BAP1-TPDS. METHODS We edited five rare BAP1 variants with differing functional characteristics identified from patients with UM in HAP1 cells using CRISPR-Cas9 and assayed their effect on cell adhesion/spreading (at 4 h) and proliferation (at 48 h), measured as cell index (CI), using xCELLigence real-time analysis system. RESULTS In BAP1 knockout HAP1 cultures, cell number was half of wild type (WT) cultures at 48 h (p = 0.00021), reaching confluence later, and CI was 78% reduced (p < 0.0001). BAP1-TPDS-associated null variants c.67+1G>T and c.1780_1781insT, and a likely pathogenic missense variant c.281A>G reduced adhesion (all p ≤ 0.015) and proliferation by 74%-83% (all p ≤ 0.032). Another likely pathogenic missense variant c.680G>A reduced both by at least 50% (all p ≤ 0.032), whereas cells edited with likely benign one c.1526C>T grew similarly to WT. CONCLUSIONS BAP1 is essential for optimal fitness of HAP1 cells. Pathogenic and likely pathogenic BAP1 variants reduced cell fitness, reflected in adhesion/spreading and proliferation properties. Further, moderate effects were quantifiable. Variant modelling in HAP1 with CRISPR-Cas9 enabled functional analysis of coding and non-coding region variants in an endogenous expression system.
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Affiliation(s)
- Pauliina E Repo
- Eye Genetics Group, Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, FI-00290, Helsinki, Finland
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4 C, PL220, FI-00029 HUS, Helsinki, Finland
| | - Michael P Backlund
- Eye Genetics Group, Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, FI-00290, Helsinki, Finland
| | - Tero T Kivelä
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4 C, PL220, FI-00029 HUS, Helsinki, Finland
| | - Joni A Turunen
- Eye Genetics Group, Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, FI-00290, Helsinki, Finland
- Ophthalmic Genetics and Rare Eye Diseases Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4 C, PL220, FI-00029 HUS, Helsinki, Finland
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2
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Barili V, Ambrosini E, Bortesi B, Minari R, De Sensi E, Cannizzaro IR, Taiani A, Michiara M, Sikokis A, Boggiani D, Tommasi C, Serra O, Bonatti F, Adorni A, Luberto A, Caggiati P, Martorana D, Uliana V, Percesepe A, Musolino A, Pellegrino B. Genetic Basis of Breast and Ovarian Cancer: Approaches and Lessons Learnt from Three Decades of Inherited Predisposition Testing. Genes (Basel) 2024; 15:219. [PMID: 38397209 PMCID: PMC10888198 DOI: 10.3390/genes15020219] [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: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Germline variants occurring in BRCA1 and BRCA2 give rise to hereditary breast and ovarian cancer (HBOC) syndrome, predisposing to breast, ovarian, fallopian tube, and peritoneal cancers marked by elevated incidences of genomic aberrations that correspond to poor prognoses. These genes are in fact involved in genetic integrity, particularly in the process of homologous recombination (HR) DNA repair, a high-fidelity repair system for mending DNA double-strand breaks. In addition to its implication in HBOC pathogenesis, the impairment of HR has become a prime target for therapeutic intervention utilizing poly (ADP-ribose) polymerase (PARP) inhibitors. In the present review, we introduce the molecular roles of HR orchestrated by BRCA1 and BRCA2 within the framework of sensitivity to PARP inhibitors. We examine the genetic architecture underneath breast and ovarian cancer ranging from high- and mid- to low-penetrant predisposing genes and taking into account both germline and somatic variations. Finally, we consider higher levels of complexity of the genomic landscape such as polygenic risk scores and other approaches aiming to optimize therapeutic and preventive strategies for breast and ovarian cancer.
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Affiliation(s)
- Valeria Barili
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Beatrice Bortesi
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Antonietta Taiani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Maria Michiara
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Angelica Sikokis
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Daniela Boggiani
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Chiara Tommasi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Olga Serra
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Francesco Bonatti
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Alessia Adorni
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Anita Luberto
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonio Percesepe
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonino Musolino
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Benedetta Pellegrino
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
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3
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Huang H, Hu C, Na J, Hart SN, Gnanaolivu RD, Abozaid M, Rao T, Tecleab YA, Pesaran T, Lyra PCM, Karam R, Yadav S, Domchek SM, de la Hoya M, Robson M, Mehine M, Bandlamudi C, Mandelker D, Monteiro ANA, Boddicker N, Chen W, Richardson ME, Couch FJ. Saturation genome editing-based functional evaluation and clinical classification of BRCA2 single nucleotide variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571597. [PMID: 38168194 PMCID: PMC10760149 DOI: 10.1101/2023.12.14.571597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to breast, ovarian, prostate and pancreatic cancer. However, variants of uncertain significance (VUS) (n>4000) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants. Here we report on comprehensive saturation genome editing-based functional characterization of 97% of all possible single nucleotide variants (SNVs) in the BRCA2 DNA Binding Domain hotspot for pathogenic missense variants that is encoded by exons 15 to 26. The assay was based on deep sequence analysis of surviving endogenously targeted haploid cells. A total of 7013 SNVs were characterized as functionally abnormal (n=955), intermediate/uncertain, or functionally normal (n=5224) based on 95% agreement with ClinVar known pathogenic and benign standards. Results were validated relative to batches of nonsense and synonymous variants and variants evaluated using a homology directed repair (HDR) functional assay. Breast cancer case-control association studies showed that pooled SNVs encoding functionally abnormal missense variants were associated with increased risk of breast cancer (odds ratio (OR) 3.89, 95%CI: 2.77-5.51). In addition, 86% of tumors associated with abnormal missense SNVs displayed loss of heterozygosity (LOH), whereas 26% of tumors with normal variants had LOH. The functional data were added to other sources of information in a ClinGen/ACMG/AMP-like model and 700 functionally abnormal SNVs, including 220 missense SNVs, were classified as pathogenic or likely pathogenic, while 4862 functionally normal SNVs, including 3084 missense SNVs, were classified as benign or likely benign. These classified variants can now be used for risk assessment and clinical care of variant carriers and the remaining functional scores can be used directly for clinical classification and interpretation of many additional variants. Summary Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to several types of cancer. However, variants of uncertain significance (VUS) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants to facilitate current and future clinical management of individuals with these variants. Here we show the results from a saturation genome editing (SGE) and functional analysis of all possible single nucleotide variants (SNVs) from exons 15 to 26 that encode the BRCA2 DNA Binding Domain hotspot for pathogenic missense variants. The assay was based on deep sequence analysis of surviving endogenously targeted human haploid HAP1 cells. The assay was calibrated relative to ClinVar known pathogenic and benign missense standards and 95% prevalence thresholds for functionally abnormal and normal variants were identified. Thresholds were validated based on nonsense and synonymous variants. SNVs encoding functionally abnormal missense variants were associated with increased risks of breast and ovarian cancer. The functional assay results were integrated into a ClinGen/ACMG/AMP-like model for clinical classification of the majority of BRCA2 SNVs as pathogenic/likely pathogenic or benign/likely benign. The classified variants can be used for improved clinical management of variant carriers.
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Sahu S, Sullivan T, Southon E, Caylor D, Geh J, Sharan SK. Protocol for the saturation and multiplexing of genetic variants using CRISPR-Cas9. STAR Protoc 2023; 4:102702. [PMID: 37948185 PMCID: PMC10658368 DOI: 10.1016/j.xpro.2023.102702] [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: 09/26/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Here, we present a multiplexed assay for variant effect protocol to assess the functional impact of all possible genetic variations within a particular genomic region. We describe steps for saturation genome editing by designing and cloning of single-guide RNA (sgRNA). We then detail steps for nucleofection of sgRNA, testing drug response on variants, and amplification of genomic DNA for next-generation sequencing. For complete details on the use and execution of this protocol, please refer to Sahu et al.1.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Dylan Caylor
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Josephine Geh
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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5
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Mishra AP, Hartford S, Chittela RK, Sahu S, Kharat SS, Alvaro-Aranda L, Contreras-Perez A, Sullivan T, Martin BK, Albaugh M, Southon E, Burkett S, Karim B, Carreira A, Tessarollo L, Sharan SK. Characterization of BRCA2 R3052Q variant in mice supports its functional impact as a low-risk variant. Cell Death Dis 2023; 14:753. [PMID: 37980415 PMCID: PMC10657400 DOI: 10.1038/s41419-023-06289-8] [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: 07/13/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Pathogenic variants in BRCA2 are known to significantly increase the lifetime risk of developing breast and ovarian cancers. Sequencing-based genetic testing has resulted in the identification of thousands of BRCA2 variants that are considered to be variants of uncertain significance (VUS) because the disease risk associated with them is unknown. One such variant is p.Arg3052Gln, which has conflicting interpretations of pathogenicity in the ClinVar variant database. Arginine at position 3052 in BRCA2 plays an important role in stabilizing its C-terminal DNA binding domain. We have generated a knock-in mouse model expressing this variant to examine its role on growth and survival in vivo. Homozygous as well as hemizygous mutant mice are viable, fertile and exhibit no overt phenotype. While we did not observe any hematopoietic defects in adults, we did observe a marked reduction in the in vitro proliferative ability of fetal liver cells that were also hypersensitive to PARP inhibitor, olaparib. In vitro studies performed on embryonic and adult fibroblasts derived from the mutant mice showed significant reduction in radiation induced RAD51 foci formation as well as increased genomic instability after mitomycin C treatment. We observed mis-localization of a fraction of R3052Q BRCA2 protein to the cytoplasm which may explain the observed in vitro phenotypes. Our findings suggest that BRCA2 R3052Q should be considered as a hypomorphic variant.
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Affiliation(s)
- Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suzanne Hartford
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Rajani Kant Chittela
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Applied Genomics Section, Bhabha Atomic Research Center, Trombay, Mumbai, 400085, India
| | - Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suhas S Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Lucia Alvaro-Aranda
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Aida Contreras-Perez
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Betty K Martin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Aura Carreira
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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6
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Sahu S, Poplawska M, Lim SH, Dutta D. CRISPR-based precision medicine for hematologic disorders: Advancements, challenges, and prospects. Life Sci 2023; 333:122165. [PMID: 37832631 DOI: 10.1016/j.lfs.2023.122165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
The development of programmable nucleases to introduce defined alterations in genomic sequences has been a powerful tool for precision medicine. While several nucleases such as zinc-finger nucleases (ZFN), transcriptor activator-like effector nucleases (TALEN), and meganucleases have been explored, the advent of CRISPR/Cas9 technology has revolutionized the field of genome engineering. In addition to disease modeling, the CRISPR/Cas9 technology has contributed to safer and more effective treatment strategies for hematologic diseases and personalized T-cell-based therapies. Here we discuss the applications of the CRISPR technology in the treatment of hematologic diseases, their efficacy, and ongoing clinical trials. We examine the obstacles to their successful use and the approaches investigated to overcome these challenges. Finally, we provide our perspectives to improve this genome editing tool for targeted therapies.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Building 560, Room 32-04, Frederick, MD 21702, USA.
| | - Maria Poplawska
- Department of Medicine (Division of Hematology and Oncology), State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Seah H Lim
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA
| | - Dibyendu Dutta
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA.
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