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Zhao H, Du H, Zhao S, Chen Z, Li Y, Xu K, Liu B, Cheng X, Wen W, Li G, Chen G, Zhao Z, Qiu G, Liu P, Zhang TJ, Wu Z, Wu N. SIGMA leverages protein structural information to predict the pathogenicity of missense variants. CELL REPORTS METHODS 2024; 4:100687. [PMID: 38211594 PMCID: PMC10831939 DOI: 10.1016/j.crmeth.2023.100687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/15/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024]
Abstract
Leveraging protein structural information to evaluate pathogenicity has been hindered by the scarcity of experimentally determined 3D protein. With the aid of AlphaFold2 predictions, we developed the structure-informed genetic missense mutation assessor (SIGMA) to predict missense variant pathogenicity. In comparison with existing predictors across labeled variant datasets and experimental datasets, SIGMA demonstrates superior performance in predicting missense variant pathogenicity (AUC = 0.933). We found that the relative solvent accessibility of the mutated residue contributed greatly to the predictive ability of SIGMA. We further explored combining SIGMA with other top-tier predictors to create SIGMA+, proving highly effective for variant pathogenicity prediction (AUC = 0.966). To facilitate the application of SIGMA, we pre-computed SIGMA scores for over 48 million possible missense variants across 3,454 disease-associated genes and developed an interactive online platform (https://www.sigma-pred.org/). Overall, by leveraging protein structure information, SIGMA offers an accurate structure-based approach to evaluating the pathogenicity of missense variants.
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Affiliation(s)
- Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Wen Wen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
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2
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Maes S, Deploey N, Peelman F, Eyckerman S. Deep mutational scanning of proteins in mammalian cells. CELL REPORTS METHODS 2023; 3:100641. [PMID: 37963462 PMCID: PMC10694495 DOI: 10.1016/j.crmeth.2023.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Protein mutagenesis is essential for unveiling the molecular mechanisms underlying protein function in health, disease, and evolution. In the past decade, deep mutational scanning methods have evolved to support the functional analysis of nearly all possible single-amino acid changes in a protein of interest. While historically these methods were developed in lower organisms such as E. coli and yeast, recent technological advancements have resulted in the increased use of mammalian cells, particularly for studying proteins involved in human disease. These advancements will aid significantly in the classification and interpretation of variants of unknown significance, which are being discovered at large scale due to the current surge in the use of whole-genome sequencing in clinical contexts. Here, we explore the experimental aspects of deep mutational scanning studies in mammalian cells and report the different methods used in each step of the workflow, ultimately providing a useful guide toward the design of such studies.
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Affiliation(s)
- Stefanie Maes
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Nick Deploey
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Frank Peelman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.
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3
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Nagy G, Diabate M, Banerjee T, Adamovich AI, Smith N, Jeon H, Dhar S, Liu W, Burgess K, Chung D, Starita LM, Parvin JD. Multiplexed assay of variant effect reveals residues of functional importance in the BRCA1 coiled-coil and serine cluster domains. PLoS One 2023; 18:e0293422. [PMID: 37917606 PMCID: PMC10621863 DOI: 10.1371/journal.pone.0293422] [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: 06/23/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Delineating functionally normal variants from functionally abnormal variants in tumor suppressor proteins is critical for cancer surveillance, prognosis, and treatment options. BRCA1 is a protein that has many variants of uncertain significance which are not yet classified as functionally normal or abnormal. In vitro functional assays can be used to identify the functional impact of a variant when the variant has not yet been categorized through clinical observation. Here we employ a homology-directed repair (HDR) reporter assay to evaluate over 300 missense and nonsense BRCA1 variants between amino acid residues 1280 and 1576, which encompasses the coiled-coil and serine cluster domains. Functionally abnormal variants tended to cluster in residues known to interact with PALB2, which is critical for homology-directed repair. Multiplexed results were confirmed by singleton assay and by ClinVar database variant interpretations. Comparison of multiplexed results to designated benign or likely benign or pathogenic or likely pathogenic variants in the ClinVar database yielded 100% specificity and 100% sensitivity of the multiplexed assay. Clinicians can reference the results of this functional assay for help in guiding cancer treatment and surveillance options. These results are the first to evaluate this domain of BRCA1 using a multiplexed approach and indicate the importance of this domain in the DNA repair process.
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Affiliation(s)
- Gregory Nagy
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Mariame Diabate
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Tapahsama Banerjee
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Aleksandra I. Adamovich
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Nahum Smith
- Department of Genome Sciences, University of Washington and Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Hyeongseon Jeon
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Shruti Dhar
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Wenfang Liu
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Katherine Burgess
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington and Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Jeffrey D. Parvin
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
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4
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Wang M, Li W, Tomimatsu N, Yu CH, Ji JH, Alejo S, Witus SR, Alimbetov D, Fitzgerald O, Wu B, Wang Q, Huang Y, Gan Y, Dong F, Kwon Y, Sareddy GR, Curiel TJ, Habib AA, Hromas R, Dos Santos Passos C, Yao T, Ivanov DN, Brzovic PS, Burma S, Klevit RE, Zhao W. Crucial roles of the BRCA1-BARD1 E3 ubiquitin ligase activity in homology-directed DNA repair. Mol Cell 2023; 83:3679-3691.e8. [PMID: 37797621 PMCID: PMC10591799 DOI: 10.1016/j.molcel.2023.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/08/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
The tumor-suppressor breast cancer 1 (BRCA1) in complex with BRCA1-associated really interesting new gene (RING) domain 1 (BARD1) is a RING-type ubiquitin E3 ligase that modifies nucleosomal histone and other substrates. The importance of BRCA1-BARD1 E3 activity in tumor suppression remains highly controversial, mainly stemming from studying mutant ligase-deficient BRCA1-BARD1 species that we show here still retain significant ligase activity. Using full-length BRCA1-BARD1, we establish robust BRCA1-BARD1-mediated ubiquitylation with specificity, uncover multiple modes of activity modulation, and construct a truly ligase-null variant and a variant specifically impaired in targeting nucleosomal histones. Cells expressing either of these BRCA1-BARD1 separation-of-function alleles are hypersensitive to DNA-damaging agents. Furthermore, we demonstrate that BRCA1-BARD1 ligase is not only required for DNA resection during homology-directed repair (HDR) but also contributes to later stages for HDR completion. Altogether, our findings reveal crucial, previously unrecognized roles of BRCA1-BARD1 ligase activity in genome repair via HDR, settle prior controversies regarding BRCA1-BARD1 ligase functions, and catalyze new efforts to uncover substrates related to tumor suppression.
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Affiliation(s)
- Meiling Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenjing Li
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nozomi Tomimatsu
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jae-Hoon Ji
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Salvador Alejo
- Department of Obstetrics & Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Samuel R Witus
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Dauren Alimbetov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - O'Taveon Fitzgerald
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Qijing Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yuxin Huang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yaqi Gan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Felix Dong
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Gangadhara R Sareddy
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tyler J Curiel
- Geisel School of Medicine at Dartmouth and Department of Medicine, Dartmouth Health, Lebanon, NH 03765, USA
| | - Amyn A Habib
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert Hromas
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Carolina Dos Santos Passos
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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5
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Wang Y, Zhao Y, Li Y, Zhang K, Fan Y, Li B, Su W, Li S. piggyBac-mediated genomic integration of linear dsDNA-based library for deep mutational scanning in mammalian cells. Cell Mol Life Sci 2023; 80:321. [PMID: 37815732 PMCID: PMC11071730 DOI: 10.1007/s00018-023-04976-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Deep mutational scanning (DMS) makes it possible to perform massively parallel quantification of the relationship between genetic variants and phenotypes of interest. However, the difficulties in introducing large variant libraries into mammalian cells greatly hinder DMS under physiological states. Here, we developed two novel strategies for DMS library construction in mammalian cells, namely 'piggyBac-in vitro ligation' and 'piggyBac-in vitro ligation-PCR'. For the first strategy, we took the 'in vitro ligation' approach to prepare high-diversity linear dsDNAs, and integrate them into the mammalian genome with a piggyBac transposon system. For the second strategy, we further added a PCR step using the in vitro ligation dsDNAs as templates, for the construction of high-content genome-integrated libraries via large-scale transfection. Both strategies could successfully establish genome-integrated EGFP-chromophore-randomized libraries in HEK293T cells and enrich the green fluorescence-chromophore amino-acid sequences. And we further identified a novel transcriptional activator peptide with the 'piggyBac-in vitro ligation-PCR' strategy. Our novel strategies greatly facilitate the construction of large variant DMS library in mammalian cells, and may have great application potential in the future.
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Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yan Fan
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Bo Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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6
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Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V. Genome-wide prediction of disease variant effects with a deep protein language model. Nat Genet 2023; 55:1512-1522. [PMID: 37563329 PMCID: PMC10484790 DOI: 10.1038/s41588-023-01465-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
Predicting the effects of coding variants is a major challenge. While recent deep-learning models have improved variant effect prediction accuracy, they cannot analyze all coding variants due to dependency on close homologs or software limitations. Here we developed a workflow using ESM1b, a 650-million-parameter protein language model, to predict all ~450 million possible missense variant effects in the human genome, and made all predictions available on a web portal. ESM1b outperformed existing methods in classifying ~150,000 ClinVar/HGMD missense variants as pathogenic or benign and predicting measurements across 28 deep mutational scan datasets. We further annotated ~2 million variants as damaging only in specific protein isoforms, demonstrating the importance of considering all isoforms when predicting variant effects. Our approach also generalizes to more complex coding variants such as in-frame indels and stop-gains. Together, these results establish protein language models as an effective, accurate and general approach to predicting variant effects.
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Affiliation(s)
- Nadav Brandes
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Grant Goldman
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte H Wang
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Vasilis Ntranos
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
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7
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Diabate M, Islam MM, Nagy G, Banerjee T, Dhar S, Smith N, Adamovich AI, Starita LM, Parvin JD. DNA repair function scores for 2172 variants in the BRCA1 amino-terminus. PLoS Genet 2023; 19:e1010739. [PMID: 37578980 PMCID: PMC10449183 DOI: 10.1371/journal.pgen.1010739] [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: 04/06/2023] [Revised: 08/24/2023] [Accepted: 07/16/2023] [Indexed: 08/16/2023] Open
Abstract
Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1.
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Affiliation(s)
- Mariame Diabate
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Muhtadi M. Islam
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Gregory Nagy
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Tapahsama Banerjee
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Shruti Dhar
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Nahum Smith
- The University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Aleksandra I. Adamovich
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Lea M. Starita
- The University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Jeffrey D. Parvin
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
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8
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Hu C, Nagaraj AB, Shimelis H, Montalban G, Lee KY, Huang H, Lumby CA, Na J, Susswein LR, Roberts ME, Marshall ML, Hiraki S, LaDuca H, Chao E, Yussuf A, Pesaran T, Neuhausen SL, Haiman CA, Kraft P, Lindstrom S, Palmer JR, Teras LR, Vachon CM, Yao S, Ong I, Nathanson KL, Weitzel JN, Boddicker N, Gnanaolivu R, Polley EC, Mer G, Cui G, Karam R, Richardson ME, Domchek SM, Yadav S, Hruska KS, Dolinsky J, Weroha SJ, Hart SN, Simard J, Masson JY, Pang YP, Couch FJ. Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C. Cancer Res 2023; 83:2557-2571. [PMID: 37253112 PMCID: PMC10390864 DOI: 10.1158/0008-5472.can-22-2319] [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: 07/21/2022] [Revised: 10/07/2022] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C-/- cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case-control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18-7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71-30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers. SIGNIFICANCE Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants.
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Affiliation(s)
| | | | | | - Gemma Montalban
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | | | | | | | - Jie Na
- Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | | | | | | | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lauren R. Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irene Ong
- University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques Simard
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Jean Yves Masson
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
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9
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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10
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Bassi N, Hovland HN, Rasheed K, Jarhelle E, Pedersen N, Mchaina EK, Bakkan SME, Iversen N, Høberg-Vetti H, Haukanes BI, Knappskog PM, Aukrust I, Ognedal E, Van Ghelue M. Functional analyses of rare germline BRCA1 variants by transcriptional activation and homologous recombination repair assays. BMC Cancer 2023; 23:368. [PMID: 37085799 PMCID: PMC10122298 DOI: 10.1186/s12885-023-10790-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/30/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Damaging alterations in the BRCA1 gene have been extensively described as one of the main causes of hereditary breast and ovarian cancer (HBOC). BRCA1 alterations can lead to impaired homologous recombination repair (HRR) of double-stranded DNA breaks, a process which involves the RING, BRCT and coiled-coil domains of the BRCA1 protein. In addition, the BRCA1 protein is involved in transcriptional activation (TA) of several genes through its C-terminal BRCT domain. METHODS In this study, we have investigated the effect on HRR and TA of 11 rare BRCA1 missense variants classified as variants of uncertain clinical significance (VUS), located within or in close proximity to the BRCT domain, with the aim of generating additional knowledge to guide the correct classification of these variants. The variants were selected from our previous study "BRCA1 Norway", which is a collection of all BRCA1 variants detected at the four medical genetic departments in Norway. RESULTS All variants, except one, showed a significantly reduced HRR activity compared to the wild type (WT) protein. Two of the variants (p.Ala1708Val and p.Trp1718Ser) also exhibited low TA activity similar to the pathogenic controls. The variant p.Trp1718Ser could be reclassified to likely pathogenic. However, for ten of the variants, the total strength of pathogenic evidence was not sufficient for reclassification according to the CanVIG-UK BRCA1/BRCA2 gene-specific guidelines for variant interpretation. CONCLUSIONS When including the newly achieved functional evidence with other available information, one VUS was reclassified to likely pathogenic. Eight of the investigated variants affected only one of the assessed activities of BRCA1, highlighting the importance of comparing results obtained from several functional assays to better understand the consequences of BRCA1 variants on protein function. This is especially important for multifunctional proteins such as BRCA1.
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Affiliation(s)
- Nicola Bassi
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | - Henrikke Nilsen Hovland
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kashif Rasheed
- Department of Medical Biology, University of Tromsø, Tromsø, Norway
- Present address: Institute for Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
- Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
| | - Nikara Pedersen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Eunice Kabanyana Mchaina
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | | | - Nina Iversen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Hildegunn Høberg-Vetti
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Per Morten Knappskog
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Elisabet Ognedal
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
- Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
- Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
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11
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Diabate M, Islam MM, Nagy G, Banerjee T, Dhar S, Smith N, Adamovich AI, Starita LM, Parvin JD. DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536331. [PMID: 37090572 PMCID: PMC10120616 DOI: 10.1101/2023.04.10.536331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1 . AUTHOR SUMMARY Most missense substitutions in BRCA1 are variants of unknown significance (VUS), and individuals with a VUS in BRCA1 cannot know from genetic information alone whether this variant predisposes to breast or ovarian cancer. We apply a multiplexed functional assay for homology directed repair of DNA double strand breaks to assess variant impact on this important BRCA1 protein function. We analyzed 2172 variants in the amino-terminus of BRCA1 and demonstrate that variants that are known as pathogenic have a loss of function in the DNA repair assay. Conversely, variants that are known to be benign are functionally normal in the multiplexed assay. We suggest that these functional determinations of BRCA1 variants can be used to augment the information that clinical cancer geneticists provide to patients who have a VUS in BRCA1 .
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Affiliation(s)
- Mariame Diabate
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Muhtadi M Islam
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Gregory Nagy
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Tapahsama Banerjee
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Shruti Dhar
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Nahum Smith
- The University of Washington, Department of Genome Sciences, Seattle, WA 98195
- Brotman Baty Institute for Precision Medicine, Seattle WA, 98195
| | - Aleksandra I Adamovich
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Lea M Starita
- The University of Washington, Department of Genome Sciences, Seattle, WA 98195
- Brotman Baty Institute for Precision Medicine, Seattle WA, 98195
| | - Jeffrey D Parvin
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
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12
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Giacoletto CJ, Schiller MR. The history and conceptual framework of assays and screens. Bioessays 2023; 45:e2200191. [PMID: 36789580 PMCID: PMC10024921 DOI: 10.1002/bies.202200191] [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: 09/25/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 02/16/2023]
Abstract
Since the 16th century, assays and screens have been essential for scientific investigation. However, most methods could be significantly improved, especially in accuracy, scalability, and often lack adequate comparisons to negative controls. There is a lack of consistency in distinguishing assays, in which accuracy is the main goal, from screens, in which scalability is prioritized over accuracy. We dissected and modernized the original definitions of assays and screens based upon recent developments and the conceptual framework of the original definitions. All methods have three components: design/measurement, performance, and interpretation. We propose a model of method development in which reproducible observations become new methods, initially assessed by sensitivity. Further development can proceed along a path to either screens or assays. The screen path focuses on scalability first, but can later prioritize analysis of negatives. Alternatively, the assay path first compares results to negative controls, assessing specificity and accuracy, later adding scalability. Both pathways converge on a high-accuracy and throughput (HAT) assay, like next generation sequencing, which we suggest should be the ultimate goal of all testing methods. Our model will help scientists better select among available methods, as well as improve existing methods, expanding their impact on science.
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Affiliation(s)
- Christopher J. Giacoletto
- Nevada Institute of Personalized Medicine, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, Nevada, 89154 USA
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, Nevada, 89154 USA
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, Nevada, 89154 USA
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, Nevada, 89154 USA
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
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13
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Functional Analyses of Rare Germline Missense BRCA1 Variants Located within and outside Protein Domains with Known Functions. Genes (Basel) 2023; 14:genes14020262. [PMID: 36833189 PMCID: PMC9957003 DOI: 10.3390/genes14020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The BRCA1 protein is implicated in numerous important cellular processes to prevent genomic instability and tumorigenesis, and pathogenic germline variants predispose carriers to hereditary breast and ovarian cancer (HBOC). Most functional studies of missense variants in BRCA1 focus on variants located within the Really Interesting New Gene (RING), coiled-coil and BRCA1 C-terminal (BRCT) domains, and several missense variants in these regions have been shown to be pathogenic. However, the majority of these studies focus on domain specific assays, and have been performed using isolated protein domains and not the full-length BRCA1 protein. Furthermore, it has been suggested that BRCA1 missense variants located outside domains with known function are of no functional importance, and could be classified as (likely) benign. However, very little is known about the role of the regions outside the well-established domains of BRCA1, and only a few functional studies of missense variants located within these regions have been published. In this study, we have, therefore, functionally evaluated the effect of 14 rare BRCA1 missense variants considered to be of uncertain clinical significance, of which 13 are located outside the well-established domains and one within the RING domain. In order to investigate the hypothesis stating that most BRCA1 variants located outside the known protein domains are benign and of no functional importance, multiple protein assays including protein expression and stability, subcellular localisation and protein interactions have been performed, utilising the full-length protein to better mimic the native state of the protein. Two variants located outside the known domains (p.Met297Val and p.Asp1152Asn) and one variant within the RING domain (p.Leu52Phe) were found to make the BRCA1 protein more prone to proteasome-mediated degradation. In addition, two variants (p.Leu1439Phe and p.Gly890Arg) also located outside known domains were found to have reduced protein stability compared to the wild type protein. These findings indicate that variants located outside the RING, BRCT and coiled-coiled domains could also affect the BRCA1 protein function. For the nine remaining variants, no significant effects on BRCA1 protein functions were observed. Based on this, a reclassification of seven variants from VUS to likely benign could be suggested.
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14
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Functional Analysis of Variants in BRCA1 Using CRISPR Base Editors. Methods Mol Biol 2023; 2606:73-85. [PMID: 36592309 DOI: 10.1007/978-1-0716-2879-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To date, methods such as fluorescent reporter assays, embryonic stem cell viability assays, and therapeutic drug-based sensitivity assays have been used to evaluate the function of the variants of uncertain significance (VUS) of the BRCA genes. However, these methods have limitations as they are associated with overexpression and do not apply to post-transcriptional regulation. Therefore, there are several VUS whose functions are unclear. Recently, we devised a new way to assess the functionality of variants in BRCA1 via a CRISPR-mediated base editor to overcome these limitations. We precisely introduced the target nucleotide substitution in living cells and identified variants whose functions were not defined. Here, we describe the methods for the functional appraisal of BRCA1 variants using CRISPR-based base editors.
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15
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Fu Y, Bedő J, Papenfuss AT, Rubin AF. Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants. Gigascience 2022; 12:giad073. [PMID: 37721410 PMCID: PMC10506130 DOI: 10.1093/gigascience/giad073] [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: 02/14/2023] [Revised: 07/02/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
BACKGROUND Evaluating the impact of amino acid variants has been a critical challenge for studying protein function and interpreting genomic data. High-throughput experimental methods like deep mutational scanning (DMS) can measure the effect of large numbers of variants in a target protein, but because DMS studies have not been performed on all proteins, researchers also model DMS data computationally to estimate variant impacts by predictors. RESULTS In this study, we extended a linear regression-based predictor to explore whether incorporating data from alanine scanning (AS), a widely used low-throughput mutagenesis method, would improve prediction results. To evaluate our model, we collected 146 AS datasets, mapping to 54 DMS datasets across 22 distinct proteins. CONCLUSIONS We show that improved model performance depends on the compatibility of the DMS and AS assays, and the scale of improvement is closely related to the correlation between DMS and AS results.
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Affiliation(s)
- Yunfan Fu
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
| | - Justin Bedő
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
| | - Anthony T Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Alan F Rubin
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
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16
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Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annu Rev Genet 2022; 56:441-465. [PMID: 36055970 DOI: 10.1146/annurev-genet-072920-032107] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Scalable sequence-function studies have enabled the systematic analysis and cataloging of hundreds of thousands of coding and noncoding genetic variants in the human genome. This has improved clinical variant interpretation and provided insights into the molecular, biophysical, and cellular effects of genetic variants at an astonishing scale and resolution across the spectrum of allele frequencies. In this review, we explore current applications and prospects for the field and outline the principles underlying scalable functional assay design, with a focus on the study of single-nucleotide coding and noncoding variants.
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Affiliation(s)
- Daniel Tabet
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Victoria Parikh
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine and Endocrine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA;
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17
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Bilyalov A, Nikolaev S, Shigapova L, Khatkov I, Danishevich A, Zhukova L, Smolin S, Titova M, Lisica T, Bodunova N, Shagimardanova E, Gusev O. Application of Multigene Panels Testing for Hereditary Cancer Syndromes. BIOLOGY 2022; 11:biology11101461. [PMID: 36290365 PMCID: PMC9598138 DOI: 10.3390/biology11101461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Approximately 5-10% of all cancers are associated with hereditary cancer predisposition syndromes (HCPS). Early identification of HCPS is facilitated by widespread use of next-generation sequencing (NGS) and brings significant benefits to both the patient and their relatives. This study aims to evaluate the landscape of genetic variants in patients with personal and/or family history of cancer using NGS-based multigene panel testing. MATERIALS AND METHODS The study cohort included 1117 probands from Russia: 1060 (94.9%) patients with clinical signs of HCPS and 57 (5.1%) healthy individuals with family history of cancer. NGS analysis of 76 HCPS genes was performed using a custom Roche NimbleGen enrichment panel. RESULTS Pathogenic/likely pathogenic variants were identified in 378 of 1117 individuals (33.8%). The predominant number (59.8%) of genetic variants was identified in BRCA1/BRCA2 genes. CHEK2 was the second most commonly altered gene with a total of 28 (7.4%) variants, and 124 (32.8%) genetic variants were found in other 35 cancer-associated genes with variable penetrance. CONCLUSIONS Multigene panel testing allows for a differential diagnosis and identification of high-risk group for oncological diseases. Our results demonstrate that inclusion of non-coding gene regions into HCPS gene panels is highly important for the identification of rare spliceogenic variants with high penetrance.
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Affiliation(s)
- Airat Bilyalov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
- Correspondence: ; Tel.: +7-9625-6038-02
| | - Sergey Nikolaev
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Leila Shigapova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Igor Khatkov
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | | | - Ludmila Zhukova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Sergei Smolin
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Marina Titova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Tatyana Lisica
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia
| | - Natalia Bodunova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Endocrinology Research Centre, 117036 Moscow, Russia
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18
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Nepomuceno TC, Dos Santos APP, Fernandes VC, Elias ABR, Gomes TT, Suarez-Kurtz G, Iversen ES, Couch FJ, Monteiro ANA, Carvalho MA. Assessment of small in-frame indels and C-terminal nonsense variants of BRCA1 using a validated functional assay. Sci Rep 2022; 12:16203. [PMID: 36171434 PMCID: PMC9519549 DOI: 10.1038/s41598-022-20500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
BRCA1 (Breast Cancer 1, early onset) is linked to breast and ovarian cancer predisposition. Still, the risks conferred by a significant portion of BRCA1 variants identified in the population remains unknown. Most of these variants of uncertain significance are missense alterations. However, the functional implications of small in-frame deletions and/or insertions (indels) are also difficult to predict. Our group has previously evaluated the functional impact of 347 missense variants using an extensively validated transcriptional activity assay. Here we show a systematic assessment of 30 naturally occurring in-frame indels located at the C-terminal region of BRCA1. We identified positions sensitive and tolerant to alterations, expanding the knowledge of structural determinants of BRCA1 function. We further designed and assessed the impact of four single codon deletions in the tBRCT linker region and six nonsense variants at the C-terminus end of BRCA1. Amino acid substitutions, deletions or insertions in the disordered region do not significantly impact activity and are not likely to constitute pathogenic alleles. On the other hand, a sizeable fraction of in-frame indels at the BRCT domain significantly impact function. We then use a Bayesian integrative statistical model to derive the probability of pathogenicity for each variant. Our data highlights the importance of assessing the impact of small in-frame indels in BRCA1 to improve risk assessment and clinical decisions for carriers.
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Affiliation(s)
- Thales C Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil.,Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Ana P P Dos Santos
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Vanessa C Fernandes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Anna B R Elias
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Thiago T Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | | | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Marcelo A Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil. .,Laboratório de Genética Molecular, Instituto Federal Do Rio de Janeiro, Rua Senador Furtado, Campus Rio de Janeiro121, Rio de Janeiro, RJ, 20270-021, Brazil.
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19
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Aljarf R, Shen M, Pires DEV, Ascher DB. Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2. Sci Rep 2022; 12:10458. [PMID: 35729312 PMCID: PMC9213547 DOI: 10.1038/s41598-022-13508-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
BRCA1 and BRCA2 are tumour suppressor genes that play a critical role in maintaining genomic stability via the DNA repair mechanism. DNA repair defects caused by BRCA1 and BRCA2 missense variants increase the risk of developing breast and ovarian cancers. Accurate identification of these variants becomes clinically relevant, as means to guide personalized patient management and early detection. Next-generation sequencing efforts have significantly increased data availability but also the discovery of variants of uncertain significance that need interpretation. Experimental approaches used to measure the molecular consequences of these variants, however, are usually costly and time-consuming. Therefore, computational tools have emerged as faster alternatives for assisting in the interpretation of the clinical significance of newly discovered variants. To better understand and predict variant pathogenicity in BRCA1 and BRCA2, various machine learning algorithms have been proposed, however presented limited performance. Here we present BRCA1 and BRCA2 gene-specific models and a generic model for quantifying the functional impacts of single-point missense variants in these genes. Across tenfold cross-validation, our final models achieved a Matthew's Correlation Coefficient (MCC) of up to 0.98 and comparable performance of up to 0.89 across independent, non-redundant blind tests, outperforming alternative approaches. We believe our predictive tool will be a valuable resource for providing insights into understanding and interpreting the functional consequences of missense variants in these genes and as a tool for guiding the interpretation of newly discovered variants and prioritizing mutations for experimental validation.
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Affiliation(s)
- Raghad Aljarf
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Mengyuan Shen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3053, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia. .,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3053, Australia.
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia. .,Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge, CB2 1GA, UK.
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20
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Kim Y, Lee S, Cho S, Park J, Chae D, Park T, Minna JD, Kim HH. High-throughput functional evaluation of human cancer-associated mutations using base editors. Nat Biotechnol 2022; 40:874-884. [PMID: 35411116 PMCID: PMC10243181 DOI: 10.1038/s41587-022-01276-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 03/10/2022] [Indexed: 12/26/2022]
Abstract
Comprehensive phenotypic characterization of the many mutations found in cancer tissues is one of the biggest challenges in cancer genomics. In this study, we evaluated the functional effects of 29,060 cancer-related transition mutations that result in protein variants on the survival and proliferation of non-tumorigenic lung cells using cytosine and adenine base editors and single guide RNA (sgRNA) libraries. By monitoring base editing efficiencies and outcomes using surrogate target sequences paired with sgRNA-encoding sequences on the lentiviral delivery construct, we identified sgRNAs that induced a single primary protein variant per sgRNA, enabling linking those mutations to the cellular phenotypes caused by base editing. The functions of the vast majority of the protein variants (28,458 variants, 98%) were classified as neutral or likely neutral; only 18 (0.06%) and 157 (0.5%) variants caused outgrowing and likely outgrowing phenotypes, respectively. We expect that our approach can be extended to more variants of unknown significance and other tumor types.
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Affiliation(s)
- Younggwang Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seungho Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soohyuk Cho
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongwoo Chae
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Taeyoung Park
- Department of Applied Statistics, Yonsei University, Seoul, Republic of Korea
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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21
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Ng PS, Boonen RA, Wijaya E, Chong CE, Sharma M, Knaup S, Mariapun S, Ho WK, Lim J, Yoon SY, Mohd Taib NA, See MH, Li J, Lim SH, Tan EY, Tan BKT, Tan SM, Tan VKM, van Dam RM, Rahmat K, Yip CH, Carvalho S, Luccarini C, Baynes C, Dunning AM, Antoniou A, van Attikum H, Easton DF, Hartman M, Teo SH. Characterisation of protein-truncating and missense variants in PALB2 in 15 768 women from Malaysia and Singapore. J Med Genet 2022; 59:481-491. [PMID: 33811135 PMCID: PMC9046754 DOI: 10.1136/jmedgenet-2020-107471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Rare protein-truncating variants (PTVs) in partner and localiser of BRCA2 (PALB2) confer increased risk to breast cancer, but relatively few studies have reported the prevalence in South-East Asian populations. Here, we describe the prevalence of rare variants in PALB2 in a population-based study of 7840 breast cancer cases and 7928 healthy Chinese, Malay and Indian women from Malaysia and Singapore, and describe the functional impact of germline missense variants identified in this population. METHODS Mutation testing was performed on germline DNA (n=15 768) using targeted sequencing panels. The functional impact of missense variants was tested in mouse embryonic stem cell based functional assays. RESULTS PTVs in PALB2 were found in 0.73% of breast cancer patients and 0.14% of healthy individuals (OR=5.44; 95% CI 2.85 to 10.39, p<0.0001). In contrast, rare missense variants in PALB2 were not associated with increased risk of breast cancer. Whereas PTVs were associated with later stage of presentation and higher-grade tumours, no significant association was observed with missense variants in PALB2. However, two novel rare missense variants (p.L1027R and p.G1043V) produced unstable proteins and resulted in a decrease in homologous recombination-mediated repair of DNA double-strand breaks. CONCLUSION Despite genetic and lifestyle differences between Asian and other populations, the population prevalence of PALB2 PTVs and associated relative risk of breast cancer, are similar to those reported in European populations.
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Affiliation(s)
- Pei Sze Ng
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Rick Acm Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Chan Eng Chong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Milan Sharma
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Sabine Knaup
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Weang Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University of Nottingham - Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Sook-Yee Yoon
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Mee Hoong See
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Swee Ho Lim
- Breast Department, KK Women's and Children's Hospital, Singapore
- Duke-NUS Breast Centre, Singhealth, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Benita Kiat-Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore
| | - Su-Ming Tan
- Division of Breast Surgery, Changi General Hospital Department of General Surgery, Singapore
| | - Veronique Kiat-Mien Tan
- Singhealth Duke-NUS Breast Centre, Singhealth, Singapore
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Rob Martinus van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Nutrition, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Kartini Rahmat
- Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Antonis Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
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22
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Boonen RA, Vreeswijk MP, van Attikum H. CHEK2 variants: linking functional impact to cancer risk. Trends Cancer 2022; 8:759-770. [DOI: 10.1016/j.trecan.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/23/2022]
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23
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Thirumal Kumar D, Udhaya Kumar S, Jain N, Sowmya B, Balsekar K, Siva R, Kamaraj B, Sidenna M, George Priya Doss C, Zayed H. Computational structural assessment of BReast CAncer type 1 susceptibility protein (BRCA1) and BRCA1-Associated Ring Domain protein 1 (BARD1) mutations on the protein-protein interface. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:375-397. [PMID: 35534113 DOI: 10.1016/bs.apcsb.2022.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Breast cancer type 1 susceptibility protein (BRCA1) is closely related to the BRCA2 (breast cancer type 2 susceptibility protein) and BARD1 (BRCA1-associated RING domain-1) proteins. The homodimers were formed through their RING fingers; however they form more compact heterodimers preferentially, influencing BRCA1 residues 1-109 and BARD1 residues 26-119. We implemented an integrative computational pipeline to screen all the mutations in BRCA1 and identify the most significant mutations influencing the Protein-Protein Interactions (PPI) in the BRCA1-BARD1 protein complex. The amino acids involved in the PPI regions were identified from the PDBsum database with the PDB ID: 1JM7. We screened 2118 missense mutations in BRCA1 and none in BARD1 for pathogenicity and stability and analyzed the amino acid sequences for conserved residues. We identified the most significant mutations from these screenings as V11G, M18K, L22S, and T97R positioned in the PPI regions of the BRCA1-BARD1 protein complex. We further performed protein-protein docking using the ZDOCK server. The native protein-protein complex showed the highest binding score of 2118.613, and the V11G mutant protein complex showed the least binding score of 1992.949. The other three mutation protein complexes had binding scores between the native and V11G protein complexes. Finally, a molecular dynamics simulation study using GROMACS was performed to comprehend changes in the BRCA1-BARD1 complex's binding pattern due to the mutation. From the analysis, we observed the highest deviation with lowest compactness and a decrease in the intramolecular h-bonds in the BRCA1-BARD1 protein complex with the V11G mutation compared to the native complex or the complexes with other mutations.
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Affiliation(s)
- D Thirumal Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India; Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Nikita Jain
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Baviri Sowmya
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kamakshi Balsekar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - R Siva
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
| | - Mariem Sidenna
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar.
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24
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Adamovich AI, Diabate M, Banerjee T, Nagy G, Smith N, Duncan K, Mendoza Mendoza E, Prida G, Freitas MA, Starita LM, Parvin JD. The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays. Am J Hum Genet 2022; 109:618-630. [PMID: 35196514 DOI: 10.1016/j.ajhg.2022.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/26/2022] [Indexed: 11/30/2022] Open
Abstract
Pathogenic variants in BRCA1 are associated with a greatly increased risk of hereditary breast and ovarian cancer (HBOC). With the increased availability and affordability of genetic testing, many individuals have been identified with BRCA1 variants of uncertain significance (VUSs), which are individually detected in the population too infrequently to ascertain a clinical risk. Functional assays can be used to experimentally assess the effects of these variants. In this study, we used multiplexed DNA repair assays of variants in the BRCA1 carboxyl terminus to functionally characterize 2,271 variants for homology-directed repair function (HDR) and 1,427 variants for cisplatin resistance (CR). We found a high level of consistent results (Pearson's r = 0.74) in the two multiplexed functional assays with non-functional variants located within regions of the BRCA1 protein necessary for its tumor suppression activity. In addition, functional categorizations of variants tested in the multiplex HDR and CR assays correlated with known clinical significance and with other functional assays for BRCA1 (Pearson's r = 0.53 to 0.71). The results of the multiplex HDR and CR assays are useful resources for characterizing large numbers of BRCA1 VUSs.
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Affiliation(s)
- Aleksandra I Adamovich
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Mariame Diabate
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Tapahsama Banerjee
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Gregory Nagy
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Nahum Smith
- Department of Genome Sciences, University of Washington and Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Kathryn Duncan
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Erika Mendoza Mendoza
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Gisselle Prida
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington and Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jeffrey D Parvin
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA.
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25
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Bellè F, Mercatanti A, Lodovichi S, Congregati C, Guglielmi C, Tancredi M, Caligo MA, Cervelli T, Galli A. Validation and Data-Integration of Yeast-Based Assays for Functional Classification of BRCA1 Missense Variants. Int J Mol Sci 2022; 23:ijms23074049. [PMID: 35409408 PMCID: PMC8999655 DOI: 10.3390/ijms23074049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/23/2022] Open
Abstract
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory to develop new tools to evaluate their functional impact and pathogenicity. As the expression of pathogenic BRCA1 variants in Saccharomyces cerevisiae increases the frequency of intra- and inter-chromosomal homologous recombination (HR), and gene reversion (GR), we validated the two HR and the GR assays by testing 23 benign and 23 pathogenic variants and compared the results with those that were obtained in the small colony phenotype (SCP) assay, an additional yeast-based assay, that was validated previously. We demonstrated that they scored high accuracy, sensitivity, and sensibility. By using a classifier that was based on majority of voting, we have integrated data from HR, GR, and SCP assays and developed a reliable method, named yBRCA1, with high sensitivity to obtain an accurate VUS functional classification (benign or pathogenic). The classification of BRCA1 variants, important for assessing the risk of developing BOC, is often difficult to establish with genetic methods because they occur rarely in the population. This study provides a new tool to get insights on the functional impact of the BRCA1 variants.
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Affiliation(s)
- Francesca Bellè
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alberto Mercatanti
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56125 Pisa, Italy;
| | - Chiara Guglielmi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
- Correspondence: (M.A.C.); (A.G.)
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alvaro Galli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
- Correspondence: (M.A.C.); (A.G.)
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26
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Ali A, Rehman MU, Ahmad SM, Mehraj T, Hussain I, Nadeem A, Mir MUR, Ganie SA. In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene. Animals (Basel) 2022; 12:ani12060693. [PMID: 35327090 PMCID: PMC8944579 DOI: 10.3390/ani12060693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Dairy cattle with a high milk yield are susceptible to many infectious diseases, such as mastitis. Subclinical mastitis (SCM) is the most prevalent form of mastitis that predominantly affects animal health, and causes adverse effects on the quality and quantity of milk. In dairy animals, subclinical mastitis often remains undetected, as no gross changes in udder characteristics are visible. In the present study, 135 Holstein Friesian dairy animals were selected and screened as healthy (n = 25) and mastitic (n = 110) based on diagnostic tests such as the California mastitis test, pH, electrical conductivity, and somatic cell count. In this study, the somatic cell count was used as a gold-standard test in differentiating subclinical mastitis animals from healthy ones. The present study was carried out to study polymorphisms in the bovine transferrin gene in cows (with subclinical mastitis and healthy). For the early detection of resistant/or susceptible animals, a useful marker could be provided by the detection of single-nucleotide polymorphisms (SNPs) in the transferrin gene, which are often associated with mammary innate immune response. The sequencing results revealed three nucleotide substitutions: two transversions (230 A > C, 231 C > A) and one transition (294 A > G) in susceptible cows as compared to disease-free subjects. The nucleotide variations at position 230 (GAC > GCA) and 231 (GAC > GCA) were nonsynonymous, and corresponded to an amino acid change from aspartic acid to alanine; whereas at position 294 (GAA > GAG), the mutation was synonymous. In the present study, many in silico tools were taken into consideration to determine the effect of SNPs on protein structure and function. The PROVEAN tool found the amino acid substitution to be neutral and deleterious. PolyPhen-2 revealed the amino acid variations at positions 320 and 321 to most likely be damaging; and at the 341 position, the variations were benign. The I-Mutant and MUpro tools found that the protein stability decreased for nonsynonymous variations. The SIFT tool revealed the protein function was likely to be affected in nonsynonymous variations, with no change in the case of synonymous ones. Phylogenetic analysis of the bovine transferrin gene revealed a close relation of the CA allele with the Bos taurus transferrin, while the G allele was closely related to a cross of Bos indicus × Bos taurus serotransferrins, followed by the Bison bison transferrin. The least relation was shown by both alleles to Capra hircus, Ovis aries, and Bubalus bubalis.
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Affiliation(s)
- Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India;
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Muneeb U. Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (M.U.R.); (S.A.G.)
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India;
| | - Tabish Mehraj
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA;
| | - Ishraq Hussain
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Ahmed Nadeem
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Manzoor Ur Rahman Mir
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India;
- Correspondence: (M.U.R.); (S.A.G.)
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Endo S, Yoshino Y, Shirota M, Watanabe G, Chiba N. BRCA1/ATF1-Mediated Transactivation is Involved in Resistance to PARP Inhibitors and Cisplatin. CANCER RESEARCH COMMUNICATIONS 2021; 1:90-105. [PMID: 36860287 PMCID: PMC9973406 DOI: 10.1158/2767-9764.crc-21-0064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR)-deficient cells are sensitive to PARP inhibitors through a synthetic lethal effect. We previously developed an HR activity assay named Assay of Site-Specific HR Activity (ASHRA). Here, we evaluated the HR activity of 30 missense variants of BRCA1 by ASHRA and found that several BRCA1 variants showed intermediate HR activity, which was not clearly discerned by our previous analyses using a conventional method. HR activity measured by ASHRA was significantly correlated with sensitivity to olaparib. However, cells expressing the severely HR-deficient BRCA1-C61G variant were resistant to olaparib, and resistance was dependent on high expression of activating transcription factor 1 (ATF1), which binds to BRCA1 and activates the transcription of target genes to regulate cell proliferation. The BRCA1-C61G variant bound to ATF1 and stimulated ATF1-mediated transactivation similar to wild-type BRCA1. High expression of ATF1 conferred resistance to olaparib and cisplatin activating BRCA1/ATF1-mediated transcription without affecting HR activity in BRCA2-knockdown or RAD51-knockdown cells, but not in BRCA1-knockdown cells. These results suggest that ASHRA is a useful method to evaluate HR activity in cells and to predict the sensitivity to PARP inhibitors. The expression level of ATF1 might be an important biomarker of the effect of PARP inhibitors and platinum agents on HR-deficient tumors with the BRCA1-C61G variant or alteration of non-BRCA1 HR factors such as BRCA2 and RAD51. Significance ASHRA could evaluate HR activity in cells and predict the sensitivity to PARP inhibitors. High expression level of ATF1 may predict the resistance of BRCAness tumors with alterations of non-BRCA1 HR factors to PARP inhibitors and platinum agents.
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Affiliation(s)
- Shino Endo
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, Sendai, Japan
- Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuki Yoshino
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, Sendai, Japan
- Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Science, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Gou Watanabe
- Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Natsuko Chiba
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, Sendai, Japan
- Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Tam B, Sinha S, Qin Z, Wang SM. Comprehensive Identification of Deleterious TP53 Missense VUS Variants Based on Their Impact on TP53 Structural Stability. Int J Mol Sci 2021; 22:11345. [PMID: 34768775 PMCID: PMC8583684 DOI: 10.3390/ijms222111345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
TP53 plays critical roles in maintaining genome stability. Deleterious genetic variants damage the function of TP53, causing genome instability and increased cancer risk. Of the large quantity of genetic variants identified in TP53, however, many remain functionally unclassified as variants of unknown significance (VUS) due to the lack of evidence. This is reflected by the presence of 749 (42%) VUS of the 1785 germline variants collected in the ClinVar database. In this study, we addressed the deleteriousness of TP53 missense VUS. Utilizing the protein structure-based Ramachandran Plot-Molecular Dynamics Simulation (RPMDS) method that we developed, we measured the effects of missense VUS on TP53 structural stability. Of the 340 missense VUS tested, we observed deleterious evidence for 193 VUS, as reflected by the TP53 structural changes caused by the VUS-substituted residues. We compared the results from RPMDS with those from other in silico methods and observed higher specificity of RPMDS in classification of TP53 missense VUS than these methods. Data from our current study address a long-standing challenge in classifying the missense VUS in TP53, one of the most important tumor suppressor genes.
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Affiliation(s)
| | | | | | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; (B.T.); (S.S.); (Z.Q.)
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29
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Findlay GM. Linking genome variants to disease: scalable approaches to test the functional impact of human mutations. Hum Mol Genet 2021; 30:R187-R197. [PMID: 34338757 PMCID: PMC8490018 DOI: 10.1093/hmg/ddab219] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
The application of genomics to medicine has accelerated the discovery of mutations underlying disease and has enhanced our knowledge of the molecular underpinnings of diverse pathologies. As the amount of human genetic material queried via sequencing has grown exponentially in recent years, so too has the number of rare variants observed. Despite progress, our ability to distinguish which rare variants have clinical significance remains limited. Over the last decade, however, powerful experimental approaches have emerged to characterize variant effects orders of magnitude faster than before. Fueled by improved DNA synthesis and sequencing and, more recently, by CRISPR/Cas9 genome editing, multiplex functional assays provide a means of generating variant effect data in wide-ranging experimental systems. Here, I review recent applications of multiplex assays that link human variants to disease phenotypes and I describe emerging strategies that will enhance their clinical utility in coming years.
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Affiliation(s)
- Gregory M Findlay
- The Francis Crick Institute, The Genome Function Laboratory, London NW1 1AT, UK
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30
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The BRCA1/BARD1 ubiquitin ligase and its substrates. Biochem J 2021; 478:3467-3483. [PMID: 34591954 DOI: 10.1042/bcj20200864] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/19/2022]
Abstract
Mutations in breast cancer type 1 susceptibility protein (BRCA1) and its heterodimeric binding partner BARD1 confer a high risk for the development of breast and ovarian cancers. The sole enzymatic function of the BRCA1/BARD1 complex is as a RING-type E3 ubiquitin (Ub) ligase, leading to the deposition of Ub signals onto a variety of substrate proteins. Distinct types of Ub signals deposited by BRCA1/BARD1 (i.e. degradative vs. non-degradative; mono-Ub vs. poly-Ub chains) on substrate proteins mediate aspects of its function in DNA double-stranded break repair, cell-cycle regulation, and transcriptional regulation. While cancer-predisposing mutations in both subunits lead to the inactivation of BRCA1/BARD1 ligase activity, controversy remains as to whether its Ub ligase activity directly inhibits tumorigenesis. Investigation of BRCA1/BARD1 substrates using rigorous, well-validated mutants and experimental systems will ultimately clarify the role of its ligase activity in cancer and possibly establish prognostic and diagnostic metrics for patients with mutations. In this review, we discuss the Ub ligase function of BRCA1/BARD1, highlighting experimental approaches, mechanistic considerations, and reagents that are useful in the study of substrate ubiquitylation. We also discuss the current understanding of two well-established BRCA1/BARD1 substrates (nucleosomal H2A and estrogen receptor α) and several recently discovered substrates (p50, NF2, Oct1, and LARP7). Lessons from the current body of work should provide a road map to researchers examining novel substrates and biological functions attributed to BRCA1/BARD1 Ub ligase activity.
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A complex of BRCA2 and PP2A-B56 is required for DNA repair by homologous recombination. Nat Commun 2021; 12:5748. [PMID: 34593815 PMCID: PMC8484605 DOI: 10.1038/s41467-021-26079-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Mutations in the tumour suppressor gene BRCA2 are associated with predisposition to breast and ovarian cancers. BRCA2 has a central role in maintaining genome integrity by facilitating the repair of toxic DNA double-strand breaks (DSBs) by homologous recombination (HR). BRCA2 acts by controlling RAD51 nucleoprotein filament formation on resected single-stranded DNA, but how BRCA2 activity is regulated during HR is not fully understood. Here, we delineate a pathway where ATM and ATR kinases phosphorylate a highly conserved region in BRCA2 in response to DSBs. These phosphorylations stimulate the binding of the protein phosphatase PP2A-B56 to BRCA2 through a conserved binding motif. We show that the phosphorylation-dependent formation of the BRCA2-PP2A-B56 complex is required for efficient RAD51 filament formation at sites of DNA damage and HR-mediated DNA repair. Moreover, we find that several cancer-associated mutations in BRCA2 deregulate the BRCA2-PP2A-B56 interaction and sensitize cells to PARP inhibition. Collectively, our work uncovers PP2A-B56 as a positive regulator of BRCA2 function in HR with clinical implications for BRCA2 and PP2A-B56 mutated cancers.
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32
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Pulver EM, Mukherjee C, van de Kamp G, Roobol SJ, Rother MB, van der Gulden H, de Bruijn R, Lattanzio MV, van der Burg E, Drenth AP, Verkaik NS, Hahn K, Klarenbeek S, de Korte-Grimmerink R, van de Ven M, Pritchard CEJ, Huijbers IJ, Xia B, van Gent DC, Essers J, van Attikum H, Ray Chaudhuri A, Bouwman P, Jonkers J. A BRCA1 coiled-coil domain variant disrupting PALB2 interaction promotes the development of mammary tumors and confers a targetable defect in homologous recombination repair. Cancer Res 2021; 81:6171-6182. [PMID: 34548335 PMCID: PMC7612117 DOI: 10.1158/0008-5472.can-21-1415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/21/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022]
Abstract
The BRCA1 tumor suppressor gene encodes a multi-domain protein for which several functions have been described. These include a key role in homologous recombination repair (HRR) of DNA double-strand breaks (DSB), which is shared with two other high-risk hereditary breast cancer suppressors, BRCA2 and PALB2. Although both BRCA1 and BRCA2 interact with PALB2, BRCA1 missense variants affecting its PALB2-interacting coiled-coil domain are considered variants of uncertain clinical significance (VUS). Using genetically engineered mice, we show here that a BRCA1 coiled-coil domain VUS, Brca1 p.L1363P, disrupts the interaction with PALB2 and leads to embryonic lethality. Brca1 p.L1363P led to a similar acceleration in the development of Trp53-deficient mammary tumors as Brca1 loss, but the tumors showed distinct histopathological features, with more stable DNA copy number profiles in Brca1 p.L1363P tumors. Nevertheless, Brca1 p.L1363P mammary tumors were HRR-incompetent and responsive to cisplatin and PARP inhibition. Overall, these results provide the first direct evidence that a BRCA1 missense variant outside of the RING and BRCT domains increases the risk of breast cancer.
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Affiliation(s)
- Emilia M Pulver
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute
| | | | | | - Stefan J Roobol
- Molecular Genetics, Radiology and Nuclear Medicine, Erasmus MC
| | | | - Hanneke van der Gulden
- Division of Molecular Pathology and Cancer Genomics Centre, The Netherlands Cancer Institute
| | - Roebi de Bruijn
- Division of Molecular Pathology, The Netherlands Cancer Institute
| | | | | | | | | | - Kerstin Hahn
- Molecular Pathology, Oncode Institute-Netherlands Cancer Institute
| | | | - Renske de Korte-Grimmerink
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute
| | | | - Ivo J Huijbers
- Transgenic core facility, Mouse Clinic for Cancer and Aging (MCCA), The Netherlands Cancer Institute
| | - Bing Xia
- Radiation Oncology, Rutgers Cancer Institute of New Jersey
| | - Dik C van Gent
- Molecular Genetics, Erasmus MC University Medical Center Rotterdam and Oncode Institute, The Netherlands
| | | | | | | | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute
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Geck RC, Boyle G, Amorosi CJ, Fowler DM, Dunham MJ. Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Annu Rev Pharmacol Toxicol 2021; 62:531-550. [PMID: 34516287 DOI: 10.1146/annurev-pharmtox-032221-085807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes (ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Gabriel Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; , .,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
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34
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Frederiksen JH, Jensen SB, Tümer Z, Hansen TVO. Classification of MSH6 Variants of Uncertain Significance Using Functional Assays. Int J Mol Sci 2021; 22:ijms22168627. [PMID: 34445333 PMCID: PMC8395337 DOI: 10.3390/ijms22168627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022] Open
Abstract
Lynch syndrome (LS) is one of the most common hereditary cancer predisposition syndromes worldwide. Individuals with LS have a high risk of developing colorectal or endometrial cancer, as well as several other cancers. LS is caused by autosomal dominant pathogenic variants in one of the DNA mismatch repair (MMR) genes MLH1, MSH2, PMS2 or MSH6, and typically include truncating variants, such as frameshift, nonsense or splicing variants. However, a significant number of missense, intronic, or silent variants, or small in-frame insertions/deletions, are detected during genetic screening of the MMR genes. The clinical effects of these variants are often more difficult to predict, and a large fraction of these variants are classified as variants of uncertain significance (VUS). It is pivotal for the clinical management of LS patients to have a clear genetic diagnosis, since patients benefit widely from screening, preventive and personal therapeutic measures. Moreover, in families where a pathogenic variant is identified, testing can be offered to family members, where non-carriers can be spared frequent surveillance, while carriers can be included in cancer surveillance programs. It is therefore important to reclassify VUSs, and, in this regard, functional assays can provide insight into the effect of a variant on the protein or mRNA level. Here, we briefly describe the disorders that are related to MMR deficiency, as well as the structure and function of MSH6. Moreover, we review the functional assays that are used to examine VUS identified in MSH6 and discuss the results obtained in relation to the ACMG/AMP PS3/BS3 criterion. We also provide a compiled list of the MSH6 variants examined by these assays. Finally, we provide a future perspective on high-throughput functional analyses with specific emphasis on the MMR genes.
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Affiliation(s)
- Jane H. Frederiksen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
- Correspondence: (J.H.F.); (T.v.O.H.)
| | - Sara B. Jensen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
| | - Zeynep Tümer
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Thomas v. O. Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark; (S.B.J.); (Z.T.)
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
- Correspondence: (J.H.F.); (T.v.O.H.)
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35
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Hosoya N, Miyagawa K. Implications of the germline variants of DNA damage response genes detected by cancer precision medicine for radiological risk communication and cancer therapy decisions. JOURNAL OF RADIATION RESEARCH 2021; 62:i44-i52. [PMID: 33978181 PMCID: PMC8114223 DOI: 10.1093/jrr/rrab009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/22/2021] [Indexed: 05/08/2023]
Abstract
Large-scale cancer-associated gene testing is now being rapidly incorporated into clinical settings, and is leading to incidental identification of the germline variants present in cancer patients. Because many cancer susceptibility genes are related to DNA damage response and repair, the variants may reflect not only the susceptibility to cancer but also the genetically defined radiation sensitivity of the patients and their relatives. When the presence of a certain germline variant increases the risk for developing radiation toxicity or radiation-induced secondary cancers, it will greatly influence the clinical decision-making. In order to achieve optimal radiological risk communication and to select the best cancer management for a given patient based on information from gene testing, healthcare professionals including genetic counselors, risk communicators and clinicians need to increase their knowledge of the health effects of various genetic variants. While germline loss-of-function mutations in both of the alleles of the DNA damage response genes cause rare hereditary diseases characterized by extreme hypersensitivity to radiation, the health effects of the carriers who have germline variants in one allele of such genes would be a matter of debate, especially when the significance of the variants is currently unknown. In this review, we describe the clinical significance of the genetic variants of the important DNA damage response genes, including ATM and TP53, and discuss how we can apply current knowledge to the management of cancer patients and their relatives from a radiological point of view.
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Affiliation(s)
- Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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36
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Yoshino Y, Fang Z, Qi H, Kobayashi A, Chiba N. Dysregulation of the centrosome induced by BRCA1 deficiency contributes to tissue-specific carcinogenesis. Cancer Sci 2021; 112:1679-1687. [PMID: 33606355 PMCID: PMC8088922 DOI: 10.1111/cas.14859] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Alterations in breast cancer gene 1 (BRCA1), a tumor suppressor gene, increase the risk of breast and ovarian cancers. BRCA1 forms a heterodimer with BRCA1-associated RING domain protein 1 (BARD1) and functions in multiple cellular processes, including DNA repair and centrosome regulation. BRCA1 acts as a tumor suppressor by promoting homologous recombination (HR) repair, and alterations in BRCA1 cause HR deficiency, not only in breast and ovarian tissues but also in other tissues. The molecular mechanisms underlying BRCA1 alteration-induced carcinogenesis remain unclear. Centrosomes are the major microtubule-organizing centers and function in bipolar spindle formation. The regulation of centrosome number is critical for chromosome segregation in mitosis, which maintains genomic stability. BRCA1/BARD1 function in centrosome regulation together with Obg-like ATPase (OLA1) and receptor for activating protein C kinase 1 (RACK1). Cancer-derived variants of BRCA1, BARD1, OLA1, and RACK1 do not interact, and aberrant expression of these proteins results in abnormal centrosome duplication in mammary-derived cells, and rarely in other cell types. RACK1 is involved in centriole duplication in the S phase by promoting polo-like kinase 1 activation by Aurora A, which is critical for centrosome duplication. Centriole number is higher in cells derived from mammary tissues compared with in those derived from other tissues, suggesting that tissue-specific centrosome characterization may shed light on the tissue specificity of BRCA1-associated carcinogenesis. Here, we explored the role of the BRCA1-containing complex in centrosome regulation and the effect of its deficiency on tissue-specific carcinogenesis.
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Affiliation(s)
- Yuki Yoshino
- Department of Cancer BiologyInstitute of Aging, Development, and CancerTohoku UniversitySendaiJapan
- Laboratory of Cancer BiologyGraduate School of Life SciencesTohoku UniversitySendaiJapan
- Department of Cancer BiologyTohoku University Graduate School of MedicineSendaiJapan
| | - Zhenzhou Fang
- Department of Cancer BiologyInstitute of Aging, Development, and CancerTohoku UniversitySendaiJapan
- Department of Cancer BiologyTohoku University Graduate School of MedicineSendaiJapan
| | - Huicheng Qi
- Department of Cancer BiologyInstitute of Aging, Development, and CancerTohoku UniversitySendaiJapan
- Department of Cancer BiologyTohoku University Graduate School of MedicineSendaiJapan
| | - Akihiro Kobayashi
- Department of Cancer BiologyInstitute of Aging, Development, and CancerTohoku UniversitySendaiJapan
- Department of Cancer BiologyTohoku University Graduate School of MedicineSendaiJapan
| | - Natsuko Chiba
- Department of Cancer BiologyInstitute of Aging, Development, and CancerTohoku UniversitySendaiJapan
- Laboratory of Cancer BiologyGraduate School of Life SciencesTohoku UniversitySendaiJapan
- Department of Cancer BiologyTohoku University Graduate School of MedicineSendaiJapan
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37
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Kuang D, Truty R, Weile J, Johnson B, Nykamp K, Araya C, Nussbaum RL, Roth FP. Prioritizing genes for systematic variant effect mapping. Bioinformatics 2021; 36:5448-5455. [PMID: 33300982 PMCID: PMC8016487 DOI: 10.1093/bioinformatics/btaa1008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION When rare missense variants are clinically interpreted as to their pathogenicity, most are classified as variants of uncertain significance (VUS). Although functional assays can provide strong evidence for variant classification, such results are generally unavailable. Multiplexed assays of variant effect can generate experimental 'variant effect maps' that score nearly all possible missense variants in selected protein targets for their impact on protein function. However, these efforts have not always prioritized proteins for which variant effect maps would have the greatest impact on clinical variant interpretation. RESULTS Here, we mined databases of clinically interpreted variants and applied three strategies, each building on the previous, to prioritize genes for systematic functional testing of missense variation. The strategies ranked genes (i) by the number of unique missense VUS that had been reported to ClinVar; (ii) by movability- and reappearance-weighted impact scores, to give extra weight to reappearing, movable VUS and (iii) by difficulty-adjusted impact scores, to account for the more resource-intensive nature of generating variant effect maps for longer genes. Our results could be used to guide systematic functional testing of missense variation toward greater impact on clinical variant interpretation. AVAILABILITY AND IMPLEMENTATION Source code available at: https://github.com/rothlab/mave-gene-prioritization. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Da Kuang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | | | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | | | - Keith Nykamp
- Invitae Corporation, San Francisco, CA 94103, USA
| | - Carlos Araya
- Invitae Corporation, San Francisco, CA 94103, USA
| | | | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
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38
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Huang C, Li G, Wu J, Liang J, Wang X. Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction. Genome Biol 2021; 22:80. [PMID: 33691754 PMCID: PMC7945310 DOI: 10.1186/s13059-021-02305-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/24/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Millions of nucleotide variants are identified through cancer genome sequencing and it is clinically important to identify the pathogenic variants among them. By introducing base substitutions at guide RNA target regions in the genome, CRISPR-Cas9-based base editors provide the possibility for evaluating a large number of variants in their genomic context. However, the variability in editing efficiency and the complexity of outcome mapping are two existing problems for assigning guide RNA effects to variants in base editing screens. RESULTS To improve the identification of pathogenic variants, we develop a framework to combine base editing screens with sgRNA efficiency and outcome mapping. We apply the method to evaluate more than 9000 variants across all the exons of BRCA1 and BRCA2 genes. Our efficiency-corrected scoring model identifies 910 loss-of-function variants for BRCA1/2, including 151 variants in the noncoding part of the genes such as the 5' untranslated regions. Many of them are identified in cancer patients and are reported as "benign/likely benign" or "variants of uncertain significance" by clinicians. Our data suggest a need to re-evaluate their clinical significance, which may be helpful for risk assessment and treatment of breast and ovarian cancer. CONCLUSIONS Our results suggest that base editing screens with efficiency correction is a powerful strategy to identify pathogenic variants in a high-throughput manner. Applying this strategy to assess variants in both coding and noncoding regions of the genome could have a direct impact on the interpretation of cancer variants.
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Affiliation(s)
- Changcai Huang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Guangyu Li
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jiayu Wu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Junbo Liang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
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39
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Abeykoon JP, Wu X, Nowakowski KE, Dasari S, Paludo J, Weroha SJ, Hu C, Hou X, Sarkaria JN, Mladek AC, Phillips JL, Feldman AL, Ravindran A, King RL, Boysen J, Stenson MJ, Carr RM, Manske MK, Molina JR, Kapoor P, Parikh SA, Kumar S, Robinson SI, Yu J, Boughey JC, Wang L, Goetz MP, Couch FJ, Patnaik MM, Witzig TE. Salicylates enhance CRM1 inhibitor antitumor activity by induction of S-phase arrest and impairment of DNA-damage repair. Blood 2021; 137:513-523. [PMID: 33507295 PMCID: PMC7845010 DOI: 10.1182/blood.2020009013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/30/2020] [Indexed: 01/10/2023] Open
Abstract
Chromosome region maintenance protein 1 (CRM1) mediates protein export from the nucleus and is a new target for anticancer therapeutics. Broader application of KPT-330 (selinexor), a first-in-class CRM1 inhibitor recently approved for relapsed multiple myeloma and diffuse large B-cell lymphoma, have been limited by substantial toxicity. We discovered that salicylates markedly enhance the antitumor activity of CRM1 inhibitors by extending the mechanisms of action beyond CRM1 inhibition. Using salicylates in combination enables targeting of a range of blood cancers with a much lower dose of selinexor, thereby potentially mitigating prohibitive clinical adverse effects. Choline salicylate (CS) with low-dose KPT-330 (K+CS) had potent, broad activity across high-risk hematological malignancies and solid-organ cancers ex vivo and in vivo. The K+CS combination was not toxic to nonmalignant cells as compared with malignant cells and was safe without inducing toxicity to normal organs in mice. Mechanistically, compared with KPT-330 alone, K+CS suppresses the expression of CRM1, Rad51, and thymidylate synthase proteins, leading to more efficient inhibition of CRM1-mediated nuclear export, impairment of DNA-damage repair, reduced pyrimidine synthesis, cell-cycle arrest in S-phase, and cell apoptosis. Moreover, the addition of poly (ADP-ribose) polymerase inhibitors further potentiates the K+CS antitumor effect. K+CS represents a new class of therapy for multiple types of blood cancers and will stimulate future investigations to exploit DNA-damage repair and nucleocytoplasmic transport for cancer therapy in general.
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MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Cell Cycle Checkpoints/drug effects
- Choline/administration & dosage
- Choline/adverse effects
- Choline/analogs & derivatives
- Choline/pharmacology
- DNA Repair/drug effects
- DNA Replication/drug effects
- DNA, Neoplasm/drug effects
- Drug Combinations
- Drug Synergism
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Hydrazines/administration & dosage
- Hydrazines/adverse effects
- Hydrazines/pharmacology
- Karyopherins/antagonists & inhibitors
- Lymphoma, Mantle-Cell/drug therapy
- Lymphoma, Mantle-Cell/pathology
- Lymphoma, Non-Hodgkin/drug therapy
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/pathology
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Phthalazines/administration & dosage
- Phthalazines/pharmacology
- Piperazines/administration & dosage
- Piperazines/pharmacology
- Random Allocation
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- S Phase Cell Cycle Checkpoints/drug effects
- Salicylates/administration & dosage
- Salicylates/adverse effects
- Salicylates/pharmacology
- Triazoles/administration & dosage
- Triazoles/adverse effects
- Triazoles/pharmacology
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
- Exportin 1 Protein
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Affiliation(s)
| | - Xiaosheng Wu
- Division of Hematology, Department of Internal Medicine
| | | | | | - Jonas Paludo
- Division of Hematology, Department of Internal Medicine
| | | | - Chunling Hu
- Department of Laboratory Medicine and Pathology
| | | | | | | | | | | | - Aishwarya Ravindran
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, and
| | - Rebecca L King
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, and
| | - Justin Boysen
- Division of Hematology, Department of Internal Medicine
| | | | | | | | | | | | | | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine
| | | | | | | | | | | | - Fergus J Couch
- Department of Health Sciences Research
- Department of Laboratory Medicine and Pathology
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40
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Li K, Zhong Y, Lin X, Quan Z. Predicting the Disease Risk of Protein Mutation Sequences With Pre-training Model. Front Genet 2020; 11:605620. [PMID: 33408741 PMCID: PMC7780924 DOI: 10.3389/fgene.2020.605620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/11/2020] [Indexed: 12/05/2022] Open
Abstract
Accurately identifying the missense mutations is of great help to alleviate the loss of protein function and structural changes, which might greatly reduce the risk of disease for tumor suppressor genes (e.g., BRCA1 and PTEN). In this paper, we propose a hybrid framework, called BertVS, that predicts the disease risk for the missense mutation of proteins. Our framework is able to learn sequence representations from the protein domain through pre-training BERT models, and also integrates with the hydrophilic properties of amino acids to obtain the sequence representations of biochemical characteristics. The concatenation of two learned representations are then sent to the classifier to predict the missense mutations of protein sequences. Specifically, we use the protein family database (Pfam) as a corpus to train the BERT model to learn the contextual information of protein sequences, and our pre-training BERT model achieves a value of 0.984 on accuracy in the masked language model prediction task. We conduct extensive experiments on BRCA1 and PTEN datasets. With comparison to the baselines, results show that BertVS achieves higher performance of 0.920 on AUROC and 0.915 on AUPR in the functionally critical domain of the BRCA1 gene. Additionally, the extended experiment on the ClinVar dataset can illustrate that gene variants with known clinical significance can also be efficiently classified by our method. Therefore, BertVS can learn the functional information of the protein sequences and effectively predict the disease risk of variants with an uncertain clinical significance.
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Affiliation(s)
- Kuan Li
- School of Cyberspace Security, Dongguan University of Technology, Guangdong, China
- Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen, China
| | - Yue Zhong
- Department of Computer Science, Xiamen University, Xiamen, China
| | - Xuan Lin
- College of Information Science and Engineering, Hunan University, Changsha, China
| | - Zhe Quan
- College of Information Science and Engineering, Hunan University, Changsha, China
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41
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Zhang Y, Park JY, Zhang F, Olson SH, Orlow I, Li Y, Kurtz RC, Ladanyi M, Chen J, Toland AE, Zhang L, Andreassen PR. The p.Ser64Leu and p.Pro104Leu missense variants of PALB2 identified in familial pancreatic cancer patients compromise the DNA damage response. Hum Mutat 2020; 42:150-163. [PMID: 33169439 DOI: 10.1002/humu.24133] [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: 04/25/2020] [Revised: 09/17/2020] [Accepted: 11/01/2020] [Indexed: 11/12/2022]
Abstract
PALB2 has been identified as a breast and pancreatic cancer susceptibility gene. Utilizing a targeted sequencing approach, we discovered two novel germline missense PALB2 variants c.191C>T and c.311C>T, encoding p.Ser64Leu and p.Pro104Leu, respectively, in individuals in a pancreatic cancer registry. No missense PALB2 variants from familial pancreatic cancer patients, and few PALB2 variants overall, have been functionally characterized. Given the known role of PALB2, we tested the impact of p.Ser64Leu and p.Pro104Leu variants on DNA damage responses. Neither p.Ser64Leu nor p.Pro104Leu have clear effects on interactions with BRCA1 and KEAP1, which are mediated by adjacent motifs in PALB2. However, both variants are associated with defective recruitment of PALB2, and the RAD51 recombinase downstream, to DNA damage foci. Furthermore, p.Ser64Leu and p.Pro104Leu both largely compromise DNA double-strand break-initiated homologous recombination, and confer increased cellular sensitivity to ionizing radiation (IR) and the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib. Taken together, our results represent the first demonstration of functionally deleterious PALB2 missense variants associated with familial pancreatic cancer and of deleterious variants in the N-terminus outside of the coiled-coil domain. Furthermore, our results suggest the possibility of personalized treatments, using IR or PARP inhibitor, of pancreatic and other cancers that carry a deleterious PALB2 variant.
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Affiliation(s)
- Yue Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Jung-Young Park
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jie Chen
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.,Division of Human Genetics, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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42
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Pauly R, Ziats CA, Abenavoli L, Schwartz CE, Boccuto L. New Strategies for Clinical Trials in Autism Spectrum Disorder. Rev Recent Clin Trials 2020; 16:131-137. [PMID: 33222679 DOI: 10.2174/1574887115666201120093634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/10/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex neurodevelopmental condition that poses several challenges in terms of clinical diagnosis and investigation of molecular etiology. The lack of knowledge on the pathogenic mechanisms underlying ASD has hampered the clinical trials that so far have tried to target ASD behavioral symptoms. In order to improve our understanding of the molecular abnormalities associated with ASD, a deeper and more extensive genetic profiling of targeted individuals with ASD was needed. METHODS The recent availability of new and more powerful sequencing technologies (third-generation sequencing) has allowed to develop novel strategies for the characterization of comprehensive genetic profiles of individuals with ASD. In particular, this review will describe integrated approaches based on the combination of various omics technologies that will lead to a better stratification of targeted cohorts for the design of clinical trials in ASD. RESULTS In order to analyze the big data collected by assays such as the whole genome, epigenome, transcriptome, and proteome, it is critical to develop an efficient computational infrastructure. Machine learning models are instrumental to identify non-linear relationships between the omics technologies and, therefore, establish a functional informative network among the different data sources. CONCLUSION The potential advantage provided by these new integrated omics-based strategies is better characterization of the genetic background of ASD cohorts, to identify novel molecular targets for drug development, and ultimately offer a more personalized approach in the design of clinical trials for ASD.
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Affiliation(s)
- Rini Pauly
- Greenwood Genetic Center, Greenwood, SC, United States
| | | | - Ludovico Abenavoli
- Department of Health Sciences, University "Magna Graecia", Catanzaro, Italy
| | | | - Luigi Boccuto
- Greenwood Genetic Center, Greenwood, SC, United States
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43
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Groopman EE, Povysil G, Goldstein DB, Gharavi AG. Rare genetic causes of complex kidney and urological diseases. Nat Rev Nephrol 2020; 16:641-656. [PMID: 32807983 PMCID: PMC7772719 DOI: 10.1038/s41581-020-0325-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/08/2023]
Abstract
Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York, NY, USA.
- Center for Precision Medicine and Genomics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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44
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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45
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Lyra PCM, Nepomuceno TC, de Souza MLM, Machado GF, Veloso MF, Henriques TB, Dos Santos DZ, Ribeiro IG, Ribeiro RS, Rangel LBA, Richardson M, Iversen ES, Goldgar D, Couch FJ, Carvalho MA, Monteiro ANA. Integration of functional assay data results provides strong evidence for classification of hundreds of BRCA1 variants of uncertain significance. Genet Med 2020; 23:306-315. [PMID: 33087888 PMCID: PMC7862071 DOI: 10.1038/s41436-020-00991-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose BRCA1 pathogenic variant heterozygotes are at a substantially increased risk for breast and ovarian cancer. The widespread uptake of testing has led to a significant increase in the detection of missense variants in BRCA1, the vast majority of which are variants of uncertain clinical significance (VUS), posing a challenge to genetic counseling. Here, we harness a wealth of functional data for thousands of variants to aid in variant classification. Methods We have collected, curated, and harmonized functional data for 2701 missense variants representing 24.5% of possible missense variants in BRCA1. Results were harmonized across studies by converting data into binary categorical variables (functional impact versus no functional impact). Using a panel of reference variants we identified a subset of assays with high sensitivity and specificity (≥80%) and apply the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines to assign evidence criteria for classification. Results Integration of data from validated assays provided ACMG/AMP evidence criteria in favor of pathogenicity for 297 variants or against pathogenicity for 2058 representing 96.2% of current VUS functionally assessed. We also explore discordant results and identify limitations in the approach. Conclusion High quality functional data are available for BRCA1 missense variants and provide evidence for classification of 2355 VUS according to their pathogenicity.
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Affiliation(s)
- Paulo C M Lyra
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Thales C Nepomuceno
- Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil.,Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Marcele L M de Souza
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Géssica F Machado
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Mariana F Veloso
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Taciane B Henriques
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Diandra Z Dos Santos
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Iuly G Ribeiro
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Roberto S Ribeiro
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Leticia B A Rangel
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil
| | | | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - David Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Marcelo A Carvalho
- Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil.,Instituto Federal do Rio de Janeiro-IFRJ, Rio de Janeiro, Brazil
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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46
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Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. eLife 2020; 9:54895. [PMID: 33084570 PMCID: PMC7707821 DOI: 10.7554/elife.54895] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
The >800 human G protein–coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we identify residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - A J Venkatakrishnan
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Alex M Tseng
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Daniel Cancilla
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Megan Satyadi
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ron O Dror
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
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47
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Yazar M, Özbek P. In Silico Tools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:23-37. [PMID: 33058752 DOI: 10.1089/omi.2020.0141] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are single-base variants that contribute to human biological variation and pathogenesis of many human diseases. Among all SNP types, nonsynonymous single-nucleotide polymorphisms (nsSNPs) can alter many structural, biochemical, and functional features of a protein such as folding characteristics, charge distribution, stability, dynamics, and interactions with other proteins/nucleotides. These modifications in the protein structure can lead nsSNPs to be closely associated with many multifactorial diseases such as cancer, diabetes, and neurodegenerative diseases. Predicting structural and functional effects of nsSNPs with experimental approaches can be time-consuming and costly; hence, computational prediction tools and algorithms are being widely and increasingly utilized in biology and medical research. This expert review examines the in silico tools and algorithms for the prediction of functional or structural effects of SNP variants, in addition to the description of the phenotypic effects of nsSNPs on protein structure, association between pathogenicity of variants, and functional or structural features of disease-associated variants. Finally, case studies investigating the functional and structural effects of nsSNPs on selected protein structures are highlighted. We conclude that creating a consistent workflow with a combination of in silico approaches or tools should be considered to increase the performance, accuracy, and precision of the biological and clinical predictions made in silico.
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Affiliation(s)
- Metin Yazar
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey.,Department of Genetics and Bioengineering, Istanbul Okan University, Tuzla, Istanbul, Turkey
| | - Pemra Özbek
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey
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48
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Boonen RACM, Vreeswijk MPG, van Attikum H. Functional Characterization of PALB2 Variants of Uncertain Significance: Toward Cancer Risk and Therapy Response Prediction. Front Mol Biosci 2020; 7:169. [PMID: 33195396 PMCID: PMC7525363 DOI: 10.3389/fmolb.2020.00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years it has become clear that pathogenic variants in PALB2 are associated with a high risk for breast, ovarian and pancreatic cancer. However, the clinical relevance of variants of uncertain significance (VUS) in PALB2, which are increasingly identified through clinical genetic testing, is unclear. Here we review recent advances in the functional characterization of VUS in PALB2. A combination of assays has been used to assess the impact of PALB2 VUS on its function in DNA repair by homologous recombination, cell cycle regulation and the control of cellular levels of reactive oxygen species (ROS). We discuss the outcome of this comprehensive analysis of PALB2 VUS, which showed that VUS in PALB2’s Coiled-Coil (CC) domain can impair the interaction with BRCA1, whereas VUS in its WD40 domain affect PALB2 protein stability. Accordingly, the CC and WD40 domains of PALB2 represent hotspots for variants that impair PALB2 protein function. We also provide a future perspective on the high-throughput analysis of VUS in PALB2, as well as the functional characterization of variants that affect PALB2 RNA splicing. Finally, we discuss how results from these functional assays can be valuable for predicting cancer risk and responsiveness to cancer therapy, such as treatment with PARP inhibitor- or platinum-based chemotherapy.
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Affiliation(s)
- Rick A C M Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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49
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Masso M, Bansal A, Bansal A, Henderson A. Structure-based functional analysis of BRCA1 RING domain variants: Concordance of computational mutagenesis, experimental assay, and clinical data. Biophys Chem 2020; 266:106442. [PMID: 32916545 DOI: 10.1016/j.bpc.2020.106442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 07/26/2020] [Indexed: 01/16/2023]
Abstract
A significant impediment to the improvement of clinical outcomes in treating breast and ovarian cancers rests with the lack of available interpretations for BRCA1 variants of unknown significance. Two research groups recently implemented large-scale functional assays for quantifying effects of single missense mutations on homology-directed DNA repair activity of BRCA1 variants, which is critical for tumor suppression and strongly correlates with cancer risk, and their results are significantly concordant with each other as well as with known pathogenic and benign variant clinical data. In this work, we implemented an established computational mutagenesis procedure to characterize structural impacts of single residue replacements to the BRCA1 RING domain. The computational data showed similarly strong concordance with known clinical data as well as with experimental data from both functional assays. Predictions made by models trained on our computational data offer a complementary and orthogonal approach for classifying all remaining unexplored BRCA1 RING domain variants.
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Affiliation(s)
- Majid Masso
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA.
| | - Anirudh Bansal
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA
| | - Arnav Bansal
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA
| | - Andrea Henderson
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA
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50
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Shaw T, Chan SH, Teo JX, Chong ST, Li ST, Courtney E, Ishak D, Sankar H, Ang ZLT, Chiang J, Loh M, Zhou L, Lee SC, Yeh HY, Kolinjivadi AM, Lim WK, Ngeow J. Investigation into the origins of an ancient BRCA1 founder mutation identified among Chinese families in Singapore. Int J Cancer 2020; 148:637-645. [PMID: 32745242 DOI: 10.1002/ijc.33241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 11/07/2022]
Abstract
Identification of ancestry-specific pathogenic variants is imperative for diagnostic, treatment, management and prevention strategies, and to understand penetrance/modifiers on risk. Our study aimed to determine the clinical significance of a recurrent BRCA1 c.442-22_442-13del variant of unknown significance identified among 13 carriers from six Chinese families, all with a significant history of breast and/or ovarian cancer. We further aimed to establish whether this was due to a founder effect and explore its origins. Haplotype analysis, using nine microsatellite markers encompassing 2.5 megabase pairs around the BRCA1 locus, identified a common haploblock specific to the variant carriers, confirming a founder effect. Variant age was estimated to date back 77.9 generations to 69 bc using the Gamma approach. On principal component analysis using single nucleotide polymorphisms merged with 1000 Genomes dataset, variant carriers were observed to overlap predominantly with the southern Han Chinese population. To determine pathogenicity of the variant, we assessed the functional effect on RAD51 foci formation as well as replication fork stability upon induction of DNA damage and observed an impaired DNA repair response associated with the variant. In summary, we identified an ancient Chinese founder mutation dating back 77.9 generations, possibly common among individuals of southern Han Chinese descent. Using evidence from phenotypic/family history studies, segregation analysis and functional characterization, the BRCA1 variant was reclassified from uncertain significance to pathogenic.
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Affiliation(s)
- Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Siao Ting Chong
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Shao-Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Eliza Courtney
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Diana Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Haresh Sankar
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Zoe Li Ting Ang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Li Zhou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Hui-Yuan Yeh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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