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Gunning AC, Wright CF. Evaluating the use of paralogous protein domains to increase data availability for missense variant classification. Genome Med 2023; 15:110. [PMID: 38087376 PMCID: PMC10714540 DOI: 10.1186/s13073-023-01264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Classification of rare missense variants remains an ongoing challenge in genomic medicine. Evidence of pathogenicity is often sparse, and decisions about how to weigh different evidence classes may be subjective. We used a Bayesian variant classification framework to investigate the performance of variant co-localisation, missense constraint, and aggregating data across paralogous protein domains ("meta-domains"). METHODS We constructed a database of all possible coding single nucleotide variants in the human genome and used PFam predictions to annotate structurally-equivalent positions across protein domains. We counted the number of pathogenic and benign missense variants at these equivalent positions in the ClinVar database, calculated a regional constraint score for each meta-domain, and assessed this approach versus existing missense constraint metrics for classifying variant pathogenicity and benignity. RESULTS Alternative pathogenic missense variants at the same amino acid position in the same protein provide strong evidence of pathogenicity (positive likelihood ratio, LR+ = 85). Additionally, clinically annotated pathogenic or benign missense variants at equivalent positions in different proteins can provide moderate evidence of pathogenicity (LR+ = 7) or benignity (LR+ = 5), respectively. Applying these approaches sequentially (through PM5) increases sensitivity for classifying pathogenic missense variants from 27 to 41%. Missense constraint can also provide strong evidence of pathogenicity for some variants, but its absence provides no evidence of benignity. CONCLUSIONS We propose using structurally equivalent positions across related protein domains from different genes to augment evidence for variant co-localisation when classifying novel missense variants. Additionally, we advocate adopting a numerical evidence-based approach to integrating diverse data in variant interpretation.
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Affiliation(s)
- Adam Colin Gunning
- Department of Clinical and Biomedical Sciences (Medical School, Faculty of Health and Life Sciences, University of Exeter, RILD, Barrack Road, Exeter, EX2 5DW, UK.
- Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon University Healthcare NHS Foundation Trust, RILD, Barrack Road, Exeter, EX2 5DW, UK.
| | - Caroline Fiona Wright
- Department of Clinical and Biomedical Sciences (Medical School, Faculty of Health and Life Sciences, University of Exeter, RILD, Barrack Road, Exeter, EX2 5DW, UK.
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Bi C, Zhang T, Li Y, Zhao H, Zhang P, Wang Y, Xu Y, Gu K, Liu Y, Yu J, Qi W, Fan S, Li Y, Zhang Y. A Proteomics- and Metabolomics-Based Study Revealed That Disorder of Palmitic Acid Metabolism by Aconitine Induces Cardiac Injury. Chem Res Toxicol 2020; 33:3031-3040. [PMID: 33236894 DOI: 10.1021/acs.chemrestox.0c00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, research on cardiac injury by aconitine focuses on its effect to directly interfere with the function of cardiac ion channels. Further, abnormal lipid metabolism could cause cardiac injury via inflammatory signaling pathway. In our preliminary study, we discovered that aconitine could alter the metabolism processes of various substances, including palmitic acid. Inspired by these studies, we investigated how elevation of palmitic acid by aconitine causes cardiac injury. Aconitine induced cardiac injury in rats (0.32 mg/kg, d = 7), and the cardiac injury was confirmed by electrocardiogram and serum biochemical study. The proteomic and metabolomic results showed that the palmitic acid level increases in heart tissue, and the NOD-like receptor (NLR) signaling pathway showed a strong effect of cardiac injury. The palmitic acid results in cell viability decline and activates NLR signaling in vitro. The shRNA-mediated knockdown of NLRP3 and NOD1/2 attenuates palmitic acid-induced inhibitory effect on cells and inhibited activation of the NLR signaling pathway. Collectively, this study reveals that aconitine provoked palmitic acid elevation could aggravate cardiac injury via the NLR signaling pathway. This study suggests that drug triggered disorder of the metabolism process could evoke cardiac injury and could propose a new strategy to study drug cardiac injury.
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Affiliation(s)
- Chenghao Bi
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Tianpu Zhang
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yamei Li
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Huan Zhao
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Pengjie Zhang
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yuming Wang
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yanyan Xu
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Kun Gu
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yuechen Liu
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Jiao Yu
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310000, China
| | - Wulin Qi
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310000, China
| | - Simiao Fan
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yubo Li
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yanjun Zhang
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
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Bocher O, Génin E. Rare variant association testing in the non-coding genome. Hum Genet 2020; 139:1345-1362. [PMID: 32500240 DOI: 10.1007/s00439-020-02190-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022]
Abstract
The development of next-generation sequencing technologies has opened-up some new possibilities to explore the contribution of genetic variants to human diseases and in particular that of rare variants. Statistical methods have been developed to test for association with rare variants that require the definition of testing units and, in these testing units, the selection of qualifying variants to include in the test. In the coding regions of the genome, testing units are usually the different genes and qualifying variants are selected based on their functional effects on the encoded proteins. Extending these tests to the non-coding regions of the genome is challenging. Testing units are difficult to define as the non-coding genome organisation is still rather unknown. Qualifying variants are difficult to select as the functional impact of non-coding variants on gene expression is hard to predict. These difficulties could explain why very few investigators so far have analysed the non-coding parts of their whole genome sequencing data. These non-coding parts yet represent the vast majority of the genome and some studies suggest that they could play a major role in disease susceptibility. In this review, we discuss recent experimental and statistical developments to gain knowledge on the non-coding genome and how this knowledge could be used to include rare non-coding variants in association tests. We describe the few studies that have considered variants from the non-coding genome in association tests and how they managed to define testing units and select qualifying variants.
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Affiliation(s)
- Ozvan Bocher
- Génétique, Génomique Fonctionnelle Et Biotechnologies, Faculté de Médecine, Univ Brest, Inserm, Inserm UMR1078, Bâtiment E-IBRBS 2ieme étage, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France.
| | - Emmanuelle Génin
- Génétique, Génomique Fonctionnelle Et Biotechnologies, Faculté de Médecine, Univ Brest, Inserm, Inserm UMR1078, Bâtiment E-IBRBS 2ieme étage, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France.
- CHU Brest, Brest, France.
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Dershem R, Metpally RPR, Jeffreys K, Krishnamurthy S, Smelser DT, Hershfinkel M, Carey DJ, Robishaw JD, Breitwieser GE. Rare-variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations of orphan G protein-coupled receptors. J Biol Chem 2019; 294:18109-18121. [PMID: 31628190 DOI: 10.1074/jbc.ra119.009253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/08/2019] [Indexed: 02/02/2023] Open
Abstract
The pace of deorphanization of G protein-coupled receptors (GPCRs) has slowed, and new approaches are required. Small molecule targeting of orphan GPCRs can potentially be of clinical benefit even if the endogenous receptor ligand has not been identified. Many GPCRs lack common variants that lead to reproducible genome-wide disease associations, and rare-variant approaches have emerged as a viable alternative to identify disease associations for such genes. Therefore, our goal was to prioritize orphan GPCRs by determining their associations with human diseases in a large clinical population. We used sequence kernel association tests to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Using rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants that cause large changes in local codon bias as independent data sets, we found strong, phenome-wide disease associations shared by two or more variant categories for 39% of the GPCRs. To validate the bioinformatics and sequence kernel association test analyses, we functionally characterized rare missense and synonymous variants of GPR39, a family A GPCR, revealing altered expression or Zn2+-mediated signaling for members of both variant classes. These results support the utility of rare variant analyses for identifying disease associations for GPCRs that lack impactful common variants. We highlight the importance of rare synonymous variants in human physiology and argue for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.
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Affiliation(s)
- Ridge Dershem
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Raghu P R Metpally
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Kirk Jeffreys
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Sarathbabu Krishnamurthy
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Diane T Smelser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Michal Hershfinkel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501 Israel
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- Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Janet D Robishaw
- Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Gerda E Breitwieser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822.
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