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Kullo IJ. Promoting equity in polygenic risk assessment through global collaboration. Nat Genet 2024:10.1038/s41588-024-01843-2. [PMID: 39103647 DOI: 10.1038/s41588-024-01843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/24/2024] [Indexed: 08/07/2024]
Abstract
The long delay before genomic technologies become available in low- and middle-income countries is a concern from both scientific and ethical standpoints. Polygenic risk scores (PRSs), a relatively recent advance in genomics, could have a substantial impact on promoting health by improving disease risk prediction and guiding preventive strategies. However, clinical use of PRSs in their current forms might widen global health disparities, as their portability to diverse groups is limited. This Perspective highlights the need for global collaboration to develop and implement PRSs that perform equitably across the world. Such collaboration requires capacity building and the generation of new data in low-resource settings, the sharing of harmonized genotype and phenotype data securely across borders, novel population genetics and statistical methods to improve PRS performance, and thoughtful clinical implementation in diverse settings. All this needs to occur while considering the ethical, legal and social implications, with support from regulatory and funding agencies and policymakers.
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Affiliation(s)
- Iftikhar J Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN, USA.
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2
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Zhang Y, Bi C, Nadeef S, Maddirevula S, Alqahtani M, Alkuraya FS, Li M. NanoRanger enables rapid single-base-pair resolution of genomic disorders. MED 2024:S2666-6340(24)00262-9. [PMID: 39047733 DOI: 10.1016/j.medj.2024.07.003] [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: 11/12/2023] [Revised: 04/13/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Delineating base-resolution breakpoints of complex rearrangements is crucial for an accurate clinical understanding of pathogenic variants and for carrier screening within family networks or the broader population. However, despite advances in genetic testing using short-read sequencing (SRS), this task remains costly and challenging. METHODS This study addresses the challenges of resolving missing disease-causing breakpoints in complex genomic disorders with suspected homozygous rearrangements by employing multiple long-read sequencing (LRS) strategies, including a novel and efficient strategy named nanopore-based rapid acquisition of neighboring genomic regions (NanoRanger). NanoRanger does not require large amounts of ultrahigh-molecular-weight DNA and stands out for its ease of use and rapid acquisition of large genomic regions of interest with deep coverage. FINDINGS We describe a cohort of 16 familial cases, each harboring homozygous rearrangements that defied breakpoint determination by SRS and optical genome mapping (OGM). NanoRanger identified the breakpoints with single-base-pair resolution, enabling accurate determination of the carrier status of unaffected family members as well as the founder nature of these genomic lesions and their frequency in the local population. The resolved breakpoints revealed that repetitive DNA, gene regulatory elements, and transcription activity contribute to genome instability in these novel recessive rearrangements. CONCLUSIONS Our data suggest that NanoRanger greatly improves the success rate of resolving base-resolution breakpoints of complex genomic disorders and expands access to LRS for the benefit of patients with Mendelian disorders. FUNDING M.L. is supported by KAUST Baseline Award no. BAS/1/1080-01-01 and KAUST Research Translation Fund Award no. REI/1/4742-01.
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Affiliation(s)
- Yingzi Zhang
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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3
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Lassen FH, Venkatesh SS, Baya N, Hill B, Zhou W, Bloemendal A, Neale BM, Kessler BM, Whiffin N, Lindgren CM, Palmer DS. Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. CELL GENOMICS 2024; 4:100602. [PMID: 38944039 PMCID: PMC11293579 DOI: 10.1016/j.xgen.2024.100602] [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: 07/31/2023] [Revised: 03/11/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
The phenotypic impact of compound heterozygous (CH) variation has not been investigated at the population scale. We phased rare variants (MAF ∼0.001%) in the UK Biobank (UKBB) exome-sequencing data to characterize recessive effects in 175,587 individuals across 311 common diseases. A total of 6.5% of individuals carry putatively damaging CH variants, 90% of which are only identifiable upon phasing rare variants (MAF < 0.38%). We identify six recessive gene-trait associations (p < 1.68 × 10-7) after accounting for relatedness, polygenicity, nearby common variants, and rare variant burden. Of these, just one is discovered when considering homozygosity alone. Using longitudinal health records, we additionally identify and replicate a novel association between bi-allelic variation in ATP2C2 and an earlier age at onset of chronic obstructive pulmonary disease (COPD) (p < 3.58 × 10-8). Genetic phase contributes to disease risk for gene-trait pairs: ATP2C2-COPD (p = 0.000238), FLG-asthma (p = 0.00205), and USH2A-visual impairment (p = 0.0084). We demonstrate the power of phasing large-scale genetic cohorts to discover phenome-wide consequences of compound heterozygosity.
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Affiliation(s)
- Frederik H Lassen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Samvida S Venkatesh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Nikolas Baya
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Barney Hill
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Novo Nordisk Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Whiffin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK.
| | - Duncan S Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK.
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4
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Sun KY, Bai X, Chen S, Bao S, Zhang C, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke AE, Ganel L, Hawes A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Di Gioia A, Rajagopal VM, Lopez A, Varela JR, Alegre-Díaz J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton JD, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalogue of protein-coding variation in 983,578 individuals. Nature 2024; 631:583-592. [PMID: 38768635 PMCID: PMC11254753 DOI: 10.1038/s41586-024-07556-0] [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: 06/19/2023] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Rare coding variants that substantially affect function provide insights into the biology of a gene1-3. However, ascertaining the frequency of such variants requires large sample sizes4-8. Here we present a catalogue of human protein-coding variation, derived from exome sequencing of 983,578 individuals across diverse populations. In total, 23% of the Regeneron Genetics Center Million Exome (RGC-ME) data come from individuals of African, East Asian, Indigenous American, Middle Eastern and South Asian ancestry. The catalogue includes more than 10.4 million missense and 1.1 million predicted loss-of-function (pLOF) variants. We identify individuals with rare biallelic pLOF variants in 4,848 genes, 1,751 of which have not been previously reported. From precise quantitative estimates of selection against heterozygous loss of function (LOF), we identify 3,988 LOF-intolerant genes, including 86 that were previously assessed as tolerant and 1,153 that lack established disease annotation. We also define regions of missense depletion at high resolution. Notably, 1,482 genes have regions that are depleted of missense variants despite being tolerant of pLOF variants. Finally, we estimate that 3% of individuals have a clinically actionable genetic variant, and that 11,773 variants reported in ClinVar with unknown significance are likely to be deleterious cryptic splice sites. To facilitate variant interpretation and genetics-informed precision medicine, we make this resource of coding variation from the RGC-ME dataset publicly accessible through a variant allele frequency browser.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Liron Ganel
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Jesús Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Jaime Berumen
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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Chen MJ, Xu YT, Sun L, Wang ZH, Little PJ, Wang L, Xian XD, Weng JP, Xu SW. A novel mouse model of familial combined hyperlipidemia and atherosclerosis. Acta Pharmacol Sin 2024; 45:1316-1320. [PMID: 38459255 PMCID: PMC11130143 DOI: 10.1038/s41401-024-01241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Within the context of residual cardiovascular risk in post-statin era, emerging evidence from epidemiologic and human genetic studies have demonstrated that triglyceride (TG)-rich lipoproteins and their remnants are causally related to cardiovascular risk. While, carriers of loss-of-function mutations of ApoC3 have low TG levels and are protected from cardiovascular disease (CVD). Of translational significance, siRNAs/antisense oligonucleotide (ASO) targeting ApoC3 is beneficial for patients with atherosclerotic CVD. Therefore, animal models of atherosclerosis with both hypercholesterolemia and hypertriglyceridemia are important for the discovery of novel therapeutic strategies targeting TG-lowering on top of traditional cholesterol-lowering. In this study, we constructed a novel mouse model of familial combined hyperlipidemia through inserting a human ApoC3 transgene (hApoC3-Tg) into C57BL/6 J mice and injecting a gain-of-function variant of adeno-associated virus-proprotein convertase subtilisin/kexin type 9 (AAV-PCSK9)-D377Y concurrently with high cholesterol diet (HCD) feeding for 16 weeks. In the last 10 weeks, hApoC3-Tg mice were orally treated with a combination of atorvastatin (10 mg·kg-1·d-1) and fenofibrate (100 mg·kg-1·d-1). HCD-treated hApoC3-Tg mice demonstrated elevated levels of serum TG, total cholesterol (TC) and low density lipoprotein-cholesterol (LDL-C). Oral administration of atorvastatin and fenofibrate significantly decreased the plaque sizes of en face aorta, aortic sinus and innominate artery accompanied by improved lipid profile and distribution. In summary, this novel mouse model is of considerable clinical relevance for evaluation of anti-atherosclerotic drugs by targeting both hypercholesterolemia and hypertriglyceridemia.
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Affiliation(s)
- Mei-Jie Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230022, China
| | - Yi-Tong Xu
- Institute of Cardiovascular Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, 100091, China
| | - Lu Sun
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230022, China
| | - Zhi-Hua Wang
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230022, China
| | - Peter J Little
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Li Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xun-de Xian
- Institute of Cardiovascular Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, 100091, China.
| | - Jian-Ping Weng
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230022, China.
| | - Suo-Wen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230022, China.
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6
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Natarajan P. Exceptional Genetics, Generalizable Therapeutics, and Coronary Artery Disease. N Engl J Med 2024. [PMID: 38809176 DOI: 10.1056/nejme2405647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Affiliation(s)
- Pradeep Natarajan
- From the Department of Medicine and Division of Cardiology, Massachusetts General Hospital and Harvard Medical School - both in Boston
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7
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Hou Z, Sun A, Li Y, Song X, Liu S, Hu X, Luan Y, Guan H, He C, Sun Y, Chen J. What Are the Reliable Plasma Biomarkers for Mild Cognitive Impairment? A Clinical 4D Proteomics Study and Validation. Mediators Inflamm 2024; 2024:7709277. [PMID: 38883967 PMCID: PMC11178428 DOI: 10.1155/2024/7709277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/20/2024] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Objective At present, Alzheimer's disease (AD) lacks effective treatment means, and early diagnosis and intervention are the keys to treatment. Therefore, for mild cognitive impairment (MCI) and AD patients, blood sample analysis using the 4D nonstandard (label-free) proteomic in-depth quantitative analysis, looking for specific protein marker expression differences, is important. These marker levels change as AD progresses, and the analysis of these biomarkers changes with this method, which has the potential to show the degree of disease progression and can be used for the diagnosis and preventive treatment of MCI and AD. Materials and Methods Patients were recruited according to the inclusion and exclusion criteria and divided into three groups according to scale scores. Elderly patients diagnosed with AD were selected as the AD group (n = 9). Patients diagnosed with MCI were classified into the MCI group (n = 10). Cognitively healthy elderly patients were included in the normal cognition control group (n = 10). Patients' blood samples were used for 4D label-free proteomic in-depth quantitative analysis to identify potential blood biomarkers. The sample size of each group was expanded (n = 30), and the selected biomarkers were verified by enzyme-linked immunosorbent assay (ELISA) to verify the accuracy of the proteomic prediction. Results Six specific blood markers, namely, APOE, MMP9, UBR5, PLA2G7, STAT5B, and S100A8, were detected by 4D label-free proteomic quantitative analysis. These markers showed a statistically significant upregulation trend in the MCI and AD groups compared with the normal cognition control group (P < 0.05). ELISA results showed that the levels of these six proteins in the MCI group were significantly higher than those in the normal cognition control group, and the levels of these six proteins in the AD group were significantly higher than those in the MCI group (P < 0.05). Conclusion The plasma levels of APOE, MMP9, UBR5, PLA2G7, STAT5B, and S100A8 in cognitively healthy elderly patients and patients with MCI and AD were significantly different and, more importantly, showed a trend of increasing expression. These results indicate that these six human plasma markers have important diagnostic and therapeutic potential in the identification of cognitive impairment and have value for in-depth research and clinical application.
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Affiliation(s)
- Zhitao Hou
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania, Philadelphia 19104, PA, USA
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education Dongzhimen Hospital Affiliated with Beijing University of Chinese Medicine, Beijing 100700, China
- The First Hospital Affiliated with Heilongjiang University of Chinese Medicine, Harbin 150010, Heilongjiang, China
| | - Ailin Sun
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
- Pudong Hospital Affiliated with Fudan University, Shanghai 200120, China
| | - Yan Li
- The First Hospital Affiliated with Heilongjiang University of Chinese Medicine, Harbin 150010, Heilongjiang, China
| | - Xiaochen Song
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Shu Liu
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Xinying Hu
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Yihan Luan
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Huibo Guan
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Changyuan He
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Yuefeng Sun
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Jing Chen
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
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8
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Abou-Karam R, Cheng F, Gady S, Fahed AC. The Role of Genetics in Advancing Cardiometabolic Drug Development. Curr Atheroscler Rep 2024; 26:153-162. [PMID: 38451435 DOI: 10.1007/s11883-024-01195-6] [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] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE OF REVIEW The objective of this review is to explore the role of genetics in cardiometabolic drug development. The declining costs of sequencing and the availability of large-scale genomic data have deepened our understanding of cardiometabolic diseases, revolutionizing drug discovery and development methodologies. We highlight four key areas in which genetics is empowering drug development for cardiometabolic disease: (1) identifying drug candidates, (2) anticipating drug target failures, (3) silencing and editing genes, and (4) enriching clinical trials. RECENT FINDINGS Identifying novel drug targets through genetic discovery studies and the use of genetic variants as indicators of potential drug efficacy and safety have become critical components of cardiometabolic drug discovery. We highlight the successes of genetically-informed therapeutic strategies, such as PCSK9 and ANGPTL3 inhibitors in lipid lowering and the emerging role of polygenic risk scores in improving the efficiency of clinical trials. Additionally, we explore the potential of gene silencing and editing technologies, such as antisense oligonucleotides and small interfering RNA, showcasing their promise in addressing diseases refractory to conventional treatments. In this review, we highlight four use cases that demonstrate the vital role of genetics in cardiometabolic drug development: (1) identifying drug candidates, (2) anticipating drug target failures, (3) silencing and editing genes, and (4) enriching clinical trials. Through these advances, genetics has paved the way to increased efficiency of drug development as well as the discovery of more personalized and effective treatments for cardiometabolic disease.
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Affiliation(s)
- Roukoz Abou-Karam
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street|CPZN 3.128, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fangzhou Cheng
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street|CPZN 3.128, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shoshana Gady
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street|CPZN 3.128, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akl C Fahed
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street|CPZN 3.128, Boston, MA, 02114, USA.
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Abassi Z, Azzam ZS, Heyman SN. Corin and Left Atrial Cardiomyopathy, Hypertension, Arrhythmia, and Fibrosis. N Engl J Med 2024; 390:1539. [PMID: 38657261 DOI: 10.1056/nejmc2313870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Affiliation(s)
- Zaid Abassi
- Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Samuel N Heyman
- Hadassah Hebrew University Hospital, Mt. Scopus, Jerusalem, Israel
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10
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Aamer W, Al-Maraghi A, Syed N, Gandhi GD, Aliyev E, Al-Kurbi AA, Al-Saei O, Kohailan M, Krishnamoorthy N, Palaniswamy S, Al-Malki K, Abbasi S, Agrebi N, Abbaszadeh F, Akil ASAS, Badii R, Ben-Omran T, Lo B, Mokrab Y, Fakhro KA. Burden of Mendelian disorders in a large Middle Eastern biobank. Genome Med 2024; 16:46. [PMID: 38584274 PMCID: PMC11000384 DOI: 10.1186/s13073-024-01307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Genome sequencing of large biobanks from under-represented ancestries provides a valuable resource for the interrogation of Mendelian disease burden at world population level, complementing small-scale familial studies. METHODS Here, we interrogate 6045 whole genomes from Qatar-a Middle Eastern population with high consanguinity and understudied mutational burden-enrolled at the national Biobank and phenotyped for 58 clinically-relevant quantitative traits. We examine a curated set of 2648 Mendelian genes from 20 panels, annotating known and novel pathogenic variants and assessing their penetrance and impact on the measured traits. RESULTS We find that 62.5% of participants are carriers of at least 1 known pathogenic variant relating to recessive conditions, with homozygosity observed in 1 in 150 subjects (0.6%) for which Peninsular Arabs are particularly enriched versus other ancestries (5.8-fold). On average, 52.3 loss-of-function variants were found per genome, 6.5 of which affect a known Mendelian gene. Several variants annotated in ClinVar/HGMD as pathogenic appeared at intermediate frequencies in this cohort (1-3%), highlighting Arab founder effect, while others have exceedingly high frequencies (> 5%) prompting reconsideration as benign. Furthermore, cumulative gene burden analysis revealed 56 genes having gene carrier frequency > 1/50, including 5 ACMG Tier 3 panel genes which would be candidates for adding to newborn screening in the country. Additionally, leveraging 58 biobank traits, we systematically assess the impact of novel/rare variants on phenotypes and discover 39 candidate large-effect variants associating with extreme quantitative traits. Furthermore, through rare variant burden testing, we discover 13 genes with high mutational load, including 5 with impact on traits relevant to disease conditions, including metabolic disorder and type 2 diabetes, consistent with the high prevalence of these conditions in the region. CONCLUSIONS This study on the first phase of the growing Qatar Genome Program cohort provides a comprehensive resource from a Middle Eastern population to understand the global mutational burden in Mendelian genes and their impact on traits in seemingly healthy individuals in high consanguinity settings.
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Affiliation(s)
- Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Najeeb Syed
- Applied Bioinformatics Core, Sidra Medicine, Doha, Qatar
| | | | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Omayma Al-Saei
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | | | | | - Saleha Abbasi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Nourhen Agrebi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | - Ramin Badii
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of pediatrics, Hamad Medical Corporation, Doha, Qatar
- Department of Pediatric, Weill Cornell Medical College, Doha, Qatar
- Division of Genetic & Genomics Medicine, Sidra Medicine, Doha, Qatar
| | - Bernice Lo
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
- College of Health Sciences, Qatar University, Doha, Qatar.
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
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11
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Gagnon E, Arsenault BJ. Drug target Mendelian randomization supports apolipoprotein C3-lowering for lipoprotein-lipid levels reductions and cardiovascular diseases prevention. Atherosclerosis 2024; 391:117501. [PMID: 38547584 DOI: 10.1016/j.atherosclerosis.2024.117501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND AND AIMS Inhibitors of apolipoprotein C-III (apoC3) are currently approved for the reduction of triglyceride levels in patients with Familial Chylomicronemia Syndrome. We used drug target Mendelian randomization (MR) to assess the effect of genetically predicted decrease in apoC3 blood protein levels on cardiometabolic traits and diseases. METHODS We quantified lifelong reductions in apoC3 blood levels by selecting all genome wide significant and independent (r2<0.1) single nucleotide polymorphisms (SNPs) in the APOC3 gene region ±1 Mb, from three genome-wide association studies (GWAS) of apoC3 blood protein levels (deCODE, n = 35,378, Fenland, n = 10,708 and ARIC, n = 7213). We included the largest GWASes on 18 cardiometabolic traits and 9 cardiometabolic diseases as study outcomes. RESULTS A one standard deviation lowering in apoC3 blood protein levels was associated with lower triglycerides, apolipoprotein B, low-density lipoprotein cholesterol, alanine aminotransferase, and glomerular filtration rate as well as higher high-density lipoprotein cholesterol levels. ApoC3 lowering was also associated with lower risk of acute pancreatitis (odds ratio [OR] = 0.91 95% CI = 0.82 to 1.00), aortic stenosis (OR = 0.82 95% CI = 0.73 to 0.93), and coronary artery disease (OR = 0.86 95% CI = 0.80 to 0.93), and was associated with increased parental lifespan (0.06 95% CI = 0.03-0.09 years). These results were concordant across robust MR methods, the three protein datasets and upon adjustment for APOA1, APOA4 and APOA5 using a multivariable MR framework. CONCLUSIONS These results provide evidence that apoC3 lowering could result in widespread benefits for cardiometabolic health and encourage the launch of trials on apoC3 inhibition for coronary artery disease prevention.
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Affiliation(s)
- Eloi Gagnon
- Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada
| | - Benoit J Arsenault
- Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada.
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12
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Faundes V, Repetto GM, Valdivia LE. Discovery of novel genetic syndromes in Latin America: Opportunities and challenges. Genet Mol Biol 2024; 47Suppl 1:e20230318. [PMID: 38466870 DOI: 10.1590/1678-4685-gmb-2023-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Latin America (LatAm) has a rich and historically significant role in delineating both novel and well-documented genetic disorders. However, the ongoing advancements in the field of human genetics pose challenges to the relatively slow adaption of LatAm in the field. Here, we describe past and present contributions of LatAm to the discovery of novel genetic disorders, often referred as novel gene-disease associations (NGDA). We also describe the current methodologies for discovery of NGDA, taking into account the latest developments in genomics. We provide an overview of opportunities and challenges for NGDA research in LatAm considering the steps currently performed to identify and validate such associations. Given the multiple and diverse needs of populations and countries in LatAm, it is imperative to foster collaborations amongst patients, indigenous people, clinicians and scientists. Such collaborative effort is essential for sustaining and enhancing the LatAm´s contributions to the field of NGDA.
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Affiliation(s)
- Víctor Faundes
- Universidad de Chile, Instituto de Nutrición y Tecnología de los Alimentos, Laboratorio de Genética y Enfermedades Metabólicas, Santiago, Chile
| | - Gabriela M Repetto
- Universidad del Desarrollo, Facultad de Medicina, Instituto de Ciencias e Innovación en Medicina, Centro de Genética y Genómica, Programa de Enfermedades Raras, Santiago, Chile
| | - Leonardo E Valdivia
- Universidad Mayor, Facultad de Ciencias, Centro de Biología Integrativa, Santiago, Chile
- Universidad Mayor, Facultad de Ciencias, Escuela de Biotecnología, Santiago, Chile
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13
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Wang J, Zhang C, Zhang L, Yao HJ, Liu X, Shi Y, Zhao J, Bo X, Chen H, Li L. Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework. Cancer Gene Ther 2024; 31:439-453. [PMID: 38146007 DOI: 10.1038/s41417-023-00714-y] [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: 08/09/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/27/2023]
Abstract
Recurrence and extraocular metastasis in advanced intraocular retinoblastoma (RB) are still major obstacles for successful treatment of Chinese children. Tuberous sclerosis complex (TSC) is a very rare, multisystemic genetic disorder characterized by hamartomatous growth. In this study, we aimed to compare genomic and epigenomic profiles with human RB or TSC using recently developed nanopore sequencing, and to identify disease-associated variations or genes. Peripheral blood samples were collected from either RB or RB/TSC patients plus their normal siblings, followed by nanopore sequencing and identification of disease-specific structural variations (SVs) and differentially methylated regions (DMRs) by a systematic biology strategy named as multiomics-based joint screening framework. In total, 316 RB- and 1295 TSC-unique SVs were identified, as well as 1072 RB- and 1114 TSC-associated DMRs, respectively. We eventually identified 6 key genes for RB for further functional validation. Knockdown of CDK19 with specific siRNAs significantly inhibited Y79 cellular proliferation and increased sensitivity to carboplatin, whereas downregulation of AHNAK2 promoted the cell growth as well as drug resistance. Those two genes might serve as potential diagnostic markers or therapeutic targets of RB. The systematic biology strategy combined with functional validation might be an effective approach for rare pediatric malignances with limited samples and challenging collection process.
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Affiliation(s)
- Junting Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China
| | - Chengyue Zhang
- Department of Ophthalmology, Beijing Children's Hospital affiliated with Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Li Zhang
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Hong-Juan Yao
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Xiaohong Liu
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, No.5 BeiXianGe St., Beijing, 100053, China
| | - Yuchen Shi
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang, Beijing, 100700, China
| | - Junyang Zhao
- Department of Ophthalmology, Beijing Children's Hospital affiliated with Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China.
| | - Liang Li
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China.
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14
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Morvaridzadeh M, Zoubdane N, Heshmati J, Alami M, Berrougui H, Khalil A. High-Density Lipoprotein Metabolism and Function in Cardiovascular Diseases: What about Aging and Diet Effects? Nutrients 2024; 16:653. [PMID: 38474781 DOI: 10.3390/nu16050653] [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: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Cardiovascular diseases (CVDs) have become the leading global cause of mortality, prompting a heightened focus on identifying precise indicators for their assessment and treatment. In this perspective, the plasma levels of HDL have emerged as a pivotal focus, given the demonstrable correlation between plasma levels and cardiovascular events, rendering them a noteworthy biomarker. However, it is crucial to acknowledge that HDLs, while intricate, are not presently a direct therapeutic target, necessitating a more nuanced understanding of their dynamic remodeling throughout their life cycle. HDLs exhibit several anti-atherosclerotic properties that define their functionality. This functionality of HDLs, which is independent of their concentration, may be impaired in certain risk factors for CVD. Moreover, because HDLs are dynamic parameters, in which HDL particles present different atheroprotective properties, it remains difficult to interpret the association between HDL level and CVD risk. Besides the antioxidant and anti-inflammatory activities of HDLs, their capacity to mediate cholesterol efflux, a key metric of HDL functionality, represents the main anti-atherosclerotic property of HDL. In this review, we will discuss the HDL components and HDL structure that may affect their functionality and we will review the mechanism by which HDL mediates cholesterol efflux. We will give a brief examination of the effects of aging and diet on HDL structure and function.
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Affiliation(s)
- Mojgan Morvaridzadeh
- Department of Medicine, Geriatric Service, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 4N4, Canada
| | - Nada Zoubdane
- Department of Medicine, Geriatric Service, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 4N4, Canada
| | - Javad Heshmati
- Department of Medicine, Geriatric Service, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 4N4, Canada
| | - Mehdi Alami
- Department of Medicine, Geriatric Service, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 4N4, Canada
| | - Hicham Berrougui
- Department of Medicine, Geriatric Service, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 4N4, Canada
| | - Abdelouahed Khalil
- Department of Medicine, Geriatric Service, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 4N4, Canada
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15
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Packard CJ, Pirillo A, Tsimikas S, Ference BA, Catapano AL. Exploring apolipoprotein C-III: pathophysiological and pharmacological relevance. Cardiovasc Res 2024; 119:2843-2857. [PMID: 38039351 DOI: 10.1093/cvr/cvad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 12/03/2023] Open
Abstract
The availability of pharmacological approaches able to effectively reduce circulating LDL cholesterol (LDL-C) has led to a substantial reduction in the risk of atherosclerosis-related cardiovascular disease (CVD). However, a residual cardiovascular (CV) risk persists in treated individuals with optimal levels of LDL-C. Additional risk factors beyond LDL-C are involved, and among these, elevated levels of triglycerides (TGs) and TG-rich lipoproteins are causally associated with an increased CV risk. Apolipoprotein C-III (apoC-III) is a key regulator of TG metabolism and hence circulating levels through several mechanisms including the inhibition of lipoprotein lipase activity and alterations in the affinity of apoC-III-containing lipoproteins for both the hepatic receptors involved in their removal and extracellular matrix in the arterial wall. Genetic studies have clarified the role of apoC-III in humans, establishing a causal link with CVD and showing that loss-of-function mutations in the APOC3 gene are associated with reduced TG levels and reduced risk of coronary heart disease. Currently available hypolipidaemic drugs can reduce TG levels, although to a limited extent. Substantial reductions in TG levels can be obtained with new drugs that target specifically apoC-III; these include two antisense oligonucleotides, one small interfering RNA and an antibody.
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Affiliation(s)
- Chris J Packard
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Angela Pirillo
- Center for the Study of Atherosclerosis, E. Bassini Hospital, Milan, Italy
- Center for the Study of Dyslipidaemias, IRCCS MultiMedica, Sesto S. Giovanni, 20099 Milan, Italy
| | - Sotirios Tsimikas
- Division of Cardiovascular Medicine, Sulpizio Cardiovascular Center, University of California San Diego, La Jolla, CA, USA
| | - Brian A Ference
- Centre for Naturally Randomized Trials, University of Cambridge, Cambridge, UK
| | - Alberico L Catapano
- Center for the Study of Dyslipidaemias, IRCCS MultiMedica, Sesto S. Giovanni, 20099 Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133 Milan, Italy
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16
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Schiaffino S, Hughes SM, Murgia M, Reggiani C. MYH13, a superfast myosin expressed in extraocular, laryngeal and syringeal muscles. J Physiol 2024; 602:427-443. [PMID: 38160435 DOI: 10.1113/jp285714] [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: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
MYH13 is a unique type of sarcomeric myosin heavy chain (MYH) first detected in mammalian extraocular (EO) muscles and later also in vocal muscles, including laryngeal muscles of some mammals and syringeal muscles of songbirds. All these muscles are specialized in generating very fast contractions while producing relatively low force, a design appropriate for muscles acting against a much lower load than most skeletal muscles inserting into the skeleton. The definition of the physiological properties of muscle fibres containing MYH13 has been complicated by the mixed fibre type composition of EO muscles and the coexistence of different MYH types within the same fibre. A major advance in this area came from studies on isolated recombinant myosin motors and the demonstration that the affinity of actin-bound human MYH13 for ADP is much weaker than those of fast-type MYH1 (type 2X) and MYH2 (type 2A). This property is consistent with a very fast detachment of myosin from actin, a major determinant of shortening velocity. The MYH13 gene arose early during vertebrate evolution but was characterized only in mammals and birds and appears to have been lost in some teleost fish. The MYH13 gene is located at the 3' end of the mammalian fast/developmental gene cluster and in a similar position to the orthologous cluster in syntenic regions of the songbird genome. MYH13 gene regulation is controlled by a super-enhancer in the mammalian locus and deletion of the neighbouring fast MYH1 and MYH4 genes leads to abnormal MYH13 expression in mouse leg muscles.
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Affiliation(s)
| | - Simon M Hughes
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College, London, UK
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Science and Research Center Koper, Institute for Kinesiology Research, Koper, Slovenia
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17
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Gazzellone A, Sangiorgi E. From Churchill to Elephants: The Role of Protective Genes against Cancer. Genes (Basel) 2024; 15:118. [PMID: 38255007 PMCID: PMC10815068 DOI: 10.3390/genes15010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Richard Peto's paradox, first described in 1975 from an epidemiological perspective, established an inverse correlation between the probability of developing cancer in multicellular organisms and the number of cells. Larger animals exhibit fewer tumors compared to smaller ones, though exceptions exist. Mice are more susceptible to cancer than humans, while elephants and whales demonstrate significantly lower cancer prevalence rates than humans. How nature and evolution have addressed the issue of cancer in the animal kingdom remains largely unexplored. In the field of medicine, much attention has been devoted to cancer-predisposing genes, as they offer avenues for intervention, including blocking, downregulating, early diagnosis, and targeted treatment. Predisposing genes also tend to manifest clinically earlier and more aggressively, making them easier to identify. However, despite significant strides in modern medicine, the role of protective genes lags behind. Identifying genes with a mild predisposing effect poses a significant challenge. Consequently, comprehending the protective function conferred by genes becomes even more elusive, and their very existence is subject to questioning. While the role of variable expressivity and penetrance defects of the same variant in a family is well-documented for many hereditary cancer syndromes, attempts to delineate the function of protective/modifier alleles have been restricted to a few instances. In this review, we endeavor to elucidate the role of protective genes observed in the animal kingdom, within certain genetic syndromes that appear to act as cancer-resistant/repressor alleles. Additionally, we explore the role of protective alleles in conditions predisposing to cancer. The ultimate goal is to discern why individuals, like Winston Churchill, managed to live up to 91 years of age, despite engaging in minimal physical activity, consuming large quantities of alcohol daily, and not abstaining from smoking.
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Affiliation(s)
| | - Eugenio Sangiorgi
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
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18
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Khan MR, Akbari A, Nicholas TJ, Castillo-Madeen H, Ajmal M, Haq TU, Laan M, Quinlan AR, Ahuja JS, Shah AA, Conrad DF. Genome sequencing of Pakistani families with male infertility identifies deleterious genotypes in SPAG6, CCDC9, TKTL1, TUBA3C, and M1AP. Andrology 2023:10.1111/andr.13570. [PMID: 38073178 PMCID: PMC11163020 DOI: 10.1111/andr.13570] [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: 08/09/2023] [Revised: 10/29/2023] [Accepted: 11/30/2023] [Indexed: 06/12/2024]
Abstract
BACKGROUND There are likely to be hundreds of monogenic forms of human male infertility. Whole genome sequencing (WGS) is the most efficient way to make progress in mapping the causative genetic variants, and ultimately improve clinical management of the disease in each patient. Recruitment of consanguineous families is an effective approach to ascertain the genetic forms of many diseases. OBJECTIVES To apply WGS to large consanguineous families with likely hereditary male infertility and identify potential genetic cases. MATERIALS AND METHODS We recruited seven large families with clinically diagnosed male infertility from rural Pakistan, including five with a history of consanguinity. We generated WGS data on 26 individuals (3-5 per family) and analyzed the resulting data with a computational pipeline to identify potentially causal single nucleotide variants, indels, and copy number variants. RESULTS We identified plausible genetic causes in five of the seven families, including a homozygous 10 kb deletion of exon 2 in a well-established male infertility gene (M1AP), and biallelic missense substitutions (SPAG6, CCDC9, TUBA3C) and an in-frame hemizygous deletion (TKTL1) in genes with emerging relevance. DISCUSSION AND CONCLUSION The rate of genetic findings using the current approach (71%) was much higher than what we recently achieved using whole-exome sequencing (WES) of unrelated singleton cases (20%). Furthermore, we identified a pathogenic single-exon deletion in M1AP that would be undetectable by WES. Screening more families with WGS, especially in underrepresented populations, will further reveal the types of variants underlying male infertility and accelerate the use of genetics in the patient management.
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Affiliation(s)
- Muhammad Riaz Khan
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Arvand Akbari
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
| | - Thomas J Nicholas
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Helen Castillo-Madeen
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
| | - Muhammad Ajmal
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Taqweem Ul Haq
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Maris Laan
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Jasvinder S Ahuja
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
| | - Aftab Ali Shah
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Donald F Conrad
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
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19
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Sun KY, Bai X, Chen S, Bao S, Kapoor M, Zhang C, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Gioia AD, Rajagopal V, Lopez A, Varela JR, Alegre J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton J, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalog of protein-coding variation in 985,830 individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539329. [PMID: 37214792 PMCID: PMC10197621 DOI: 10.1101/2023.05.09.539329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Locke
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | - Jesus Alegre
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Roberto Tapia-Conyer
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Pablo Kuri-Morales
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jason Torres
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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20
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Lipov A, Jurgens SJ, Mazzarotto F, Allouba M, Pirruccello JP, Aguib Y, Gennarelli M, Yacoub MH, Ellinor PT, Bezzina CR, Walsh R. Exploring the complex spectrum of dominance and recessiveness in genetic cardiomyopathies. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1078-1094. [PMID: 38666070 PMCID: PMC11041721 DOI: 10.1038/s44161-023-00346-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/07/2023] [Indexed: 04/28/2024]
Abstract
Discrete categorization of Mendelian disease genes into dominant and recessive models often oversimplifies their underlying genetic architecture. Cardiomyopathies (CMs) are genetic diseases with complex etiologies for which an increasing number of recessive associations have recently been proposed. Here, we comprehensively analyze all published evidence pertaining to biallelic variation associated with CM phenotypes to identify high-confidence recessive genes and explore the spectrum of monoallelic and biallelic variant effects in established recessive and dominant disease genes. We classify 18 genes with robust recessive association with CMs, largely characterized by dilated phenotypes, early disease onset and severe outcomes. Several of these genes have monoallelic association with disease outcomes and cardiac traits in the UK Biobank, including LMOD2 and ALPK3 with dilated and hypertrophic CM, respectively. Our data provide insights into the complex spectrum of dominance and recessiveness in genetic heart disease and demonstrate how such approaches enable the discovery of unexplored genetic associations.
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Affiliation(s)
- Alex Lipov
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
| | - Sean J. Jurgens
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Francesco Mazzarotto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - James P. Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Division of Cardiology, University of California, San Francisco, San Francisco, CA USA
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Magdi H. Yacoub
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
- Harefield Heart Science Centre, Uxbridge, UK
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA USA
| | - Connie R. Bezzina
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, Amsterdam, the Netherlands
| | - Roddy Walsh
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
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21
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Singer-Berk M, Gudmundsson S, Baxter S, Seaby EG, England E, Wood JC, Son RG, Watts NA, Karczewski KJ, Harrison SM, MacArthur DG, Rehm HL, O'Donnell-Luria A. Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data. Am J Hum Genet 2023; 110:1496-1508. [PMID: 37633279 PMCID: PMC10502856 DOI: 10.1016/j.ajhg.2023.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023] Open
Abstract
Predicted loss of function (pLoF) variants are often highly deleterious and play an important role in disease biology, but many pLoF variants may not result in loss of function (LoF). Here we present a framework that advances interpretation of pLoF variants in research and clinical settings by considering three categories of LoF evasion: (1) predicted rescue by secondary sequence properties, (2) uncertain biological relevance, and (3) potential technical artifacts. We also provide recommendations on adjustments to ACMG/AMP guidelines' PVS1 criterion. Applying this framework to all high-confidence pLoF variants in 22 genes associated with autosomal-recessive disease from the Genome Aggregation Database (gnomAD v.2.1.1) revealed predicted LoF evasion or potential artifacts in 27.3% (304/1,113) of variants. The major reasons were location in the last exon, in a homopolymer repeat, in a low proportion expressed across transcripts (pext) scored region, or the presence of cryptic in-frame splice rescues. Variants predicted to evade LoF or to be potential artifacts were enriched for ClinVar benign variants. PVS1 was downgraded in 99.4% (162/163) of pLoF variants predicted as likely not LoF/not LoF, with 17.2% (28/163) downgraded as a result of our framework, adding to previous guidelines. Variant pathogenicity was affected (mostly from likely pathogenic to VUS) in 20 (71.4%) of these 28 variants. This framework guides assessment of pLoF variants beyond standard annotation pipelines and substantially reduces false positive rates, which is key to ensure accurate LoF variant prediction in both a research and clinical setting.
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Affiliation(s)
- Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Genomic Informatics Group, University Hospital Southampton, Southampton, UK
| | - Eleina England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jordan C Wood
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel G Son
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ambry Genetics, Aliso Viejo, CA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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22
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Holling T, Brylka L, Scholz T, Bierhals T, Herget T, Meinecke P, Schinke T, Oheim R, Kutsche K. TMCO3, a Putative K + :Proton Antiporter at the Golgi Apparatus, Is Important for Longitudinal Growth in Mice and Humans. J Bone Miner Res 2023; 38:1334-1349. [PMID: 37554015 DOI: 10.1002/jbmr.4827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 04/27/2023] [Accepted: 05/07/2023] [Indexed: 08/10/2023]
Abstract
Isolated short stature, defined as short stature without any other abnormalities, is a common heterogeneous condition in children. Exome sequencing identified the homozygous nonsense variant c.1832G>A/p.(Trp611*) in TMCO3 in two sisters with isolated short stature. Radiological studies, biochemical measurements, assessment of the skeletal status, and three-dimensional bone microarchitecture revealed no relevant skeletal and bone abnormalities in both sisters. The homozygous TMCO3 variant segregated with short stature in the family. TMCO3 transcript levels were reduced by ~50% in leukocyte-derived RNA of both sisters compared with controls, likely due to nonsense-mediated mRNA decay. In primary urinary cells of heterozygous family members, we detected significantly reduced TMCO3 protein levels. TMCO3 is functionally uncharacterized. We ectopically expressed wild-type TMCO3 in HeLa and ATDC5 chondrogenic cells and detected TMCO3 predominantly at the Golgi apparatus, whereas the TMCO3W611* mutant did not reach the Golgi. Coordinated co-expression of TMCO3W611* -HA and EGFP in HeLa cells confirmed intrinsic instability and/or degradation of the mutant. Tmco3 is expressed in all relevant mouse skeletal cell types. Highest abundance of Tmco3 was found in chondrocytes of the prehypertrophic zone in mouse and minipig growth plates where it co-localizes with a Golgi marker. Knockdown of Tmco3 in differentiated ATDC5 cells caused reduced and increased expression of Pthlh and Ihh, respectively. Measurement of long bones in Tmco3tm1b(KOMP)Wtsi knockout mice revealed significant shortening of forelimbs and hindlimbs. TMCO3 is a potential member of the monovalent cation:proton antiporter 2 (CPA2) family. By in silico tools and homology modeling, TMCO3 is predicted to have an N-terminal secretory signal peptide, forms a dimer localized to the membrane, and is organized in a dimerization and a core domain. The core domain contains the CPA2 motif essential for K+ binding and selectivity. Collectively, our data demonstrate that loss of TMCO3 causes growth defects in both humans and mice. © 2023 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Brylka
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tasja Scholz
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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23
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Felix JF, Grant SF. Keeping It in the Family: Consanguinity Reveals P4HTM as a Novel Syndromic Obesity Gene. Diabetes 2023; 72:1184-1186. [PMID: 37603723 PMCID: PMC10450820 DOI: 10.2337/dbi23-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/07/2023] [Indexed: 08/23/2023]
Affiliation(s)
- Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Struan F.A. Grant
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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24
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Schroader JH, Handley MT, Reddy K. Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1790. [PMID: 37092460 DOI: 10.1002/wrna.1790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Inosine triphosphate pyrophosphatase (ITPase), encoded by the ITPA gene in humans, is an important enzyme that preserves the integrity of cellular nucleotide pools by hydrolyzing the noncanonical purine nucleotides (deoxy)inosine and (deoxy)xanthosine triphosphate into monophosphates and pyrophosphate. Variants in the ITPA gene can cause partial or complete ITPase deficiency. Partial ITPase deficiency is benign but clinically relevant as it is linked to altered drug responses. Complete ITPase deficiency causes a severe multisystem disorder characterized by seizures and encephalopathy that is frequently associated with fatal infantile dilated cardiomyopathy. In the absence of ITPase activity, its substrate noncanonical nucleotides have the potential to accumulate and become aberrantly incorporated into DNA and RNA. Hence, the pathophysiology of ITPase deficiency could arise from metabolic imbalance, altered DNA or RNA regulation, or from a combination of these factors. Here, we review the known functions of ITPase and highlight recent work aimed at determining the molecular basis for ITPA-associated pathogenesis which provides evidence for RNA dysfunction. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jacob H Schroader
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Mark T Handley
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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25
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Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
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Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
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26
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Feng J, Zhang X, Li R, Zhao P, Han X, Wu Q, Tian Q, Tang G, Song J, Bi H. Widespread Involvement of Acetylation in the Retinal Metabolism of Form-Deprivation Myopia in Guinea Pigs. ACS OMEGA 2023; 8:23825-23839. [PMID: 37426266 PMCID: PMC10324097 DOI: 10.1021/acsomega.3c02219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023]
Abstract
Myopia has become the major cause of visual impairment worldwide. Although the pathogenesis of myopia remains controversial, proteomic studies suggest that dysregulation of retinal metabolism is potentially involved in the pathology of myopia. Lysine acetylation of proteins plays a key role in regulating cellular metabolism, but little is known about its role in the form-deprived myopic retina. Hence, a comprehensive analysis of proteomic and acetylomic changes in the retinas of guinea pigs with form-deprivation myopia was performed. In total, 85 significantly differential proteins and 314 significantly differentially acetylated proteins were identified. Notably, the differentially acetylated proteins were markedly enriched in metabolic pathways such as glycolysis/gluconeogenesis, the pentose phosphate pathway, retinol metabolism, and the HIF-1 signaling pathway. HK2, HKDC1, PKM, LDH, GAPDH, and ENO1 were the key enzymes in these metabolic pathways with decreased acetylation levels in the form-deprivation myopia group. Altered lysine acetylation of key enzymes in the form-deprived myopic retina might affect the dynamic balance of metabolism in the retinal microenvironment by altering their activity. In conclusion, as the first report on the myopic retinal acetylome, this study provides a reliable basis for further studies on myopic retinal acetylation.
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Affiliation(s)
- Jiaojiao Feng
- Shandong
University of Traditional Chinese Medicine, Jinan 250014, Shandong, China
| | - Xiuyan Zhang
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
- Shandong
Provincial Key Laboratory of Integrated Traditional Chinese and Western
Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Jinan 250002, Shandong, China
| | - Runkuan Li
- Shandong
University of Traditional Chinese Medicine, Jinan 250014, Shandong, China
| | - Ping Zhao
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
- Shandong
Provincial Key Laboratory of Integrated Traditional Chinese and Western
Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Jinan 250002, Shandong, China
| | - Xudong Han
- School
of Medicine, Southeast University, Nanjing 210009, Jiangsu, China
| | - Qiuxin Wu
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
- Shandong
Provincial Key Laboratory of Integrated Traditional Chinese and Western
Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Jinan 250002, Shandong, China
| | - Qingmei Tian
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
- Shandong
Provincial Key Laboratory of Integrated Traditional Chinese and Western
Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Jinan 250002, Shandong, China
| | - Guodong Tang
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
- Shandong
Provincial Key Laboratory of Integrated Traditional Chinese and Western
Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Jinan 250002, Shandong, China
| | - Jike Song
- Shandong
University of Traditional Chinese Medicine, Jinan 250014, Shandong, China
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
| | - Hongsheng Bi
- Affiliated
Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250002, Shandong, China
- Shandong
Provincial Key Laboratory of Integrated Traditional Chinese and Western
Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Jinan 250002, Shandong, China
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27
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Lassen FH, Venkatesh SS, Baya N, Zhou W, Bloemendal A, Neale BM, Kessler BM, Whiffin N, Lindgren CM, Palmer DS. Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.29.23291992. [PMID: 37461573 PMCID: PMC10350147 DOI: 10.1101/2023.06.29.23291992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Exome-sequencing association studies have successfully linked rare protein-coding variation to risk of thousands of diseases. However, the relationship between rare deleterious compound heterozygous (CH) variation and their phenotypic impact has not been fully investigated. Here, we leverage advances in statistical phasing to accurately phase rare variants (MAF ~ 0.001%) in exome sequencing data from 175,587 UK Biobank (UKBB) participants, which we then systematically annotate to identify putatively deleterious CH coding variation. We show that 6.5% of individuals carry such damaging variants in the CH state, with 90% of variants occurring at MAF < 0.34%. Using a logistic mixed model framework, systematically accounting for relatedness, polygenic risk, nearby common variants, and rare variant burden, we investigate recessive effects in common complex diseases. We find six exome-wide significant (P < 1.68 × 10 - 7 ) and 17 nominally significant (P < 5.25 × 10 - 5 ) gene-trait associations. Among these, only four would have been identified without accounting for CH variation in the gene. We further incorporate age-at-diagnosis information from primary care electronic health records, to show that genetic phase influences lifetime risk of disease across 20 gene-trait combinations (FDR < 5%). Using a permutation approach, we find evidence for genetic phase contributing to disease susceptibility for a collection of gene-trait pairs, including FLG-asthma (P = 0.00205 ) and USH2A-visual impairment (P = 0.0084 ). Taken together, we demonstrate the utility of phasing large-scale genetic sequencing cohorts for robust identification of the phenome-wide consequences of compound heterozygosity.
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Affiliation(s)
- Frederik H. Lassen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Samvida S. Venkatesh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Nikolas Baya
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Wei Zhou
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola Whiffin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Population Health Health, Medical Sciences Division University of Oxford, Oxford, United Kingdom
| | - Duncan S. Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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28
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De La Torre AL, Huynh TN, Chang CCY, Pooler DB, Ness DB, Lewis LD, Pannem S, Feng Y, Samkoe KS, Hickey WF, Chang TY. Stealth Liposomes Encapsulating a Potent ACAT1/SOAT1 Inhibitor F12511: Pharmacokinetic, Biodistribution, and Toxicity Studies in Wild-Type Mice and Efficacy Studies in Triple Transgenic Alzheimer's Disease Mice. Int J Mol Sci 2023; 24:11013. [PMID: 37446191 PMCID: PMC10341764 DOI: 10.3390/ijms241311013] [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: 05/07/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Cholesterol is essential for cellular function and is stored as cholesteryl esters (CEs). CEs biosynthesis is catalyzed by the enzymes acyl-CoA:cholesterol acyltransferase 1 and 2 (ACAT1 and ACAT2), with ACAT1 being the primary isoenzyme in most cells in humans. In Alzheimer's Disease, CEs accumulate in vulnerable brain regions. Therefore, ACATs may be promising targets for treating AD. F12511 is a high-affinity ACAT1 inhibitor that has passed phase 1 safety tests for antiatherosclerosis. Previously, we developed a nanoparticle system to encapsulate a large concentration of F12511 into a stealth liposome (DSPE-PEG2000 with phosphatidylcholine). Here, we injected the nanoparticle encapsulated F12511 (nanoparticle F) intravenously (IV) in wild-type mice and performed an HPLC/MS/MS analysis and ACAT enzyme activity measurement. The results demonstrated that F12511 was present within the mouse brain after a single IV but did not overaccumulate in the brain or other tissues after repeated IVs. A histological examination showed that F12511 did not cause overt neurological or systemic toxicity. We then showed that a 2-week IV delivery of nanoparticle F to aging 3xTg AD mice ameliorated amyloidopathy, reduced hyperphosphorylated tau and nonphosphorylated tau, and reduced neuroinflammation. This work lays the foundation for nanoparticle F to be used as a possible therapy for AD and other neurodegenerative diseases.
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Affiliation(s)
- Adrianna L. De La Torre
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (A.L.D.L.T.)
| | - Thao N. Huynh
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (A.L.D.L.T.)
| | - Catherine C. Y. Chang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (A.L.D.L.T.)
| | - Darcy B. Pooler
- Clinical Pharmacology Shared Resource, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03766, USA
| | - Dylan B. Ness
- Clinical Pharmacology Shared Resource, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03766, USA
| | - Lionel D. Lewis
- Clinical Pharmacology Shared Resource, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03766, USA
| | - Sanjana Pannem
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; (S.P.); (Y.F.)
| | - Yichen Feng
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; (S.P.); (Y.F.)
| | - Kimberley S. Samkoe
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; (S.P.); (Y.F.)
| | - William F. Hickey
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03766, USA;
| | - Ta Yuan Chang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (A.L.D.L.T.)
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29
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Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J, Tanneeru D, Deshmukh M, Bassi A, Robinson J, Chaudhary R, Murugan S, Ul-Asar Z, Saleem I, Ishtiaq U, Fatima A, Sheikh SS, Hameed S, Ishaq M, Rasheed SZ, Memon FUR, Jalal A, Abbas S, Frossard P, Fuchsberger C, Forer L, Schoenherr S, Bei Q, Bhangale T, Tom J, Gadde SGK, B V P, Naik NK, Wang M, Kwok PY, Khera AV, Lakshmi BR, Butterworth AS, Chowdhury R, Danesh J, di Angelantonio E, Naheed A, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Ramprasad VL, Kukkle PL, Seshagiri S, Kathiresan S, Ghosh A, Mohan V, Saleheen D, Stawiski EW, Peterson AS. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity. Nat Commun 2023; 14:3377. [PMID: 37291107 PMCID: PMC10250394 DOI: 10.1038/s41467-023-38766-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
- Dept of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - J Fah Sathirapongsasuti
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
| | - Ravi Gupta
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Asif Rasheed
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Radha Venkatesan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Saurabh Belsare
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Ramesh Menon
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Sameer Phalke
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - John Fang
- Thermo Fisher Scientific, Santa Clara, CA, 95051, USA
| | - Deepak Tanneeru
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - Akshi Bassi
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | | | | | - Zameer Ul-Asar
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Imran Saleem
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Unzila Ishtiaq
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Areej Fatima
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | | | | | | | | | | | - Anjum Jalal
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Philippe Frossard
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Qixin Bei
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Product Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA
| | | | - Priya B V
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | | | - Minxian Wang
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Amit V Khera
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, MA, 02115, Boston, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
| | - B R Lakshmi
- MDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Emanuele di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Aliya Naheed
- Initiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh
| | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | | | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Soaham Desai
- Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
| | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod Kumar Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Uday B Muthane
- Parkinson and Ageing Research Foundation, Bengaluru, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Prashanth L Kukkle
- All India Institute of Medical Sciences, Rishikesh, India
- Manipal Hospital, Miller Road, Bengaluru, India
- Parkinson's Disease and Movement Disorders Clinic, Bengaluru, India
| | - Somasekar Seshagiri
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arkasubhra Ghosh
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | - V Mohan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Danish Saleheen
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
- Seymour, Paul and Gloria Milstein Division of Cardiology at Columbia University, New York, NY, 10032, USA
| | - Eric W Stawiski
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
- Caribou Biosciences, Berkeley, CA, 94710, USA
| | - Andrew S Peterson
- MedGenome Inc., Foster City, CA, 94404, USA.
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
- Broadwing Bio, South San Francisco, CA, 94080, USA.
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30
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Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Precise modulation of transcription factor levels identifies features underlying dosage sensitivity. Nat Genet 2023; 55:841-851. [PMID: 37024583 PMCID: PMC10181932 DOI: 10.1038/s41588-023-01366-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Harold S Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ophir D Klein
- Departments of Orofacial Sciences and Pediatrics, Program in Craniofacial Biology, and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | | | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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31
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Spagnuolo CM, Hegele RA. Recent advances in treating hypertriglyceridemia in patients at high risk of cardiovascular disease with apolipoprotein C-III inhibitors. Expert Opin Pharmacother 2023; 24:1013-1020. [PMID: 37114828 DOI: 10.1080/14656566.2023.2206015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
INTRODUCTION Mild-to-moderate hypertriglyceridemia (HTG) is commonly encountered and is associated with atherosclerotic cardiovascular disease (ASCVD). Elevated plasma triglyceride (TG) levels reflect high levels of triglyceride-rich lipoproteins, against which lipid-lowering therapies that reduce low-density lipoprotein cholesterol are relatively ineffective. Apolipoprotein (apo) C-III is a new pharmacological target to reduce triglycerides and potentially also cardiovascular disease risk. AREAS COVERED Here, we evaluate current lipid-lowering therapies and their effect on TG levels; genetic, pre-clinical, cellular, molecular biology, and translational studies that emphasize the importance of apo C-III in the metabolism of TG-rich lipoproteins and ASCVD risk; and clinical trials of pharmacotherapies that reduce TG levels via apo C-III inhibition. The PubMed database was searched using terms: apolipoprotein C-III, ARO-APOC3, atherosclerotic cardiovascular disease, olezarsen, triglycerides, and volanesorsen; study types: clinical trials, systematic reviews, and meta-analyses; and time criterion 2005 to present. EXPERT OPINION Apo C-III inhibition is a promising treatment approach for adults with mild-to-moderate HTG and either established atherosclerotic cardiovascular disease or its risk factors. Biologic agents such as volanesorsen, olezarsen, and ARO-APOC3 significantly reduce plasma levels of apo C-III and TG, although data on cardiovascular outcomes are lacking. Volanesorsen is associated with thrombocytopenia in patients with severe HTG, but other agents appear to be better tolerated. Clinical trials with long-term follow-up of cardiovascular outcomes will establish the validity of apo C-III inhibition.
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Affiliation(s)
- Catherine M Spagnuolo
- Depatment of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Depatment of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Vascular Biology Research Group, Robarts Research Institute, London, Ontario, Canada
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32
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Kostes WW, Brafman DA. The Multifaceted Role of WNT Signaling in Alzheimer's Disease Onset and Age-Related Progression. Cells 2023; 12:cells12081204. [PMID: 37190113 DOI: 10.3390/cells12081204] [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: 03/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The evolutionary conserved WNT signaling pathway orchestrates numerous complex biological processes during development and is critical to the maintenance of tissue integrity and homeostasis in the adult. As it relates to the central nervous system, WNT signaling plays several roles as it relates to neurogenesis, synaptic formation, memory, and learning. Thus, dysfunction of this pathway is associated with multiple diseases and disorders, including several neurodegenerative disorders. Alzheimer's disease (AD) is characterized by several pathologies, synaptic dysfunction, and cognitive decline. In this review, we will discuss the various epidemiological, clinical, and animal studies that demonstrate a precise link between aberrant WNT signaling and AD-associated pathologies. In turn, we will discuss the manner in which WNT signaling influences multiple molecular, biochemical, and cellular pathways upstream of these end-point pathologies. Finally, we will discuss how merging tools and technologies can be used to generate next generation cellular models to dissect the relationship between WNT signaling and AD.
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Affiliation(s)
- William W Kostes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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33
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Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia. Eur J Hum Genet 2023:10.1038/s41431-023-01327-7. [PMID: 36935417 PMCID: PMC10400601 DOI: 10.1038/s41431-023-01327-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/21/2023] Open
Abstract
Ribonuclease inhibitor 1, also known as angiogenin inhibitor 1, encoded by RNH1, is a ubiquitously expressed leucine-rich repeat protein, which is highly conserved in mammalian species. Inactivation of rnh1 in mice causes an embryonically lethal anemia, but the exact biological function of RNH1 in humans remains unknown and no human genetic disease has so far been associated with RNH1. Here, we describe a family with two out of seven siblings affected by a disease characterized by congenital cataract, global developmental delay, myopathy and psychomotor deterioration, seizures and periodic anemia associated with upper respiratory tract infections. A homozygous splice-site variant (c.615-2A > C) in RNH1 segregated with the disease. Sequencing of RNA derived from patient fibroblasts and cDNA analysis of skeletal muscle mRNA showed aberrant splicing with skipping of exon 7. Western blot analysis revealed a total lack of the RNH1 protein. Functional analysis revealed that patient fibroblasts were more sensitive to RNase A exposure, and this phenotype was reversed by transduction with a lentivirus expressing RNH1 to complement patient cells. Our results demonstrate that loss-of-function of RNH1 in humans is associated with a multiorgan developmental disease with recessive inheritance. It may be speculated that the infection-induced deterioration resulted from an increased susceptibility toward extracellular RNases and/or other inflammatory responses normally kept in place by the RNase inhibitor RNH1.
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34
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Singer-Berk M, Gudmundsson S, Baxter S, Seaby EG, England E, Wood JC, Son RG, Watts NA, Karczewski KJ, Harrison SM, MacArthur DG, Rehm HL, O'Donnell-Luria A. Advanced variant classification framework reduces the false positive rate of predicted loss of function (pLoF) variants in population sequencing data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.08.23286955. [PMID: 36945502 PMCID: PMC10029069 DOI: 10.1101/2023.03.08.23286955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Predicted loss of function (pLoF) variants are highly deleterious and play an important role in disease biology, but many of these variants may not actually result in loss-of-function. Here we present a framework that advances interpretation of pLoF variants in research and clinical settings by considering three categories of LoF evasion: (1) predicted rescue by secondary sequence properties, (2) uncertain biological relevance, and (3) potential technical artifacts. We also provide recommendations on adjustments to ACMG/AMP guidelines's PVS1 criterion. Applying this framework to all high-confidence pLoF variants in 22 autosomal recessive disease-genes from the Genome Aggregation Database (gnomAD, v2.1.1) revealed predicted LoF evasion or potential artifacts in 27.3% (304/1,113) of variants. The major reasons were location in the last exon, in a homopolymer repeat, in low per-base expression (pext) score regions, or the presence of cryptic splice rescues. Variants predicted to be potential artifacts or to evade LoF were enriched for ClinVar benign variants. PVS1 was downgraded in 99.4% (162/163) of LoF evading variants assessed, with 17.2% (28/163) downgraded as a result of our framework, adding to previous guidelines. Variant pathogenicity was affected (mostly from likely pathogenic to VUS) in 20 (71.4%) of these 28 variants. This framework guides assessment of pLoF variants beyond standard annotation pipelines, and substantially reduces false positive rates, which is key to ensure accurate LoF variant prediction in both a research and clinical setting.
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Affiliation(s)
- Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Eleina England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jordan C Wood
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel G Son
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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Stankov S, Cuchel M. Gene editing for dyslipidemias: New tools to "cut" lipids. Atherosclerosis 2023; 368:14-24. [PMID: 36725417 PMCID: PMC10493168 DOI: 10.1016/j.atherosclerosis.2023.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/23/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
Effective lipid lowering therapies are essential for the prevention of atherosclerosis and cardiovascular disease. Available treatments have evolved in both their efficacy and their frequency of administration, and currently include monoclonal antibodies, antisense oligonucleotides and siRNA approaches. However, an unmet need remains for more effective and long-lasting therapeutics. Gene editing permanently alters endogenous gene expression and has the potential to revolutionize disease treatment. Despite the existence of several gene editing approaches, the CRISPR/Cas9 system has emerged as the preferred technology because of its high efficiency and relative simplicity. This review provides a general overview of this promising technology and an update on the progress made towards the development of treatments of dyslipidemia. The recently started phase 1b gene editing clinical trial targeting PCSK9 in patients with heterozygous familial hypercholesterolemia and cardiovascular disease highlights how gene editing may become available to treat not only patients affected by rare disorders of lipid metabolism, but also patients that are difficult-to-treat or at high risk. Other targets like ANGPTL3, LDLR, and APOC3 are on track for further pre-clinical development. The identification of novel targets using electronic health record-linked biobanks and human sequencing studies will continue to expand the potential target pool, and clinical assessment of treated patients will provide essential efficacy and safety information on current strategies. Gene editing of genes regulating lipid metabolism holds promise as an exciting new therapeutic approach. However, since gene editing permanently alters a patient's genome, its therapeutic application in humans will require careful safety assessment and ethical considerations.
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Affiliation(s)
- Sylvia Stankov
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Marina Cuchel
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, PA, USA.
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36
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Carss KJ, Deaton AM, Del Rio-Espinola A, Diogo D, Fielden M, Kulkarni DA, Moggs J, Newham P, Nelson MR, Sistare FD, Ward LD, Yuan J. Using human genetics to improve safety assessment of therapeutics. Nat Rev Drug Discov 2023; 22:145-162. [PMID: 36261593 DOI: 10.1038/s41573-022-00561-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.
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Affiliation(s)
| | - Aimee M Deaton
- Amgen, Cambridge, MA, USA.,Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Alberto Del Rio-Espinola
- Novartis Institutes for BioMedical Research, Basel, Switzerland.,GentiBio Inc., Cambridge, MA, USA
| | | | - Mark Fielden
- Amgen, Thousand Oaks, MA, USA.,Kate Therapeutics, San Diego, CA, USA
| | | | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Frank D Sistare
- Merck & Co., West Point, PA, USA.,315 Meadowmont Ln, Chapel Hill, NC, USA
| | - Lucas D Ward
- Amgen, Cambridge, MA, USA. .,Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Jing Yuan
- Amgen, Cambridge, MA, USA.,Pfizer, Cambridge, MA, USA
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Abstract
Hundreds of different genetic causes of chronic kidney disease are now recognized, and while individually rare, taken together they are significant contributors to both adult and pediatric diseases. Traditional genetics approaches relied heavily on the identification of large families with multiple affected members and have been fundamental to the identification of genetic kidney diseases. With the increased utilization of massively parallel sequencing and improvements to genotype imputation, we can analyze rare variants in large cohorts of unrelated individuals, leading to personalized care for patients and significant research advancements. This review evaluates the contribution of rare disorders to patient care and the study of genetic kidney diseases and highlights key advancements that utilize new techniques to improve our ability to identify new gene-disease associations.
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Affiliation(s)
- Mark D Elliott
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA;
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA;
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA;
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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38
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Vihinen M. Systematic errors in annotations of truncations, loss-of-function and synonymous variants. Front Genet 2023; 14:1015017. [PMID: 36713076 PMCID: PMC9880313 DOI: 10.3389/fgene.2023.1015017] [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: 08/09/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.
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Pan K, Xu C, Chen C, Chen S, Zhang Y, Ding X, Xu X, Lv Q. Soluble interleukin-2 receptor combined with interleukin-8 is a powerful predictor of future adverse cardiovascular events in patients with acute myocardial infarction. Front Cardiovasc Med 2023; 10:1110742. [PMID: 37139133 PMCID: PMC10150071 DOI: 10.3389/fcvm.2023.1110742] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/21/2023] [Indexed: 05/05/2023] Open
Abstract
Background Little is known about the role of interleukin (IL) in patients with acute myocardial infarction (MI), especially soluble IL-2 receptor (sIL-2R) and IL-8. We aim to evaluate, in MI patients, the predictive value of serum sIL-2R and IL-8 for future major adverse cardiovascular events (MACEs), and compare them with current biomarkers reflecting myocardial inflammation and injury. Methods This was a prospective, single-center cohort study. We measured serum concentrations of IL-1β, sIL-2R, IL-6, IL-8 and IL-10. Levels of current biomarkers for predicting MACEs were measured, including high-sensitivity C reactive protein, cardiac troponin T and N-terminal pro-brain natriuretic peptide. Clinical events were collected during 1-year and a median of 2.2 years (long-term) follow-up. Results Twenty-four patients (13.8%, 24/173) experienced MACEs during 1-year follow-up and 40 patients (23.1%, 40/173) during long-term follow-up. Of the five interleukins studied, only sIL-2R and IL-8 were independently associated with endpoints during 1-year or long-term follow-up. Patients with high sIL-2R or IL-8 levels (higher than the cutoff value) had a significantly higher risk of MACEs during 1-year (sIL-2R: HR 7.7, 3.3-18.0, p < 0.001; IL-8: HR 4.8, 2.1-10.7, p < 0.001) and long-term (sIL-2R: HR 7.7, 3.3-18.0, p < 0.001; IL-8: HR 4.8, 2.1-10.7, p < 0.001) follow-up. Receiver operator characteristic curve analysis regarding predictive accuracy for MACEs during 1-year follow-up showed that the area under the curve for sIL-2R, IL-8, sIL-2R combined with IL-8 was 0.66 (0.54-0.79, p = 0.011), 0.69 (0.56-0.82, p < 0.001) and 0.720 (0.59-0.85, p < 0.001), whose predictive value were superior to that of current biomarkers. The addition of sIL-2R combined with IL-8 to the existing prediction model resulted in a significant improvement in predictive power (p = 0.029), prompting a 20.8% increase in the proportion of correct classifications. Conclusions High serum sIL-2R combined with IL-8 levels was significantly associated with MACEs during follow-up in patients with MI, suggesting that sIL-2R combined with IL-8 may be a helpful biomarker for identifying the increased risk of new cardiovascular events. IL-2 and IL-8 would be promising therapeutic targets for anti-inflammatory therapy.
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Affiliation(s)
- Kunming Pan
- Department of Pharmacy, Zhongshan Hospital Fudan University, Shanghai, China
| | - Chenqi Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Kidney Disease and Dialysis, Shanghai, China
- Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai, China
- Shanghai Medical Center of Kidney Disease, Shanghai, China
| | - Can Chen
- Department of Pharmacy, Zhongshan Hospital Fudan University, Shanghai, China
| | - Shuqing Chen
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqian Zhang
- Department of Pharmacy, Zhongshan Hospital Fudan University, Shanghai, China
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Kidney Disease and Dialysis, Shanghai, China
- Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai, China
- Shanghai Medical Center of Kidney Disease, Shanghai, China
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Kidney Disease and Dialysis, Shanghai, China
- Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai, China
- Shanghai Medical Center of Kidney Disease, Shanghai, China
- Correspondence: Qianzhou Lv Xialian Xu
| | - Qianzhou Lv
- Department of Pharmacy, Zhongshan Hospital Fudan University, Shanghai, China
- Correspondence: Qianzhou Lv Xialian Xu
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Chen Z, Lehertshuber C, Schunkert H. Genome Editing in Dyslipidemia and Atherosclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:139-156. [DOI: 10.1007/978-981-19-5642-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Tabata T, Masumura Y, Higo S, Kunimatsu S, Kameda S, Inoue H, Okuno S, Ogawa S, Takashima S, Watanabe M, Miyagawa S, Hikoso S, Sakata Y. Multiplexed measurement of cell type-specific calcium kinetics using high-content image analysis combined with targeted gene disruption. Biochem Biophys Res Commun 2022; 637:40-49. [PMID: 36375249 DOI: 10.1016/j.bbrc.2022.10.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Kinetic analysis of intracellular calcium (Ca2+) in cardiomyocytes is commonly used to determine the pathogenicity of genetic mutations identified in patients with dilated cardiomyopathy (DCM). Conventional methods for measuring Ca2+ kinetics target whole-well cultured cardiomyocytes and therefore lack information concerning individual cells. Results are also affected by heterogeneity in cell populations. Here, we developed an analytical method using CRISPR/Cas9 genome editing combined with high-content image analysis (HCIA) that links cell-by-cell Ca2+ kinetics and immunofluorescence images in thousands of cardiomyocytes at a time. After transfecting cultured mouse cardiomyocytes that constitutively express Cas9 with gRNAs, we detected a prolonged action potential duration specifically in Serca2a-depleted ventricular cardiomyocytes in mixed culture. To determine the phenotypic effect of a frameshift mutation in PKD1 in a patient with DCM, we introduced the mutation into Cas9-expressing cardiomyocytes by gRNA transfection and found that it decreases the expression of PKD1-encoded PC1 protein that co-localizes specifically with Serca2a and L-type voltage-gated calcium channels. We also detected the suppression of Ca2+ amplitude in ventricular cardiomyocytes with decreased PC1 expression in mixed culture. Our HCIA method provides comprehensive kinetic and static information on individual cardiomyocytes and allows the pathogenicity of mutations to be determined rapidly.
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Affiliation(s)
- Tomoka Tabata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yuki Masumura
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shuichiro Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan; Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - Suzuka Kunimatsu
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Satoshi Kameda
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hiroyuki Inoue
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shota Okuno
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shou Ogawa
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Seiji Takashima
- Department of Medical Biochemistry, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Mikio Watanabe
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shungo Hikoso
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
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Khera AV, Wang M, Chaffin M, Emdin CA, Samani NJ, Schunkert H, Watkins H, McPherson R, Elosua R, Boerwinkle E, Ardissino D, Butterworth AS, Di Angelantonio E, Naheed A, Danesh J, Chowdhury R, Krumholz HM, Sheu WHH, Rich SS, Rotter JI, Chen YDI, Gabriel S, Lander ES, Saleheen D, Kathiresan S. Gene Sequencing Identifies Perturbation in Nitric Oxide Signaling as a Nonlipid Molecular Subtype of Coronary Artery Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003598. [PMID: 36215124 PMCID: PMC9771961 DOI: 10.1161/circgen.121.003598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/24/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND A key goal of precision medicine is to disaggregate common, complex diseases into discrete molecular subtypes. Rare coding variants in the low-density lipoprotein receptor gene (LDLR) are identified in 1% to 2% of coronary artery disease (CAD) patients, defining a molecular subtype with risk driven by hypercholesterolemia. METHODS To search for additional subtypes, we compared the frequency of rare, predicted loss-of-function and damaging missense variants aggregated within a given gene in 41 081 CAD cases versus 217 115 controls. RESULTS Rare variants in LDLR were most strongly associated with CAD, present in 1% of cases and associated with 4.4-fold increased CAD risk. A second subtype was characterized by variants in endothelial nitric oxide synthase gene (NOS3), a key enzyme regulating vascular tone, endothelial function, and platelet aggregation. A rare predicted loss-of-function or damaging missense variants in NOS3 was present in 0.6% of cases and associated with 2.42-fold increased risk of CAD (95% CI, 1.80-3.26; P=5.50×10-9). These variants were associated with higher systolic blood pressure (+3.25 mm Hg; [95% CI, 1.86-4.65]; P=5.00×10-6) and increased risk of hypertension (adjusted odds ratio 1.31; [95% CI, 1.14-1.51]; P=2.00×10-4) but not circulating cholesterol concentrations, suggesting that, beyond lipid pathways, nitric oxide synthesis is a key nonlipid driver of CAD risk. CONCLUSIONS Beyond LDLR, we identified an additional nonlipid molecular subtype of CAD characterized by rare variants in the NOS3 gene.
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Affiliation(s)
- Amit V. Khera
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
- Cardiology Division, Dept of Medicine, Massachusetts General Hospital, Boston, MA
| | - Minxian Wang
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
- CAS Key Laboratory of Genome Sciences & Information, Beijing Inst of Genomics, Chinese Academy of Sciences & China National Ctr for Bioinformation, Beijing, China
| | - Mark Chaffin
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
| | - Connor A. Emdin
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
| | - Nilesh J. Samani
- Dept of Cardiovascular Sciences, Univ of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Ctr, Glenfield Hospital, Leicester, UK
| | - Heribert Schunkert
- Dept of Cardiology, German Heart Ctr Munich, Technical Univ of Munich, Munich, Germany
- DZHK (German Ctr for Cardiovascular Research), Partner site Munich, Munich Heart Alliance, Munich, Germany
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Dept of Medicine, Univ of Oxford, Headington, UK
- Wellcome Trust Ctr for Human Genetics, Univ of Oxford, Oxford, UK
| | - Ruth McPherson
- Inst for Cardiogenetics, Univ of Lübeck, Lübeck, Schleswig-Holstein, Germany
- German Research Ctr for Cardiovascular Research, Partner Site Hamburg/Lübeck/Kiel & Univ Heart Center Lübeck (J.E.), Berlin, Brandenburg, Germany
- Depts of Medicine & Biochemistry, Univ of Ottawa Heart Inst, Ottawa, ON, Canada
| | - Roberto Elosua
- Cardiovascular Epidemiology & Genetics, Hospital del Mar Research Inst, Barcelona, Spain
- CIBER Enfermedades Cardiovasculares, Barcelona, Spain
- Facultat de Medicina, Universitat de Vic-Central de Cataluña, Barcelona, Spain
| | - Eric Boerwinkle
- Ctr for Human Genetics & Dept. of Epidemiology, Univ of Texas Health Science Ctr School of Public Health, Houston, TX
| | - Diego Ardissino
- Cardiology, Azienda Ospedaliero-Universitaria di Parma, Univ of Parma, Parma, Italy
- Associazione per lo Studio Della Trombosi in Cardiologia, Pavia, Italy
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- National Inst for Health Research Blood & Transplant Research Unit in Donor Health & Genomics, Univ of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus & Univ of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus & Univ of Cambridge, Cambridge, UK
- NIHR Blood & Transplant Research Unit in Donor Health & Genomics, Univ of Cambridge, Cambridge, UK
- BHF Ctr of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, Univ of Cambridge, Cambridge, UK
- Health Data Science Research Ctr, Human Technopole, Milan, Italy
| | - Aliya Naheed
- Initiative for Noncommunicable Bangladesh, Diseases, Health Systems & Population Studies Division, International Ctr for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- National Inst for Health Research Blood & Transplant Research Unit in Donor Health & Genomics, Univ of Cambridge, Cambridge, UK
- British Heart Foundation Ctr of Research Excellence, Univ of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus & Univ of Cambridge, Cambridge, UK
- Dept of Human Genetics, Wellcome Sanger Inst, Hinxton, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- Centre for Non-Communicable Disease Research, Dhaka, Bangladesh
| | - Harlan M. Krumholz
- Section of Cardiovascular Medicine, Dept of Medicine, Yale Univ, New Haven, CT
- Ctr for Outcomes Research & Evaluation, Yale-New Haven Hospital, New Haven, CT
| | - Wayne H-H Sheu
- Cardiovascular Research Ctr, Dept of Medicine, National Yang Ming Univ School of Medicine, Taipei, Taiwan
| | - Stephen S. Rich
- Ctr for Public Health Genomics, Univ of Virginia, Charlottesville, VA
| | - Jerome I. Rotter
- The Inst for Translational Genomics & Population Sciences, Dept of Pediatrics, The Lundquist Inst for Biomedical Innovation at Harbor-UCLA Medical Ctr, Torrance, CA
| | - Yii-der Ida Chen
- The Inst for Translational Genomics & Population Sciences, Dept of Pediatrics, The Lundquist Inst for Biomedical Innovation at Harbor-UCLA Medical Ctr, Torrance, CA
| | - Stacey Gabriel
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
| | - Eric S. Lander
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
- Dept of Biology, MIT, Cambridge, MA
- Dept of Systems Biology, Harvard Medical School, Boston, MA
| | - Danish Saleheen
- Dept of Medicine, Columbia Univ, New York, NY
- Ctr for Non-Communicable Diseases, Karachi, Sindh, Pakistan
| | - Sekar Kathiresan
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
- Cardiology Division, Dept of Medicine, Massachusetts General Hospital, Boston, MA
- Verve Therapeutics, Cambridge, MA
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Federico A, Pavel A, Möbus L, McKean D, del Giudice G, Fortino V, Niehues H, Rastrick J, Eyerich K, Eyerich S, van den Bogaard E, Smith C, Weidinger S, de Rinaldis E, Greco D. The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis. Hum Genomics 2022; 16:62. [PMID: 36437479 PMCID: PMC9703794 DOI: 10.1186/s40246-022-00431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
In recent years, a growing interest in the characterization of the molecular basis of psoriasis has been observed. However, despite the availability of a large amount of molecular data, many pathogenic mechanisms of psoriasis are still poorly understood. In this study, we performed an integrated analysis of 23 public transcriptomic datasets encompassing both lesional and uninvolved skin samples from psoriasis patients. We defined comprehensive gene co-expression network models of psoriatic lesions and uninvolved skin. Moreover, we curated and exploited a wide range of functional information from multiple public sources in order to systematically annotate the inferred networks. The integrated analysis of transcriptomics data and co-expression networks highlighted genes that are frequently dysregulated and show aberrant patterns of connectivity in the psoriatic lesion compared with the unaffected skin. Our approach allowed us to also identify plausible, previously unknown, actors in the expression of the psoriasis phenotype. Finally, we characterized communities of co-expressed genes associated with relevant molecular functions and expression signatures of specific immune cell types associated with the psoriasis lesion. Overall, integrating experimental driven results with curated functional information from public repositories represents an efficient approach to empower knowledge generation about psoriasis and may be applicable to other complex diseases.
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Affiliation(s)
- Antonio Federico
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Tampere Institute for Advanced Studies, Tampere University, Tampere, Finland
| | - Alisa Pavel
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - Lena Möbus
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - David McKean
- Sanofi Immunology and Inflammation Research Therapeutic Area, Precision Immunology Cluster, Cambridge, Massachusetts USA
| | - Giusy del Giudice
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - Vittorio Fortino
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna Niehues
- grid.461760.20000 0004 0580 1253Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Joe Rastrick
- grid.418727.f0000 0004 5903 3819Immunology Therapeutic Area, UCB Pharma, Slough, UK
| | - Kilian Eyerich
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany ,grid.24381.3c0000 0000 9241 5705Unit of Dermatology and Venerology, Department of Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Stefanie Eyerich
- grid.6936.a0000000123222966ZAUM-Center of Allergy and Environment, Technical University and Helmholtz Center Munich, Munich, Germany
| | - Ellen van den Bogaard
- grid.461760.20000 0004 0580 1253Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Catherine Smith
- grid.13097.3c0000 0001 2322 6764St. John’s Institute of Dermatology, King’s College London, London, UK
| | - Stephan Weidinger
- grid.9764.c0000 0001 2153 9986Department of Dermatology, Kiel University, 24105 Kiel, Germany
| | - Emanuele de Rinaldis
- Sanofi Immunology and Inflammation Research Therapeutic Area, Precision Immunology Cluster, Cambridge, Massachusetts USA
| | - Dario Greco
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland ,grid.7737.40000 0004 0410 2071Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Belkadi A, Thareja G, Abbaszadeh F, Badii R, Fauman E, Albagha OM, Suhre K. Identification of PCSK9-like human gene knockouts using metabolomics, proteomics, and whole-genome sequencing in a consanguineous population. CELL GENOMICS 2022; 3:100218. [PMID: 36777185 PMCID: PMC9903797 DOI: 10.1016/j.xgen.2022.100218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/16/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Natural human knockouts of genes associated with desirable outcomes, such as PCSK9 with low levels of LDL-cholesterol, can lead to the discovery of new drug targets and treatments. Rare loss-of-function variants are more likely to be found in the homozygous state in consanguineous populations, and deep molecular phenotyping of blood samples from homozygous carriers can help to discriminate between silent and functional variants. Here, we combined whole-genome sequencing with proteomics and metabolomics for 2,935 individuals from the Qatar Biobank (QBB) to evaluate the power of this approach for finding genes of clinical and pharmaceutical interest. As proof-of-concept, we identified a homozygous carrier of a very rare PCSK9 variant with extremely low circulating PCSK9 levels and low LDL. Our study demonstrates that the chances of finding such variants are about 168 times higher in QBB compared with GnomAD and emphasizes the potential of consanguineous populations for drug discovery.
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Affiliation(s)
- Aziz Belkadi
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Omar M.E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar,Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA,Corresponding author
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Chen A, Tapia H, Goddard JM, Gibney PA. Trehalose and its applications in the food industry. Compr Rev Food Sci Food Saf 2022; 21:5004-5037. [PMID: 36201393 DOI: 10.1111/1541-4337.13048] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/29/2022] [Accepted: 08/31/2022] [Indexed: 01/28/2023]
Abstract
Trehalose is a nonreducing disaccharide composed of two glucose molecules linked by α, α-1,1-glycosidic bond. It is present in a wide variety of organisms, including bacteria, fungi, insects, plants, and invertebrate animals. Trehalose has distinct physical and chemical properties that have been investigated for their biological importance in a range of prokaryotic and eukaryotic species. Emerging research on trehalose has identified untapped opportunities for its application in the food, medical, pharmaceutical, and cosmetics industries. This review summarizes the chemical and biological properties of trehalose, its occurrence and metabolism in living organisms, its protective role in molecule stabilization, and natural and commercial production methods. Utilization of trehalose in the food industry, in particular how it stabilizes protein, fat, carbohydrate, and volatile compounds, is also discussed in depth. Challenges and opportunities of its application in specific applications (e.g., diagnostics, bioprocessing, ingredient technology) are described. We conclude with a discussion on the potential of leveraging the unique molecular properties of trehalose in molecular stabilization for improving the safety, quality, and sustainability of our food systems.
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Affiliation(s)
- Anqi Chen
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Hugo Tapia
- Biology Program, California State University - Channel Islands, Camarillo, California, USA
| | - Julie M Goddard
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
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46
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Selvaraj MS, Li X, Li Z, Pampana A, Zhang DY, Park J, Aslibekyan S, Bis JC, Brody JA, Cade BE, Chuang LM, Chung RH, Curran JE, de Las Fuentes L, de Vries PS, Duggirala R, Freedman BI, Graff M, Guo X, Heard-Costa N, Hidalgo B, Hwu CM, Irvin MR, Kelly TN, Kral BG, Lange L, Li X, Lisa M, Lubitz SA, Manichaikul AW, Michael P, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Reupena MS, Smith JA, Sun X, Taylor KD, Tracy RP, Tsai MY, Wang Z, Wang Y, Bao W, Wilkins JT, Yanek LR, Zhao W, Arnett DK, Blangero J, Boerwinkle E, Bowden DW, Chen YDI, Correa A, Cupples LA, Dutcher SK, Ellinor PT, Fornage M, Gabriel S, Germer S, Gibbs R, He J, Kaplan RC, Kardia SLR, Kim R, Kooperberg C, Loos RJF, Viaud-Martinez KA, Mathias RA, McGarvey ST, Mitchell BD, Nickerson D, North KE, Psaty BM, Redline S, Reiner AP, Vasan RS, Rich SS, Willer C, Rotter JI, Rader DJ, Lin X, Peloso GM, Natarajan P. Whole genome sequence analysis of blood lipid levels in >66,000 individuals. Nat Commun 2022; 13:5995. [PMID: 36220816 PMCID: PMC9553944 DOI: 10.1038/s41467-022-33510-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 09/21/2022] [Indexed: 01/05/2023] Open
Abstract
Blood lipids are heritable modifiable causal factors for coronary artery disease. Despite well-described monogenic and polygenic bases of dyslipidemia, limitations remain in discovery of lipid-associated alleles using whole genome sequencing (WGS), partly due to limited sample sizes, ancestral diversity, and interpretation of clinical significance. Among 66,329 ancestrally diverse (56% non-European) participants, we associate 428M variants from deep-coverage WGS with lipid levels; ~400M variants were not assessed in prior lipids genetic analyses. We find multiple lipid-related genes strongly associated with blood lipids through analysis of common and rare coding variants. We discover several associated rare non-coding variants, largely at Mendelian lipid genes. Notably, we observe rare LDLR intronic variants associated with markedly increased LDL-C, similar to rare LDLR exonic variants. In conclusion, we conducted a systematic whole genome scan for blood lipids expanding the alleles linked to lipids for multiple ancestries and characterize a clinically-relevant rare non-coding variant model for lipids.
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Affiliation(s)
- Margaret Sunitha Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Akhil Pampana
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Y Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 350, Taiwan
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston university School of Medicine, Boston, MA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
- Tulane University Translational Science Institute, New Orleans, LA, 70112, USA
| | - Brian G Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Martin Lisa
- Department of Medicine, George Washington University, Washingron, DC, USA
| | - Steven A Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Ani W Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Preuss Michael
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - May E Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Samoa, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minneosta, Minneapolis, MN, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Wei Bao
- Institute of Public Health, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - John T Wilkins
- Department of Medicine (Cardiology) and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, KY, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Adolfo Correa
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Susan K Dutcher
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 7722, USA
| | | | - Soren Germer
- New York Genome Center, New York, NY, 10013, USA
| | - Richard Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, 77030, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
- Tulane University Translational Science Institute, New Orleans, LA, 70112, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan Kim
- Psomagen, Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- NNF Center for Basic Metabolic Research, University of Copenhagen, Cophenhagen, Denmark
| | | | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Deborah Nickerson
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Kari E North
- Department of Epidemiology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Ramachandran S Vasan
- Sections of Preventive medicine and Epidemiology, Cardiovascular medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Cristen Willer
- University of Michigan, Internal Medicine, Ann Arbor, MI, 48109, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Statistics, Harvard University, Cambridge, MA, 02138, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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de Leusse C, Roman C, Roquelaure B, Fabre A. Estimating the prevalence of congenital disaccharidase deficiencies using allele frequencies from gnomAD. Arch Pediatr 2022; 29:599-603. [PMID: 36167617 DOI: 10.1016/j.arcped.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/04/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND There are currently three known congenital disaccharidase deficiencies: congenital lactase deficiency (CLD), congenital sucrase-isomaltase deficiency (CSD), and congenital trehalase deficiency (CTD). No congenital deficiency has been described for maltase-glucoamylase (MGAM). METHODS A literature search was performed in PubMed for the pathogenic variants CLD, CSD, and CTD and the articles retrieved were analyzed to estimate the prevalence of congenital disaccharidase deficiencies. RESULTS Based on reported variants, the estimated prevalence was 1.3 per 106 births (95% CI: 1.1-1.7) for CLD, and 31.4 per 106 births (95% CI: 28.3-34.8) for CSD. Using data on previously reported variants and variants predicted to be loss-of-function in gnomAD, the overall estimated prevalence was 2.3 per 106 births (95% CI: 1.9-2.9) for CLD, 57.6 per 106 births (95% CI:52.5-63.2) for CSD, and 9.2 per 106 births (95% CI: 2.5-3.7) for CTD. CONCLUSION The prevalence of CSD was found to be relatively high, while for other congenital disaccharidase deficiencies, the estimated prevalence was very low.
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Affiliation(s)
- C de Leusse
- AP-HM, Hôpital de la Timone Enfants, Service de pédiatrie multidisciplinaire, Marseille, France
| | - C Roman
- AP-HM, Hôpital de la Timone Enfants, Service de pédiatrie multidisciplinaire, Marseille, France
| | - B Roquelaure
- AP-HM, Hôpital de la Timone Enfants, Service de pédiatrie multidisciplinaire, Marseille, France
| | - A Fabre
- AP-HM, Hôpital de la Timone Enfants, Service de pédiatrie multidisciplinaire, Marseille, France; Aix Marseille Univ, INSERM, MMG, Marseille, France.
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48
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Lee JH, Oh HK, Choi BS, Lee HH, Lee KJ, Kim UG, Lee J, Lee H, Lee GS, Ahn SJ, Han JP, Kim S, Yeom SC, Song DW. Genome editing-mediated knock-in of therapeutic genes ameliorates the disease phenotype in a model of hemophilia. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:551-562. [PMID: 36090746 PMCID: PMC9403902 DOI: 10.1016/j.omtn.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/01/2022] [Indexed: 11/27/2022]
Abstract
Recently, clinical trials of adeno-associated virus-mediated replacement therapy have suggested long-term therapeutic effects for several genetic diseases of the liver, including hemophilia. However, there remain concerns regarding decreased therapeutic effects when the liver is regenerated or when physiological proliferation occurs. Although genome editing using the clustered regularly interspaced short palindromic repeats/Cas9 system provides an opportunity to solve this problem, low knock-in efficiency may limit its application for therapeutically relevant expression. Here, we identified a novel gene, APOC3, in which a strong promoter facilitated the expression of knocked-in genes in hepatocytes. We also investigated the effects of APOC3 editing using a small Cas9 protein derived from Campylobacter jejuni (CjCas9) in a hemophilic model. We demonstrated that adeno-associated virus-mediated delivery of CjCas9 and donor led to moderate levels of human factor 9 expression in APOC3-humanized mice. Moreover, knock-in-driven expression induced substantial recovery of clotting function in mice with hemophilia B. There was no evidence of off-target editing in vitro or in vivo. Collectively, our findings demonstrated therapeutically relevant expression using a precise and efficient APOC3-editing platform, providing insights into the development of further long-term therapeutics for diverse monogenic liver diseases.
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Li Q, Ren Z, Cao K, Li MM, Wang K, Zhou Y. CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer. SCIENCE ADVANCES 2022; 8:eabj1624. [PMID: 35544644 PMCID: PMC9075800 DOI: 10.1126/sciadv.abj1624] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 03/21/2022] [Indexed: 05/12/2023]
Abstract
Several knowledgebases are manually curated to support clinical interpretations of thousands of hotspot somatic mutations in cancer. However, discrepancies or even conflicting interpretations are observed among these databases. Furthermore, many previously undocumented mutations may have clinical or functional impacts on cancer but are not systematically interpreted by existing knowledgebases. To address these challenges, we developed CancerVar to facilitate automated and standardized interpretations for 13 million somatic mutations based on the AMP/ASCO/CAP 2017 guidelines. We further introduced a deep learning framework to predict oncogenicity for these variants using both functional and clinical features. CancerVar achieved satisfactory performance when compared to several independent knowledgebases and, using clinically curated datasets, demonstrated practical utility in classifying somatic variants. In summary, by integrating clinical guidelines with a deep learning framework, CancerVar facilitates clinical interpretation of somatic variants, reduces manual work, improves consistency in variant classification, and promotes implementation of the guidelines.
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Affiliation(s)
- Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G2C1, Canada
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zilin Ren
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marilyn M. Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Lynch MT, Maloney KA, Pollin TI, Streeten EA, Puffenberger EG, Strauss KA, Shuldiner AR, Mitchell BD. Impact of parental relatedness on reproductive outcomes among the Old Order Amish of Lancaster County. Am J Med Genet A 2022; 188:2119-2128. [PMID: 35442562 DOI: 10.1002/ajmg.a.62757] [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: 10/26/2021] [Revised: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 11/06/2022]
Abstract
Genetically isolated populations that arise due to recent bottleneck events have reduced genetic variation reflecting the common set of founders. Increased genetic relatedness among members of isolated populations puts them at increased risk for some recessive disorders that are rare in outbred populations. To assess the burden on reproductive health, we compared frequencies of adverse reproductive outcomes between Amish couples who were both heterozygous carriers of a highly penetrant pathogenic or likely pathogenic variant and noncarrier couples from the same Amish community. In addition, we evaluated whether overall genetic relatedness of parents was associated with reproductive outcomes. Of the 1824 couples included in our study, 11.1% were at risk of producing a child with an autosomal recessive disorder. Carrier couples reported a lower number of miscarriages compared to noncarrier couples (p = 0.02), although the number of stillbirths (p = 0.3), live births (p = 0.9), and number of pregnancies (p = 0.9) did not differ significantly between groups. In contrast, higher overall relatedness between spouses was positively correlated with number of live births (p < 0.0001), pregnancies (p < 0.0001), and stillbirths (p = 0.03), although not with the number of miscarriages (p = 0.4). These results highlight a complex association between relatedness of parents and reproductive health outcomes in this community.
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Affiliation(s)
- Megan T Lynch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin A Maloney
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Streeten
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
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- Regeneron Genetics Center LLC, Tarrytown, New York, USA
| | | | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
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