1
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Rieder E, Li J, Rodriguez-Flores JL, Taimur Malik M, Abedi V, Zand R. Cysteine-Altering NOTCH3 Variants Are Associated with an Increased Risk of Autoimmune Diseases. J Clin Med 2023; 12:6278. [PMID: 37834922 PMCID: PMC10573689 DOI: 10.3390/jcm12196278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Autoimmune conditions have been reported among patients with cysteine-altering NOTCH3 variants and CADASIL. This study aimed to investigate the occurrence of autoimmune illnesses and markers of inflammation in such populations. Cases were identified who had a NOTCH3 cysteine-altering variant from the Geisinger MyCode® Community Health Initiative (MyCode®). We further performed external validation using the UK Biobank cohort. A cohort of 121 individuals with a NOTCH3 cysteine-altering variant from MyCode® was compared to a control group with no non-synonymous variation in NOTCH3 (n = 184). Medical records were evaluated for inflammatory markers and autoimmune conditions, which were grouped by the organ systems involved. A similar analysis was conducted using data from the UK Biobank (n~450,000). An overall increase in inflammatory markers among participants with a NOTCH3 cysteine-altering variant was observed when compared to an age- and sex-matched MyCode® control group (out of participants with laboratory testing: 50.9% versus 26.7%; p = 0.0047; out of total participants: 23.1% versus 10.9%; p = 0.004). Analysis of UK Biobank data indicated any autoimmune diagnosis (1.63 [1.14, 2.09], p= 2.665 × 10-3) and multiple sclerosis (3.42 [1.67, 6.02], p = 9.681 × 10-4) are associated with a NOTCH3 cysteine-altering variant in any domain. Our findings suggest a possible association between NOTCH3 cysteine-altering variants and autoimmune conditions.
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Affiliation(s)
- Emily Rieder
- Geisinger Commonwealth School of Medicine, Geisinger Health System, Scranton, PA 18510, USA;
- Department of Pediatrics, Duke University, Durham, NC 27705, USA
| | - Jiang Li
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA; (J.L.); (V.A.)
| | | | | | - Vida Abedi
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA; (J.L.); (V.A.)
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
| | - Ramin Zand
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
- Department of Neurology, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
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2
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Rodriguez-Flores JL, Messai-Badji R, Robay A, Temanni R, Syed N, Markovic M, Al-Khayat E, Qafoud F, Nawaz Z, Badii R, Al-Sarraj Y, Mbarek H, Al-Muftah W, Alvi M, Rostami MR, Cruzado JCM, Mezey JG, Shakaki AA, Malek JA, Greenblatt MB, Fakhro KA, Machaca K, Al-Nabet A, Afifi N, Brooks A, Ismail SI, Althani A, Crystal RG. The QChip1 knowledgebase and microarray for precision medicine in Qatar. NPJ Genom Med 2022; 7:3. [PMID: 35046417 PMCID: PMC8770564 DOI: 10.1038/s41525-021-00270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022] Open
Abstract
Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Ramzi Temanni
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Monika Markovic
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Eiman Al-Khayat
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Fatima Qafoud
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Zafar Nawaz
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Ramin Badii
- Weill Cornell Medicine, Doha, Qatar
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
| | | | | | | | | | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | | | | | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Khalid A Fakhro
- Weill Cornell Medicine, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Ajayeb Al-Nabet
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Nahla Afifi
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Andrew Brooks
- RUCDR Infinite Biologics, Piscataway, NJ, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | | | - Asmaa Althani
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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3
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Feusier JE, Arunachalam S, Tashi T, Baker MJ, VanSant-Webb C, Ferdig A, Welm BE, Rodriguez-Flores JL, Ours C, Jorde LB, Prchal JT, Mason CC. Large-Scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers. Blood Cancer Discov 2021; 2:226-237. [PMID: 34027416 DOI: 10.1158/2643-3230.bcd-20-0094] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by detectable hematopoietic-associated gene mutations in a person without evidence of hematologic malignancy. We sought to identify additional cancer-presenting mutations useable for CHIP detection by performing a data mining analysis of 48 somatic mutation studies reporting mutations at diagnoses of 7,430 adult and pediatric patients with hematologic malignancies. Following extraction of 20,141 protein-altering mutations, we identified 434 significantly recurrent mutation hotspots, 364 of which occurred at loci confidently assessable for CHIP. We then performed an additional large-scale analysis of whole exome sequencing data from 4,538 persons belonging to three non-cancer cohorts for clonal mutations. We found the combined cohort prevalence of CHIP with mutations identical to those reported at blood cancer mutation hotspots to be 1.8%, and that some of these CHIP mutations occurred in children. Our findings may help to improve CHIP detection and pre-cancer surveillance for both children and adults.
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Affiliation(s)
- Julie E Feusier
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA.,Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Sasi Arunachalam
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tsewang Tashi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,VA Medical Center, Salt Lake City, UT, USA
| | - Monika J Baker
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Chad VanSant-Webb
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Amber Ferdig
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Bryan E Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | | | - Christopher Ours
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Josef T Prchal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,VA Medical Center, Salt Lake City, UT, USA
| | - Clinton C Mason
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
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4
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Dashti M, Alsaleh H, Rodriguez-Flores JL, Eaaswarkhanth M, Al-Mulla F, Thanaraj TA. Mitochondrial haplogroup J associated with higher risk of obesity in the Qatari population. Sci Rep 2021; 11:1091. [PMID: 33441698 PMCID: PMC7806807 DOI: 10.1038/s41598-020-80040-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
Obesity, a major risk factor for metabolic disorders, is highly prevalent in Qatari population. Maternal transmission of obesity traits can be significant; for example, X haplogroup is known to be associated with lower BMI and body fat mass in Northern Europeans and T haplogroup which is a sister haplogroup of J is known to be associated with obesity in Caucasian subjects from Austria and Southern Italy. We aimed to delineate the mitochondrial haplogroups and variants associated with obesity in Qatari population. Mitochondrial genomes of 864 Qatari individuals were extracted from whole exome sequencing data with an average coverage of 77X. We distributed the participants into 2 sub-cohorts: obese (BMI ≥ 30) and non-obese (BMI < 30); the mean value of BMI from these two groups were 36.5 ± 5.7 and 26.5 ± 2.6, respectively. Mitochondrial haplogroup profiling followed by uni- and multivariant association tests adjusted for covariates were performed. Qatari individuals with mitochondrial haplogroup J had an increased (twofold) risk of obesity (odds ratio [OR] 1.925; 95% CI 1.234–3.002; P = 0.0038; the Bonferroni adjusted P value threshold is 0.0041), whereas the individuals with haplogroup X were at low risk of obesity (OR 0.387; 95% CI 0.175–0.857; P = 0.019). Further, a set of 38 mitochondrial variants were found to be associated (at P ≤ 0.05) with obesity in models adjusted for age, sex and haplogroup.
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Affiliation(s)
- Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Hussain Alsaleh
- Kuwait Identification DNA Laboratory, General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | | | | | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait.
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5
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Oleksyk TK, Wolfsberger WW, Weber AM, Shchubelka K, Oleksyk OT, Levchuk O, Patrus A, Lazar N, Castro-Marquez SO, Hasynets Y, Boldyzhar P, Neymet M, Urbanovych A, Stakhovska V, Malyar K, Chervyakova S, Podoroha O, Kovalchuk N, Rodriguez-Flores JL, Zhou W, Medley S, Battistuzzi F, Liu R, Hou Y, Chen S, Yang H, Yeager M, Dean M, Mills RE, Smolanka V. Genome diversity in Ukraine. Gigascience 2021; 10:6079618. [PMID: 33438729 PMCID: PMC7804371 DOI: 10.1093/gigascience/giaa159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.
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Affiliation(s)
- Taras K Oleksyk
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Walter W Wolfsberger
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khrystyna Shchubelka
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA.,Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Olga T Oleksyk
- A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, Ukraine
| | | | | | | | - Stephanie O Castro-Marquez
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Yaroslava Hasynets
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine
| | - Patricia Boldyzhar
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Mikhailo Neymet
- Velyka Kopanya Family Hospital, Transcarpatia 90330, Ukraine
| | | | | | - Kateryna Malyar
- I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, Ukraine
| | | | | | - Natalia Kovalchuk
- Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, Ukraine
| | | | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Medley
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Fabia Battistuzzi
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Ryan Liu
- BGI Shenzhen, Shenzhen, 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen, 518083, China
| | - Siru Chen
- BGI Shenzhen, Shenzhen, 518083, China
| | | | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Volodymyr Smolanka
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
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6
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Kolchanova S, Kliver S, Komissarov A, Dobrinin P, Tamazian G, Grigorev K, Wolfsberger WW, Majeske AJ, Velez-Valentin J, Valentin de la Rosa R, Paul-Murphy JR, Guzman DSM, Court MH, Rodriguez-Flores JL, Martínez-Cruzado JC, Oleksyk TK. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes (Basel) 2019; 10:E54. [PMID: 30654561 PMCID: PMC6356210 DOI: 10.3390/genes10010054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/13/2018] [Accepted: 01/08/2019] [Indexed: 11/17/2022] Open
Abstract
Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.
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Affiliation(s)
- Sofiia Kolchanova
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany.
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Aleksei Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Pavel Dobrinin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Kirill Grigorev
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
| | - Walter W Wolfsberger
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biological Sciences, Oakland University, 118 Library Drive, Rochester, MI 48309, USA.
- Department of Biological Sciences, Uzhhorod National University, 88000 Uzhhorod, Ukraine.
| | - Audrey J Majeske
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Beaumont BioBank, William Beaumont Hospital, Royal Oak, MI 48073, USA.
| | - Jafet Velez-Valentin
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande, PR 00745, USA.
| | - Ricardo Valentin de la Rosa
- The Recovery Program of the Puerto Rican Parrot at the Rio Abajo State Forest, Departamento de Recursos Naturales y Ambientales de Puerto Rico, Arecibo, PR 00613, USA.
| | - Joanne R Paul-Murphy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - David Sanchez-Migallon Guzman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - Michael H Court
- Program in Individualized Medicine (PrIMe), Pharmacogenomics Laboratory, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, 100 Grimes Way, Pullman, WA 99164, USA.
| | | | | | - Taras K Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biological Sciences, Oakland University, 118 Library Drive, Rochester, MI 48309, USA.
- Department of Biological Sciences, Uzhhorod National University, 88000 Uzhhorod, Ukraine.
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7
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O’Beirne SL, Salit J, Rodriguez-Flores JL, Staudt MR, Abi Khalil C, Fakhro KA, Robay A, Ramstetter MD, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Nabet Al-Marri A, Bener A, Mahmoud M, Chiuchiolo MJ, Al-Shakaki A, Chidiac O, Stadler D, Mezey JG, Crystal RG. Exome sequencing-based identification of novel type 2 diabetes risk allele loci in the Qatari population. PLoS One 2018; 13:e0199837. [PMID: 30212457 PMCID: PMC6136697 DOI: 10.1371/journal.pone.0199837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 06/14/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) susceptibility is influenced by genetic and lifestyle factors. To date, the majority of genetic studies of T2D have been in populations of European and Asian descent. The focus of this study is on genetic variations underlying T2D in Qataris, a population with one of the highest incidences of T2D worldwide. RESULTS Illumina HiSeq exome sequencing was performed on 864 Qatari subjects (574 T2D cases, 290 controls). Sequence kernel association test (SKAT) gene-based analysis identified an association for low frequency potentially deleterious variants in 6 genes. However, these findings were not replicated by SKAT analysis in an independent cohort of 12,699 exomes, primarly due to the absence of low frequency potentially deleterious variants in 5 of the 6 genes. Interestingly one of the genes identified, catenin beta 1 (CTNNB1, β-catenin), is the key effector of the Wnt pathway and interacts with the nuclear receptor transcription factor 7-like 2 (TCF7L2), variants which are the most strongly associated with risk of developing T2D worldwide. Single variant analysis did not identify any associated variants, suggesting the SKAT association signal was not driven by individual variants. None of the 6 associated genes were among 634 previously described T2D genes. CONCLUSIONS The observation that genes not previously linked to T2D in prior studies of European and Asian populations are associated with T2D in Qatar provides new insights into the complexity of T2D pathogenesis and emphasizes the importance of understudied populations when assessing genetic variation in the pathogenesis of common disorders.
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Affiliation(s)
- Sarah L. O’Beirne
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Juan L. Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Michelle R. Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Khalid A. Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
- Division of Translational Medicine, Sidra Medical Research Centre, Doha, Qatar
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Monica D. Ramstetter
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Joel A. Malek
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Mahmoud Zirie
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Amin Jayyousi
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Ramin Badii
- Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Abdulbari Bener
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Mai Mahmoud
- Department of Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Maria J. Chiuchiolo
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Alya Al-Shakaki
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Omar Chidiac
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Dora Stadler
- Department of Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
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8
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Fakhro KA, Elbardisi H, Arafa M, Robay A, Rodriguez-Flores JL, Al-Shakaki A, Syed N, Mezey JG, Abi Khalil C, Malek JA, Al-Ansari A, Al Said S, Crystal RG. Point-of-care whole-exome sequencing of idiopathic male infertility. Genet Med 2018; 20:1365-1373. [PMID: 29790874 DOI: 10.1038/gim.2018.10] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/09/2018] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Nonobstructive azoospermia (NOA) affects 1% of the male population; however, despite state-of-the-art clinical assessment, for most patients the cause is unknown. We capitalized on an analysis of multiplex families in the Middle East to identify highly penetrant genetic causes. METHODS We used whole-exome sequencing (WES) in 8 consanguineous families and combined newly discovered genes with previously reported ones to create a NOA gene panel, which was used to identify additional variants in 75 unrelated idiopathic NOA subjects and 74 fertile controls. RESULTS In five of eight families, we identified rare deleterious recessive variants in CCDC155, NANOS2, SPO11, TEX14, and WNK3 segregating with disease. These genes, which are novel to human NOA, have remarkable testis-specific expression, and murine functional evidence supports roles for them in spermatogenesis. Among 75 unrelated NOA subjects, we identified 4 (~5.3%) with additional recessive variants in these newly discovered genes and 6 with deleterious variants in previously reported NOA genes, yielding an overall genetic etiology for 13.3% subjects versus 0 fertile controls (p = 0.001). CONCLUSION NOA affects millions of men, many of whom remain idiopathic despite extensive laboratory evaluation. The genetic etiology for a substantial fraction of these patients (>50% familial and >10% sporadic) may be discovered by WES at the point of care.
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Affiliation(s)
- Khalid A Fakhro
- Translational Medicine, Sidra Medical and Research Center, Doha, Qatar.,Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | | | - Mohamed Arafa
- Department of Urology, Hamada Medical Corporation, Doha, Qatar.,Andrology Department, Cairo University, Egypt, Egypt
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | | | | | | | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
| | | | | | | | | | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA.
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9
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Yousri NA, Fakhro KA, Robay A, Rodriguez-Flores JL, Mohney RP, Zeriri H, Odeh T, Kader SA, Aldous EK, Thareja G, Kumar M, Al-Shakaki A, Chidiac OM, Mohamoud YA, Mezey JG, Malek JA, Crystal RG, Suhre K. Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population. Nat Commun 2018; 9:333. [PMID: 29362361 PMCID: PMC5780481 DOI: 10.1038/s41467-017-01972-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/30/2017] [Indexed: 12/30/2022] Open
Abstract
Metabolomics-genome-wide association studies (mGWAS) have uncovered many metabolic quantitative trait loci (mQTLs) influencing human metabolic individuality, though predominantly in European cohorts. By combining whole-exome sequencing with a high-resolution metabolomics profiling for a highly consanguineous Middle Eastern population, we discover 21 common variant and 12 functional rare variant mQTLs, of which 45% are novel altogether. We fine-map 10 common variant mQTLs to new metabolite ratio associations, and 11 common variant mQTLs to putative protein-altering variants. This is the first work to report common and rare variant mQTLs linked to diseases and/or pharmacological targets in a consanguineous Arab cohort, with wide implications for precision medicine in the Middle East. Blood metabolites are influenced by a combination of genetic and environmental factors. Here, Yousri and colleagues perform a whole-exome sequencing study in combination with a metabolomics analysis to identify metabolic quantitative trait loci in a Middle Eastern population.
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Affiliation(s)
- Noha A Yousri
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar. .,Computer and Systems Engineering, Alexandria University, Alexandria, Egypt.
| | - Khalid A Fakhro
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar. .,Sidra Medical Research Center, Department of Human Genetics, PO Box 26999, Doha, Qatar.
| | - Amal Robay
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | | | | | - Hassina Zeriri
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Tala Odeh
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Sara Abdul Kader
- Physiology and Biophysics, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Eman K Aldous
- Genomics Core, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Gaurav Thareja
- Physiology and Biophysics, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Manish Kumar
- Physiology and Biophysics, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Alya Al-Shakaki
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Omar M Chidiac
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Yasmin A Mohamoud
- Genomics Core, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Jason G Mezey
- Genetic Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Joel A Malek
- Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar.,Genomics Core, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | - Ronald G Crystal
- Genetic Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Karsten Suhre
- Physiology and Biophysics, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar.
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10
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Song M, Mathews CA, Stewart SE, Shmelkov SV, Mezey JG, Rodriguez-Flores JL, Rasmussen SA, Britton JC, Oh YS, Walkup JT, Lee FS, Glatt CE. Rare Synaptogenesis-Impairing Mutations in SLITRK5 Are Associated with Obsessive Compulsive Disorder. PLoS One 2017; 12:e0169994. [PMID: 28085938 PMCID: PMC5234816 DOI: 10.1371/journal.pone.0169994] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/27/2016] [Indexed: 01/02/2023] Open
Abstract
Obsessive compulsive disorder (OCD) is substantially heritable, but few molecular genetic risk factors have been identified. Knockout mice lacking SLIT and NTRK-Like Family, Member 5 (SLITRK5) display OCD-like phenotypes including serotonin reuptake inhibitor-sensitive pathologic grooming, and corticostriatal dysfunction. Thus, mutations that impair SLITRK5 function may contribute to the genetic risk for OCD. We re-sequenced the protein-coding sequence of the human SLITRK5 gene (SLITRK5) in three hundred and seventy seven OCD subjects and compared rare non-synonymous mutations (RNMs) in that sample with similar mutations in the 1000 Genomes database. We also performed in silico assessments and in vitro functional synaptogenesis assays on the Slitrk5 mutations identified. We identified four RNM's among these OCD subjects. There were no significant differences in the prevalence or in silico effects of rare non-synonymous mutations in the OCD sample versus controls. Direct functional testing of recombinant SLITRK5 proteins found that all mutations identified in OCD subjects impaired synaptogenic activity whereas none of the pseudo-matched mutations identified in 1000 Genomes controls had significant effects on SLITRK5 function (Fisher's exact test P = 0.028). These results demonstrate that rare functional mutations in SLITRK5 contribute to the genetic risk for OCD in human populations. They also highlight the importance of biological characterization of allelic effects in understanding genotype-phenotype relationships as there were no statistical differences in overall prevalence or bioinformatically predicted effects of OCD case versus control mutations. Finally, these results converge with others to highlight the role of aberrant synaptic function in corticostriatal neurons in the pathophysiology of OCD.
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Affiliation(s)
- Minseok Song
- Synaptic Circuit Plasticity Laboratory, Department of Structure & Function of Neural Network, Korea Brain Research Institute, 61 Cheomdan-ro, Dong-gu, Daegu, Korea
| | - Carol A. Mathews
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
| | - S. Evelyn Stewart
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Sergey V. Shmelkov
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, United States of America
- Department of Psychiatry, New York University School of Medicine, New York, NY, United States of America
| | - Jason G. Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, NY, NY United States of America
| | | | - Steven A. Rasmussen
- Department of Psychiatry and Human Behavior, Alpert Medical School, Brown University, Providence, RI, United States of America
| | - Jennifer C. Britton
- Department of Psychology, University of Miami, Miami, FL, United States of America
| | - Yong-Seok Oh
- Department of Brain-Cognitive Science, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpung-myeon, Dalseong-gun, Daegu, Republic of Korea
| | - John T. Walkup
- Department of Psychiatry, Weill Cornell Medical College, New York, New York, United States of America
| | - Francis S. Lee
- Department of Psychiatry, Weill Cornell Medical College, New York, New York, United States of America
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medical College, New York, New York, United States of America
| | - Charles E. Glatt
- Department of Psychiatry, Weill Cornell Medical College, New York, New York, United States of America
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11
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O'Beirne SL, Salit J, Rodriguez-Flores JL, Staudt MR, Abi Khalil C, Fakhro KA, Robay A, Ramstetter MD, Al-Azwani IK, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Nabet Al-Marri A, Chiuchiolo MJ, Al-Shakaki A, Chidiac O, Gharbiah M, Bener A, Stadler D, Hackett NR, Mezey JG, Crystal RG. Correction: Type 2 Diabetes Risk Allele Loci in the Qatari Population. PLoS One 2016; 11:e0161910. [PMID: 27551721 PMCID: PMC4995036 DOI: 10.1371/journal.pone.0161910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0156834.].
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12
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Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, Robay A, Malek JA, Suhre K, Chouchane L, Badii R, Al-Nabet Al-Marri A, Abi Khalil C, Zirie M, Jayyousi A, Salit J, Keinan A, Clark AG, Crystal RG, Mezey JG. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res 2016; 26:151-62. [PMID: 26728717 PMCID: PMC4728368 DOI: 10.1101/gr.191478.115] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/15/2015] [Indexed: 12/26/2022]
Abstract
An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Khalid Fakhro
- Sidra Medical and Research Center, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Francisco Agosto-Perez
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Monica D Ramstetter
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Leonardo Arbiza
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Thomas L Vincent
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Ramin Badii
- Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Mahmoud Zirie
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Amin Jayyousi
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Andrew G Clark
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
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13
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Fakhro KA, Yousri NA, Rodriguez-Flores JL, Robay A, Staudt MR, Agosto-Perez F, Salit J, Malek JA, Suhre K, Jayyousi A, Zirie M, Stadler D, Mezey JG, Crystal RG. Copy number variations in the genome of the Qatari population. BMC Genomics 2015; 16:834. [PMID: 26490036 PMCID: PMC4618522 DOI: 10.1186/s12864-015-1991-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/06/2015] [Indexed: 12/25/2022] Open
Abstract
Background The populations of the Arabian Peninsula remain the least represented in public genetic databases, both in terms of single nucleotide variants and of larger genomic mutations. We present the first high-resolution copy number variation (CNV) map for a Gulf Arab population, using a hybrid approach that integrates array genotyping intensity data and next-generation sequencing reads to call CNVs in the Qatari population. Methods CNVs were detected in 97 unrelated Qatari individuals by running two calling algorithms on each of two primary datasets: high-resolution genotyping (Illumina Omni 2.5M) and high depth whole-genome sequencing (Illumina PE 100bp). The four call-sets were integrated to identify high confidence CNV regions, which were subsequently annotated for putative functional effect and compared to public databases of CNVs in other populations. The availability of genome sequence was leveraged to identify tagging SNPs in high LD with common deletions in this population, enabling their imputation from genotyping experiments in the future. Results Genotyping intensities and genome sequencing data from 97 Qataris were analyzed with four different algorithms and integrated to discover 16,660 high confidence CNV regions (CNVRs) in the total population, affecting ~28 Mb in the median Qatari genome. Up to 40 % of all CNVs affected genes, including novel CNVs affecting Mendelian disease genes, segregating at different frequencies in the 3 major Qatari subpopulations, including those with Bedouin, Persian/South Asian, and African ancestry. Consistent with high consanguinity levels in the Bedouin subpopulation, we found an increased burden for homozygous deletions in this group. In comparison to known CNVs in the comprehensive Database of Genomic Variants, we found that 5 % of all CNVRs in Qataris were completely novel, with an enrichment of CNVs affecting several known chromosomal disorder loci and genes known to regulate sugar metabolism and type 2 diabetes in the Qatari cohort. Finally, we leveraged the availability of genome sequence to find suitable tagging SNPs for common deletions in this population. Conclusion We combine four independently generated datasets from 97 individuals to study CNVs for the first time at high-resolution in a Gulf Arab population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1991-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Khalid A Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar. .,Division of Translational Medicine, Sidra Medical Research Centre, Doha, Qatar.
| | - Noha A Yousri
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar. .,Computer and Systems Engineering, Alexandria University, Alexandria, Egypt.
| | - Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Michelle R Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Francisco Agosto-Perez
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Amin Jayyousi
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar.
| | - Mahmoud Zirie
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar.
| | - Dora Stadler
- Department of Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Jason G Mezey
- Computer and Systems Engineering, Alexandria University, Alexandria, Egypt. .,Department Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA.
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar. .,Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
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14
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Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet 2013; 9:e1004023. [PMID: 24385924 PMCID: PMC3873240 DOI: 10.1371/journal.pgen.1004023] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
Abstract
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations. Populations of the Americas have a rich and heterogeneous genetic and cultural heritage that draws from a diversity of pre-Columbian Native American, European, and African populations. Characterizing this diversity facilitates the development of medical genetics research in diverse populations and the transfer of medical knowledge across populations. It also represents an opportunity to better understand the peopling of the Americas, from the crossing of Beringia to the post-Columbian era. Here, we take advantage sequencing of individuals of Colombian (CLM), Mexican (MXL), and Puerto Rican (PUR) origin by the 1000 Genomes project to improve our demographic models for the peopling of the Americas. The divergence among African, European, and Native American ancestors to these populations enables us to infer the continent of origin at each locus in the sampled genomes. The resulting patterns of ancestry suggest complex post-Columbian migration histories, starting later in CLM than in MXL and PUR. Whereas European ancestral segments show evidence of relatedness, a demographic model of synonymous variation suggests that the Native American Ancestors to MXL, PUR, and CLM panels split within a few hundred years over 12 thousand years ago. Together with early archeological sites in South America, these results support rapid divergence during the initial peopling of the Americas.
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Affiliation(s)
- Simon Gravel
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
- * E-mail:
| | - Fouad Zakharia
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Andres Moreno-Estrada
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jake K. Byrnes
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Ancestry.com DNA LLC, San Francisco, California, United States of America
| | - Marina Muzzio
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE). CCT- CONICET-La Plata, Argentina and Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Eimear E. Kenny
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, Center for Statistical Genetics, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher R. Gignoux
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Maples
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Wilfried Guiblet
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Marc Via
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
- Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - Karla Sandoval
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | | | | | - Taras K. Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | | | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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15
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Rodriguez-Flores JL, Fakhro K, Hackett NR, Salit J, Fuller J, Agosto-Perez F, Gharbiah M, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Nabet Al-Marri A, Chouchane L, Stadler DJ, Mezey JG, Crystal RG. Exome sequencing identifies potential risk variants for Mendelian disorders at high prevalence in Qatar. Hum Mutat 2013; 35:105-16. [PMID: 24123366 DOI: 10.1002/humu.22460] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 09/25/2013] [Indexed: 11/06/2022]
Abstract
Exome sequencing of families of related individuals has been highly successful in identifying genetic polymorphisms responsible for Mendelian disorders. Here, we demonstrate the value of the reverse approach, where we use exome sequencing of a sample of unrelated individuals to analyze allele frequencies of known causal mutations for Mendelian diseases. We sequenced the exomes of 100 individuals representing the three major genetic subgroups of the Qatari population (Q1 Bedouin, Q2 Persian-South Asian, Q3 African) and identified 37 variants in 33 genes with effects on 36 clinically significant Mendelian diseases. These include variants not present in 1000 Genomes and variants at high frequency when compared with 1000 Genomes populations. Several of these Mendelian variants were only segregating in one Qatari subpopulation, where the observed subpopulation specificity trends were confirmed in an independent population of 386 Qataris. Premarital genetic screening in Qatar tests for only four out of the 37, such that this study provides a set of Mendelian disease variants with potential impact on the epidemiological profile of the population that could be incorporated into the testing program if further experimental and clinical characterization confirms high penetrance.
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Rodriguez-Flores JL, Fuller J, Hackett NR, Salit J, Malek JA, Al-Dous E, Chouchane L, Zirie M, Jayoussi A, Mahmoud MA, Crystal RG, Mezey JG. Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population. PLoS One 2012; 7:e47614. [PMID: 23139751 PMCID: PMC3490971 DOI: 10.1371/journal.pone.0047614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/19/2012] [Indexed: 01/30/2023] Open
Abstract
The Qatari population, located at the Arabian migration crossroads of African and Eurasia, is comprised of Bedouin, Persian and African genetic subgroups. By deep exome sequencing of only 7 Qataris, including individuals in each subgroup, we identified 2,750 nonsynonymous SNPs predicted to be deleterious, many of which are linked to human health, or are in genes linked to human health. Many of these SNPs were at significantly elevated deleterious allele frequency in Qataris compared to other populations worldwide. Despite the small sample size, SNP allele frequency was highly correlated with a larger Qatari sample. Together, the data demonstrate that exome sequencing of only a small number of individuals can reveal genetic variations with potential health consequences in understudied populations.
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Affiliation(s)
- Juan L. Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jennifer Fuller
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Neil R. Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Joel A. Malek
- Department of Genetic Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Eman Al-Dous
- Department of Genetic Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Mahmoud Zirie
- Hamad Medical Corporation, Doha, Qatar
- Department of Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | | | - Mai A. Mahmoud
- Department of Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
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17
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Omberg L, Salit J, Hackett N, Fuller J, Matthew R, Chouchane L, Rodriguez-Flores JL, Bustamante C, Crystal RG, Mezey JG. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations. BMC Genet 2012; 13:49. [PMID: 22734698 PMCID: PMC3512499 DOI: 10.1186/1471-2156-13-49] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 06/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. RESULTS Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. CONCLUSIONS By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.
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Affiliation(s)
- Larsson Omberg
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
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18
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Hackett NR, Butler MW, Shaykhiev R, Salit J, Omberg L, Rodriguez-Flores JL, Mezey JG, Strulovici-Barel Y, Wang G, Didon L, Crystal RG. RNA-Seq quantification of the human small airway epithelium transcriptome. BMC Genomics 2012; 13:82. [PMID: 22375630 PMCID: PMC3337229 DOI: 10.1186/1471-2164-13-82] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/29/2012] [Indexed: 01/04/2023] Open
Abstract
Background The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting state and in response to chronic cigarette smoking using massive parallel mRNA sequencing (RNA-Seq). Results The data demonstrate that 48% of SAE expressed genes are ubiquitous, shared with many tissues, with 52% enriched in this cell population. The most highly expressed gene, SCGB1A1, is characteristic of Clara cells, the cell type unique to the human SAE. Among other genes expressed by the SAE are those related to Clara cell differentiation, secretory mucosal defense, and mucociliary differentiation. The high sensitivity of RNA-Seq permitted quantification of gene expression related to infrequent cell populations such as neuroendocrine cells and epithelial stem/progenitor cells. Quantification of the absolute smoking-induced changes in SAE gene expression revealed that, compared to ubiquitous genes, more SAE-enriched genes responded to smoking with up-regulation, and those with the highest basal expression levels showed most dramatic changes. Smoking had no effect on SAE gene splicing, but was associated with a shift in molecular pattern from Clara cell-associated towards the mucus-secreting cell differentiation pathway with multiple features of cancer-associated molecular phenotype. Conclusions These observations provide insights into the unique biology of human SAE by providing quantit-ative assessment of the global transcriptome under physiological conditions and in response to the stress of chronic cigarette smoking.
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Affiliation(s)
- Neil R Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA.
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19
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Courel M, Soler-Jover A, Rodriguez-Flores JL, Mahata SK, Elias S, Montero-Hadjadje M, Anouar Y, Giuly RJ, O'Connor DT, Taupenot L. Pro-hormone secretogranin II regulates dense core secretory granule biogenesis in catecholaminergic cells. J Biol Chem 2010; 285:10030-10043. [PMID: 20061385 PMCID: PMC2843166 DOI: 10.1074/jbc.m109.064196] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 12/16/2009] [Indexed: 11/06/2022] Open
Abstract
Processes underlying the formation of dense core secretory granules (DCGs) of neuroendocrine cells are poorly understood. Here, we present evidence that DCG biogenesis is dependent on the secretory protein secretogranin (Sg) II, a member of the granin family of pro-hormone cargo of DCGs in neuroendocrine cells. Depletion of SgII expression in PC12 cells leads to a decrease in both the number and size of DCGs and impairs DCG trafficking of other regulated hormones. Expression of SgII fusion proteins in a secretory-deficient PC12 variant rescues a regulated secretory pathway. SgII-containing dense core vesicles share morphological and physical properties with bona fide DCGs, are competent for regulated exocytosis, and maintain an acidic luminal pH through the V-type H(+)-translocating ATPase. The granulogenic activity of SgII requires a pH gradient along this secretory pathway. We conclude that SgII is a critical factor for the regulation of DCG biogenesis in neuroendocrine cells, mediating the formation of functional DCGs via its pH-dependent aggregation at the trans-Golgi network.
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Affiliation(s)
- Maïté Courel
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0838.
| | - Alex Soler-Jover
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0838
| | | | - Sushil K Mahata
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0838; Veteran Affairs San Diego Healthcare System, San Diego, California 92093
| | - Salah Elias
- INSERM U982, University of Rouen, 76821 Mont-St.-Aignan Cedex, France
| | | | - Youssef Anouar
- INSERM U982, University of Rouen, 76821 Mont-St.-Aignan Cedex, France
| | - Richard J Giuly
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California 92093
| | - Daniel T O'Connor
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0838; Veteran Affairs San Diego Healthcare System, San Diego, California 92093.
| | - Laurent Taupenot
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0838; Veteran Affairs San Diego Healthcare System, San Diego, California 92093.
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Zhang K, Rao F, Rana BK, Gayen JR, Calegari F, King A, Rosa P, Huttner WB, Stridsberg M, Mahata M, Vaingankar S, Mahboubi V, Salem RM, Rodriguez-Flores JL, Fung MM, Smith DW, Schork NJ, Ziegler MG, Taupenot L, Mahata SK, O'Connor DT. Autonomic function in hypertension; role of genetic variation at the catecholamine storage vesicle protein chromogranin B. ACTA ACUST UNITED AC 2010; 2:46-56. [PMID: 20011129 DOI: 10.1161/circgenetics.108.785659] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kuixing Zhang
- Department of Medicine and CHGG, UCSD School of Medicine, 9500 GilmanDrive, La Jolla, CA 92093-0838. E-mail: or
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21
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Zhang K, Zhang L, Rao F, Brar B, Rodriguez-Flores JL, Taupenot L, O'Connor DT. Human tyrosine hydroxylase natural genetic variation: delineation of functional transcriptional control motifs disrupted in the proximal promoter. ACTA ACUST UNITED AC 2010; 3:187-98. [PMID: 20124442 DOI: 10.1161/circgenetics.109.904813] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Tyrosine hydroxylase (TH) is the rate-limiting enzyme in catecholamine biosynthesis. Common genetic variation at the human TH promoter predicts alterations in autonomic activity and blood pressure, but how such variation influences human traits and, specifically, whether such variation affects transcription are not yet known. METHODS AND RESULTS Pairwise linkage disequilibrium across the TH locus indicated that common promoter variants (C-824T, G-801C, A-581G, and G-494A) were located in a single 5' linkage disequilibrium block in white, black, Hispanic, and Asian populations. Polymorphisms C-824T and A-581G were located in highly conserved regions and were predicted to disrupt known transcriptional control motifs myocyte enhancer factor-2 (MEF2), sex-determining region Y (SRY), and forkhead box D1 (FOXD1) at C-824T and G/C-rich binding factors specificity protein 1 (SP1), activating enhancer-binding protein 2 (AP2)], early growth response protein 1 (EGR1) at A-581G. At C-824T and A-581G, promoter and luciferase reporter plasmids indicated differential allele strength (T>C at C-824T; G>A at A-581G) under both basal circumstances and secretory stimulation. C-824T and A-581G displayed the most pronounced effects on both transcription in cella and catecholamine secretion in vivo. We further probed the functional significance of C-824T and A-581G by cotransfection of trans-activating factors in cella; MEF2, SRY, and FOXD1 differentially activated C-824T, whereas the G/C-rich binding factors SP1, AP2, and EGR1 differentially activated A-581G. At C-824T, factor MEF2 acted in a directionally coordinate fashion (at T>C) to explain the in vivo trait associations, whereas at A-581G, factors SP1, AP2, and EGR1 displayed similar differential actions (at G>A). Finally, chromatin immunoprecipitation demonstrated that the endogenous factors bound to the motifs in cella. CONCLUSIONS We conclude that common genetic variants in the proximal TH promoter, especially at C-824T and A-581G, are functional in cella and alter transcription so as to explain promoter marker-on-trait associations in vivo. MEF2, FOXD1, and SRY contribute to functional differences in C-824T expression, whereas SP1, AP2, and EGR1 mediate those of A-581G. The SRY effect on TH transcription suggests a mechanism whereby male and female sex may differ in sympathetic activity and hence blood pressure. These results point to new strategies for diagnostic and therapeutic intervention into disorders of human autonomic function and their cardiovascular consequences.
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Affiliation(s)
- Kuixing Zhang
- Department of Medicine and Pharmacology, Center for Human Genetics and Genomics, University of California at San Diego, USA
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22
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Wang L, Rao F, Zhang K, Mahata M, Rodriguez-Flores JL, Fung MM, Waalen J, Cockburn MG, Hamilton BA, Mahata SK, O'Connor DT. Neuropeptide Y1Receptor NPY1R. J Am Coll Cardiol 2009; 54:944-54. [DOI: 10.1016/j.jacc.2009.05.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 10/20/2022]
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23
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Biswas N, Rodriguez-Flores JL, Courel M, Gayen JR, Vaingankar SM, Mahata M, Torpey JW, Taupenot L, O'Connor DT, Mahata SK. Cathepsin L colocalizes with chromogranin a in chromaffin vesicles to generate active peptides. Endocrinology 2009; 150:3547-57. [PMID: 19372204 PMCID: PMC2717865 DOI: 10.1210/en.2008-1613] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chromogranin A (CgA), the major soluble protein in chromaffin granules, is proteolytically processed to generate biologically active peptides including the catecholamine release inhibitory peptide catestatin. Here we sought to determine whether cysteine protease cathepsin L (CTSL), a novel enzyme for proteolytic processing of neuropeptides, acts like the well-established serine proteases [prohormone convertase (PC)1/3 or PC2] to generate catestatin by proteolytic processing of CgA. We found that endogenous CTSL colocalizes with CgA in the secretory vesicles of primary rat chromaffin cells. Transfection of PC12 cells with an expression plasmid encoding CTSL directed expression of CTSL toward secretory vesicles. Deconvolution fluorescence microscopy suggested greater colocalization of CTSL with CgA than the lysosomal marker LGP110. The overexpression of CTSL in PC12 cells caused cleavage of full-length CgA. CTSL also cleaved CgA in vitro, in time- and dose-dependent fashion, and specificity of the process was documented through E64 (thiol reagent) inhibition. Mass spectrometry on CTSL-digested recombinant CgA identified a catestatin-region peptide, corresponding to CgA(360-373). The pool of peptides generated from the CTSL cleavage of CgA inhibited nicotine-induced catecholamine secretion from PC12 cells. CTSL processing in the catestatin region was diminished by naturally occurring catestatin variants, especially Pro370Leu and Gly364Ser. Among the CTSL-generated peptides, a subset matched those found in the catestatin region in vivo. These findings indicate that CgA can be a substrate for the cysteine protease CTSL both in vitro and in cella, and their colocalization within chromaffin granules in cella suggests the likelihood of an enzyme/substrate relationship in vivo.
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Affiliation(s)
- Nilima Biswas
- Department of Medicine (0838), University of California, San Diego, La Jolla, California 92093-0838, USA
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24
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Rao F, Zhang L, Wessel J, Zhang K, Wen G, Kennedy BP, Rana BK, Das M, Rodriguez-Flores JL, Smith DW, Cadman PE, Salem RM, Mahata SK, Schork NJ, Taupenot L, Ziegler MG, O'Connor DT. Adrenergic polymorphism and the human stress response. Ann N Y Acad Sci 2009; 1148:282-96. [PMID: 19120120 DOI: 10.1196/annals.1410.085] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Tyrosine hydroxylase (TH) is the rate-limiting enzyme in catecholamine biosynthesis. Does common genetic variation at human TH alter autonomic activity and predispose to cardiovascular disease? We undertook systematic polymorphism discovery at the TH locus, and then tested variants for contributions to sympathetic function and blood pressure. We resequenced 80 ethnically diverse individuals across the TH locus. One hundred seventy-two twin pairs were evaluated for sympathetic traits, including catecholamine production and environmental (cold) stress responses. To evaluate hypertension, we genotyped subjects selected from the most extreme diastolic blood pressure percentiles in the population. Human TH promoter haplotype/reporter plasmids were transfected into chromaffin cells. Forty-nine single nucleotide polymorphisms (SNPs) and one tetranucleotide repeat were discovered, but coding region polymorphism did not account for common phenotypic variation. A block of linkage disequilibrium spanned four common variants in the proximal promoter. Catecholamine secretory traits were significantly heritable, as were stress-induced blood pressure changes. In the TH promoter, significant associations were found for urinary catecholamine excretion, as well as blood pressure response to stress. TH promoter haplotype #2 (TGGG) showed pleiotropy, increasing both norepinephrine excretion and blood pressure during stress. In hypertension, a case-control study (1266 subjects, 53% women) established the effect of C-824T in determination of blood pressure. We conclude that human catecholamine secretory traits are heritable, displaying joint genetic determination (pleiotropy) with autonomic activity and finally with blood pressure in the population. Catecholamine secretion is influenced by genetic variation in the adrenergic pathway encoding catecholamine synthesis, especially at the classically rate-limiting step, TH. The results suggest novel pathophysiological links between a key adrenergic locus, catecholamine metabolism, and blood pressure, and suggest new strategies to approach the mechanism, diagnosis, and treatment of systemic hypertension.
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Affiliation(s)
- Fangwen Rao
- Department of Medicine, University of California at San Diego, La Jolla, California 92093-0838, USA.
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25
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Chen Y, Rao F, Rodriguez-Flores JL, Mahata M, Fung MM, Stridsberg M, Vaingankar SM, Wen G, Salem RM, Das M, Cockburn MG, Schork NJ, Ziegler MG, Hamilton BA, Mahata SK, Taupenot L, O'Connor DT. Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion. J Am Coll Cardiol 2008; 52:1468-81. [PMID: 19017515 DOI: 10.1016/j.jacc.2008.07.047] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 07/14/2008] [Accepted: 07/17/2008] [Indexed: 02/07/2023]
Abstract
OBJECTIVES We aimed to determine whether the common variation at the chromogranin A (CHGA) locus increases susceptibility to hypertension. BACKGROUND CHGA regulates catecholamine storage and release. Previously we systematically identified genetic variants across CHGA. METHODS We carried out dense genotyping across the CHGA locus in >1,000 individuals with the most extreme blood pressures (BPs) in the population, as well as twin pairs with autonomic phenotypes. We also characterized the function of a trait-associated 3'-untranslated region (3'-UTR) variant with transfected CHGA 3'-UTR/luciferase reporter plasmids. RESULTS CHGA was overexpressed in patients with hypertension, especially hypertensive men, and CHGA predicted catecholamines. In individuals with extreme BPs, CHGA genetic variants predicted BP, especially in men, with a peak association occurring in the 3'-UTR at C+87T, accounting for up to approximately 12/ approximately 9 mm Hg. The C+87T genotype predicted CHGA secretion in vivo, with the +87T allele (associated with lower BP) also diminishing plasma CHGA by approximately 10%. The C+87T 3'-UTR variant also predicted the BP response to environmental (cold) stress; the same allele (+87T) that diminished basal BP in the population also decreased the systolic BP response to stress by approximately 12 mm Hg, and the response was smaller in women (by approximately 6 mm Hg). In a chromaffin cell-transfected CHGA 3'-UTR/luciferase reporter plasmid, the +87T allele associated with lower BP also decreased reporter expression by approximately 30%. In cultured chromaffin cells, reducing endogenous CHGA expression by small interfering ribonucleic acid caused approximately two-thirds depletion of catecholamine storage vesicles. CONCLUSIONS Common variant C+87T in the CHGA 3'-UTR is a functional polymorphism causally associated with hypertension especially in men of the population, and we propose steps ("intermediate phenotypes") whereby in a sex-dependent fashion this genetic variant influences the ultimate disease trait. These observations suggest new molecular strategies to probe the pathophysiology, risk, and rational treatment of hypertension.
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Affiliation(s)
- Yuqing Chen
- Department of Medicine, Center for Human Genetics and Genomics, University of California at San Diego, San Diego, California 92093, USA
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26
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Zhang L, Rao F, Zhang K, Khandrika S, Das M, Vaingankar SM, Bao X, Rana BK, Smith DW, Wessel J, Salem RM, Rodriguez-Flores JL, Mahata SK, Schork NJ, Ziegler MG, O’Connor DT. Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk. J Clin Invest 2007; 117:2658-71. [PMID: 17717598 PMCID: PMC1950457 DOI: 10.1172/jci31093] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Accepted: 05/18/2007] [Indexed: 11/17/2022] Open
Abstract
GTP cyclohydrolase 1 (GCH1) is rate limiting in the provision of the cofactor tetrahydrobiopterin for biosynthesis of catecholamines and NO. We asked whether common genetic variation at GCH1 alters transmitter synthesis and predisposes to disease. Here we undertook a systematic search for polymorphisms in GCH1, then tested variants' contributions to NO and catecholamine release as well as autonomic function in twin pairs. Renal NO and neopterin excretions were significantly heritable, as were baroreceptor coupling (heart rate response to BP fluctuation) and pulse interval (1/heart rate). Common GCH1 variant C+243T in the 3'-untranslated region (3'-UTRs) predicted NO excretion, as well as autonomic traits: baroreceptor coupling, maximum pulse interval, and pulse interval variability, though not catecholamine secretion. In individuals with the most extreme BP values in the population, C+243T affected both diastolic and systolic BP, principally in females. In functional studies, C+243T decreased reporter expression in transfected 3'-UTRs plasmids. We conclude that human NO secretion traits are heritable, displaying joint genetic determination with autonomic activity by functional polymorphism at GCH1. Our results document novel pathophysiological links between a key biosynthetic locus and NO metabolism and suggest new strategies for approaching the mechanism, diagnosis, and treatment of risk predictors for cardiovascular diseases such as hypertension.
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Affiliation(s)
- Lian Zhang
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Fangwen Rao
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Kuixing Zhang
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Srikrishna Khandrika
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Madhusudan Das
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Sucheta M. Vaingankar
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Xuping Bao
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Brinda K. Rana
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Douglas W. Smith
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Jennifer Wessel
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Rany M. Salem
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Juan L. Rodriguez-Flores
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Sushil K. Mahata
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Nicholas J. Schork
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Michael G. Ziegler
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
| | - Daniel T. O’Connor
- Department of Medicine,
Department of Psychiatry, and
Department of Biology, UCSD School of Medicine, San Diego, California, USA.
VA San Diego Healthcare System, San Diego, California, USA.
Center for Human Genetics and Genomics and
Department of Pharmacology, UCSD School of Medicine, San Diego, California, USA
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Rao F, Zhang L, Wessel J, Zhang K, Wen G, Kennedy BP, Rana BK, Das M, Rodriguez-Flores JL, Smith DW, Cadman PE, Salem RM, Mahata SK, Schork NJ, Taupenot L, Ziegler MG, O'Connor DT. Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis: discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo. Circulation 2007; 116:993-1006. [PMID: 17698732 DOI: 10.1161/circulationaha.106.682302] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Tyrosine hydroxylase (TH) is the rate-limiting enzyme in catecholamine biosynthesis. Does common genetic variation at human TH alter autonomic activity and predispose to cardiovascular disease? We undertook systematic polymorphism discovery at the TH locus and then tested variants for contributions to sympathetic function and blood pressure. METHODS AND RESULTS We resequenced 80 ethnically diverse individuals across the TH locus. One hundred seventy-two twin pairs were evaluated for sympathetic traits, including catecholamine production, reflex control of the circulation, and environmental (cold) stress responses. To evaluate hypertension, we genotyped subjects selected from the most extreme diastolic blood pressure percentiles in the population. Human TH promoter haplotype/reporter plasmids were transfected into chromaffin cells. Forty-nine single-nucleotide polymorphisms were discovered, but coding region polymorphism did not account for common phenotypic variation. A block of linkage disequilibrium spanned 4 common variants in the proximal promoter. Catecholamine secretory traits were significantly heritable (h2), as were stress-induced blood pressure changes. In the TH promoter, significant associations were found for urinary catecholamine excretion and for blood pressure response to stress. TH promoter haplotype 2 (TGGG) showed pleiotropy, increasing both norepinephrine excretion and blood pressure during stress. Coalescent simulations suggest that TH haplotype 2 likely arose approximately 380,000 years ago. In hypertension, 2 independent case-control studies (1266 subjects with 53% women and 927 subjects with 24% women) replicated the effect of C-824T in the determination of blood pressure. CONCLUSIONS We conclude that human catecholamine secretory traits are heritable, displaying joint genetic determination (pleiotropy) with autonomic activity and finally with blood pressure in the population. Catecholamine secretion is influenced by genetic variation in the adrenergic pathway encoding catecholamine synthesis, especially at the classically rate-limiting step, TH. The results suggest novel pathophysiological links between a key adrenergic locus, catecholamine metabolism, and blood pressure and suggest new strategies to approach the mechanism, diagnosis, and treatment of systemic hypertension.
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Affiliation(s)
- Fangwen Rao
- Department of Medicine, University of California at San Diego, San Diego, Calif, USA
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