1
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Walker CG, Thayer ZM, Marks EJ, Ly KN, Pillai A, Waldie K, Underwood L, Snell RG, Knowles SD, Cha JE, Morton SMB. Association between maternal depression symptoms and child telomere length. J Psychiatr Res 2024; 174:319-325. [PMID: 38685189 DOI: 10.1016/j.jpsychires.2024.04.037] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
The biological mechanisms that explain how adverse early life events influence adult disease risk are poorly understood. One proposed mechanism is via the induction of accelerated biological aging, for which telomere length is considered a biomarker. We aimed to determine if maternal depression pre- and post-partum was associated with telomere length in children at 4 years of age (n = 4299). Mothers completed structured questionnaires assessing depression during pregnancy (Edinburgh Depression Scale), at 9 months (Edinburgh Depression Scale), and at 54 months postpartum (Patient Health Questionnaire 9). Regression methods were used to investigate the relationship between telomere length (DNA from saliva) and maternal depression score recorded at each stage. Significant covariates included in the final model were: maternal age at pregnancy; child sex; child ethnicity; gestational age group, and rurality group. Child telomere length was found to be longer if their mother had a higher depression score at both postpartum time points tested (9 months of age; coefficient 0.003, SE = 0.001, P = 0.01, 54 months of age; coefficient 0.003, SE = 0.002, P = 0.02). Although these findings seem paradoxical, increased telomere length may be an adaptive response to early life stressors. We propose several testable hypotheses for these results and to determine if the positive association between depression and telomere length is a developmental adaptation or an indirect consequence of environmental factors.
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Affiliation(s)
- Caroline G Walker
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand.
| | - Zaneta M Thayer
- Department of Anthropology, Dartmouth College, Hanover, NH, USA
| | - Emma J Marks
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand
| | - Kien N Ly
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand
| | - Avinesh Pillai
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand; Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Karen Waldie
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand; School of Psychology, University of Auckland, Auckland, New Zealand
| | - Lisa Underwood
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Sarah D Knowles
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand; Auckland Museum, Auckland, New Zealand
| | - Jane E Cha
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand
| | - Susan M B Morton
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, New Zealand
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2
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Jiang A, Snell RG, Lehnert K. ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells. Bioinformatics 2024; 40:btae167. [PMID: 38539041 PMCID: PMC11007236 DOI: 10.1093/bioinformatics/btae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
MOTIVATION In recent years, improvements in throughput of single-cell RNA-seq have resulted in a significant increase in the number of cells profiled. The generation of single-cell RNA-seq datasets comprising >1 million cells is becoming increasingly common, giving rise to demands for more efficient computational workflows. RESULTS We present an update to our single-cell RNA-seq analysis web server application, ICARUS (available at https://launch.icarus-scrnaseq.cloud.edu.au) that allows effective analysis of large-scale single-cell RNA-seq datasets. ICARUS v3 utilizes the geometric cell sketching method to subsample cells from the overall dataset for dimensionality reduction and clustering that can be then projected to the large dataset. We then extend this functionality to select a representative subset of cells for downstream data analysis applications including differential expression analysis, gene co-expression network construction, gene regulatory network construction, trajectory analysis, cell-cell communication inference, and cell cluster associations to GWAS traits. We demonstrate analysis of single-cell RNA-seq datasets using ICARUS v3 of 1.3 million cells completed within the hour. AVAILABILITY AND IMPLEMENTATION ICARUS is available at https://launch.icarus-scrnaseq.cloud.edu.au.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
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3
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Lopdell TJ, Trevarton AJ, Moody J, Prowse-Wilkins C, Knowles S, Tiplady K, Chamberlain AJ, Goddard ME, Spelman RJ, Lehnert K, Snell RG, Davis SR, Littlejohn MD. A common regulatory haplotype doubles lactoferrin concentration in milk. Genet Sel Evol 2024; 56:22. [PMID: 38549172 DOI: 10.1186/s12711-024-00890-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/10/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is economically valuable and has an extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence has also been previously observed to regulate lactoferrin content in milk. Here, we conducted genetic mapping of lactoferrin protein concentration in conjunction with RNA-seq, ChIP-seq, and ATAC-seq data to pinpoint candidate causative variants that regulate lactoferrin concentrations in milk. RESULTS We identified a highly-significant lactoferrin protein quantitative trait locus (pQTL), as well as a cis lactotransferrin (LTF) expression QTL (cis-eQTL) mapping to the LTF locus. Using ChIP-seq and ATAC-seq datasets representing lactating mammary tissue samples, we also report a number of regions where the openness of chromatin is under genetic influence. Several of these also show highly significant QTL with genetic signatures similar to those highlighted through pQTL and eQTL analysis. By performing correlation analysis between these QTL, we revealed an ATAC-seq peak in the putative promotor region of LTF, that highlights a set of 115 high-frequency variants that are potentially responsible for these effects. One of the 115 variants (rs110000337), which maps within the ATAC-seq peak, was predicted to alter binding sites of transcription factors known to be involved in lactation-related pathways. CONCLUSIONS Here, we report a regulatory haplotype of 115 variants with conspicuously large impacts on milk lactoferrin concentration. These findings could enable the selection of animals for high-producing specialist herds.
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Affiliation(s)
- Thomas J Lopdell
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand.
| | - Alexander J Trevarton
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Janelle Moody
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Claire Prowse-Wilkins
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- Faculty of Veterinarian and Agricultural Science, The University of Melbourne, Parkville, VIC, Australia
| | - Sarah Knowles
- Auckland War Memorial Museum, Victoria Street West, Auckland, New Zealand
| | - Kathryn Tiplady
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Michael E Goddard
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- Faculty of Veterinarian and Agricultural Science, The University of Melbourne, Parkville, VIC, Australia
| | - Richard J Spelman
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Stephen R Davis
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Mathew D Littlejohn
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
- AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North, New Zealand
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4
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Whitford W, Taylor J, Hayes I, Smith W, Snell RG, Lehnert K, Jacobsen JC. A novel 11 base pair deletion in KMT2C resulting in Kleefstra syndrome 2. Mol Genet Genomic Med 2024; 12:e2350. [PMID: 38146907 PMCID: PMC10767577 DOI: 10.1002/mgg3.2350] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023] Open
Abstract
BACKGROUND Haploinsufficiency of the Lysine Methyltransferase 2C (KMT2C) gene results in the autosomal dominant disorder, Kleefstra syndrome 2. It is an extremely rare neurodevelopmental condition, with 14 previous reports describing varied clinical manifestations including dysmorphic features, delayed psychomotor development and delayed growth. METHODS Here, we describe a female with global developmental delay, attention deficit disorder, dyspraxia, short stature and subtle non-specific dysmorphic features. To identify causative mutations, whole exome sequencing was performed on the proband and her younger brother with discrete clinical presentation. RESULTS Whole exome sequencing identified a novel de novo heterozygous 11 bp deletion in KMT2C (c.1759_1769del), resulting in a frameshift mutation and early termination of the protein (p.Gln587SerfsTer7). This variant is the second-most N-terminal reported mutation, located 4171 amino acids upstream of the critical enzymatically active SET domain (required for chromatin modification and histone methylation). CONCLUSION The majority of the other reported mutations are frameshift mutations upstream of the SET domain and are predicted to result in protein truncation. It is thought that truncation of the SET domain, results functionally in an inability to modify chromatin through histone methylation. This report expands the clinical and genetic characterisation of Kleefstra syndrome 2.
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Affiliation(s)
- Whitney Whitford
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Juliet Taylor
- Genetic Health Service NZTe Whatu OraAucklandNew Zealand
| | - Ian Hayes
- Genetic Health Service NZTe Whatu OraAucklandNew Zealand
| | - Warwick Smith
- Kidz First Child Development ServiceTe Whatu OraAucklandNew Zealand
| | - Russell G. Snell
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Klaus Lehnert
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Jessie C. Jacobsen
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
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5
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Handley RR, Reid SJ, Burch Z, Jacobsen JC, Gillis T, Correia K, Rudiger SR, McLaughlin CJ, Bawden CS, MacDonald ME, Wheeler VC, Snell RG. Somatic CAG Repeat Stability in a Transgenic Sheep Model of Huntington's Disease. J Huntingtons Dis 2024; 13:33-40. [PMID: 38393920 DOI: 10.3233/jhd-231516] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Somatic instability of the huntingtin (HTT) CAG repeat mutation modifies age-at-onset of Huntington's disease (HD). Understanding the mechanism and pathogenic consequences of instability may reveal therapeutic targets. Using small-pool PCR we analyzed CAG instability in the OVT73 sheep model which expresses a full-length human cDNA HTT transgene. Analyses of five- and ten-year old sheep revealed the transgene (CAG)69 repeat was remarkably stable in liver, striatum, and other brain tissues. As OVT73 sheep at ten years old have minimal cell death and behavioral changes, our findings support instability of the HTT expanded-CAG repeat as being required for the progression of HD.
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Affiliation(s)
- Renee R Handley
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Suzanne J Reid
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Zoe Burch
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessie C Jacobsen
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy Gillis
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin Correia
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Skye R Rudiger
- Molecular Biology and Reproductive Technology, Laboratories, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Clive J McLaughlin
- Molecular Biology and Reproductive Technology, Laboratories, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - C Simon Bawden
- Molecular Biology and Reproductive Technology, Laboratories, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Marcy E MacDonald
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Russell G Snell
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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6
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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Author Correction: Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1462. [PMID: 37674040 PMCID: PMC10645586 DOI: 10.1038/s43587-023-00499-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
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Sugrue VJ, Zoller JA, Narayan P, Lu AT, Ortega-Recalde OJ, Grant MJ, Bawden CS, Rudiger SR, Haghani A, Bond DM, Hore RR, Garratt M, Sears KE, Wang N, Yang XW, Snell RG, Hore TA, Horvath S. Correction: Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci. eLife 2023; 12:e92968. [PMID: 37831065 PMCID: PMC10575626 DOI: 10.7554/elife.92968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
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8
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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1144-1166. [PMID: 37563227 PMCID: PMC10501909 DOI: 10.1038/s43587-023-00462-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.
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Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
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9
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Jiang A, Handley RR, Lehnert K, Snell RG. From Pathogenesis to Therapeutics: A Review of 150 Years of Huntington's Disease Research. Int J Mol Sci 2023; 24:13021. [PMID: 37629202 PMCID: PMC10455900 DOI: 10.3390/ijms241613021] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Huntington's disease (HD) is a debilitating neurodegenerative genetic disorder caused by an expanded polyglutamine-coding (CAG) trinucleotide repeat in the huntingtin (HTT) gene. HD behaves as a highly penetrant dominant disorder likely acting through a toxic gain of function by the mutant huntingtin protein. Widespread cellular degeneration of the medium spiny neurons of the caudate nucleus and putamen are responsible for the onset of symptomology that encompasses motor, cognitive, and behavioural abnormalities. Over the past 150 years of HD research since George Huntington published his description, a plethora of pathogenic mechanisms have been proposed with key themes including excitotoxicity, dopaminergic imbalance, mitochondrial dysfunction, metabolic defects, disruption of proteostasis, transcriptional dysregulation, and neuroinflammation. Despite the identification and characterisation of the causative gene and mutation and significant advances in our understanding of the cellular pathology in recent years, a disease-modifying intervention has not yet been clinically approved. This review includes an overview of Huntington's disease, from its genetic aetiology to clinical presentation and its pathogenic manifestation. An updated view of molecular mechanisms and the latest therapeutic developments will also be discussed.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand; (R.R.H.); (K.L.); (R.G.S.)
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10
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Poquérusse J, Nolan M, Thorburn DR, Van Hove JLK, Friederich MW, Love DR, Taylor J, Powell CA, Minczuk M, Snell RG, Lehnert K, Glamuzina E, Jacobsen JC. Severe neonatal onset neuroregression with paroxysmal dystonia and apnoea: Expanding the phenotypic and genotypic spectrum of CARS2-related mitochondrial disease. JIMD Rep 2023; 64:223-232. [PMID: 37151360 PMCID: PMC10159863 DOI: 10.1002/jmd2.12360] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Disorders of mitochondrial function are a collectively common group of genetic diseases in which deficits in core mitochondrial translation machinery, including aminoacyl tRNA synthetases, are key players. Biallelic variants in the CARS2 gene (NM_024537.4), which encodes the mitochondrial aminoacyl-tRNA synthetase for cysteine (CARS2, mt-aaRScys; MIM*612800), result in childhood onset epileptic encephalopathy and complex movement disorder with combined oxidative phosphorylation deficiency (MIM#616672). Prior to this report, eight unique pathogenic variants in the CARS2 gene had been reported in seven individuals. Here, we describe a male who presented in the third week of life with apnoea. He rapidly deteriorated with paroxysmal dystonic crises and apnoea resulting in death at 16 weeks. He had no evidence of seizure activity or multisystem disease and had normal brain imaging. Skeletal muscle biopsy revealed a combined disorder of oxidative phosphorylation. Whole-exome sequencing identified biallelic variants in the CARS2 gene: one novel (c.1478T>C, p.Phe493Ser), and one previously reported (c.655G>A, p.Ala219Thr; rs727505361). Northern blot analysis of RNA isolated from the patient's fibroblasts confirmed a clear defect in aminoacylation of the mitochondrial tRNA for cysteine (mt-tRNACys). To our knowledge, this is the earliest reported case of CARS2 deficiency with severe, early onset dystonia and apnoea, without epilepsy.
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Affiliation(s)
- Jessie Poquérusse
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Melinda Nolan
- Department of NeurologyStarship Children's HealthAucklandNew Zealand
| | - David R. Thorburn
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsThe University of MelbourneMelbourneVictoriaAustralia
| | - Johan L. K. Van Hove
- Department of Pediatrics, School of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Marisa W. Friederich
- Department of Pediatrics, School of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Donald R. Love
- Diagnostic GeneticsLabPLUS, Auckland City HospitalAucklandNew Zealand
- Present address:
Division Chief, Pathology GeneticsSidra MedicineDohaQatar
| | - Juliet Taylor
- Genetic Health Service New ZealandAuckland City HospitalAucklandNew Zealand
| | | | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Russell G. Snell
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Klaus Lehnert
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic ServiceAuckland City HospitalAucklandNew Zealand
| | - Jessie C. Jacobsen
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
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11
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Jiang A, You L, Snell RG, Lehnert K. Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0. NAR Genom Bioinform 2023; 5:lqad032. [PMID: 37007589 PMCID: PMC10052380 DOI: 10.1093/nargab/lqad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/17/2023] [Accepted: 03/18/2023] [Indexed: 04/01/2023] Open
Abstract
Complex biological traits and disease often involve patterns of gene expression that can be characterised and examined. Here we present ICARUS v2.0, an update to our single cell RNA-seq analysis web server with additional tools to investigate gene networks and understand core patterns of gene regulation in relation to biological traits. ICARUS v2.0 enables gene co-expression analysis with MEGENA, transcription factor regulated network identification with SCENIC, trajectory analysis with Monocle3, and characterisation of cell-cell communication with CellChat. Cell cluster gene expression profiles may be examined against Genome Wide Association Studies with MAGMA to find significant associations with GWAS traits. Additionally, differentially expressed genes may be compared against the Drug-Gene Interaction database (DGIdb 4.0) to facilitate drug discovery. ICARUS v2.0 offers a comprehensive toolbox of the latest single cell RNA-seq analysis methodologies packed into an efficient, user friendly, tutorial style web server application (accessible at https://launch.icarus-scrnaseq.cloud.edu.au/) that enables single cell RNA-seq analysis tailored to the user's dataset.
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Affiliation(s)
- Andrew Jiang
- To whom correspondence should be addressed. Tel: +64 3737599 (Ext 85059);
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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12
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Trevarton AJ, Mears ER, Moody J, Lopdell TJ, Chometon TQ, Taylor JA, Wang CJ, Littlejohn MD, Snell RG. Development of SpCas9-expressing bovine mammary epithelial cell lines. In Vitro Cell Dev Biol Anim 2023; 59:163-165. [PMID: 36930414 DOI: 10.1007/s11626-023-00756-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Affiliation(s)
- Alexander J Trevarton
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand.
| | - Emily R Mears
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Janelle Moody
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | | | - Thaize Q Chometon
- Auckland Cytometry, Faculty of Sciences, The University of Auckland, Auckland, New Zealand
| | - John A Taylor
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Carol J Wang
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Mathew D Littlejohn
- Livestock Improvement Corporation, Newstead, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
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13
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Whitford W, Hawkins V, Moodley KS, Grant MJ, Lehnert K, Snell RG, Jacobsen JC. Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer. Sci Rep 2022; 12:8572. [PMID: 35595858 PMCID: PMC9122479 DOI: 10.1038/s41598-022-12613-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
Rapid, cost-effective identification of genetic variants in small candidate genomic regions remains a challenge, particularly for less well equipped or lower throughput laboratories. The application of Oxford Nanopore Technologies’ MinION sequencer has the potential to fulfil this requirement. We demonstrate a proof of concept for a multiplexing assay that pools PCR amplicons for MinION sequencing to enable sequencing of multiple templates from multiple individuals, which could be applied to gene-targeted diagnostics. A combined strategy of barcoding and sample pooling was developed for simultaneous multiplex MinION sequencing of 100 PCR amplicons. The amplicons are family-specific, spanning a total of 30 loci in DNA isolated from 82 human neurodevelopmental cases and family members. The target regions were chosen for further interrogation because a potentially disease-causative variant had been identified in affected individuals following Illumina exome sequencing. The pooled MinION sequences were deconvoluted by aligning to custom references using the minimap2 aligner software. Our multiplexing approach produced an interpretable and expected sequence from 29 of the 30 targeted genetic loci. The sequence variant which was not correctly resolved in the MinION sequence was adjacent to a five nucleotide homopolymer. It is already known that homopolymers present a resolution problem with the MinION approach. Interestingly despite equimolar quantities of PCR amplicon pooled for sequencing, significant variation in the depth of coverage (127×–19,626×; mean = 8321×, std err = 452.99) was observed. We observed independent relationships between depth of coverage and target length, and depth of coverage and GC content. These relationships demonstrate biases of the MinION sequencer for longer templates and those with lower GC content. We demonstrate an efficient approach for variant discovery or confirmation from short DNA templates using the MinION sequencing device. With less than 130 × depth of coverage required for accurate genotyping, the methodology described here allows for rapid highly multiplexed targeted sequencing of large numbers of samples in a minimally equipped laboratory with a potential cost as much 200 × less than that from Sanger sequencing.
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Affiliation(s)
- Whitney Whitford
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. .,Centre for Brain Research, The University of Auckland, Auckland, New Zealand.
| | - Victoria Hawkins
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Kriebashne S Moodley
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Matthew J Grant
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
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14
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Jiang A, Lehnert K, You L, Snell RG. ICARUS, an interactive web server for single cell RNA-seq analysis. Nucleic Acids Res 2022; 50:W427-W433. [PMID: 35536286 PMCID: PMC9252722 DOI: 10.1093/nar/gkac322] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 03/24/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023] Open
Abstract
Here we present ICARUS, a web server to enable users without experience in R to undertake single cell RNA-seq analysis. The focal point of ICARUS is its intuitive tutorial-style user interface, designed to guide logical navigation through the multitude of pre-processing, analysis and visualization steps. ICARUS is easily accessible through a dedicated web server (https://launch.icarus-scrnaseq.cloud.edu.au/) and avoids installation of software on the user's computer. Notable features include the facility to apply quality control thresholds and adjust dimensionality reduction and cell clustering parameters. Data is visualized through 2D/3D UMAP and t-SNE plots and may be curated to remove potential confounders such as cell cycle heterogeneity. ICARUS offers flexible differential expression analysis with user-defined cell groups and gene set enrichment analysis to identify likely affected biological pathways. Eleven organisms including human, dog, mouse, rat, zebrafish, fruit fly, nematode, yeast, cattle, chicken and pig are currently supported. Visualization of multimodal data including those generated by CITE-seq and the 10X Genomics Multiome kit is included. ICARUS incorporates a function to save the current state of analysis avoiding computationally intensive steps during repeat analysis. The complete analysis of a typical single cell RNA-seq dataset by inexperienced users may be achieved in 1-2 h.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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15
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Davis SR, Ward HE, Kelly V, Palmer D, Ankersmit-Udy AE, Lopdell TJ, Berry SD, Littlejohn MD, Tiplady K, Adams LF, Carnie K, Burrett A, Thomas N, Snell RG, Spelman RJ, Lehnert K. Screening for phenotypic outliers identifies an unusually low concentration of a β-lactoglobulin B protein isoform in bovine milk caused by a synonymous SNP. Genet Sel Evol 2022; 54:22. [PMID: 35296234 PMCID: PMC8925192 DOI: 10.1186/s12711-022-00711-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
Background Milk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms of the whey protein, β-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration. Results A cohort of cows, from a single sire family, was identified that produced milk containing a low concentration of the BLG B protein isoform. A genome-wide association study (GWAS) of BLG B protein isoform concentration in milk from AB heterozygous cows, detected a group of highly significant single nucleotide polymorphisms (SNPs) within or close to the BLG gene. Among these was a synonymous G/A variation at position + 78 bp in exon 1 of the BLG gene (chr11:103256256G > A). The effect of the A allele of this SNP (which we named B’) on BLG expression was evaluated in a luciferase reporter assay in transfected CHO-K1 and MCF-7 cells. In both cell types, the presence of the B’ allele in a plasmid containing the bovine BLG gene from -922 to + 898 bp (relative to the transcription initiation site) resulted in a 60% relative reduction in mRNA expression, compared to the plasmid containing the wild-type B sequence allele. Examination of a mammary RNAseq dataset (n = 391) identified 14 heterozygous carriers of the B’ allele which were homozygous for the BLG B protein isoform (BB’). The level of expression of the BLG B’ allele was 41.9 ± 1.0% of that of the wild-type BLG B allele. Milk samples from three cows, homozygous for the A allele at chr11:103,256,256 (B’B’), were analysed (HPLC) and showed BLG concentrations of 1.04, 1.26 and 1.83 g/L relative to a mean of 4.84 g/L in milk from 16 herd contemporaries of mixed (A and B) BLG genotypes. The mechanism by which B’ downregulates milk BLG concentration remains to be determined. Conclusions High-throughput screening and identification of outliers, enabled the discovery of a synonymous G > A mutation in exon 1 of the B allele of the BLG gene (B’), which reduced the milk concentration of β-lactoglobulin B protein isoform, by more than 50%. Milk from cows carrying the B’ allele is expected to have improved processing characteristics, particularly for cheese-making. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00711-z.
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Affiliation(s)
- Stephen R Davis
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand. .,ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand.
| | - Hamish E Ward
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Van Kelly
- School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - David Palmer
- School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Alexandra E Ankersmit-Udy
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Thomas J Lopdell
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Sarah D Berry
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Mathew D Littlejohn
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Kathryn Tiplady
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Linda F Adams
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Katie Carnie
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Alayna Burrett
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Natalie Thomas
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
| | - Russell G Snell
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Richard J Spelman
- Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Klaus Lehnert
- ViaLactia Biosciences Ltd., a subsidiary (now closed) of Fonterra Co-Operative Ltd., Fanshawe Street, Auckland, New Zealand
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16
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Shelling AN, Bicknell LS, Bohlander SS, Cox MP, Filoche SK, Fraser HG, Gamet K, Lacaze P, Murphy R, Snell RG, Sporle A, Te Aika B, Purcell RV, Tiller JM. Genomic discrimination in New Zealand health and life insurance. AGenDA: Against Genomic Discrimination in Aotearoa. N Z Med J 2022; 135:7-12. [PMID: 35728166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Andrew N Shelling
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, University of Auckland, Auckland
| | | | - Stefan S Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North
| | - Sara K Filoche
- Department of Obstetrics, Gynaecology and Women's Health, University of Otago Wellington, Wellington
| | | | | | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Rinki Murphy
- Department of Medicine, School of Medicine, University of Auckland, Auckland
| | - Russell G Snell
- Centre for Brain Research and School of Biological Sciences, University of Auckland, Auckland
| | - Andrew Sporle
- Department of Statistics, University of Auckland, Auckland
| | - Ben Te Aika
- Genomics Aotearoa, University of Otago, Dunedin
| | | | - Jane M Tiller
- School of Public Health and Preventive Medicine, Monash University, Faculty of Medicine, Nursing and Health Sciences, Melbourne, Australia
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17
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Jiang A, Ankersmit-Udy A, Turner SA, Scholtens M, Littlejohn MD, Lopez-Villalobos N, Proser CG, Snell RG, Lehnert K. A Capra hircus chromosome 19 locus linked to milk production influences mammary conformation. J Anim Sci Biotechnol 2022; 13:4. [PMID: 35144696 PMCID: PMC8832686 DOI: 10.1186/s40104-021-00667-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/01/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background Economically important milk production traits including milk volume, milk fat and protein yield vary considerably across dairy goats in New Zealand. A significant portion of the variation is attributable to genetic variation. Discovery of genetic markers linked to milk production traits can be utilised to drive selection of high-performance animals. A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait locus (QTL) located on chromosome 19. The most significantly associated single nucleotide polymorphism (SNP) marker for this locus is located at position 26,610,610 (SNP marker rs268292132). This locus is associated with multiple milk production traits including fat, protein and volume. The predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2 kg fat, 1.9 kg protein and 73.6 kg milk yield. An outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic effects. An adverse relationship between milk production and udder health traits has been reported at this locus. Therefore, a genome wide association study was undertaken looking for loci associated with udder traits. Results The QTL and production associated marker rs268292132 was identified in this study to also be associated with several goat udder traits including udder depth (UD), fore udder attachment (FUA) and rear udder attachment (RUA). Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610 (SNP marker rs268292132) associated with an adverse change in UD, FUA and RUA. Conclusions Our study has confirmed the negative relationship between udder traits and production traits in the NZ goat population. We have found that the frequency of the high production allele is relatively high in the NZ goat population, indicating that its effect on udder conformation is not significantly detrimental on animal health. It will however be important to monitor udder conformation as the chromosome 19 locus is progressively implemented for marker assisted selection. It will also be of interest to determine if the gene underlying the production QTL has a direct effect on mammary gland morphology or whether the changes observed are a consequence of the increased milk volume. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00667-y.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alex Ankersmit-Udy
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - Mathew D Littlejohn
- AL Rae Centre of Genetics and Breeding, Massey University, Hamilton, New Zealand
| | - Nicolas Lopez-Villalobos
- Dairy Cattle Breeding and Genetics, School of Agriculture & Environment, Massey University, Hamilton, New Zealand
| | | | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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18
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Mears ER, Handley RR, Grant MJ, Reid SJ, Day BT, Rudiger SR, McLaughlan CJ, Verma PJ, Bawden SC, Patassini S, Unwin RD, Cooper GJS, Gusella JF, MacDonald ME, Brauning R, Maclean P, Pearson JF, Waldvogel HJ, Faull RLM, Snell RG. A Multi-omic Huntington's Disease Transgenic Sheep-Model Database for Investigating Disease Pathogenesis. J Huntingtons Dis 2021; 10:423-434. [PMID: 34420978 PMCID: PMC8673501 DOI: 10.3233/jhd-210482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 11/15/2022]
Abstract
Background: The pathological mechanism of cellular dysfunction and death in Huntington’s disease (HD) is not well defined. Our transgenic HD sheep model (OVT73) was generated to investigate these mechanisms and for therapeutic testing. One particular cohort of animals has undergone focused investigation resulting in a large interrelated multi-omic dataset, with statistically significant changes observed comparing OVT73 and control ‘omic’ profiles and reported in literature. Objective: Here we make this dataset publicly available for the advancement of HD pathogenic mechanism discovery. Methods: To enable investigation in a user-friendly format, we integrated seven multi-omic datasets from a cohort of 5-year-old OVT73 (n = 6) and control (n = 6) sheep into a single database utilising the programming language R. It includes high-throughput transcriptomic, metabolomic and proteomic data from blood, brain, and other tissues. Results: We present the ‘multi-omic’ HD sheep database as a queryable web-based platform that can be used by the wider HD research community (https://hdsheep.cer.auckland.ac.nz/). The database is supported with a suite of simple automated statistical analysis functions for rapid exploratory analyses. We present examples of its use that validates the integrity relative to results previously reported. The data may also be downloaded for user determined analysis. Conclusion: We propose the use of this online database as a hypothesis generator and method to confirm/refute findings made from patient samples and alternate model systems, to expand our understanding of HD pathogenesis. Importantly, additional tissue samples are available for further investigation of this cohort.
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Affiliation(s)
- Emily R Mears
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Renee R Handley
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Matthew J Grant
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Suzanne J Reid
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Benjamin T Day
- High Performance Sport New Zealand, Mairangi Bay, Auckland, New Zealand
| | - Skye R Rudiger
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, Livestock Sciences Division, Rosedale, SA, Australia
| | - Clive J McLaughlan
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, Livestock Sciences Division, Rosedale, SA, Australia
| | - Paul J Verma
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, Livestock Sciences Division, Rosedale, SA, Australia
| | - Simon C Bawden
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, Livestock Sciences Division, Rosedale, SA, Australia
| | - Stefano Patassini
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK.,Division of Cardiovascular Science, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK.,Division of Cardiovascular Science, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Garth J S Cooper
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK.,Division of Cardiovascular Science, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Rudiger Brauning
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Paul Maclean
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Henry J Waldvogel
- Centre for Brain Research, Faculty of Medical and Health Science, the University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Centre for Brain Research, Faculty of Medical and Health Science, the University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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19
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Sugrue VJ, Zoller JA, Narayan P, Lu AT, Ortega-Recalde OJ, Grant MJ, Bawden CS, Rudiger SR, Haghani A, Bond DM, Hore RR, Garratt M, Sears KE, Wang N, Yang XW, Snell RG, Hore TA, Horvath S. Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci. eLife 2021; 10:e64932. [PMID: 34227937 PMCID: PMC8260231 DOI: 10.7554/elife.64932] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
In mammals, females generally live longer than males. Nevertheless, the mechanisms underpinning sex-dependent longevity are currently unclear. Epigenetic clocks are powerful biological biomarkers capable of precisely estimating chronological age and identifying novel factors influencing the aging rate using only DNA methylation data. In this study, we developed the first epigenetic clock for domesticated sheep (Ovis aries), which can predict chronological age with a median absolute error of 5.1 months. We have discovered that castrated male sheep have a decelerated aging rate compared to intact males, mediated at least in part by the removal of androgens. Furthermore, we identified several androgen-sensitive CpG dinucleotides that become progressively hypomethylated with age in intact males, but remain stable in castrated males and females. Comparable sex-specific methylation differences in MKLN1 also exist in bat skin and a range of mouse tissues that have high androgen receptor expression, indicating that it may drive androgen-dependent hypomethylation in divergent mammalian species. In characterizing these sites, we identify biologically plausible mechanisms explaining how androgens drive male-accelerated aging.
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Affiliation(s)
| | - Joseph Alan Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los AngelesLos AngelesUnited States
| | - Pritika Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | | | - Matthew J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - C Simon Bawden
- Livestock and Farming Systems, South Australian Research and Development InstituteRoseworthyAustralia
| | - Skye R Rudiger
- Livestock and Farming Systems, South Australian Research and Development InstituteRoseworthyAustralia
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Donna M Bond
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Reuben R Hore
- Blackstone Hill Station, Becks, RD2OmakauNew Zealand
| | - Michael Garratt
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLALos AngelesUnited States
| | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (UCLA)Los AngelesUnited States
| | - Xiangdong William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (UCLA)Los AngelesUnited States
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - Timothy A Hore
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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20
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McLean ZL, Appleby SJ, Wei J, Snell RG, Oback B. Front Cover Image, Volume 88, Issue 1, January 2021. Mol Reprod Dev 2021. [DOI: 10.1002/mrd.23453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Zachariah L. McLean
- Reproduction, AgResearch, Ruakura Research Centre Hamilton
- Applied Translational Research Group and Centre for Brain Research, School of Biological Sciences University of Auckland Auckland New Zealand
| | - Sarah J. Appleby
- Reproduction, AgResearch, Ruakura Research Centre Hamilton
- Department of Molecular Medicine and Pathology University of Auckland Auckland New Zealand
| | - Jingwei Wei
- Reproduction, AgResearch, Ruakura Research Centre Hamilton
| | - Russell G. Snell
- Applied Translational Research Group and Centre for Brain Research, School of Biological Sciences University of Auckland Auckland New Zealand
| | - Björn Oback
- Reproduction, AgResearch, Ruakura Research Centre Hamilton
- Department of Molecular Medicine and Pathology University of Auckland Auckland New Zealand
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21
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McLean ZL, Appleby SJ, Wei J, Snell RG, Oback B. Testes of DAZL null neonatal sheep lack prospermatogonia but maintain normal somatic cell morphology and marker expression. Mol Reprod Dev 2020; 88:3-14. [PMID: 33251684 DOI: 10.1002/mrd.23443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 01/21/2023]
Abstract
Multiplying the germline would increase the number of offspring that can be produced from selected animals, accelerating genetic improvement for livestock breeding. This could be achieved by producing multiple chimaeric animals, each carrying a mix of donor and host germ cells in their gonads. However, such chimaeric germlines would produce offspring from both donor and host genotypes, limiting the rate of genetic improvement. To resolve this problem, we disrupted the RNA-binding protein DAZL and generated germ cell-deficient host animals. Using Cas9-mediated homology-directed repair (HDR), we introduced a DAZL loss-of-function mutation in male ovine fetal fibroblasts. Following manual single cell isolation, 4/48 (8.3%) of donor cell strains were homozygously HDR-edited. Sequence-validated strains were used as nuclear donors for somatic cell cloning to generate three lambs, which died at birth. All DAZL null male neonatal sheep lacked germ cells on histological sections and showed greatly reduced germ cell markers. Somatic cells within their testes were morphologically intact and expressed normal levels of lineage-specific markers, suggesting that the germ cell niche remained intact. This extends the DAZL mutant phenotype beyond mice into agriculturally relevant ruminants, providing a pathway for using absolute germline transmitters in rapid livestock improvement.
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Affiliation(s)
- Zachariah L McLean
- Reproduction, AgResearch, Ruakura Research Centre, Hamilton.,Applied Translational Research Group and Centre for Brain Research, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sarah J Appleby
- Reproduction, AgResearch, Ruakura Research Centre, Hamilton.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Jingwei Wei
- Reproduction, AgResearch, Ruakura Research Centre, Hamilton
| | - Russell G Snell
- Applied Translational Research Group and Centre for Brain Research, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Björn Oback
- Reproduction, AgResearch, Ruakura Research Centre, Hamilton.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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22
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Samson CA, Whitford W, Snell RG, Jacobsen JC, Lehnert K. Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing. Sci Rep 2020; 10:19255. [PMID: 33159102 PMCID: PMC7648094 DOI: 10.1038/s41598-020-76022-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/04/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022] Open
Abstract
Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequence comparisons of atypically aligning reads from eight human saliva-derived samples to RefSeq genomes revealed the majority to be of bacterial origin (63.46%). To partition the non-human reads during the alignment step, a decoy of the most prevalent bacterial genome sequences was designed and utilised. This reduced the number of atypically aligning reads when trialled on the eight saliva-derived samples by 44% and most importantly prevented the associated anomalous genotype calls. Saliva derived DNA is often contaminated by DNA from other species. This can lead to non-human reads aligning to the human reference genome using current alignment best-practices, impacting variant identification. This problem can be diminished by using a bacterial decoy in the alignment process.
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Affiliation(s)
- C A Samson
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - W Whitford
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - R G Snell
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - J C Jacobsen
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand.
| | - K Lehnert
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
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23
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Narayan P, Reid S, Scotter EL, McGregor AL, Mehrabi NF, Singh-Bains MK, Glass M, Faull RLM, Snell RG, Dragunow M. Inconsistencies in histone acetylation patterns among different HD model systems and HD post-mortem brains. Neurobiol Dis 2020; 146:105092. [PMID: 32979507 DOI: 10.1016/j.nbd.2020.105092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/28/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in exon 1 of the huntingtin gene. Emerging evidence shows that additional epigenetic factors can modify disease phenotypes. Harnessing the ability of the epigenome to modify the disease for therapeutic purposes is therefore of interest. Epigenome modifiers, such as histone deacetylase inhibitors (HDACi), have improved pathology in a range of HD models. Yet in clinical trials, HDACi have failed to alleviate HD symptoms in patients. This study investigated potential reasons for the lack of translation of the therapeutic benefits of HDACi from lab to clinic. We analysed histone acetylation patterns of immuno-positive nuclei from brain sections and tissue microarrays from post-mortem human control and HD cases alongside several well-established HD models (OVT73 transgenic HD sheep, YAC128 mice, and an in vitro cell model expressing 97Q mutant huntingtin). Significant increases in histone H4 acetylation were observed in post-mortem HD cases, OVT73 transgenic HD sheep and in vitro models; these changes were absent in YAC128 mice. In addition, nuclear labelling for acetyl-histone H4 levels were inversely proportional to mutant huntingtin aggregate load in HD human cortex. Our data raise concerns regarding the utility of HDACi for the treatment of HD when regions of pathology exhibit already elevated histone acetylation patterns and emphasize the importance of searching for alternative epigenetic targets in future therapeutic strategies aiming to rescue HD phenotypes.
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Affiliation(s)
- Pritika Narayan
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
| | - Suzanne Reid
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
| | - Emma L Scotter
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand.
| | - Ailsa L McGregor
- School of Pharmacy, University of Otago, Dunedin 9016, New Zealand.
| | - Nasim F Mehrabi
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand.
| | | | - Michelle Glass
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand; Department of Pharmacology and Toxicology, University of Otago, Dunedin 9016, New Zealand.
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand.
| | - Russell G Snell
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
| | - Mike Dragunow
- Centre for Brain Research, University of Auckland, Auckland 1023, New Zealand.
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24
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Fink T, Lopdell TJ, Tiplady K, Handley R, Johnson TJJ, Spelman RJ, Davis SR, Snell RG, Littlejohn MD. A new mechanism for a familiar mutation - bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement. BMC Genomics 2020; 21:591. [PMID: 32847516 PMCID: PMC7449055 DOI: 10.1186/s12864-020-07004-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 03/18/2020] [Accepted: 08/19/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following in-vitro studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. RESULTS We used a large RNAseq dataset to re-examine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA > GC variant that encodes the DGAT1 K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL for DGAT1, where the K232A mutation appears as one of the top associated variants for this effect. By conducting in vitro expression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. CONCLUSIONS The relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear; however, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at the DGAT1 locus.
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Affiliation(s)
- Tania Fink
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas J Lopdell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand. .,Livestock Improvement Corporation, Hamilton, New Zealand.
| | - Kathryn Tiplady
- Livestock Improvement Corporation, Hamilton, New Zealand.,Al Rae Centre, Massey University, Hamilton, New Zealand
| | - Renee Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mathew D Littlejohn
- Livestock Improvement Corporation, Hamilton, New Zealand.,Al Rae Centre, Massey University, Hamilton, New Zealand
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25
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Lopez-Villalobos N, Spelman RJ, Melis J, Davis SR, Berry SD, Lehnert K, Sneddon NW, Holroyd SE, MacGibbon AK, Snell RG. Genetic correlations of milk fatty acid contents predicted from milk mid-infrared spectra in New Zealand dairy cattle. J Dairy Sci 2020; 103:7238-7248. [PMID: 32534926 DOI: 10.3168/jds.2019-17971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/27/2019] [Accepted: 04/02/2020] [Indexed: 12/29/2022]
Abstract
The objective of this study was to estimate genetic correlations among milk fatty acid (FA) concentrations in New Zealand dairy cattle. Concentrations of each of the most common FA, expressed as a percentage of the total FA, were determined by gas chromatography on a specific cohort of animals. Using this data set, prediction equations were derived using mid-infrared (MIR) spectroscopy data collected from the same samples. These prediction equations were applied to a large data set of MIR measurements in 34,141 milk samples from 3,445 Holstein-Friesian, 2,935 Jersey, and 3,609 crossbred Holstein-Friesian × Jersey cows, sampled an average of 3.42 times during the 2007-2008 season. Data were analyzed using univariate and bivariate repeatability animal models. Heritability of predicted FA concentration in milk fat ranged from 0.21 to 0.42, indicating that genetic selection could be used to change the FA composition of milk. The de novo synthesized FA (C6:0, C8:0, C10:0, C12:0, and C14:0) showed strong positive genetic correlations with each other, ranging from 0.24 to 0.99. Saturated FA were negatively correlated with unsaturated (-0.93) and polyunsaturated (-0.84) FA. The saturated FA were positively correlated with milk fat yield and fat percentage, whereas the unsaturated FA were negatively associated with fat yield and fat percentage. Our results indicate that bovine milk FA composition can be changed through genetic selection using MIR as a phenotypic proxy.
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Affiliation(s)
- N Lopez-Villalobos
- School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
| | - R J Spelman
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - J Melis
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - S R Davis
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - S D Berry
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - K Lehnert
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - N W Sneddon
- School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; Fonterra Research and Development Centre, Palmerston North 4442, New Zealand
| | - S E Holroyd
- Fonterra Research and Development Centre, Palmerston North 4442, New Zealand
| | - A K MacGibbon
- Fonterra Research and Development Centre, Palmerston North 4442, New Zealand
| | - R G Snell
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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26
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Whitford W, Lehnert K, Snell RG, Jacobsen JC. RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions. Sci Rep 2019; 9:16934. [PMID: 31729446 PMCID: PMC6858463 DOI: 10.1038/s41598-019-53181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/17/2018] [Accepted: 10/25/2019] [Indexed: 11/11/2022] Open
Abstract
The popularisation and decreased cost of genome resequencing has resulted in an increased use in molecular diagnostics. While there are a number of established and high quality bioinfomatic tools for identifying small genetic variants including single nucleotide variants and indels, currently there is no established standard for the detection of copy number variants (CNVs) from sequence data. The requirement for CNV detection from high throughput sequencing has resulted in the development of a large number of software packages. These tools typically utilise the sequence data characteristics: read depth, split reads, read pairs, and assembly-based techniques. However, the additional source of information from read balance (defined as relative proportion of reads of each allele at each position) has been underutilised in the existing applications. Here we present Read Balance Validator (RBV), a bioinformatic tool that uses read balance for prioritisation and validation of putative CNVs. The software simultaneously interrogates nominated regions for the presence of deletions or multiplications, and can differentiate larger CNVs from diploid regions. Additionally, the utility of RBV to test for inheritance of CNVs is demonstrated in this report. RBV is a CNV validation and prioritisation bioinformatic tool for both genome and exome sequencing available as a python package from https://github.com/whitneywhitford/RBV.
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Affiliation(s)
- Whitney Whitford
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand. .,Centre for Brain Research, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland, New Zealand
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27
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Jivanji S, Worth G, Lopdell TJ, Yeates A, Couldrey C, Reynolds E, Tiplady K, McNaughton L, Johnson TJJ, Davis SR, Harris B, Spelman R, Snell RG, Garrick D, Littlejohn MD. Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle. Genet Sel Evol 2019; 51:62. [PMID: 31703548 PMCID: PMC6839108 DOI: 10.1186/s12711-019-0506-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 12/11/2018] [Accepted: 10/25/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date. RESULTS Using imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genes KIT and MITF as likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to the PAX3 gene, which encodes a known transcription factor that controls MITF expression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation in PAX3 (p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 of MITF transcripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involving KIT and/or other genes in this region. CONCLUSIONS Our findings extend those of previous studies that reported KIT as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the MITF and PAX3 genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics.
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Affiliation(s)
- Swati Jivanji
- Massey University Manawatu, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Gemma Worth
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Thomas J. Lopdell
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Anna Yeates
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Christine Couldrey
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Edwardo Reynolds
- Massey University Manawatu, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Kathryn Tiplady
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Lorna McNaughton
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Thomas J. J. Johnson
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Stephen R. Davis
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Bevin Harris
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Richard Spelman
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Russell G. Snell
- The University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Dorian Garrick
- Massey University Manawatu, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Mathew D. Littlejohn
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
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28
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Torres Cleuren YN, Ewe CK, Chipman KC, Mears ER, Wood CG, Al-Alami CEA, Alcorn MR, Turner TL, Joshi PM, Snell RG, Rothman JH. Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network. eLife 2019; 8:48220. [PMID: 31414984 PMCID: PMC6754231 DOI: 10.7554/elife.48220] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 05/06/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm GRN. While some natural isolates show a nearly absolute requirement for these two regulators, in others, most embryos differentiate endoderm in their absence. GWAS and analysis of recombinant inbred lines reveal multiple genetic regions underlying this broad phenotypic variation. We observe a reciprocal trend, in which genomic variants, or knockdown of endoderm regulatory genes, that result in a high SKN-1 requirement often show low MOM-2/Wnt requirement and vice-versa, suggesting that cryptic variation in the endoderm GRN may be tuned by opposing requirements for these two key regulatory inputs. These findings reveal that while the downstream components in the endoderm GRN are common across metazoan phylogeny, initiating regulatory inputs are remarkably plastic even within a single species.
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Affiliation(s)
- Yamila N Torres Cleuren
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chee Kiang Ewe
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Kyle C Chipman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Emily R Mears
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cricket G Wood
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | | | - Melissa R Alcorn
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Thomas L Turner
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Pradeep M Joshi
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joel H Rothman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
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29
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Patassini S, Begley P, Xu J, Church SJ, Kureishy N, Reid SJ, Waldvogel HJ, Faull RLM, Snell RG, Unwin RD, Cooper GJS. Cerebral Vitamin B5 (D-Pantothenic Acid) Deficiency as a Potential Cause of Metabolic Perturbation and Neurodegeneration in Huntington's Disease. Metabolites 2019; 9:E113. [PMID: 31212603 PMCID: PMC6630497 DOI: 10.3390/metabo9060113] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 05/09/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by an expanded CAG repeat in exon 1 of the HTT gene. HD usually manifests in mid-life with loss of GABAergic projection neurons from the striatum accompanied by progressive atrophy of the putamen followed by other brain regions, but linkages between the genetics and neurodegeneration are not understood. We measured metabolic perturbations in HD-human brain in a case-control study, identifying pervasive lowering of vitamin B5, the obligatory precursor of coenzyme A (CoA) that is essential for normal intermediary metabolism. Cerebral pantothenate deficiency is a newly-identified metabolic defect in human HD that could potentially: (i) impair neuronal CoA biosynthesis; (ii) stimulate polyol-pathway activity; (iii) impair glycolysis and tricarboxylic acid cycle activity; and (iv) modify brain-urea metabolism. Pantothenate deficiency could lead to neurodegeneration/dementia in HD that might be preventable by treatment with vitamin B5.
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Affiliation(s)
- Stefano Patassini
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland 1142, New Zealand.
- Owlstone Medical, Cambridge Science Park, Cambridge CB4 0GJ, UK.
| | - Paul Begley
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
| | - Jingshu Xu
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
- Manchester Cancer Research Centre Building, The University of Manchester, Manchester M20 4GJ, UK.
| | - Stephanie J Church
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
| | - Nina Kureishy
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
| | - Suzanne J Reid
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland 1142, New Zealand.
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Henry J Waldvogel
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Richard L M Faull
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Russell G Snell
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland 1142, New Zealand.
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
| | - Garth J S Cooper
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M19 9NT, UK.
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland 1142, New Zealand.
- Manchester Cancer Research Centre Building, The University of Manchester, Manchester M20 4GJ, UK.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.
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30
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Whitford W, Lehnert K, Snell RG, Jacobsen JC. Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data. J Biomed Inform 2019; 94:103174. [PMID: 30965134 DOI: 10.1016/j.jbi.2019.103174] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 12/12/2018] [Revised: 03/12/2019] [Accepted: 04/06/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Whole genome sequencing (WGS) has increased in popularity and decreased in cost over the past decade, rendering this approach as a viable and sensitive method for variant detection. In addition to its utility for single nucleotide variant detection, WGS data has the potential to detect Copy Number Variants (CNV) to fine resolution. Many CNV detection software packages have been developed exploiting four main types of data: read pair, split read, read depth, and assembly based methods. The aim of this study was to evaluate the efficiency of each of these main approaches in detecting germline deletions. METHODS WGS data and high confidence deletion calls for the individual NA12878 from the Genome in a Bottle consortium were the benchmark dataset. The performance of BreakDancer, CNVnator, Delly, FermiKit, and Pindel was assessed by comparing the accuracy and sensitivity of each software package in detecting deletions exceeding 1 kb. RESULTS There was considerable variability in the outputs of the different WGS CNV detection programs. The best performance was seen from BreakDancer and Delly, with 92.6% and 96.7% sensitivity, respectively and 34.5% and 68.5% false discovery rate (FDR), respectively. In comparison, Pindel, CNVnator, and FermiKit were less effective with sensitivities of 69.1%, 66.0%, and 15.8%, respectively and FDR of 91.3%, 69.0%, and 31.7%, respectively. Concordance across software packages was poor, with only 27 of the total 612 benchmark deletions identified by all five methodologies. CONCLUSIONS The WGS based CNV detection tools evaluated show disparate performance in identifying deletions ≥1 kb, particularly those utilising different input data characteristics. Software that exploits read pair based data had the highest sensitivity, namely BreakDancer and Delly. BreakDancer also had the second lowest false discovery rate. Therefore, in this analysis read pair methods (BreakDancer in particular) were the best performing approaches for the identification of deletions ≥1 kb, balancing accuracy and sensitivity. There is potential for improvement in the detection algorithms, particularly for reducing FDR. This analysis has validated the utility of WGS based CNV detection software to reliably identify deletions, and these findings will be of use when choosing appropriate software for deletion detection, in both research and diagnostic medicine.
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Affiliation(s)
- Whitney Whitford
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
| | - Klaus Lehnert
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
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31
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Murray SJ, Black BL, Reid SJ, Rudiger SR, Simon Bawden C, Snell RG, Waldvogel HJ, Faull RL. Chemical neuroanatomy of the substantia nigra in the ovine brain. J Chem Neuroanat 2019; 97:43-56. [DOI: 10.1016/j.jchemneu.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/20/2023]
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32
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Helbig KL, Lauerer RJ, Bahr JC, Souza IA, Myers CT, Uysal B, Schwarz N, Gandini MA, Huang S, Keren B, Mignot C, Afenjar A, Billette de Villemeur T, Héron D, Nava C, Valence S, Buratti J, Fagerberg CR, Soerensen KP, Kibaek M, Kamsteeg EJ, Koolen DA, Gunning B, Schelhaas HJ, Kruer MC, Fox J, Bakhtiari S, Jarrar R, Padilla-Lopez S, Lindstrom K, Jin SC, Zeng X, Bilguvar K, Papavasileiou A, Xing Q, Zhu C, Boysen K, Vairo F, Lanpher BC, Klee EW, Tillema JM, Payne ET, Cousin MA, Kruisselbrink TM, Wick MJ, Baker J, Haan E, Smith N, Sadeghpour A, Davis EE, Katsanis N, Corbett MA, MacLennan AH, Gecz J, Biskup S, Goldmann E, Rodan LH, Kichula E, Segal E, Jackson KE, Asamoah A, Dimmock D, McCarrier J, Botto LD, Filloux F, Tvrdik T, Cascino GD, Klingerman S, Neumann C, Wang R, Jacobsen JC, Nolan MA, Snell RG, Lehnert K, Sadleir LG, Anderlid BM, Kvarnung M, Guerrini R, Friez MJ, Lyons MJ, Leonhard J, Kringlen G, Casas K, El Achkar CM, Smith LA, Rotenberg A, Poduri A, Sanchis-Juan A, Carss KJ, Rankin J, Zeman A, Raymond FL, Blyth M, Kerr B, Ruiz K, Urquhart J, Hughes I, Banka S, Hedrich UB, Scheffer IE, Helbig I, Zamponi GW, Lerche H, Mefford HC, Allori A, Angrist M, Ashley P, Bidegain M, Boyd B, Chambers E, Cope H, Cotten CM, Curington T, Davis EE, Ellestad S, Fisher K, French A, Gallentine W, Goldberg R, Hill K, Kansagra S, Katsanis N, Katsanis S, Kurtzberg J, Marcus J, McDonald M, Mikati M, Miller S, Murtha A, Perilla Y, Pizoli C, Purves T, Ross S, Sadeghpour A, Smith E, Wiener J. De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias. Am J Hum Genet 2019; 104:562. [PMID: 30849329 DOI: 10.1016/j.ajhg.2019.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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33
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Lopdell TJ, Hawkins V, Couldrey C, Tiplady K, Davis SR, Harris BL, Snell RG, Littlejohn MD. Widespread cis-regulation of RNA editing in a large mammal. RNA 2019; 25:319-335. [PMID: 30530731 PMCID: PMC6380278 DOI: 10.1261/rna.066902.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Post-transcriptional RNA editing may regulate transcript expression and diversity in cells, with potential impacts on various aspects of physiology and environmental adaptation. A small number of recent genome-wide studies in Drosophila, mouse, and human have shown that RNA editing can be genetically modulated, highlighting loci that quantitatively impact editing of transcripts. The potential gene expression and physiological consequences of these RNA-editing quantitative trait loci (edQTL), however, are almost entirely unknown. Here, we present analyses of RNA editing in a large domestic mammal (Bos taurus), where we use whole-genome and high-depth RNA sequencing to discover, characterize, and conduct genetic mapping studies of novel transcript edits. Using a discovery population of nine deeply sequenced cows, we identify 2413 edit sites in the mammary transcriptome, the majority of which are adenosine to inosine edits (98.6%). Most sites are predicted to reside in double-stranded secondary structures (85.1%), and quantification of the rates of editing in an additional 355 cows reveals editing is negatively correlated with gene expression in the majority of cases. Genetic analyses of RNA editing and gene expression highlight 152 cis-regulated edQTL, of which 15 appear to cosegregate with expression QTL effects. Trait association analyses in a separate population of 9989 lactating cows also shows 12 of the cis-edQTL coincide with at least one cosegregating lactation QTL. Together, these results enhance our understanding of RNA-editing dynamics in mammals, and suggest mechanistic links by which loci may impact phenotype through RNA editing mediated processes.
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Affiliation(s)
- Thomas J Lopdell
- Research and Development, Livestock Improvement Corporation, Hamilton 3296, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1071, New Zealand
| | - Victoria Hawkins
- School of Biological Sciences, University of Auckland, Auckland 1071, New Zealand
| | - Christine Couldrey
- Research and Development, Livestock Improvement Corporation, Hamilton 3296, New Zealand
| | - Kathryn Tiplady
- Research and Development, Livestock Improvement Corporation, Hamilton 3296, New Zealand
| | - Stephen R Davis
- Research and Development, Livestock Improvement Corporation, Hamilton 3296, New Zealand
| | - Bevin L Harris
- Research and Development, Livestock Improvement Corporation, Hamilton 3296, New Zealand
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland 1071, New Zealand
| | - Mathew D Littlejohn
- Research and Development, Livestock Improvement Corporation, Hamilton 3296, New Zealand
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34
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Lopdell TJ, Tiplady K, Couldrey C, Johnson TJJ, Keehan M, Davis SR, Harris BL, Spelman RJ, Snell RG, Littlejohn MD. Multiple QTL underlie milk phenotypes at the CSF2RB locus. Genet Sel Evol 2019; 51:3. [PMID: 30678637 PMCID: PMC6346582 DOI: 10.1186/s12711-019-0446-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 09/13/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022] Open
Abstract
Background Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously reported QTL located at the CSF2RB locus on chromosome 5, for several milk production phenotypes, to better understand its underlying genetic and molecular causes. Results Using a population of 29,350 taurine dairy cows, we conducted association analyses for milk yield and composition traits, and identified highly significant QTL for milk yield, milk fat concentration, and milk protein concentration. Strikingly, protein concentration and milk yield appear to show co-located yet genetically distinct QTL. To attempt to understand the molecular mechanisms that might be mediating these effects, gene expression data were used to investigate eQTL for 11 genes in the broader interval. This analysis highlighted genetic impacts on CSF2RB and NCF4 expression that share similar association signatures to those observed for lactation QTL, strongly implicating one or both of these genes as responsible for these effects. Using the same gene expression dataset representing 357 lactating cows, we also identified 38 novel RNA editing sites in the 3′ UTR of CSF2RB transcripts. The extent to which two of these sites were edited also appears to be genetically co-regulated with lactation QTL, highlighting a further layer of regulatory complexity that involves the CSF2RB gene. Conclusions This locus presents a diversity of molecular and lactation QTL, likely representing multiple overlapping effects that, at a minimum, highlight the CSF2RB gene as having a causal role in these processes. Electronic supplementary material The online version of this article (10.1186/s12711-019-0446-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J Lopdell
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand. .,School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand.
| | - Kathryn Tiplady
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Christine Couldrey
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Thomas J J Johnson
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Michael Keehan
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Stephen R Davis
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Bevin L Harris
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Richard J Spelman
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Mathew D Littlejohn
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
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35
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Young AT, Ly KN, Wilson C, Lehnert K, Snell RG, Reid SJ, Jacobsen JC. Modelling brain dopamine-serotonin vesicular transport disease in Caenorhabditis elegans. Dis Model Mech 2018; 11:dmm.035709. [PMID: 30266839 PMCID: PMC6262812 DOI: 10.1242/dmm.035709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/10/2018] [Indexed: 11/26/2022] Open
Abstract
Brain dopamine-serotonin vesicular transport disease is a rare disease caused by autosomal recessive mutations in the SLC18A2 gene, which encodes the VMAT2 protein. VMAT2 is a membrane protein responsible for vesicular transport of monoamines, and its disruption negatively affects neurotransmission. This results in a severe neurodevelopmental disorder affecting motor skills and development, and causes muscular hypotonia. The condition was initially described in a consanguineous Saudi Arabian family with affected siblings homozygous for a P387L mutation. We subsequently found a second mutation in a New Zealand family (homozygous P237H), which was later also identified in an Iraqi family. Pramipexole has been shown to have some therapeutic benefit. Transgenic Caenorhabditis elegans were developed to model the P237H and P387L mutations. Investigations into dopamine- and serotonin-related C. elegans phenotypes, including pharyngeal pumping and grazing, showed that both mutations cause significant impairment of these processes when compared with a non-transgenic N2 strain and a transgenic containing the wild-type human SLC18A2 gene. Preliminary experiments investigating the therapeutic effects of serotonin and pramipexole demonstrated that serotonin could successfully restore the pharyngeal pumping phenotype. These analyses provide further support for the role of these mutations in this disease. Summary: The first Caenorhabditis elegans model to study brain dopamine-serotonin vesicular transport disease, demonstrating impairment of pharyngeal pumping and grazing phenotypes.
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Affiliation(s)
- Alexander T Young
- The School of Biological Sciences and Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Kien N Ly
- The School of Biological Sciences and Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Callum Wilson
- Adult and Paediatric National Metabolic Service, Auckland City Hospital, Auckland 1023, New Zealand
| | - Klaus Lehnert
- The School of Biological Sciences and Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Russell G Snell
- The School of Biological Sciences and Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Suzanne J Reid
- The School of Biological Sciences and Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Jessie C Jacobsen
- The School of Biological Sciences and Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
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36
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Helbig KL, Lauerer RJ, Bahr JC, Souza IA, Myers CT, Uysal B, Schwarz N, Gandini MA, Huang S, Keren B, Mignot C, Afenjar A, Billette de Villemeur T, Héron D, Nava C, Valence S, Buratti J, Fagerberg CR, Soerensen KP, Kibaek M, Kamsteeg EJ, Koolen DA, Gunning B, Schelhaas HJ, Kruer MC, Fox J, Bakhtiari S, Jarrar R, Padilla-Lopez S, Lindstrom K, Jin SC, Zeng X, Bilguvar K, Papavasileiou A, Xing Q, Zhu C, Boysen K, Vairo F, Lanpher BC, Klee EW, Tillema JM, Payne ET, Cousin MA, Kruisselbrink TM, Wick MJ, Baker J, Haan E, Smith N, Sadeghpour A, Davis EE, Katsanis N, Corbett MA, MacLennan AH, Gecz J, Biskup S, Goldmann E, Rodan LH, Kichula E, Segal E, Jackson KE, Asamoah A, Dimmock D, McCarrier J, Botto LD, Filloux F, Tvrdik T, Cascino GD, Klingerman S, Neumann C, Wang R, Jacobsen JC, Nolan MA, Snell RG, Lehnert K, Sadleir LG, Anderlid BM, Kvarnung M, Guerrini R, Friez MJ, Lyons MJ, Leonhard J, Kringlen G, Casas K, El Achkar CM, Smith LA, Rotenberg A, Poduri A, Sanchis-Juan A, Carss KJ, Rankin J, Zeman A, Raymond FL, Blyth M, Kerr B, Ruiz K, Urquhart J, Hughes I, Banka S, Hedrich UB, Scheffer IE, Helbig I, Zamponi GW, Lerche H, Mefford HC, Allori A, Angrist M, Ashley P, Bidegain M, Boyd B, Chambers E, Cope H, Cotten CM, Curington T, Davis EE, Ellestad S, Fisher K, French A, Gallentine W, Goldberg R, Hill K, Kansagra S, Katsanis N, Katsanis S, Kurtzberg J, Marcus J, McDonald M, Mikati M, Miller S, Murtha A, Perilla Y, Pizoli C, Purves T, Ross S, Sadeghpour A, Smith E, Wiener J. De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias. Am J Hum Genet 2018; 103:666-678. [PMID: 30343943 DOI: 10.1016/j.ajhg.2018.09.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are severe neurodevelopmental disorders often beginning in infancy or early childhood that are characterized by intractable seizures, abundant epileptiform activity on EEG, and developmental impairment or regression. CACNA1E is highly expressed in the central nervous system and encodes the α1-subunit of the voltage-gated CaV2.3 channel, which conducts high voltage-activated R-type calcium currents that initiate synaptic transmission. Using next-generation sequencing techniques, we identified de novo CACNA1E variants in 30 individuals with DEE, characterized by refractory infantile-onset seizures, severe hypotonia, and profound developmental impairment, often with congenital contractures, macrocephaly, hyperkinetic movement disorders, and early death. Most of the 14, partially recurring, variants cluster within the cytoplasmic ends of all four S6 segments, which form the presumed CaV2.3 channel activation gate. Functional analysis of several S6 variants revealed consistent gain-of-function effects comprising facilitated voltage-dependent activation and slowed inactivation. Another variant located in the domain II S4-S5 linker results in facilitated activation and increased current density. Five participants achieved seizure freedom on the anti-epileptic drug topiramate, which blocks R-type calcium channels. We establish pathogenic variants in CACNA1E as a cause of DEEs and suggest facilitated R-type calcium currents as a disease mechanism for human epilepsy and developmental disorders.
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Gardner RJM, Crozier IG, Binfield AL, Love DR, Lehnert K, Gibson K, Lintott CJ, Snell RG, Jacobsen JC, Jones PP, Waddell-Smith KE, Kennedy MA, Skinner JR. Penetrance and expressivity of the R858H CACNA1C variant in a five-generation pedigree segregating an arrhythmogenic channelopathy. Mol Genet Genomic Med 2018; 7:e00476. [PMID: 30345660 PMCID: PMC6382452 DOI: 10.1002/mgg3.476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 05/21/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Isolated cardiac arrhythmia due to a variant in CACNA1C is of recent knowledge. Most reports have been of singleton cases or of quite small families, and estimates of penetrance and expressivity have been difficult to obtain. We here describe a large pedigree, from which such estimates have been calculated. METHODS We studied a five-generation family, in which a CACNA1C variant c.2573G>A p.Arg858His co-segregates with syncope and cardiac arrest, documenting electrocardiographic data and cardiac symptomatology. The reported patients/families from the literature with CACNA1C gene variants were reviewed, and genotype-phenotype correlations are drawn. RESULTS The range of phenotype in the studied family is wide, from no apparent effect, through an asymptomatic QT interval prolongation on electrocardiography, to episodes of presyncope and syncope, ventricular fibrillation, and sudden death. QT prolongation showed inconsistent correlation with functional cardiology. Based upon analysis of 28 heterozygous family members, estimates of penetrance and expressivity are derived. CONCLUSIONS These estimates of penetrance and expressivity, for this specific variant, may be useful in clinical practice. Review of the literature indicates that individual CACNA1C variants have their own particular genotype-phenotype correlations. We suggest that, at least in respect of the particular variant reported here, "arrhythmogenic channelopathy" may be a more fitting nomenclature than long QT syndrome.
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Affiliation(s)
- R J McKinlay Gardner
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Genetic Health Service New Zealand (South Island Hub), Christchurch Hospital, Christchurch, New Zealand.,Clinical Genetics Group, Department of Women's and Children's Health, University of Otago, Dunedin, New Zealand
| | - Ian G Crozier
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Department of Cardiology, Christchurch Hospital, Christchurch, New Zealand
| | - Alex L Binfield
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Department of Paediatrics, Christchurch Hospital, Christchurch, New Zealand.,Department of Paediatrics, University of Otago, Christchurch, New Zealand
| | - Donald R Love
- Cardiac Inherited Disease Group, Auckland, New Zealand.,LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Klaus Lehnert
- Cardiac Inherited Disease Group, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kate Gibson
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Genetic Health Service New Zealand (South Island Hub), Christchurch Hospital, Christchurch, New Zealand
| | - Caroline J Lintott
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Genetic Health Service New Zealand (South Island Hub), Christchurch Hospital, Christchurch, New Zealand
| | - Russell G Snell
- Cardiac Inherited Disease Group, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jessie C Jacobsen
- Cardiac Inherited Disease Group, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Peter P Jones
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Department of Physiology and HeartOtago, University of Otago, Dunedin, New Zealand
| | - Kathryn E Waddell-Smith
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Department of Cardiology, Auckland City Hospital, Auckland, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Jonathan R Skinner
- Cardiac Inherited Disease Group, Auckland, New Zealand.,Department of Cardiology, Auckland City Hospital, Auckland, New Zealand
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38
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Robertson SP, Hindmarsh JH, Berry S, Cameron VA, Cox MP, Dewes O, Doughty RN, Gray G, Jacobsen JC, Laurence A, Matisoo-Smith E, Morton S, Shelling AN, Sika-Paotonu D, Rolleston A, Skinner JR, Snell RG, Sporle A, Print C, Merriman TR, Hudson M, Wilcox P. Genomic medicine must reduce, not compound, health inequities: the case for hauora-enhancing genomic resources for New Zealand. N Z Med J 2018; 131:81-89. [PMID: 30116069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Precision medicine seeks to draw on data from both individuals and populations across disparate domains to influence and support diagnosis, management and prevention in healthcare at the level of the individual patient and their family/whānau. Central to this initiative is incorporating the effects of the inherent variation that lies within genomes and can influence health outcomes. Identifying and interpreting such variation requires an accurate, valid and representative dataset to firstly define what variants are present and then assess the potential relevance for the health of a person, their family/whānau and the wider community to which they belong. Globally the variation embedded within genomes differs enormously and has been shaped by the size, constitution, historical origins and evolutionary history of their source populations. Māori, and more broadly Pacific peoples, differ substantially in terms of genomic variation compared to the more closely studied European and Asian populations. In the absence of accurate genomic information from Māori and Pacific populations, the precise interpretation of genomic data and the success and benefits of genomic medicine will be disproportionately less for those Māori and Pacific peoples. In this viewpoint article we, as a group of healthcare professionals, researchers and scientists, present a case for assembling genomic resources that catalogue the characteristics of the genomes of New Zealanders, with an emphasis on peoples of Māori and Polynesian ancestry, as a healthcare imperative. In proposing the creation of these resources, we note that their governance and management must be led by iwi and Māori and Pacific representatives. Assembling a genomic resource must be informed by cultural concepts and values most especially understanding that, at a physical and spiritual level, whakapapa is embodied within the DNA of a person. Therefore DNA and genomic data that connects to whakapapa (genealogy) is considered a taonga (something precious and significant), and its storage, utilisation and interpretation is a culturally significant activity. Furthermore, such resources are not proposed to primarily enable comparisons between those with Māori and broader Pacific ancestries and other Aotearoa peoples but to place an understanding of the genetic contributors to their health outcomes in a valid context. Ongoing oversight and governance of such taonga by Māori and Pacific representatives will maximise hauora (health) while also minimising the risk of misuse of this information.
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Affiliation(s)
- Stephen P Robertson
- Professor, Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin
| | - Jennie Harre Hindmarsh
- Research Coordinator, Ngāti Porou Hauora Charitable Trust, Te Puia Springs, Tairāwhiti, Gisborne
| | - Sarah Berry
- Senior Research Fellow, Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, The University of Auckland, Auckland
| | - Vicky A Cameron
- Professor, Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch
| | - Murray P Cox
- Professor, Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North
| | - Ofa Dewes
- Research Fellow, Maurice Wilkens Centre for Molecular Biodiscovery, Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland; School of Nursing, Faculty of Medical and Health Sciences, The University of Auckland, Auckland
| | - Robert N Doughty
- Professor, Department of Medicine, University of Auckland, Auckland
| | - George Gray
- Public Health Physician, Planning and Funding, Bay of Plenty District Health Board, Tauranga
| | - Jessie C Jacobsen
- Research Fellow, Centre for Brain Research and School of Biological Sciences, The University of Auckland, Auckland
| | | | | | - Susan Morton
- Senior Research Fellow, Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, The University of Auckland
| | - Andrew N Shelling
- Professor, Department of Obstetrics and Gynaecology, The University of Auckland, Auckland
| | - Dianne Sika-Paotonu
- Associate Dean (Pacific), Senior Lecturer Pathology & Molecular Medicine, Wellington School of Medicine and Health Sciences, University of Otago, Wellington; Honorary Research Associate, Victoria University of Wellington, Wellington; Honorary Research Associate Telethon Kids Institute, Perth, Western Australia; Affiliate Investigator, Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland
| | - Anna Rolleston
- Clinical Director, The Centre for Health, Manawa Ora Centre, Tauranga
| | - Jonathan R Skinner
- Director, Cardiac Inherited Disease Group, Auckland City Hospital and Green Lane Paediatric and Congenital Cardiac Services, Starship Children's Hospital, Auckland
| | - Russell G Snell
- Professor, Centre for Brain Research and School of Biological Sciences, The University of Auckland, Auckland
| | - Andrew Sporle
- Senior Research Fellow, Department of Statistics, The University of Auckland, Auckland
| | - Cristin Print
- Professor, Department of Medicine, University of Auckland, Auckland; Professor and Director, The Bioinformatics Institute, and the Genomics Into Medicine Programme University of Auckland, Auckland
| | - Tony R Merriman
- Professor, Department of Biochemistry, University of Otago, Dunedin and Principal Investigator, Maurice Wilkins Centre for Molecular Biodiscovery
| | - Maui Hudson
- Associate Professor, Māori and Indigenous Governance Centre, University of Waikato, Hamilton
| | - Philip Wilcox
- Senior Lecturer, Department of Mathematics and Statistics, University of Otago, Dunedin
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Berry SD, Walker CG, Ly K, Snell RG, Atatoa Carr PE, Bandara D, Mohal J, Castro TG, Marks E, Morton SMB, Grant CC. Re: "Widespread prevalence of a CREBRF variant amongst Māori and Pacific children is associated with weight and height in early childhood". Int J Obes (Lond) 2018; 42:1392-1393. [PMID: 29463920 DOI: 10.1038/s41366-018-0026-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 12/29/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah D Berry
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand.
| | - Caroline G Walker
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Kien Ly
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, Centre for Brain Research University of Auckland, Auckland, New Zealand
| | - Polly E Atatoa Carr
- National Institute of Demographic and Economic Analysis, University of Waikato, Hamilton, New Zealand
| | - Dinusha Bandara
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Jatender Mohal
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Teresa G Castro
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Emma Marks
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Susan M B Morton
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand
| | - Cameron C Grant
- Centre for Longitudinal Research - He Ara ki Mua and Growing Up in New Zealand, University of Auckland, Auckland, New Zealand.,Department of Paediatrics: Child and Youth Health, University of Auckland, Auckland, New Zealand.,Starship Children's Hospital, Auckland District Health Board, Auckland, New Zealand
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40
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Lopdell TJ, Tiplady K, Struchalin M, Johnson TJJ, Keehan M, Sherlock R, Couldrey C, Davis SR, Snell RG, Spelman RJ, Littlejohn MD. DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content. BMC Genomics 2017; 18:968. [PMID: 29246110 PMCID: PMC5731188 DOI: 10.1186/s12864-017-4320-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 05/23/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Abstract
Background Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS focussed on analysis of milk lactose traits. Results Using a discovery population of 12,000 taurine dairy cattle, we detail 27 QTL for lactose concentration and yield, and subsequently validate the effects of 26 of these loci in a distinct population of 18,000 cows. We next present data implicating causative genes and variants for these QTL. Fine mapping of these regions using imputed, whole genome sequence-resolution genotypes reveals protein-coding candidate causative variants affecting the ABCG2, DGAT1, STAT5B, KCNH4, NPFFR2 and RNF214 genes. Eleven of the remaining QTL appear to be driven by regulatory effects, suggested by the presence of co-locating, co-segregating eQTL discovered using mammary RNA sequence data from a population of 357 lactating cows. Pathway analysis of genes representing all lactose-associated loci shows significant enrichment of genes located in the endoplasmic reticulum, with functions related to ion channel activity mediated through the LRRC8C, P2RX4, KCNJ2 and ANKH genes. A number of the validated QTL are also found to be associated with additional milk volume, fat and protein phenotypes. Conclusions Overall, these findings highlight novel candidate genes and variants involved in milk lactose regulation, whose impacts on membrane transport mechanisms reinforce the key osmo-regulatory roles of lactose in milk. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4320-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J Lopdell
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand.,School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Kathryn Tiplady
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Maksim Struchalin
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Thomas J J Johnson
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Michael Keehan
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Ric Sherlock
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Christine Couldrey
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Stephen R Davis
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Symonds Street, Auckland, New Zealand
| | - Richard J Spelman
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand
| | - Mathew D Littlejohn
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand.
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41
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Whitford W, Hawkins I, Glamuzina E, Wilson F, Marshall A, Ashton F, Love DR, Taylor J, Hill R, Lehnert K, Snell RG, Jacobsen JC. Compound heterozygous SLC19A3 mutations further refine the critical promoter region for biotin-thiamine-responsive basal ganglia disease. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001909. [PMID: 28696212 PMCID: PMC5701311 DOI: 10.1101/mcs.a001909] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 02/14/2017] [Accepted: 05/24/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in the gene SLC19A3 result in thiamine metabolism dysfunction syndrome 2, also known as biotin-thiamine-responsive basal ganglia disease (BTBGD). This neurometabolic disease typically presents in early childhood with progressive neurodegeneration, including confusion, seizures, and dysphagia, advancing to coma and death. Treatment is possible via supplement of biotin and/or thiamine, with early treatment resulting in significant lifelong improvements. Here we report two siblings who received a refined diagnosis of BTBGD following whole-genome sequencing. Both children inherited compound heterozygous mutations from unaffected parents; a missense single-nucleotide variant (p.G23V) in the first transmembrane domain of the protein, and a 4808-bp deletion in exon 1 encompassing the 5′ UTR and minimal promoter region. This deletion is the smallest promoter deletion reported to date, further defining the minimal promoter region of SLC19A3. Unfortunately, one of the siblings died prior to diagnosis, but the other is showing significant improvement after commencement of therapy. This case demonstrates the power of whole-genome sequencing for the identification of structural variants and subsequent diagnosis of rare neurodevelopmental disorders.
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Affiliation(s)
- Whitney Whitford
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Isobel Hawkins
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic Service, Starship Children's Hospital, Auckland 1023, New Zealand
| | - Francessa Wilson
- Department of Paediatric Radiology, Starship Children's Hospital, Auckland 1023, New Zealand
| | - Andrew Marshall
- Department of Paediatrics and Child Health, Wellington Hospital, Wellington 6021, New Zealand
| | - Fern Ashton
- Diagnostic Genetics LabPLUS, Auckland City Hospital, Auckland 1023, New Zealand
| | - Donald R Love
- Diagnostic Genetics LabPLUS, Auckland City Hospital, Auckland 1023, New Zealand
| | - Juliet Taylor
- Genetic Health Service New Zealand, Auckland City Hospital, Auckland 1023, New Zealand
| | - Rosamund Hill
- Department of Neurology, Auckland City Hospital, Auckland 1023, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand.,Centre for Brain Research, The University of Auckland, Auckland 1010, New Zealand
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42
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Jacobsen JC, Whitford W, Swan B, Taylor J, Love DR, Hill R, Molyneux S, George PM, Mackay R, Robertson SP, Snell RG, Lehnert K. Compound Heterozygous Inheritance of Mutations in Coenzyme Q8A Results in Autosomal Recessive Cerebellar Ataxia and Coenzyme Q 10 Deficiency in a Female Sib-Pair. JIMD Rep 2017; 42:31-36. [PMID: 29159460 DOI: 10.1007/8904_2017_73] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/29/2017] [Accepted: 11/02/2017] [Indexed: 12/27/2022] Open
Abstract
Autosomal recessive ataxias are characterised by a fundamental loss in coordination of gait with associated atrophy of the cerebellum. There is significant clinical and genetic heterogeneity amongst inherited ataxias; however, an early molecular diagnosis is essential with low-risk treatments available for some of these conditions. We describe two female siblings who presented early in life with unsteady gait and cerebellar atrophy. Whole exome sequencing revealed compound heterozygous inheritance of two pathogenic mutations (p.Leu277Pro, c.1506+1G>A) in the coenzyme Q8A gene (COQ8A), a gene central to biosynthesis of coenzyme Q (CoQ). The paternally derived p.Leu277Pro mutation is predicted to disrupt a conserved motif in the substrate-binding pocket of the protein, resulting in inhibition of CoQ10 production. The maternal c.1506+1G>A mutation destroys a canonical splice donor site in exon 12 affecting transcript processing and subsequent protein translation. Mutations in this gene can result in primary coenzyme Q10 deficiency type 4, which is characterized by childhood onset of cerebellar ataxia and exercise intolerance, both of which were observed in this sib-pair. Muscle biopsies revealed unequivocally low levels of CoQ10, and the siblings were subsequently established on a therapeutic dose of CoQ10 with distinct clinical evidence of improvement after 1 year of treatment. This case emphasises the importance of an early and accurate molecular diagnosis for suspected inherited ataxias, particularly given the availability of approved treatments for some subtypes.
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Affiliation(s)
- Jessie C Jacobsen
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Whitney Whitford
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Brendan Swan
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Juliet Taylor
- Genetic Health Service New Zealand, Auckland City Hospital, Auckland, New Zealand
| | - Donald R Love
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Rosamund Hill
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Sarah Molyneux
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Peter M George
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Richard Mackay
- Canterbury Health Laboratories, Christchurch, New Zealand
| | | | - Russell G Snell
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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43
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Geraerts FCA, Snell RG, Faull RLM, Williams L, Jacobsen JC, Reid SJ. Comparison of Huntington's disease CAG Repeat Length Stability in Human Motor Cortex and Cingulate Gyrus. J Huntingtons Dis 2017; 5:297-301. [PMID: 27716680 DOI: 10.3233/jhd-160203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Huntington's disease is caused by expansion of the CAG repeat in Huntingtin. This repeat has shown tissue-specific instability in mouse models and in a small number of post-mortem human samples. We used small-pool PCR to generate a modified instability index to quantify CAG instability within two brain regions from six human samples where cell loss has been associated with motor and mood symptoms: the motor cortex and cingulate gyrus. The expanded allele demonstrated instability in both regions, with minimal instability in the unexpanded allele. Region-specific differences were not observed, suggesting symptomatology may not be determined by repeat length instability.
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Affiliation(s)
- Fiona C A Geraerts
- School of Biological Sciences, Centre for Brain Research, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, Centre for Brain Research, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Liam Williams
- School of Biological Sciences, Centre for Brain Research, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Jessie C Jacobsen
- School of Biological Sciences, Centre for Brain Research, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Suzanne J Reid
- School of Biological Sciences, Centre for Brain Research, Faculty of Science, The University of Auckland, Auckland, New Zealand
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44
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Fink T, Tiplady K, Lopdell T, Johnson T, Snell RG, Spelman RJ, Davis SR, Littlejohn MD. Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics. Sci Rep 2017; 7:44793. [PMID: 28322319 PMCID: PMC5359603 DOI: 10.1038/srep44793] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 06/09/2016] [Accepted: 02/14/2017] [Indexed: 12/23/2022] Open
Abstract
A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds. These QTL have been attributed to two functional variants in the bidirectional promoter of PLAG1 and CHCHD7. Although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given that these variants are also associated with expression of five additional genes at the broader locus. In the current study, we conducted expression QTL (eQTL) mapping of this region using a large, high depth mammary RNAseq dataset representing 375 lactating cows. Here we show that of the seven previously implicated genes, only PLAG1 and LYN are differentially expressed by QTL genotype, and only PLAG1 bears the same association signature of the growth and body weight QTLs. For the first time, we also report significant association of PLAG1 genotype with milk production traits, including milk fat, volume, and protein yield. Collectively, these data strongly suggest PLAG1 as the causative gene underlying this diverse range of traits, and demonstrate new effects for the locus on lactation phenotypes.
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Affiliation(s)
- Tania Fink
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Thomas Lopdell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Livestock Improvement Corporation, Hamilton, New Zealand
| | - Thomas Johnson
- Livestock Improvement Corporation, Hamilton, New Zealand
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | | | - Mathew D Littlejohn
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Livestock Improvement Corporation, Hamilton, New Zealand
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45
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Jacobsen JC, Erdin S, Chiang C, Hanscom C, Handley RR, Barker DD, Stortchevoi A, Blumenthal I, Reid SJ, Snell RG, MacDonald ME, Morton AJ, Ernst C, Gusella JF, Talkowski ME. Potential molecular consequences of transgene integration: The R6/2 mouse example. Sci Rep 2017; 7:41120. [PMID: 28120936 PMCID: PMC5264158 DOI: 10.1038/srep41120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 09/23/2016] [Accepted: 11/11/2016] [Indexed: 01/09/2023] Open
Abstract
Integration of exogenous DNA into a host genome represents an important route to generate animal and cellular models for exploration into human disease and therapeutic development. In most models, little is known concerning structural integrity of the transgene, precise site of integration, or its impact on the host genome. We previously used whole-genome and targeted sequencing approaches to reconstruct transgene structure and integration sites in models of Huntington’s disease, revealing complex structural rearrangements that can result from transgenesis. Here, we demonstrate in the R6/2 mouse, a widely used Huntington’s disease model, that integration of a rearranged transgene with coincident deletion of 5,444 bp of host genome within the gene Gm12695 has striking molecular consequences. Gm12695, the function of which is unknown, is normally expressed at negligible levels in mouse brain, but transgene integration has resulted in cortical expression of a partial fragment (exons 8–11) 3’ to the transgene integration site in R6/2. This transcript shows significant expression among the extensive network of differentially expressed genes associated with this model, including synaptic transmission, cell signalling and transcription. These data illustrate the value of sequence-level resolution of transgene insertions and transcription analysis to inform phenotypic characterization of transgenic models utilized in therapeutic research.
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Affiliation(s)
- Jessie C Jacobsen
- Centre for Brain Research, School of Biological Sciences, The University of Auckland 1010, New Zealand
| | - Serkan Erdin
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute of M.I.T and Harvard, Cambridge, Massachusetts 02143, USA
| | - Colby Chiang
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Carrie Hanscom
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Renee R Handley
- Centre for Brain Research, School of Biological Sciences, The University of Auckland 1010, New Zealand
| | - Douglas D Barker
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Alex Stortchevoi
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Ian Blumenthal
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Suzanne J Reid
- Centre for Brain Research, School of Biological Sciences, The University of Auckland 1010, New Zealand
| | - Russell G Snell
- Centre for Brain Research, School of Biological Sciences, The University of Auckland 1010, New Zealand
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute of M.I.T and Harvard, Cambridge, Massachusetts 02143, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115 USA
| | - A Jennifer Morton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, United Kingdom
| | - Carl Ernst
- Department of Psychiatry, McGill University, Montreal, Quebec ON H4H 1R3, Canada
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute of M.I.T and Harvard, Cambridge, Massachusetts 02143, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Michael E Talkowski
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute of M.I.T and Harvard, Cambridge, Massachusetts 02143, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115 USA.,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, 02114 USA
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46
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Patassini S, Begley P, Xu J, Church SJ, Reid SJ, Kim EH, Curtis MA, Dragunow M, Waldvogel HJ, Snell RG, Unwin RD, Faull RLM, Cooper GJS. Metabolite mapping reveals severe widespread perturbation of multiple metabolic processes in Huntington's disease human brain. Biochim Biophys Acta 2016; 1862:1650-62. [PMID: 27267344 DOI: 10.1016/j.bbadis.2016.06.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 01/01/2023]
Abstract
Huntington's disease (HD) is a genetically-mediated neurodegenerative disorder wherein the aetiological defect is a mutation in the Huntington's gene (HTT), which alters the structure of the huntingtin protein (Htt) through lengthening of its polyglutamine tract, thus initiating a cascade that ultimately leads to premature death. However, neurodegeneration typically manifests in HD only in middle age, and mechanisms linking the causative mutation to brain disease are poorly understood. Brain metabolism is severely perturbed in HD, and some studies have indicated a potential role for mutant Htt as a driver of these metabolic aberrations. Here, our objective was to determine the effects of HD on brain metabolism by measuring levels of polar metabolites in regions known to undergo varying degrees of damage. We performed gas-chromatography/mass spectrometry-based metabolomic analyses in a case-control study of eleven brain regions in short post-mortem-delay human tissue from nine well-characterized HD patients and nine matched controls. In each patient, we measured metabolite content in representative tissue-samples from eleven brain regions that display varying degrees of damage in HD, thus identifying the presence and abundance of 63 different metabolites from several molecular classes, including carbohydrates, amino acids, nucleosides, and neurotransmitters. Robust alterations in regional brain-metabolite abundances were observed in HD patients: these included changes in levels of small molecules that play important roles as intermediates in the tricarboxylic-acid and urea cycles, and amino-acid metabolism. Our findings point to widespread disruption of brain metabolism and indicate a complex phenotype beyond the gradient of neuropathologic damage observed in HD brain.
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Affiliation(s)
- Stefano Patassini
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand; Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK.
| | - Paul Begley
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK
| | - Jingshu Xu
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand; Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Stephanie J Church
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK
| | - Suzanne J Reid
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Eric H Kim
- Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, United States
| | - Maurice A Curtis
- Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Mike Dragunow
- Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Henry J Waldvogel
- Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Russell G Snell
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand; Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK
| | - Richard L M Faull
- Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Garth J S Cooper
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand; Centre for Brain Research and Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, UK; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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47
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Jacobsen JC, Wilson C, Cunningham V, Glamuzina E, Prosser DO, Love DR, Burgess T, Taylor J, Swan B, Hill R, Robertson SP, Snell RG, Lehnert K. Brain dopamine-serotonin vesicular transport disease presenting as a severe infantile hypotonic parkinsonian disorder. J Inherit Metab Dis 2016; 39:305-8. [PMID: 26497564 DOI: 10.1007/s10545-015-9897-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/23/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022]
Abstract
Two male siblings from a consanguineous union presented in early infancy with marked truncal hypotonia, a general paucity of movement, extrapyramidal signs and cognitive delay. By mid-childhood they had made little developmental progress and remained severely hypotonic and bradykinetic. They developed epilepsy and had problems with autonomic dysfunction and oculogyric crises. They had a number of orthopaedic problems secondary to their hypotonia. Cerebrospinal fluid (CSF) neurotransmitters were initially normal, apart from mildly elevated 5-hydroxyindolacetic acid, and the children did not respond favourably to a trial of levodopa-carbidopa. The youngest died from respiratory complications at 10 years of age. Repeat CSF neurotransmitters in the older sibling at eight years of age showed slightly low homovanillic acid and 5-hydroxyindoleacetic acid levels. Whole-exome sequencing revealed a novel mutation homozygous in both children in the monoamine transporter gene SLC18A2 (p.Pro237His), resulting in brain dopamine-serotonin vesicular transport disease. This is the second family to be described with a mutation in this gene. Treatment with the dopamine agonist pramipexole in the surviving child resulted in mild improvements in alertness, communication, and eye movements. This case supports the identification of the causal mutation in the original case, expands the clinical phenotype of brain dopamine-serotonin vesicular transport disease and confirms that pramipexole treatment may lead to symptomatic improvement in affected individuals.
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Affiliation(s)
- Jessie C Jacobsen
- Centre for Brain Research and School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Callum Wilson
- Adult and Paediatric National Metabolic Service, Auckland City Hospital, Auckland, New Zealand
| | - Vicki Cunningham
- Child Health Centre, Northland District Health Board, Whangarei, New Zealand
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic Service, Auckland City Hospital, Auckland, New Zealand
| | - Debra O Prosser
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Donald R Love
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Trent Burgess
- VCGS Pathology, Murdoch Childrens' Research Institute, Parkville, Victoria, Australia
| | - Juliet Taylor
- Genetic Health Service New Zealand, Auckland City Hospital, Auckland, New Zealand
| | - Brendan Swan
- Centre for Brain Research and School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rosamund Hill
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | | | - Russell G Snell
- Centre for Brain Research and School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- Centre for Brain Research and School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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48
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Handley RR, Reid SJ, Patassini S, Rudiger SR, Obolonkin V, McLaughlan CJ, Jacobsen JC, Gusella JF, MacDonald ME, Waldvogel HJ, Bawden CS, Faull RLM, Snell RG. Metabolic disruption identified in the Huntington's disease transgenic sheep model. Sci Rep 2016; 6:20681. [PMID: 26864449 PMCID: PMC4749952 DOI: 10.1038/srep20681] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 09/25/2015] [Accepted: 12/31/2015] [Indexed: 12/02/2022] Open
Abstract
Huntington’s disease (HD) is a dominantly inherited, progressive neurodegenerative disorder caused by a CAG repeat expansion within exon 1 of HTT, encoding huntingtin. There are no therapies that can delay the progression of this devastating disease. One feature of HD that may play a critical role in its pathogenesis is metabolic disruption. Consequently, we undertook a comparative study of metabolites in our transgenic sheep model of HD (OVT73). This model does not display overt symptoms of HD but has circadian rhythm alterations and molecular changes characteristic of the early phase disease. Quantitative metabolite profiles were generated from the motor cortex, hippocampus, cerebellum and liver tissue of 5 year old transgenic sheep and matched controls by gas chromatography-mass spectrometry. Differentially abundant metabolites were evident in the cerebellum and liver. There was striking tissue-specificity, with predominantly amino acids affected in the transgenic cerebellum and fatty acids in the transgenic liver, which together may indicate a hyper-metabolic state. Furthermore, there were more strong pair-wise correlations of metabolite abundance in transgenic than in wild-type cerebellum and liver, suggesting altered metabolic constraints. Together these differences indicate a metabolic disruption in the sheep model of HD and could provide insight into the presymptomatic human disease.
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Affiliation(s)
- Renee R Handley
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
| | - Suzanne J Reid
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
| | - Stefano Patassini
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
| | - Skye R Rudiger
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development, Adelaide, SA 5350, Australia
| | - Vladimir Obolonkin
- Research &Development, Livestock Improvement Corporation, Hamilton, 3240, New Zealand
| | - Clive J McLaughlan
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development, Adelaide, SA 5350, Australia
| | - Jessie C Jacobsen
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, United States of America
| | - Marcy E MacDonald
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, United States of America
| | - Henry J Waldvogel
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
| | - C Simon Bawden
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development, Adelaide, SA 5350, Australia
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
| | - Russell G Snell
- Centre for Brain Research, University of Auckland, Auckland, 1010, New Zealand
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49
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Lehnert K, Ward H, Berry SD, Ankersmit-Udy A, Burrett A, Beattie EM, Thomas NL, Harris B, Ford CA, Browning SR, Rawson P, Verkerk GA, van der Does Y, Adams LF, Davis SR, Jordan TW, MacGibbon AKH, Spelman RJ, Snell RG. Phenotypic population screen identifies a new mutation in bovine DGAT1 responsible for unsaturated milk fat. Sci Rep 2015; 5:8484. [PMID: 25719731 PMCID: PMC4341421 DOI: 10.1038/srep08484] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 11/11/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022] Open
Abstract
Selective breeding has strongly reduced the genetic diversity in livestock species, and contemporary breeding practices exclude potentially beneficial rare genetic variation from the future gene pool. Here we test whether important traits arising by new mutations can be identified and rescued in highly selected populations. We screened milks from 2.5 million cows to identify an exceptional individual which produced milk with reduced saturated fat content, and improved unsaturated and omega-3 fatty acid concentrations. The milk traits were transmitted dominantly to her offspring, and genetic mapping and genome sequencing revealed a new mutation in a previously unknown splice enhancer of the DGAT1 gene. Homozygous carriers show features of human diarrheal disorders, and may be useful for the development of therapeutic strategies. Our study demonstrates that high-throughput phenotypic screening can uncover rich genetic diversity even in inbred populations, and introduces a novel strategy to develop novel milks with improved nutritional properties.
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Affiliation(s)
- Klaus Lehnert
- 1] ViaLactia Biosciences (NZ) Ltd., Auckland, New Zealand [2] School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Hamish Ward
- ViaLactia Biosciences (NZ) Ltd., Auckland, New Zealand
| | - Sarah D Berry
- ViaLactia Biosciences (NZ) Ltd., Auckland, New Zealand
| | | | | | | | | | | | | | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Pisana Rawson
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | | | | | - Linda F Adams
- ViaLactia Biosciences (NZ) Ltd., Auckland, New Zealand
| | | | - T William Jordan
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | | | | | - Russell G Snell
- 1] ViaLactia Biosciences (NZ) Ltd., Auckland, New Zealand [2] School of Biological Sciences, University of Auckland, Auckland, New Zealand
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50
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Abstract
Traditional RNA extraction methods rely on the use of hazardous chemicals such as phenol, chloroform, guanidinium thiocyanate to disrupt cells and inactivate RNAse simultaneously. RNA isolation from Caenorhabditis elegans presents another challenge due to its tough cuticle, therefore several repeated freeze–thaw cycles may be needed to disrupt the cuticle before the cell contents are released. In addition, a large number of animals are required for successful RNA isolation. To overcome these issues, we have developed a simple and efficient method using proteinase K and a brief heat treatment to release RNA of quality suitable for quantitative PCR analysis.The benefits of the method are: Faster and safer compared to conventional RNA extraction methods Released RNA can be used directly for cDNA synthesis without purification As little as a single worm is sufficient
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Affiliation(s)
- Kien Ly
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Suzanne J Reid
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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