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Fearnley LG, Rafehi H, Bennett MF, Bahlo M. Exploring THAP11 Repeat Expansion beyond Chinese-Ancestry Cohorts: An Examination of 1000 Genomes and UK Biobank Data. Mov Disord 2023; 38:2320-2322. [PMID: 38113319 PMCID: PMC10946534 DOI: 10.1002/mds.29636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Liam G. Fearnley
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
- Bruce Lefroy Centre for Genetic Health ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Haloom Rafehi
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
- Bruce Lefroy Centre for Genetic Health ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Mark F. Bennett
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
| | - Melanie Bahlo
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
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2
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Rafehi H, Read J, Szmulewicz DJ, Davies KC, Snell P, Fearnley LG, Scott L, Thomsen M, Gillies G, Pope K, Bennett MF, Munro JE, Ngo KJ, Chen L, Wallis MJ, Butler EG, Kumar KR, Wu KH, Tomlinson SE, Tisch S, Malhotra A, Lee-Archer M, Dolzhenko E, Eberle MA, Roberts LJ, Fogel BL, Brüggemann N, Lohmann K, Delatycki MB, Bahlo M, Lockhart PJ. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA27B/ATX-FGF14. Am J Hum Genet 2023; 110:1018. [PMID: 37267898 DOI: 10.1016/j.ajhg.2023.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
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3
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Waryah C, Cursons J, Foroutan M, Pflueger C, Wang E, Molania R, Sorolla A, Wallis C, Moses C, Glas I, Magalhães L, Thompson EW, Fearnley LG, Chaffer CL, Davis M, Papenfuss AT, Redfern A, Lister R, Esteller M, Blancafort P. Synthetic Epigenetic Reprogramming of Mesenchymal to Epithelial States Using the CRISPR/dCas9 Platform in Triple Negative Breast Cancer. Adv Sci (Weinh) 2023:e2301802. [PMID: 37217832 PMCID: PMC10401103 DOI: 10.1002/advs.202301802] [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] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 05/24/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a reversible transcriptional program invoked by cancer cells to drive cancer progression. Transcription factor ZEB1 is a master regulator of EMT, driving disease recurrence in poor-outcome triple negative breast cancers (TNBCs). Here, this work silences ZEB1 in TNBC models by CRISPR/dCas9-mediated epigenetic editing, resulting in highly-specific and nearly complete suppression of ZEB1 in vivo, accompanied by long-lasting tumor inhibition. Integrated "omic" changes promoted by dCas9 linked to the KRAB domain (dCas9-KRAB) enabled the discovery of a ZEB1-dependent-signature of 26 genes differentially-expressed and -methylated, including the reactivation and enhanced chromatin accessibility in cell adhesion loci, outlining epigenetic reprogramming toward a more epithelial state. In the ZEB1 locus transcriptional silencing is associated with induction of locally-spread heterochromatin, significant changes in DNA methylation at specific CpGs, gain of H3K9me3, and a near complete erasure of H3K4me3 in the ZEB1 promoter. Epigenetic shifts induced by ZEB1-silencing are enriched in a subset of human breast tumors, illuminating a clinically-relevant hybrid-like state. Thus, the synthetic epi-silencing of ZEB1 induces stable "lock-in" epigenetic reprogramming of mesenchymal tumors associated with a distinct and stable epigenetic landscape. This work outlines epigenome-engineering approaches for reversing EMT and customizable precision molecular oncology approaches for targeting poor outcome breast cancers.
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Affiliation(s)
- Charlene Waryah
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Centre for Medical Research, University of Western Australia, Perth, WA, 6009, Australia
| | - Joseph Cursons
- Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Momeneh Foroutan
- Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, 6 Verdun St, Perth, WA, 6009, Australia
| | - Edina Wang
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Centre for Medical Research, University of Western Australia, Perth, WA, 6009, Australia
| | - Ramyar Molania
- Population Health and Immunity Division, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Anabel Sorolla
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Centre for Medical Research, University of Western Australia, Perth, WA, 6009, Australia
| | - Christopher Wallis
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Centre for Medical Research, University of Western Australia, Perth, WA, 6009, Australia
| | - Colette Moses
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, XH 1098, The Netherlands
| | - Irina Glas
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Leandro Magalhães
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Postgraduate Program of Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, 66075-110, Brazil
| | - Erik W Thompson
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Liam G Fearnley
- Population Health and Immunity Division, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3800, Australia
| | - Christine L Chaffer
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Medicine, Darlinghurst, NSW, 2010, Australia
| | - Melissa Davis
- Population Health and Immunity Division, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Population Health and Immunity Division, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3800, Australia
| | - Andrew Redfern
- School of Medicine, University of Western Australia, Perth, WA, 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, 6 Verdun St, Perth, WA, 6009, Australia
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, 08916, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, 28029, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, 08007, Spain
| | - Pilar Blancafort
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
- Centre for Medical Research, University of Western Australia, Perth, WA, 6009, Australia
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4
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Henden L, Fearnley LG, Grima N, McCann EP, Dobson-Stone C, Fitzpatrick L, Friend K, Hobson L, Chan Moi Fat S, Rowe DB, D'Silva S, Kwok JB, Halliday GM, Kiernan MC, Mazumder S, Timmins HC, Zoing M, Pamphlett R, Adams L, Bahlo M, Blair IP, Williams KL. Short tandem repeat expansions in sporadic amyotrophic lateral sclerosis and frontotemporal dementia. Sci Adv 2023; 9:eade2044. [PMID: 37146135 PMCID: PMC10162670 DOI: 10.1126/sciadv.ade2044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pathogenic short tandem repeat (STR) expansions cause over 20 neurodegenerative diseases. To determine the contribution of STRs in sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), we used ExpansionHunter, REviewer, and polymerase chain reaction validation to assess 21 neurodegenerative disease-associated STRs in whole-genome sequencing data from 608 patients with sporadic ALS, 68 patients with sporadic FTD, and 4703 matched controls. We also propose a data-derived outlier detection method for defining allele thresholds in rare STRs. Excluding C9orf72 repeat expansions, 17.6% of clinically diagnosed ALS and FTD cases had at least one expanded STR allele reported to be pathogenic or intermediate for another neurodegenerative disease. We identified and validated 162 disease-relevant STR expansions in C9orf72 (ALS/FTD), ATXN1 [spinal cerebellar ataxia type 1 (SCA1)], ATXN2 (SCA2), ATXN8 (SCA8), TBP (SCA17), HTT (Huntington's disease), DMPK [myotonic dystrophy type 1 (DM1)], CNBP (DM2), and FMR1 (fragile-X disorders). Our findings suggest clinical and pathological pleiotropy of neurodegenerative disease genes and highlight their importance in ALS and FTD.
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Affiliation(s)
- Lyndal Henden
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam G Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Natalie Grima
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Carol Dobson-Stone
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Lauren Fitzpatrick
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Kathryn Friend
- SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Lynne Hobson
- SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Sandrine Chan Moi Fat
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Dominic B Rowe
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Susan D'Silva
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - John B Kwok
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Glenda M Halliday
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Srestha Mazumder
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Hannah C Timmins
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Margaret Zoing
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Discipline of Pathology, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Lorel Adams
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ian P Blair
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Kelly L Williams
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
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5
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Rafehi H, Read J, Szmulewicz DJ, Davies KC, Snell P, Fearnley LG, Scott L, Thomsen M, Gillies G, Pope K, Bennett MF, Munro JE, Ngo KJ, Chen L, Wallis MJ, Butler EG, Kumar KR, Wu KHC, Tomlinson SE, Tisch S, Malhotra A, Lee-Archer M, Dolzhenko E, Eberle MA, Roberts LJ, Fogel BL, Brüggemann N, Lohmann K, Delatycki MB, Bahlo M, Lockhart PJ. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA50/ATX-FGF14. Am J Hum Genet 2023; 110:105-119. [PMID: 36493768 PMCID: PMC9892775 DOI: 10.1016/j.ajhg.2022.11.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [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: 10/12/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
Adult-onset cerebellar ataxias are a group of neurodegenerative conditions that challenge both genetic discovery and molecular diagnosis. In this study, we identified an intronic (GAA) repeat expansion in fibroblast growth factor 14 (FGF14). Genetic analysis of 95 Australian individuals with adult-onset ataxia identified four (4.2%) with (GAA)>300 and a further nine individuals with (GAA)>250. PCR and long-read sequence analysis revealed these were pure (GAA) repeats. In comparison, no control subjects had (GAA)>300 and only 2/311 control individuals (0.6%) had a pure (GAA)>250. In a German validation cohort, 9/104 (8.7%) of affected individuals had (GAA)>335 and a further six had (GAA)>250, whereas 10/190 (5.3%) control subjects had (GAA)>250 but none were (GAA)>335. The combined data suggest (GAA)>335 are disease causing and fully penetrant (p = 6.0 × 10-8, OR = 72 [95% CI = 4.3-1,227]), while (GAA)>250 is likely pathogenic with reduced penetrance. Affected individuals had an adult-onset, slowly progressive cerebellar ataxia with variable features including vestibular impairment, hyper-reflexia, and autonomic dysfunction. A negative correlation between age at onset and repeat length was observed (R2 = 0.44, p = 0.00045, slope = -0.12) and identification of a shared haplotype in a minority of individuals suggests that the expansion can be inherited or generated de novo during meiotic division. This study demonstrates the power of genome sequencing and advanced bioinformatic tools to identify novel repeat expansions via model-free, genome-wide analysis and identifies SCA50/ATX-FGF14 as a frequent cause of adult-onset ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Read
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - David J. Szmulewicz
- Cerebellar Ataxia Clinic, Eye and Ear Hospital, Melbourne, VIC, Australia,The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kayli C. Davies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam G. Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam Scott
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Mark F. Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kathie J. Ngo
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Luke Chen
- Alfred Hospital, Department of Neurology, Melbourne, VIC, Australia
| | - Mathew J. Wallis
- Clinical Genetics Service, Austin Health, Melbourne, VIC, Australia,Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Kishore R. Kumar
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord, NSW, Australia,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kathy HC. Wu
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Clinical Genomics, St Vincent’s Hospital, Darlinghurst, NSW, Australia,Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,School of Medicine, University of Notre Dame, Sydney, NSW, Australia
| | - Susan E. Tomlinson
- School of Medicine, University of Notre Dame, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Stephen Tisch
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Abhishek Malhotra
- Department of Neuroscience, University Hospital Geelong, Geelong, VIC, Australia
| | - Matthew Lee-Archer
- Launceston General Hospital, Tasmanian Health Service, Launceston, TAS, Australia
| | | | | | - Leslie J. Roberts
- Department of Neurology and Neurological Research, St. Vincent’s Hospital, Melbourne, VIC, Australia
| | - Brent L. Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA,Departments of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Martin B. Delatycki
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Paul J. Lockhart
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Corresponding author
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6
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Grinton BE, Robertson E, Fearnley LG, Scheffer IE, Marson AG, O'Brien TJ, Pickrell WO, Rees MI, Sisodiya SM, Balding DJ, Bennett MF, Bahlo M, Berkovic SF, Oliver KL. A founder event causing a dominant childhood epilepsy survives 800 years through weak selective pressure. Am J Hum Genet 2022; 109:2080-2087. [PMID: 36288729 PMCID: PMC9674963 DOI: 10.1016/j.ajhg.2022.10.004] [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: 05/11/2022] [Accepted: 10/03/2022] [Indexed: 01/26/2023] Open
Abstract
Genetic epilepsy with febrile seizures plus (GEFS+) is an autosomal dominant familial epilepsy syndrome characterized by distinctive phenotypic heterogeneity within families. The SCN1B c.363C>G (p.Cys121Trp) variant has been identified in independent, multi-generational families with GEFS+. Although the variant is present in population databases (at very low frequency), there is strong clinical, genetic, and functional evidence to support pathogenicity. Recurrent variants may be due to a founder event in which the variant has been inherited from a common ancestor. Here, we report evidence of a single founder event giving rise to the SCN1B c.363C>G variant in 14 independent families with epilepsy. A common haplotype was observed in all families, and the age of the most recent common ancestor was estimated to be approximately 800 years ago. Analysis of UK Biobank whole-exome-sequencing data identified 74 individuals with the same variant. All individuals carried haplotypes matching the epilepsy-affected families, suggesting all instances of the variant derive from a single mutational event. This unusual finding of a variant causing an autosomal dominant, early-onset disease in an outbred population that has persisted over many generations can be attributed to the relatively mild phenotype in most carriers and incomplete penetrance. Founder events are well established in autosomal recessive and late-onset disorders but are rarely observed in early-onset, autosomal dominant diseases. These findings suggest variants present in the population at low frequencies should be considered potentially pathogenic in mild phenotypes with incomplete penetrance and may be more important contributors to the genetic landscape than previously thought.
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Affiliation(s)
- Bronwyn E Grinton
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Erandee Robertson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Liam G Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia; Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia; Florey Institute of Neuroscience and Mental Health, Heidelberg, VIC 3084, Australia
| | - Anthony G Marson
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3BX, UK
| | - Terence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; Department of Neurology, The Royal Melbourne Hospital, Parkville, VIC 3052, Australia; Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia; Department of Medicine, The University of Melbourne, Parkville, VIC 3010, Australia
| | - W Owen Pickrell
- Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK; Department of Neurology, Morriston Hospital, Swansea Bay University Health Board, Swansea SA2 8PP, UK
| | - Mark I Rees
- Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK; Faculty of Medicine & Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sanjay M Sisodiya
- Chalfont Centre for Epilepsy, Chalfont St Peter, Buckinghamshire HP11 2FZ, UK; Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - David J Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia.
| | - Karen L Oliver
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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7
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Grima N, Henden L, Fearnley LG, Rowe DB, D'Silva S, Pamphlett R, Adams L, Kiernan MC, Mazumder S, Timmins HC, Zoing M, Bahlo M, Blair IP, Williams KL. NEK1 and STMN2 short tandem repeat lengths are not associated with Australian amyotrophic lateral sclerosis risk. Neurobiol Aging 2022; 116:92-95. [DOI: 10.1016/j.neurobiolaging.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
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8
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Huckstep H, Fearnley LG, Davis MJ. Measuring pathway database coverage of the phosphoproteome. PeerJ 2021; 9:e11298. [PMID: 34113485 PMCID: PMC8162239 DOI: 10.7717/peerj.11298] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. There has been finite success in using data-driven approaches to reveal phosphosite functionality due to a range of limitations. The alternate, more suitable approach is making use of prior knowledge from literature-derived databases. Here, we analysed seven widely used databases to shed light on their suitability to provide functional insights into phosphoproteomics data. We first determined the global coverage of each database at both the protein and phosphosite level. We also determined how consistent each database was in its phosphorylation annotations compared to a global standard. Finally, we looked in detail at the coverage of each database over six experimental datasets. Our analysis highlights the relative strengths and weaknesses of each database, providing a guide in how each can be best used to identify biological mechanisms in phosphoproteomic data.
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Affiliation(s)
- Hannah Huckstep
- Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Liam G. Fearnley
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Division of Population Health, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Melissa J. Davis
- Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
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9
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Ritchie SC, Watts S, Fearnley LG, Holt KE, Abraham G, Inouye M. A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets. Cell Syst 2019; 3:71-82. [PMID: 27467248 DOI: 10.1016/j.cels.2016.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/09/2016] [Accepted: 06/29/2016] [Indexed: 01/15/2023]
Abstract
Network modules-topologically distinct groups of edges and nodes-that are preserved across datasets can reveal common features of organisms, tissues, cell types, and molecules. Many statistics to identify such modules have been developed, but testing their significance requires heuristics. Here, we demonstrate that current methods for assessing module preservation are systematically biased and produce skewed p values. We introduce NetRep, a rapid and computationally efficient method that uses a permutation approach to score module preservation without assuming data are normally distributed. NetRep produces unbiased p values and can distinguish between true and false positives during multiple hypothesis testing. We use NetRep to quantify preservation of gene coexpression modules across murine brain, liver, adipose, and muscle tissues. Complex patterns of multi-tissue preservation were revealed, including a liver-derived housekeeping module that displayed adipose- and muscle-specific association with body weight. Finally, we demonstrate the broader applicability of NetRep by quantifying preservation of bacterial networks in gut microbiota between men and women.
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Affiliation(s)
- Scott C Ritchie
- Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Stephen Watts
- Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Liam G Fearnley
- Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Gad Abraham
- Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Inouye
- Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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10
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Nath AP, Ritchie SC, Byars SG, Fearnley LG, Havulinna AS, Joensuu A, Kangas AJ, Soininen P, Wennerström A, Milani L, Metspalu A, Männistö S, Würtz P, Kettunen J, Raitoharju E, Kähönen M, Juonala M, Palotie A, Ala-Korpela M, Ripatti S, Lehtimäki T, Abraham G, Raitakari O, Salomaa V, Perola M, Inouye M. An interaction map of circulating metabolites, immune gene networks, and their genetic regulation. Genome Biol 2017; 18:146. [PMID: 28764798 PMCID: PMC5540552 DOI: 10.1186/s13059-017-1279-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 01/05/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking. Here, we integrate blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts (total N = 2168), including a subset of individuals with matched multi-omic data at 7-year follow-up. RESULTS We identify topologically replicable gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity. These immune gene modules show complex patterns of association with 158 circulating metabolites, including lipoprotein subclasses, lipids, fatty acids, amino acids, small molecules, and CRP. Genome-wide scans for module expression quantitative trait loci (mQTLs) reveal five modules with mQTLs that have both cis and trans effects. The strongest mQTL is in ARHGEF3 (rs1354034) and affects a module enriched for platelet function, independent of platelet counts. Modules of mast cell/basophil and neutrophil function show temporally stable metabolite associations over 7-year follow-up, providing evidence that these modules and their constituent gene products may play central roles in metabolic inflammation. Furthermore, the strongest mQTL in ARHGEF3 also displays clear temporal stability, supporting widespread trans effects at this locus. CONCLUSIONS This study provides a detailed map of natural variation at the blood immunometabolic interface and its genetic basis, and may facilitate subsequent studies to explain inter-individual variation in cardiometabolic disease.
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Affiliation(s)
- Artika P Nath
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Scott C Ritchie
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Sean G Byars
- Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Liam G Fearnley
- Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Aki S Havulinna
- National Institute for Health and Welfare, Helsinki, 00271, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland
| | - Anni Joensuu
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Antti J Kangas
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland
| | - Pasi Soininen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland
| | | | - Lili Milani
- University of Tartu, Estonian Genome Center, Tartu, 51010, Estonia
| | - Andres Metspalu
- University of Tartu, Estonian Genome Center, Tartu, 51010, Estonia
| | - Satu Männistö
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Peter Würtz
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
| | - Johannes Kettunen
- National Institute for Health and Welfare, Helsinki, 00271, Finland.,Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland.,Biocenter Oulu, University of Oulu, Oulu, 90014, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, 33014, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, FI-33521, Tampere, Finland
| | - Markus Juonala
- Department of Medicine, University of Turku and Division of Medicine, Turku University Hospital, FI-20520, Turku, Finland.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland.,Biocenter Oulu, University of Oulu, Oulu, 90014, Finland.,Computational Medicine, School of Social and Community Medicine, University of Bristol, Bristol, BS8 1TH, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland.,Department of Public Health, University of Helsinki, Helsinki, 00014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, 33014, Tampere, Finland
| | - Gad Abraham
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20520, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, 20520, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, 00271, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland.,University of Tartu, Estonian Genome Center, Tartu, 51010, Estonia
| | - Michael Inouye
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, 3010, Victoria, Australia. .,Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia. .,Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia. .,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
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11
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Abstract
Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological and analytical limitations while also highlighting recent successes in integrating these data. The use of multi-omics to infer reaction rates is discussed as a potential future direction for metabolomics research, as a means of identifying biomarkers as well as inferring causality. Furthermore, we highlight established analysis approaches as well as simulation-based methods currently used in single- and multi-cell levels in systems biology.
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Affiliation(s)
- Liam G Fearnley
- Centre for Systems Genomics.,School of BioSciences.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Michael Inouye
- Centre for Systems Genomics .,School of BioSciences.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
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12
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Ritchie SC, Würtz P, Nath AP, Abraham G, Havulinna AS, Fearnley LG, Sarin AP, Kangas AJ, Soininen P, Aalto K, Seppälä I, Raitoharju E, Salmi M, Maksimow M, Männistö S, Kähönen M, Juonala M, Ripatti S, Lehtimäki T, Jalkanen S, Perola M, Raitakari O, Salomaa V, Ala-Korpela M, Kettunen J, Inouye M. The Biomarker GlycA Is Associated with Chronic Inflammation and Predicts Long-Term Risk of Severe Infection. Cell Syst 2015; 1:293-301. [PMID: 27136058 DOI: 10.1016/j.cels.2015.09.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 11/27/2022]
Abstract
The biomarker glycoprotein acetylation (GlycA) has been shown to predict risk of cardiovascular disease and all-cause mortality. Here, we characterize biological processes associated with GlycA by leveraging population-based omics data and health records from >10,000 individuals. Our analyses show that GlycA levels are chronic within individuals for up to a decade. In apparently healthy individuals, elevated GlycA corresponded to elevation of myriad inflammatory cytokines, as well as a gene coexpression network indicative of increased neutrophil activity, suggesting that individuals with high GlycA may be in a state of chronic inflammatory response. Accordingly, analysis of infection-related hospitalization and death records showed that increased GlycA increased long-term risk of severe non-localized and respiratory infections, particularly septicaemia and pneumonia. In total, our work demonstrates that GlycA is a biomarker for chronic inflammation, neutrophil activity, and risk of future severe infection. It also illustrates the utility of leveraging multi-layered omics data and health records to elucidate the molecular and cellular processes associated with biomarkers.
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Affiliation(s)
- Scott C Ritchie
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia; Department of Pathology, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Peter Würtz
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu 90014, Finland
| | - Artika P Nath
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Gad Abraham
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia; Department of Pathology, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Aki S Havulinna
- National Institute for Health and Welfare, Helsinki 00271, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Liam G Fearnley
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia; Department of Pathology, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Antti J Kangas
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu 90014, Finland
| | - Pasi Soininen
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu 90014, Finland; NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
| | - Kristiina Aalto
- MediCity Research Laboratory, Department of Medical Microbiology and Immunology, University of Turku, Turku 20520, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories, School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Marko Salmi
- National Institute for Health and Welfare, Helsinki 00271, Finland; MediCity Research Laboratory, Department of Medical Microbiology and Immunology, University of Turku, Turku 20520, Finland
| | - Mikael Maksimow
- National Institute for Health and Welfare, Helsinki 00271, Finland; MediCity Research Laboratory, Department of Medical Microbiology and Immunology, University of Turku, Turku 20520, Finland
| | - Satu Männistö
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, FI-33521 Tampere, Finland
| | - Markus Juonala
- Department of Medicine, University of Turku and Division of Medicine, Turku University Hospital, FI-20520 Turku, Finland; Murdoch Childrens Research Institute, Parkville, 3052 Victoria, Australia
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland; Department of Public Health, University of Helsinki, Helsinki 00014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory, Department of Medical Microbiology and Immunology, University of Turku, Turku 20520, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki 00271, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu 90014, Finland; NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland; Oulu University Hospital, Oulu 90220, Finland; Computational Medicine, School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Johannes Kettunen
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu 90014, Finland; National Institute for Health and Welfare, Helsinki 00271, Finland; NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland.
| | - Michael Inouye
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia; Department of Pathology, The University of Melbourne, Parkville, 3010 Victoria, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, 3010 Victoria, Australia.
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13
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Abstract
Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge.
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14
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Abstract
Curated databases of signal transduction have grown to describe several thousand reactions, and efficient use of these data requires the development of modelling tools to elucidate and explore system properties. We present PATHLOGIC-S, a Boolean specification for a signalling model, with its associated GPL-licensed implementation using integer programming techniques. The PATHLOGIC-S specification has been designed to function on current desktop workstations, and is capable of providing analyses on some of the largest currently available datasets through use of Boolean modelling techniques to generate predictions of stable and semi-stable network states from data in community file formats. PATHLOGIC-S also addresses major problems associated with the presence and modelling of inhibition in Boolean systems, and reduces logical incoherence due to common inhibitory mechanisms in signalling systems. We apply this approach to signal transduction networks including Reactome and two pathways from the Panther Pathways database, and present the results of computations on each along with a discussion of execution time. A software implementation of the framework and model is freely available under a GPL license.
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Affiliation(s)
- Liam G. Fearnley
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Lars K. Nielsen
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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