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Lutz MW, Chiba-Falek O. Bioinformatics pipeline to guide post-GWAS studies in Alzheimer's: A new catalogue of disease candidate short structural variants. Alzheimers Dement 2023; 19:4094-4109. [PMID: 37253165 PMCID: PMC10524333 DOI: 10.1002/alz.13168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Short structural variants (SSVs), including insertions/deletions (indels), are common in the human genome and impact disease risk. The role of SSVs in late-onset Alzheimer's disease (LOAD) has been understudied. In this study, we developed a bioinformatics pipeline of SSVs within LOAD-genome-wide association study (GWAS) regions to prioritize regulatory SSVs based on the strength of their predicted effect on transcription factor (TF) binding sites. METHODS The pipeline utilized publicly available functional genomics data sources including candidate cis-regulatory elements (cCREs) from ENCODE and single-nucleus (sn)RNA-seq data from LOAD patient samples. RESULTS We catalogued 1581 SSVs in candidate cCREs in LOAD GWAS regions that disrupted 737 TF sites. That included SSVs that disrupted the binding of RUNX3, SPI1, and SMAD3, within the APOE-TOMM40, SPI1, and MS4A6A LOAD regions. CONCLUSIONS The pipeline developed here prioritized non-coding SSVs in cCREs and characterized their putative effects on TF binding. The approach integrates multiomics datasets for validation experiments using disease models.
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Affiliation(s)
- Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
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2
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Monnakgotla NR, Mahungu AC, Heckmann JM, Botha G, Mulder NJ, Wu G, Rampersaud E, Myers J, Van Blitterswijk M, Rademakers R, Taylor JP, Wuu J, Benatar M, Nel M. Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans. Neurol Genet 2023; 9:e200077. [PMID: 37346932 PMCID: PMC10281237 DOI: 10.1212/nxg.0000000000200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/03/2023] [Indexed: 06/23/2023]
Abstract
Background and Objectives Amyotrophic lateral sclerosis (ALS) is a degenerative condition of the brain and spinal cord in which protein-coding variants in known ALS disease genes explain a minority of sporadic cases. There is a growing interest in the role of noncoding structural variants (SVs) as ALS risk variants or genetic modifiers of ALS phenotype. In small European samples, specific short SV alleles in noncoding regulatory regions of SCAF4, SQSTM1, and STMN2 have been reported to be associated with ALS, and several groups have investigated the possible role of SMN1/SMN2 gene copy numbers in ALS susceptibility and clinical severity. Methods Using short-read whole genome sequencing (WGS) data, we investigated putative ALS-susceptibility SCAF4 (3'UTR poly-T repeat), SQSTM1 (intron 5 AAAC insertion), and STMN2 (intron 3 CA repeat) alleles in African ancestry patients with ALS and described the architecture of the SMN1/SMN2 gene region. South African cases with ALS (n = 114) were compared with ancestry-matched controls (n = 150), 1000 Genomes Project samples (n = 2,336), and H3Africa Genotyping Chip Project samples (n = 347). Results There was no association with previously reported SCAF4 poly-T repeat, SQSTM1 AAAC insertion, and long STMN2 CA alleles with ALS risk in South Africans (p > 0.2). Similarly, SMN1 and SMN2 gene copy numbers did not differ between South Africans with ALS and matched population controls (p > 0.9). Notably, 20% of the African samples in this study had no SMN2 gene copies, which is a higher frequency than that reported in Europeans (approximately 7%). Discussion We did not replicate the reported association of SCAF4, SQSTM1, and STMN2 short SVs with ALS in a small South African sample. In addition, we found no link between SMN1 and SMN2 copy numbers and susceptibility to ALS in this South African sample, which is similar to the conclusion of a recent meta-analysis of European studies. However, the SMN gene region findings in Africans replicate previous results from East and West Africa and highlight the importance of including diverse population groups in disease gene discovery efforts. The clinically relevant differences in the SMN gene architecture between African and non-African populations may affect the effectiveness of targeted SMN2 gene therapy for related diseases such as spinal muscular atrophy.
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Affiliation(s)
- Nomakhosazana R Monnakgotla
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Amokelani C Mahungu
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Jeannine M Heckmann
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Gerrit Botha
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Nicola J Mulder
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Gang Wu
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Evadnie Rampersaud
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Jason Myers
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Marka Van Blitterswijk
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Rosa Rademakers
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - J Paul Taylor
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Joanne Wuu
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Michael Benatar
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
| | - Melissa Nel
- From the Neurology Research Group (N.R.M., A.C.M., J.M.H., M.N.), Division of Neurology, Department of Medicine; Neuroscience Institute (N.R.M., A.C.M., J.M.H., M.N.); Computational Biology Division (G.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.V.B.), Mayo Clinic, Jacksonville, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belgium; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Department of Neurology (J.W., M.B.), University of Miami, FL
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Theunissen F, Anderton RS, Mastaglia FL, James I, Bedlack R, Akkari PA. Intronic NEFH variant is associated with reduced risk for sporadic ALS and later age of disease onset. Sci Rep 2022; 12:14739. [PMID: 36042248 PMCID: PMC9427846 DOI: 10.1038/s41598-022-18942-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Neurofilament heavy (NEFH) is one of the critical proteins required for the formation of the neuronal cytoskeleton and polymorphisms in NEFH are reported as a rare cause of sporadic ALS (sALS). In the current study, a candidate tetranucleotide (TTTA) repeat variant in NEFH was selected using an in-silico short structural variant (SSV) evaluation algorithm and investigated in two cohorts of North American sALS patients, both separately and combined (Duke cohort n = 138, Coriell cohort n = 333; combined cohort n = 471), compared to a group of healthy controls from the Coriell Institute biobank (n = 496). Stratification according to site of disease onset revealed that the 9 TTTA allele was associated with reduced disease risk, specifically confined to spinal-onset sALS patients in the Duke cohort (p = 0.001). Furthermore, carriage of the 10 TTTA allele was associated with a 2.7 year later age of disease onset in the larger combined sALS cohort (p = 0.02). These results suggest that the 9 and 10 TTTA motif length may have a protective advantage for potentially lowering the risk of sALS and delaying the age of disease onset, however, these results need to be replicated in larger multicenter and multi-ethnic cohorts.
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Affiliation(s)
- Frances Theunissen
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ryan S Anderton
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,School of Health Sciences and Institute for Health Research, University of Notre Dame Australia, Fremantle, WA, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Ian James
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | | | - P Anthony Akkari
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia. .,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia. .,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia. .,Department of Neurology, Duke University, Durham, NC, USA.
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4
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Berthold N, Pytte J, Bulik CM, Tschochner M, Medland SE, Akkari PA. Bridging the gap: Short structural variants in the genetics of anorexia nervosa. Int J Eat Disord 2022; 55:747-753. [PMID: 35470453 PMCID: PMC9545787 DOI: 10.1002/eat.23716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/07/2022]
Abstract
Anorexia nervosa (AN) is a devastating disorder with evidence of underexplored heritability. Twin and family studies estimate heritability (h2 ) to be 57%-64%, and genome-wide association studies (GWAS) reveal significant genetic correlations with psychiatric and anthropometric traits and a total of nine genome-wide significant loci. Whether significantly associated single nucleotide polymorphisms identified by GWAS are causal or tag true causal variants, remains to be elucidated. We propose a novel method for bridging this knowledge gap by fine-mapping short structural variants (SSVs) in and around GWAS-identified loci. SSV fine-mapping of loci associated with complex disorders such as schizophrenia, amyotrophic lateral sclerosis, and Alzheimer's disease has uncovered genetic risk markers, phenotypic variability between patients, new pathological mechanisms, and potential therapeutic targets. We analyze previous investigations' methods and propose utilizing an evaluation algorithm to prioritize 10 SSVs for each of the top two AN GWAS-identified loci followed by Sanger sequencing and fragment analysis via capillary electrophoresis to characterize these SSVs for case/control association studies. Success of previous SSV analyses in complex disorders and effective utilization of similar methodologies supports our proposed method. Furthermore, the structural and spatial properties of the 10 SSVs identified for each of the top two AN GWAS-associated loci, cell adhesion molecule 1 (CADM1) and NCK interacting protein with SH3 domain (NCKIPSD), are similar to previous studies. We propose SSV fine-mapping of AN-associated loci will identify causal genetic architecture. Deepening understandings of AN may lead to novel therapeutic targets and subsequently increase quality-of-life for individuals living with the illness. PUBLIC SIGNIFICANCE STATEMENT: Anorexia nervosa is a severe and complex illness, arising from a combination of environmental and genetic factors. Recent studies estimate the contribution of genetic variability; however, the specific DNA sequences and how they contribute remain unknown. We present a novel approach, arguing that the genetic variant class, short structural variants, could answer this knowledge gap and allow development of biologically targeted therapeutics, improving quality-of-life and patient outcomes for affected individuals.
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Affiliation(s)
- Natasha Berthold
- School of Nursing, Midwifery, Health Sciences & PhysiotherapyUniversity of Notre Dame AustraliaFremantleWestern AustraliaAustralia
- Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
- School of Human Sciences, University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Julia Pytte
- Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
- School of Human Sciences, University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Cynthia M. Bulik
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Department of PsychiatryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of NutritionUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Monika Tschochner
- School of Nursing, Midwifery, Health Sciences & PhysiotherapyUniversity of Notre Dame AustraliaFremantleWestern AustraliaAustralia
| | - Sarah E. Medland
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Patrick Anthony Akkari
- Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityPerthWestern AustraliaAustralia
- Centre for Neuromuscular and Neurological DisordersUniversity of Western AustraliaNedlandsWestern AustraliaAustralia
- Department of NeurologyDuke UniversityDurhamNorth Carolina
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5
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Theunissen F, Flynn LL, Anderton RS, Akkari PA. Short structural variants as informative genetic markers for ALS disease risk and progression. BMC Med 2022; 20:11. [PMID: 35034660 PMCID: PMC8762977 DOI: 10.1186/s12916-021-02206-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023] Open
Abstract
There is considerable variability in disease progression for patients with amyotrophic lateral sclerosis (ALS) including the age of disease onset, site of disease onset, and survival time. There is growing evidence that short structural variations (SSVs) residing in frequently overlooked genomic regions can contribute to complex disease mechanisms and can explain, in part, the phenotypic variability in ALS patients. Here, we discuss SSVs recently characterized by our laboratory and how these discoveries integrate into the current literature on ALS, particularly in the context of application to future clinical trials. These markers may help to identify and differentiate patients for clinical trials that have a similar ALS disease mechanism(s), thereby reducing the impact of participant heterogeneity. As evidence accumulates for the genetic markers discovered in SQSTM1, SCAF4, and STMN2, we hope to improve the outcomes of future ALS clinical trials.
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Affiliation(s)
- Frances Theunissen
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia.
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.
| | - Loren L Flynn
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Black Swan Pharmaceuticals, Wake Forrest, NC, USA
| | - Ryan S Anderton
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
- Faculty of Medicine, Nursing, Midwifery and Health Sciences, University of Notre Dame Australia, Fremantle, WA, 6160, Australia
| | - P Anthony Akkari
- Perron Institute for Neurological and Translational Science, First floor, RR block, QEII Medical Centre, 8 Verdun St, Nedlands, WA, 6009, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Black Swan Pharmaceuticals, Wake Forrest, NC, USA
- Division of Neurology, Duke University Medical Centre, Duke University, Durham, NC, USA
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6
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Genetics of synucleins in neurodegenerative diseases. Acta Neuropathol 2021; 141:471-490. [PMID: 32740728 DOI: 10.1007/s00401-020-02202-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
Abstract
The SNCA locus currently has an indisputable role in Parkinson's disease and other synucleinopathies. The role of genetic variability in the other members of the synuclein family (SNCB and SNCG) in disease is far less clear. In this review, we critically assess the pathogenicity, main characteristics, and roles of genetic variants in these genes reported to be causative of synucleinopathies. We also summarize the different association signals identified in the SNCA locus that have been associated with risk for disease. We take a bird's eye view of the variability currently reported in the general population for the three genes and use these data to infer on the potential relationship between each of the genes and human disease.
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7
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Theunissen F, Anderton RS, Mastaglia FL, Flynn LL, Winter SJ, James I, Bedlack R, Hodgetts S, Fletcher S, Wilton SD, Laing NG, MacShane M, Needham M, Saunders A, Mackay-Sim A, Melamed Z, Ravits J, Cleveland DW, Akkari PA. Novel STMN2 Variant Linked to Amyotrophic Lateral Sclerosis Risk and Clinical Phenotype. Front Aging Neurosci 2021; 13:658226. [PMID: 33841129 PMCID: PMC8033025 DOI: 10.3389/fnagi.2021.658226] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022] Open
Abstract
Objective There is a critical need to establish genetic markers that explain the complex phenotypes and pathogenicity of ALS. This study identified a polymorphism in the Stathmin-2 gene and investigated its association with sporadic ALS (sALS) disease risk, age-of onset and survival duration. Methods The candidate CA repeat was systematically analyzed using PCR, Sanger sequencing and high throughput capillary separation for genotyping. Stathmin-2 expression was investigated using RT-PCR in patient olfactory neurosphere-derived (ONS) cells and RNA sequencing in laser-captured spinal motor neurons. Results In a case-control analysis of a combined North American sALS cohort (n = 321) and population control group (n = 332), long/long CA genotypes were significantly associated with disease risk (p = 0.042), and most strongly when one allele was a 24 CA repeat (p = 0.0023). In addition, longer CA allele length was associated with earlier age-of-onset (p = 0.039), and shorter survival duration in bulbar-onset cases (p = 0.006). In an Australian longitudinal sALS cohort (n = 67), ALS functional rating scale scores were significantly lower in carriers of the long/long genotype (p = 0.034). Stathmin-2 mRNA expression was reduced in sporadic patient ONS cells. Additionally, sALS patients and controls exhibited variable expression of Stathmin-2 mRNA according to CA genotype in laser-captured spinal motor neurons. Conclusions We report a novel non-coding CA repeat in Stathmin-2 which is associated with sALS disease risk and has disease modifying effects. The potential value of this variant as a disease marker and tool for cohort enrichment in clinical trials warrants further investigation.
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Affiliation(s)
- Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ryan S Anderton
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,School of Health Sciences, Institute for Health Research, The University of Notre Dame Australia, Fremantle, WA, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Loren L Flynn
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Samantha J Winter
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Health Sciences, Institute for Health Research, The University of Notre Dame Australia, Fremantle, WA, Australia
| | - Ian James
- Institute for Immunology and Infectious Disease, Murdoch University, Perth, WA, Australia
| | - Richard Bedlack
- Department of Neurology, Duke University, Durham, NC, United States
| | - Stuart Hodgetts
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Human Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Steve D Wilton
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Nigel G Laing
- Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Mandi MacShane
- Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Merrilee Needham
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Faculty of Medicine, The University of Notre Dame Australia, Fremantle, WA, Australia.,Department of Neurology, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Ann Saunders
- Zinfandel Pharmaceuticals, Chapel Hill, NC, United States
| | - Alan Mackay-Sim
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Ze'ev Melamed
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
| | - John Ravits
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - P Anthony Akkari
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,Department of Neurology, Duke University, Durham, NC, United States
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Pytte J, Flynn LL, Anderton RS, Mastaglia FL, Theunissen F, James I, Pfaff A, Koks S, Saunders AM, Bedlack R, Burns DK, Lutz MW, Siddique N, Siddique T, Roses AD, Akkari PA. Disease-modifying effects of an SCAF4 structural variant in a predominantly SOD1 ALS cohort. Neurol Genet 2020; 6:e470. [PMID: 32754644 PMCID: PMC7357414 DOI: 10.1212/nxg.0000000000000470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To test the hypothesis that rs573116164 will have disease-modifying effects in patients with superoxide dismutase 1 (SOD1) familial amyotrophic lateral sclerosis (fALS), we characterized rs573116164 within a cohort of 190 patients with fALS and 560 healthy age-matched controls to assess the variant for association with various measures of disease. METHODS Using a previously described bioinformatics evaluation algorithm, a polymorphic short structural variant associated with SOD1 was identified according to its theoretical effect on gene expression. An 12-18 poly-T repeat (rs573116164) within the 3' untranslated region of serine and arginine rich proteins-related carboxy terminal domain associated factor 4 (SCAF4), a gene that is adjacent to SOD1, was assessed for disease association and influence on survival and age at onset in an fALS cohort using PCR, Sanger sequencing, and capillary separation techniques for allele detection. RESULTS In a North American cohort of predominantly SOD1 fALS patients (n =190) and age-matched healthy controls (n = 560), we showed that carriage of an 18T SCAF4 allele was associated with disease within this cohort (odds ratio [OR] 6.6; 95% confidence interval [CI] 3.9-11.2; p = 4.0e-11), but also within non-SOD1 cases (n = 27; OR 5.3; 95% CI 1.9-14.5; p = 0.0014). This finding suggests genetically SOD1-independent effects of SCAF4 on fALS susceptibility. Furthermore, carriage of an 18T allele was associated with a 26-month reduction in survival time (95% CI 6.6-40.8; p = 0.014), but did not affect age at onset of disease. CONCLUSIONS The findings in this fALS cohort suggest that rs573116164 could have SOD1-independent and broader relevance in ALS, warranting further investigation in other fALS and sporadic ALS cohorts, as well as studies of functional effects of the 18T variant on gene expression.
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Affiliation(s)
- Julia Pytte
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Loren L Flynn
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ryan S Anderton
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Frank L Mastaglia
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Frances Theunissen
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ian James
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Abigail Pfaff
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Sulev Koks
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ann M Saunders
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Richard Bedlack
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Daniel K Burns
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Michael W Lutz
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Nailah Siddique
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Teepu Siddique
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Allen D Roses
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - P Anthony Akkari
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
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Pytte J, Anderton RS, Flynn LL, Theunissen F, Jiang L, Pitout I, James I, Mastaglia FL, Saunders AM, Bedlack R, Siddique T, Siddique N, Akkari PA. Association of a structural variant within the SQSTM1 gene with amyotrophic lateral sclerosis. NEUROLOGY-GENETICS 2020; 6:e406. [PMID: 32185242 PMCID: PMC7061286 DOI: 10.1212/nxg.0000000000000406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/23/2020] [Indexed: 11/15/2022]
Abstract
Objective As structural variations may underpin susceptibility to complex neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), the objective of this study was to investigate a structural variant (SV) within sequestosome 1 (SQSTM1). Methods A candidate insertion/deletion variant within intron 5 of the SQSTM1 gene was identified using a previously established SV evaluation algorithm and chosen according to its subsequent theoretical effect on gene expression. The variant was systematically assessed through PCR, polyacrylamide gel fractionation, Sanger sequencing, and reverse transcriptase PCR. Results A reliable and robust assay confirmed the polymorphic nature of this variant and that the variant may influence SQSTM1 transcript levels. In a North American cohort of patients with familial ALS (fALS) and sporadic ALS (sALS) (n = 403) and age-matched healthy controls (n = 562), we subsequently showed that the SQSTM1 variant is associated with fALS (p = 0.0036), particularly in familial superoxide dismutase 1 mutation positive patients (p = 0.0005), but not with patients with sALS (p = 0.97). Conclusions This disease association highlights the importance and implications of further investigation into SVs that may provide new targets for cohort stratification and therapeutic development.
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Affiliation(s)
- Julia Pytte
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ryan S Anderton
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Loren L Flynn
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Frances Theunissen
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Leanne Jiang
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ianthe Pitout
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ian James
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Frank L Mastaglia
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ann M Saunders
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Richard Bedlack
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Teepu Siddique
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Nailah Siddique
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - P Anthony Akkari
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
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10
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Theunissen F, Flynn LL, Anderton RS, Mastaglia F, Pytte J, Jiang L, Hodgetts S, Burns DK, Saunders A, Fletcher S, Wilton SD, Akkari PA. Structural Variants May Be a Source of Missing Heritability in sALS. Front Neurosci 2020; 14:47. [PMID: 32082115 PMCID: PMC7005198 DOI: 10.3389/fnins.2020.00047] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022] Open
Abstract
The underlying genetic and molecular mechanisms that drive amyotrophic lateral sclerosis (ALS) remain poorly understood. Structural variants within the genome can play a significant role in neurodegenerative disease risk, such as the repeat expansion in C9orf72 and the tri-nucleotide repeat in ATXN2, both of which are associated with familial and sporadic ALS. Many such structural variants reside in uncharacterized regions of the human genome, and have been under studied. Therefore, characterization of structural variants located in and around genes associated with ALS could provide insight into disease pathogenesis, and lead to the discovery of highly informative genetic tools for stratification in clinical trials. Such genomic variants may provide a deeper understanding of how gene expression can affect disease etiology, disease severity and trajectory, patient response to treatment, and may hold the key to understanding the genetics of sporadic ALS. This article outlines the current understanding of amyotrophic lateral sclerosis genetics and how structural variations may underpin some of the missing heritability of this disease.
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Affiliation(s)
- Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Human Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Loren L Flynn
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ryan S Anderton
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,School of Health Sciences, Institute for Health Research, University of Notre Dame Australia, Fremantle, WA, Australia
| | - Frank Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Julia Pytte
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Human Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Leanne Jiang
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Biological Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Stuart Hodgetts
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Human Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Daniel K Burns
- Zinfandel Pharmaceuticals, Chapel Hill, NC, United States
| | - Ann Saunders
- Zinfandel Pharmaceuticals, Chapel Hill, NC, United States
| | - Sue Fletcher
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Steve D Wilton
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Patrick Anthony Akkari
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
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11
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Afek A, Tagliafierro L, Glenn OC, Lukatsky DB, Gordan R, Chiba-Falek O. Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene. Neurogenetics 2018; 19:135-144. [PMID: 29730780 DOI: 10.1007/s10048-018-0546-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/25/2018] [Indexed: 12/01/2022]
Abstract
Short structural variants-variants other than single nucleotide polymorphisms-are hypothesized to contribute to many complex diseases, possibly by modulating gene expression. However, the molecular mechanisms by which noncoding short structural variants exert their effects on gene regulation have not been discovered. Here, we study simple sequence repeats (SSRs), a common class of short structural variants. Previously, we showed that repetitive sequences can directly influence the binding of transcription factors to their proximate recognition sites, a mechanism we termed non-consensus binding. In this study, we focus on the SSR termed Rep1, which was associated with Parkinson's disease (PD) and has been implicated in the cis-regulation of the PD-risk SNCA gene. We show that Rep1 acts via the non-consensus binding mechanism to affect the binding of transcription factors from the GATA and ELK families to their specific sites located right next to the Rep1 repeat. Next, we performed an expression analysis to further our understanding regarding the GATA and ELK family members that are potentially relevant for SNCA transcriptional regulation in health and disease. Our analysis indicates a potential role for GATA2, consistent with previous reports. Our study proposes non-consensus transcription factor binding as a potential mechanism through which noncoding repeat variants could exert their pathogenic effects by regulating gene expression.
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Affiliation(s)
- A Afek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, 27710, USA.,Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - L Tagliafierro
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Neurology, Duke University Medical Center, Durham, NC, 27710, USA
| | - O C Glenn
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Neurology, Duke University Medical Center, Durham, NC, 27710, USA
| | - D B Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, 8410501, Beersheba, Israel
| | - R Gordan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, 27710, USA. .,Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA. .,Department of Computer Science, Duke University, Durham, NC, 27708, USA.
| | - O Chiba-Falek
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA. .,Department of Neurology, Duke University Medical Center, Durham, NC, 27710, USA.
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12
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Piper DA, Sastre D, Schüle B. Advancing Stem Cell Models of Alpha-Synuclein Gene Regulation in Neurodegenerative Disease. Front Neurosci 2018; 12:199. [PMID: 29686602 PMCID: PMC5900030 DOI: 10.3389/fnins.2018.00199] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/13/2018] [Indexed: 12/15/2022] Open
Abstract
Alpha-synuclein (non A4 component of amyloid precursor, SNCA, NM_000345.3) plays a central role in the pathogenesis of Parkinson's disease (PD) and related Lewy body disorders such as Parkinson's disease dementia, Lewy body dementia, and multiple system atrophy. Since its discovery as a disease-causing gene in 1997, alpha-synuclein has been a central point of scientific interest both at the protein and gene level. Mutations, including copy number variants, missense mutations, short structural variants, and single nucleotide polymorphisms, can be causative for PD and affect conformational changes of the protein, can contribute to changes in expression of alpha-synuclein and its isoforms, and can influence regulation of temporal as well as spatial levels of alpha-synuclein in different tissues and cell types. A lot of progress has been made to understand both the physiological transcriptional and epigenetic regulation of the alpha-synuclein gene and whether changes in transcriptional regulation could lead to disease and neurodegeneration in PD and related alpha-synucleinopathies. Although the histopathological changes in these neurodegenerative disorders are similar, the temporal and spatial presentation and progression distinguishes them which could be in part due to changes or disruption of transcriptional regulation of alpha-synuclein. In this review, we describe different genetic alterations that contribute to PD and neurodegenerative conditions and review aspects of transcriptional regulation of the alpha-synuclein gene in the context of the development of PD. New technologies, advanced gene engineering and stem cell modeling, are on the horizon to shed further light on a better understanding of gene regulatory processes and exploit them for therapeutic developments.
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Affiliation(s)
- Desiree A Piper
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
| | - Danuta Sastre
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
| | - Birgitt Schüle
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
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13
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Glenn OC, Tagliafierro L, Beach TG, Woltjer RL, Chiba-Falek O. Interpreting Gene Expression Effects of Disease-Associated Variants: A Lesson from SNCA rs356168. Front Genet 2017; 8:133. [PMID: 28979294 PMCID: PMC5611418 DOI: 10.3389/fgene.2017.00133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/07/2017] [Indexed: 11/13/2022] Open
Abstract
The SNCA intronic single nucleotide polymorphism (SNP), rs356168, has been associated with Parkinson's disease (PD) in large genome wide association studies (GWAS). Recently, the PD-risk allele, rs356168-G was shown to increase SNCA-mRNA expression using genome edited human induced pluripotent stem cells (iPSC)-derived neurons. In this study, as means of validation, we tested the effect of rs356168 on total SNCA-mRNA levels using brain tissues, temporal and frontal cortex, from healthy control donors. Carriers of the rs356168-G allele demonstrated a borderline significant decrease of SNCA-mRNA levels in temporal brain tissues (p = 0.02) compared to individuals homozygous for the 'A' allele. Similar trend, but weak, was observed in the analysis of frontal cortex samples, however, this analysis did not reach statistical significance. These results conflict with the recently reported effect of SNCA SNP rs356168 described above. Our study conveys the need to carefully interpret the precise molecular mechanism by which rs356168, or another tightly linked variant, affects the regulation of SNCA expression. The regulatory mechanisms that contribute to the observed associations between PD and the SNCA-3' linkage disequilibrium region warrant further investigations.
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Affiliation(s)
- Omolara-Chinue Glenn
- Department of Neurology, Duke University Medical Center, DurhamNC, United States.,Center for Genomic and Computational Biology, Duke University Medical Center, DurhamNC, United States
| | - Lidia Tagliafierro
- Department of Neurology, Duke University Medical Center, DurhamNC, United States.,Center for Genomic and Computational Biology, Duke University Medical Center, DurhamNC, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun CityAZ, United States
| | - Randy L Woltjer
- Layton Aging and Alzheimer's Disease Center, Department of Pathology, Oregon Health and Science University, PortlandOR, United States
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, DurhamNC, United States.,Center for Genomic and Computational Biology, Duke University Medical Center, DurhamNC, United States
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14
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Structural variants in SNCA gene and the implication to synucleinopathies. Curr Opin Genet Dev 2017; 44:110-116. [PMID: 28319736 DOI: 10.1016/j.gde.2017.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/30/2017] [Indexed: 01/23/2023]
Abstract
Synucleinopathies are a group of neurodegenerative diseases that share a common pathological lesion of intracellular protein inclusions largely composed of aggregates of alpha-synuclein protein. Accumulating evidence, including genome-wide association studies, has implicated the alpha-synuclein (SNCA) gene in the etiology of synucleinopathies and it has been suggested that SNCA expression levels are critical for the development of these diseases. This review focuses on genetic variants from the class of structural variants (SVs), including multiplication of large genomic segments and short (<50bp) genomic variants such as simple sequence repeats (SSRs), within the SNCA locus. We provide evidence that SNCA-SVs play a key role in the pathogenesis of synucleinopathies via their effects on gene expression and on regulatory mechanisms including transcription and splicing.
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