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Piras IS, Krate J, Schrauwen I, Corneveaux JJ, Serrano GE, Sue L, Beach TG, Huentelman MJ. Whole transcriptome profiling of the human hippocampus suggests an involvement of the KIBRA rs17070145 polymorphism in differential activation of the MAPK signaling pathway. Hippocampus 2017; 27:784-793. [PMID: 28380666 DOI: 10.1002/hipo.22731] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 02/26/2017] [Accepted: 03/27/2017] [Indexed: 11/06/2022]
Abstract
The rs17070145-T variant of the WWC1 gene, coding for the KIBRA protein, has been associated with both increased episodic memory performance and lowered risk for late onset Alzheimer's disease, although the mechanism behind this protective effect has not been completely elucidated. To achieve a better understanding of the pathways modulated by rs17070145 and its associated functional variant(s), we used laser capture microdissection (LCM) and RNA-sequencing to investigate the effect of rs17070145 genotypes on whole transcriptome expression in the human hippocampus (HP) of 22 neuropathologically normal individuals, with a specific focus on the dentate gyrus (DG) and at the pyramidal cells (PC) of CA1 and CA3 sub-regions. Differential expression analysis of RNA-seq data within the HP based on the rs17070145 genotype revealed an overexpression of genes involved in the MAPK signaling pathway, potentially driven by the T/T genotype. The most important contribution comes from genes dysregulated within the DG region. Other genes significantly dysregulated, and not involved in the MAPK pathway (Adj P < 0.01 and Fold Change > |1.00|) were: RSPO4 (HP); ARC, DUSP5, DNAJB5, EGR4, PPP1R15A, WBP11P1, EGR1, GADD45B (DG); CH25H, HSPA1A, HSPA1B, TNFSF9, and NPAS4 (PC). Several evidences suggested that the MAPK signaling pathway is linked with memory and learning processes. In non-neuronal cells, the KIBRA protein is phosphorylated by ERK1/2 (involved in the MAPK signaling) in cells as well as in vitro. Several of the other dysregulated genes are involved in memory and learning processes, as well as in Alzheimer's Disease. In conclusion, our results suggest that the effect of the WWC1 rs17070145 polymorphism on memory performance and Alzheimer's disease might be due to a differential regulation of the MAPK signaling, a key pathway involved in memory and learning processes.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, 85004
| | - Jonida Krate
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, 85004
| | - Isabelle Schrauwen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, 85004
| | - Jason J Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, 85004
| | - Geidy E Serrano
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, Arizona, 85351
| | - Lucia Sue
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, Arizona, 85351
| | - Thomas G Beach
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, Arizona, 85351
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, 85004
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2
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Moskowitz AM, Belnap N, Siniard AL, Szelinger S, Claasen AM, Richholt RF, De Both M, Corneveaux JJ, Balak C, Piras IS, Russell M, Courtright AL, Rangasamy S, Ramsey K, Craig DW, Narayanan V, Huentelman MJ, Schrauwen I. A de novo missense mutation in ZMYND11 is associated with global developmental delay, seizures, and hypotonia. Cold Spring Harb Mol Case Stud 2016; 2:a000851. [PMID: 27626064 PMCID: PMC5002929 DOI: 10.1101/mcs.a000851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recently, mutations in the zinc finger MYND-type containing 11 (ZMYND11) gene were identified in patients with autism spectrum disorders, intellectual disability, aggression, and complex neuropsychiatric features, supporting that this gene is implicated in 10p15.3 microdeletion syndrome. We report a novel de novo variant in the ZMYND11 gene (p.Ser421Asn) in a patient with a complex neurodevelopmental phenotype. The patient is a 24-yr-old Caucasian/Filipino female with seizures, global developmental delay, sensorineural hearing loss, hypotonia, dysmorphic features, and other features including a happy disposition and ataxic gait similar to Angelman syndrome. In addition, this patient had uncommon features including eosinophilic esophagitis and multiple, severe allergies not described in similar ZMYND11 cases. This new case further supports the association of ZMYND11 with autistic-like phenotypes and suggests that ZMYND11 should be included in the list of potentially causative candidate genes in cases with complex neurodevelopmental phenotypes.
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Affiliation(s)
- Abby M Moskowitz
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Newell Belnap
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Ashley L Siniard
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Ana M Claasen
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Ryan F Richholt
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Matt De Both
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jason J Corneveaux
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Chris Balak
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Ignazio S Piras
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Megan Russell
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Amanda L Courtright
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - David W Craig
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Matt J Huentelman
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
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Henderson-Smith A, Corneveaux JJ, De Both M, Cuyugan L, Liang WS, Huentelman M, Adler C, Driver-Dunckley E, Beach TG, Dunckley TL. Next-generation profiling to identify the molecular etiology of Parkinson dementia. Neurol Genet 2016; 2:e75. [PMID: 27275011 PMCID: PMC4881621 DOI: 10.1212/nxg.0000000000000075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/21/2016] [Indexed: 12/15/2022]
Abstract
OBJECTIVE We sought to determine the underlying cortical gene expression changes associated with Parkinson dementia using a next-generation RNA sequencing approach. METHODS In this study, we used RNA sequencing to evaluate differential gene expression and alternative splicing in the posterior cingulate cortex from neurologically normal control patients, patients with Parkinson disease, and patients with Parkinson disease with dementia. RESULTS Genes overexpressed in both disease states were involved with an immune response, whereas shared underexpressed genes functioned in signal transduction or as components of the cytoskeleton. Alternative splicing analysis produced a pattern of immune and RNA-processing disturbances. CONCLUSIONS Genes with the greatest degree of differential expression did not overlap with genes exhibiting significant alternative splicing activity. Such variation indicates the importance of broadening expression studies to include exon-level changes because there can be significant differential splicing activity with potential structural consequences, a subtlety that is not detected when examining differential gene expression alone, or is underrepresented with probe-limited array technology.
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Affiliation(s)
- Adrienne Henderson-Smith
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Jason J Corneveaux
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Matthew De Both
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Lori Cuyugan
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Winnie S Liang
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Matthew Huentelman
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Charles Adler
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Erika Driver-Dunckley
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Thomas G Beach
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
| | - Travis L Dunckley
- Neurogenomics Division (A.H.-S., J.J.C., M.D.B., L.C., W.S.L., M.H., T.L.D.), Collaborative Sequencing Center (L.C., W.S.L.), Translational Genomics Research Institute, Phoenix; Division of Neurology (C.A., E.D.-D.), Mayo Clinic, Scottsdale; Banner Sun Health Research Institute (T.G.B.), Sun City, AZ
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Sommen M, Schrauwen I, Vandeweyer G, Boeckx N, Corneveaux JJ, van den Ende J, Boudewyns A, De Leenheer E, Janssens S, Claes K, Verstreken M, Strenzke N, Predöhl F, Wuyts W, Mortier G, Bitner-Glindzicz M, Moser T, Coucke P, Huentelman MJ, Van Camp G. DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System. Hum Mutat 2016; 37:812-9. [PMID: 27068579 DOI: 10.1002/humu.22999] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [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: 07/06/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.
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Affiliation(s)
- Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nele Boeckx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jason J Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jenneke van den Ende
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - An Boudewyns
- Department of Otorhinolaryngology, Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Els De Leenheer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Kathleen Claes
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Margriet Verstreken
- University Department Otolaryngology, St. Augustinus Hospital, Antwerp, Belgium
| | - Nicola Strenzke
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Friederike Predöhl
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Maria Bitner-Glindzicz
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Tobias Moser
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Paul Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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5
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Kalani MYS, Siniard AL, Corneveaux JJ, Bruhns R, Richholt R, Forseth J, Zabramski JM, Nakaji P, Spetzler RF, Huentelman MJ. Rare Variants in Cardiomyopathy Genes Associated With Stress-Induced Cardiomyopathy. Neurosurgery 2015; 78:835-43. [PMID: 26606670 DOI: 10.1227/neu.0000000000001152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Stress-induced cardiomyopathy (SIC) is a poorly understood condition associated with periods of emotional and physical stress. The clinical approaches for management of SIC are supportive and reactive to patient symptoms. OBJECTIVE To utilize next-generation exome sequencing to define genetic variation associated with, and potentially responsible for, this disease. METHODS We performed exome sequencing of 7 white female patients with SIC. Filtering of the identified variants was performed to limit our investigation to those sequences that passed quality control criteria, were rare or novel, were determined algorithmically to have high impact on the associated protein, and were within regions of high species conservation. All variants were verified by using Sanger sequencing. RESULTS Exome-sequencing analysis revealed that each patient carried predicted deleterious variants affecting known cardiomyopathy genes. In each case, the identified variant was either not previously found in public human genome data or was previously annotated in a database of clinical variants associated with cardiac dysfunction. CONCLUSION Patients with SIC harbor deleterious mutations in established cardiomyopathy genes at a level higher than healthy controls. We hypothesize that patients at highest risk for SIC likely live in a compensated state of cardiac dysfunction that manifests clinically only after the myocardium is stressed. In short, we propose that SIC is another example of an occult cardiomyopathy with a distinct physiological trigger and suggest that alternative clinical approaches to these patients may be warranted. ABBREVIATIONS CADD, Combined Annotation Dependent DepletionFPKM, fragments per kilobase pair of exon per million fragments mappedNHLBI GO ESP, National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing ProjectPCR, polymerase chain reactionSIC, stress-induced cardiomyopathy.
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Affiliation(s)
- M Yashar S Kalani
- *Division of Neurological Surgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona; ‡Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona; §Division of Internal Medicine, St. Joseph's Hospital and Medical Center, Phoenix, Arizona
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6
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Schrauwen I, Szelinger S, Siniard AL, Corneveaux JJ, Kurdoglu A, Richholt R, De Both M, Malenica I, Swaminathan S, Rangasamy S, Kulkarni N, Bernes S, Buchhalter J, Ramsey K, Craig DW, Narayanan V, Huentelman MJ. A De Novo Mutation in TEAD1 Causes Non-X-Linked Aicardi Syndrome. Invest Ophthalmol Vis Sci 2015; 56:3896-904. [PMID: 26091538 DOI: 10.1167/iovs.14-16261] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Aicardi syndrome (AIC) is a congenital neurodevelopmental disorder characterized by infantile spasms, agenesis of the corpus callosum, and chorioretinal lacunae. Variation in phenotype and disease severity is well documented, but chorioretinal lacunae represent the most constant pathological feature. Aicardi syndrome is believed to be an X-linked-dominant disorder occurring almost exclusively in females, although 46, XY males with AIC have been described. The purpose of this study is to identify genetic factors and pathways involved in AIC. METHODS We performed exome/genome sequencing of 10 children diagnosed with AIC and their parents and performed RNA sequencing on blood samples from nine cases, their parents, and unrelated controls. RESULTS We identified a de novo mutation in autosomal gene TEAD1, expressed in the retina and brain, in a patient with AIC. Mutations in TEAD1 have previously been associated with Sveinsson's chorioretinal atrophy, characterized by chorioretinal degeneration. This demonstrates that TEAD1 mutations can lead to different chorioretinal complications. In addition, we found that altered expression of genes associated with synaptic plasticity, neuronal development, retinal development, and cell cycle control/apoptosis is an important underlying potential pathogenic mechanism shared among cases. Last, we found a case with skewed X inactivation, supporting the idea that nonrandom X inactivation might be important in AIC. CONCLUSIONS We expand the phenotype of TEAD1 mutations, demonstrate its importance in chorioretinal complications, and propose the first putative pathogenic mechanisms underlying AIC. Our data suggest that AIC is a genetically heterogeneous disease and is not restricted to the X chromosome, and that TEAD1 mutations may be present in male patients.
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Affiliation(s)
- Isabelle Schrauwen
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States 3Department of Medical Genetics, U
| | - Szabolcs Szelinger
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Ashley L Siniard
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Jason J Corneveaux
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Ahmet Kurdoglu
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Ryan Richholt
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Matt De Both
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Ivana Malenica
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Shanker Swaminathan
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Sampathkumar Rangasamy
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Neil Kulkarni
- Phoenix Children's Hospital, Phoenix, Arizona, United States
| | - Saunder Bernes
- Phoenix Children's Hospital, Phoenix, Arizona, United States
| | | | - Keri Ramsey
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - David W Craig
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Vinodh Narayanan
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Matthew J Huentelman
- Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, United States 2Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States
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7
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Schrauwen I, Hasin-Brumshtein Y, Corneveaux JJ, Ohmen J, White C, Allen AN, Lusis AJ, Van Camp G, Huentelman MJ, Friedman RA. A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear. Hear Res 2015; 333:266-274. [PMID: 26341477 DOI: 10.1016/j.heares.2015.08.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 08/12/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium.,Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jason J Corneveaux
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Jeffrey Ohmen
- House Ear Institute, Los Angeles 90057, CA, United States
| | - Cory White
- House Ear Institute, Los Angeles 90057, CA, United States.,Keck School of Medicine, USC, Los Angeles, CA, United States
| | - April N Allen
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Rick A Friedman
- Keck School of Medicine, USC, Los Angeles, CA, United States
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8
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Ramos P, Karnezis AN, Craig DW, Sekulic A, Russell ML, Hendricks WP, Corneveaux JJ, Barrett MT, Shumansky K, Yang Y, Shah SP, Prentice LM, Marra MA, Kiefer J, Zismann VL, McEachron TA, Salhia B, Prat J, Clarke BA, Pressey JG, Farley JH, Anthony SP, Roden RB, Cunliffe HE, Huntsman DG, Trent JM. Abstract POSTER-BIOL-1327: Small cell carcinoma of the ovary, hypercalcemic type displays frequent inactivating germline and somatic mutations in SMARCA4. Clin Cancer Res 2015. [DOI: 10.1158/1557-3265.ovcasymp14-poster-biol-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is arguably the most aggressive ovarian cancer. Most patients are diagnosed at an advanced stage, do not respond to chemotherapy, and die of disease within 1-2 years. It affects children and young women and is reported to occur in families. The cause of the disease is poorly understood. Therefore, we used next generation sequencing technology to identify the genetic basis of the disease.
Method: We performed whole genome, whole exome sequencing or targeted sequencing on tumours and germline samples from 17 SCCOHT patients and on the SCCOHT cell line BIN-67 and SCCOHT-1. Immunohistochemistry (IHC) was performed on formalin-fixed, paraffin-embedded tumors from 23 patients and on a tissue microarray of 485 primary ovarian tumours of other subtypes. BIN-67 cells harbouring biallelic inactivation of SMARCA4 were transduced with a lentivirus expressing wild type SMARCA4.
Result: We identified inactivating germline and somatic mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 79% (11/14) of SCCOHT patients, 2 of whom bore germline mutations, and in both cell lines. SMARCA4 protein was lost in 87% (20/23) of SCCOHT tumours but in only 0.4% (2/485) of other primary ovarian tumours. Reintroduction of wild-type SMARCA4 into BIN-67 cells resulted in altered cell morphology and growth arrest.
Conclusions: The mutation spectrum, IHC profile and cell culture phenotype implicate SMARCA4 as a critical tumour suppressor in SCCOHT pathogenesis.
Citation Format: Pilar Ramos, Anthony N. Karnezis, David W. Craig, Aleksandar Sekulic, Megan L. Russell, William P.D. Hendricks, Jason J. Corneveaux, Michael T. Barrett, Karey Shumansky, Yidong Yang, Sohrab P. Shah, Leah M. Prentice, Marco A. Marra, Jeffrey Kiefer, Victoria L. Zismann, Troy A. McEachron, Bodour Salhia, Jaime Prat, Blaise A. Clarke, Joseph G. Pressey, John H. Farley, Stephen P. Anthony, Richard B.S. Roden, Heather E. Cunliffe, David G. Huntsman, Jeffrey M. Trent. Small cell carcinoma of the ovary, hypercalcemic type displays frequent inactivating germline and somatic mutations in SMARCA4 [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-BIOL-1327.
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Affiliation(s)
- Pilar Ramos
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Anthony N. Karnezis
- 2Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
- 9Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - David W. Craig
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Aleksandar Sekulic
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- 3Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Megan L. Russell
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - William P.D. Hendricks
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jason J. Corneveaux
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Michael T. Barrett
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Karey Shumansky
- 8Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Yidong Yang
- 8Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Sohrab P. Shah
- 2Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
- 8Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Leah M. Prentice
- 9Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Marco A. Marra
- 10Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Jeffrey Kiefer
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Victoria L. Zismann
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Troy A. McEachron
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Bodour Salhia
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jaime Prat
- 11Department of Pathology, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Blaise A. Clarke
- 12Department of Pathology, University Health Network, Toronto, ON, Canada
| | - Joseph G. Pressey
- 4Department of Pediatric Hematology-Oncology, The Children's Hospital of Alabama, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John H. Farley
- 5Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Creighton University School of Medicine and St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | | | - Richard B.S. Roden
- 7Department of Pathology, The Johns Hopkins University, Baltimore MD, USA
| | - Heather E. Cunliffe
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - David G. Huntsman
- 2Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
- 9Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Jeffrey M. Trent
- 1Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
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9
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Decker B, Davis BW, Rimbault M, Long AH, Karlins E, Jagannathan V, Reiman R, Parker HG, Drögemüller C, Corneveaux JJ, Chapman ES, Trent JM, Leeb T, Huentelman MJ, Wayne RK, Karyadi DM, Ostrander EA. Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor. Genome Res 2015; 25:1646-55. [PMID: 26232412 PMCID: PMC4617961 DOI: 10.1101/gr.190314.115] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/15/2015] [Indexed: 12/20/2022]
Abstract
Canine transmissible venereal tumor (CTVT) is a parasitic cancer clone that has propagated for thousands of years via sexual transfer of malignant cells. Little is understood about the mechanisms that converted an ancient tumor into the world's oldest known continuously propagating somatic cell lineage. We created the largest existing catalog of canine genome-wide variation and compared it against two CTVT genome sequences, thereby separating alleles derived from the founder's genome from somatic mutations that must drive clonal transmissibility. We show that CTVT has undergone continuous adaptation to its transmissible allograft niche, with overlapping mutations at every step of immunosurveillance, particularly self-antigen presentation and apoptosis. We also identified chronologically early somatic mutations in oncogenesis- and immune-related genes that may represent key initiators of clonal transmissibility. Thus, we provide the first insights into the specific genomic aberrations that underlie CTVT's dogged perseverance in canids around the world.
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Affiliation(s)
- Brennan Decker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, CB1 8RN, United Kingdom
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Maud Rimbault
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adrienne H Long
- Pediatric Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Eric Karlins
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Rebecca Reiman
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bern, CH-3001, Switzerland
| | - Jason J Corneveaux
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Erica S Chapman
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jeffery M Trent
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, CH-3001, Switzerland
| | | | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Danielle M Karyadi
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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10
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Schrauwen I, Szelinger S, Siniard AL, Kurdoglu A, Corneveaux JJ, Malenica I, Richholt R, Van Camp G, De Both M, Swaminathan S, Turk M, Ramsey K, Craig DW, Narayanan V, Huentelman MJ. A Frame-Shift Mutation in CAV1 Is Associated with a Severe Neonatal Progeroid and Lipodystrophy Syndrome. PLoS One 2015; 10:e0131797. [PMID: 26176221 PMCID: PMC4503302 DOI: 10.1371/journal.pone.0131797] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/05/2015] [Indexed: 12/20/2022] Open
Abstract
A 3-year-old female patient presenting with an unknown syndrome of a neonatal progeroid appearance, lipodystrophy, pulmonary hypertension, cutis marmorata, feeding disorder and failure to thrive was investigated by whole-genome sequencing. This revealed a de novo, heterozygous, frame-shift mutation in the Caveolin1 gene (CAV1) (p.Phe160X). Mutations in CAV1, encoding the main component of the caveolae in plasma membranes, cause Berardinelli-Seip congenital lipodystrophy type 3 (BSCL). Although BSCL is recessive, heterozygous carriers either show a reduced phenotype of partial lipodystrophy, pulmonary hypertension, or no phenotype. To investigate the pathogenic mechanisms underlying this syndrome in more depth, we performed next generation RNA sequencing of peripheral blood, which showed several dysregulated pathways in the patient that might be related to the phenotypic progeroid features (apoptosis, DNA repair/replication, mitochondrial). Secondly, we found a significant down-regulation of known Cav1 interaction partners, verifying the dysfunction of CAV1. Other known progeroid genes and lipodystrophy genes were also dysregulated. Next, western blotting of lysates of cultured fibroblasts showed that the patient shows a significantly decreased expression of wild-type CAV1 protein, demonstrating a loss-of-function mutation, though her phenotype is more severe that other heterozygotes with similar mutations. This phenotypic variety could be explained by differences in genetic background. Indications for this are supported by additional rare variants we found in AGPAT2 and LPIN1 lipodystrophy genes. CAV1, AGPAT2 and LPIN1 all play an important role in triacylglycerol (TAG) biosynthesis in adipose tissue, and the defective function in different parts of this pathway, though not all to the same extend, could contribute to a more severe lipoatrophic phenotype in this patient. In conclusion, we report, for the first time, an association of CAV1 dysfunction with a syndrome of severe premature aging and lipodystrophy. This may contribute to a better understanding of the aging process and pathogenic mechanisms that contribute to premature aging.
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Affiliation(s)
- Isabelle Schrauwen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Ashley L. Siniard
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Ahmet Kurdoglu
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Jason J. Corneveaux
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Ivana Malenica
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Ryan Richholt
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Matt De Both
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Shanker Swaminathan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Mari Turk
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - David W. Craig
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Matthew J. Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States of America
- * E-mail:
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11
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Hunter JM, Ahearn ME, Balak CD, Liang WS, Kurdoglu A, Corneveaux JJ, Russell M, Huentelman MJ, Craig DW, Carpten J, Coons SW, DeMello DE, Hall JG, Bernes SM, Baumbach-Reardon L. Novel pathogenic variants and genes for myopathies identified by whole exome sequencing. Mol Genet Genomic Med 2015; 3:283-301. [PMID: 26247046 PMCID: PMC4521965 DOI: 10.1002/mgg3.142] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 12/25/2022] Open
Abstract
Neuromuscular diseases (NMD) account for a significant proportion of infant and childhood mortality and devastating chronic disease. Determining the specific diagnosis of NMD is challenging due to thousands of unique or rare genetic variants that result in overlapping phenotypes. We present four unique childhood myopathy cases characterized by relatively mild muscle weakness, slowly progressing course, mildly elevated creatine phosphokinase (CPK), and contractures. We also present two additional cases characterized by severe prenatal/neonatal myopathy. Prior extensive genetic testing and histology of these cases did not reveal the genetic etiology of disease. Here, we applied whole exome sequencing (WES) and bioinformatics to identify likely causal pathogenic variants in each pedigree. In two cases, we identified novel pathogenic variants in COL6A3. In a third case, we identified novel likely pathogenic variants in COL6A6 and COL6A3. We identified a novel splice variant in EMD in a fourth case. Finally, we classify two cases as calcium channelopathies with identification of novel pathogenic variants in RYR1 and CACNA1S. These are the first cases of myopathies reported to be caused by variants in COL6A6 and CACNA1S. Our results demonstrate the utility and genetic diagnostic value of WES in the broad class of NMD phenotypes.
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Affiliation(s)
- Jesse M Hunter
- Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Mary Ellen Ahearn
- Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Christopher D Balak
- Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Winnie S Liang
- Collaborative Sequencing Center, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Ahmet Kurdoglu
- Center for Bioinformatics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Jason J Corneveaux
- Neurogenomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Megan Russell
- Center for Bioinformatics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Matthew J Huentelman
- Neurogenomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - David W Craig
- Neurogenomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - John Carpten
- Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
| | - Stephen W Coons
- Section of Neuropathology, Barrow Neurological Institute Phoenix, Arizona
| | - Daphne E DeMello
- Division of Neurology, Phoenix Children's Hospital Phoenix, Arizona
| | - Judith G Hall
- Departments of Medical Genetics and Pediatrics, University of British Columbia Vancouver, British Columbia, Canada
| | - Saunder M Bernes
- Division of Neurology, Phoenix Children's Hospital Phoenix, Arizona
| | - Lisa Baumbach-Reardon
- Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona
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12
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Nho K, Kim S, Risacher SL, Shen L, Corneveaux JJ, Swaminathan S, Lin H, Ramanan VK, Liu Y, Foroud TM, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Weiner MW, Baldwin CT, Lunetta KL, Farrer LA, Furney SJ, Lovestone S, Simmons A, Mecocci P, Vellas B, Tsolaki M, Kloszewska I, Soininen H, McDonald BC, Farlow MR, Ghetti B, Huentelman MJ, Saykin AJ. Protective variant for hippocampal atrophy identified by whole exome sequencing. Ann Neurol 2015; 77:547-52. [PMID: 25559091 DOI: 10.1002/ana.24349] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 12/16/2014] [Accepted: 12/24/2014] [Indexed: 01/25/2023]
Abstract
We used whole-exome sequencing to identify variants other than APOE associated with the rate of hippocampal atrophy in amnestic mild cognitive impairment. An in-silico predicted missense variant in REST (rs3796529) was found exclusively in subjects with slow hippocampal volume loss and validated using unbiased whole-brain analysis and meta-analysis across 5 independent cohorts. REST is a master regulator of neurogenesis and neuronal differentiation that has not been previously implicated in Alzheimer's disease. These findings nominate REST and its functional pathways as protective and illustrate the potential of combining next-generation sequencing with neuroimaging to discover novel disease mechanisms and potential therapeutic targets.
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Affiliation(s)
- Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
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13
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Nasser S, Kurdolgu AA, Izatt T, Aldrich J, Russell ML, Christoforides A, Tembe W, Keifer JA, Corneveaux JJ, Byron SA, Forman KM, Zuccaro C, Keats JJ, Lorusso PM, Carpten JD, Trent JM, Craig DW. An integrated framework for reporting clinically relevant biomarkers from paired tumor/normal genomic and transcriptomic sequencing data in support of clinical trials in personalized medicine. Pac Symp Biocomput 2015:56-67. [PMID: 25592568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ability to rapidly sequence the tumor and germline DNA of an individual holds the eventual promise of revolutionizing our ability to match targeted therapies to tumors harboring the associated genetic biomarkers. Analyzing high throughput genomic data consisting of millions of base pairs and discovering alterations in clinically actionable genes in a structured and real time manner is at the crux of personalized testing. This requires a computational architecture that can monitor and track a system within a regulated environment as terabytes of data are reduced to a small number of therapeutically relevant variants, delivered as a diagnostic laboratory developed test. These high complexity assays require data structures that enable real-time and retrospective ad-hoc analysis, with a capability of updating to keep up with the rapidly changing genomic and therapeutic options, all under a regulated environment that is relevant under both CMS and FDA depending on application. We describe a flexible computational framework that uses a paired tumor/normal sample allowing for complete analysis and reporting in approximately 24 hours, providing identification of single nucleotide changes, small insertions and deletions, chromosomal rearrangements, gene fusions and gene expression with positive predictive values over 90%. In this paper we present the challenges in integrating clinical, genomic and annotation databases to provide interpreted draft reports which we utilize within ongoing clinical research protocols. We demonstrate the need to retire from existing performance measurements of accuracy and specificity and measure metrics that are meaningful to a genomic diagnostic environment. This paper presents a three-tier infrastructure that is currently being used to analyze an individual genome and provide available therapeutic options via a clinical report. Our framework utilizes a non-relational variant-centric database that is scaleable to a large amount of data and addresses the challenges and limitations of a relational database system. Our system is continuously monitored via multiple trackers each catering differently to the diversity of users involved in this process. These trackers designed in analytics web-app framework provide status updates for an individual sample accurate to a few minutes. In this paper, we also present our outcome delivery process that is designed and delivered adhering to the standards defined by various regulation agencies involved in clinical genomic testing.
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Affiliation(s)
- Sara Nasser
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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14
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Szelinger S, Malenica I, Corneveaux JJ, Siniard AL, Kurdoglu AA, Ramsey KM, Schrauwen I, Trent JM, Narayanan V, Huentelman MJ, Craig DW. Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing. PLoS One 2014; 9:e113036. [PMID: 25503791 PMCID: PMC4264736 DOI: 10.1371/journal.pone.0113036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/23/2014] [Indexed: 12/30/2022] Open
Abstract
In females, X chromosome inactivation (XCI) is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.
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Affiliation(s)
- Szabolcs Szelinger
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Molecular and Cellular Biology Interdisciplinary Graduate Program, College of Liberal Arts and Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ivana Malenica
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jason J. Corneveaux
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ashley L. Siniard
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ahmet A. Kurdoglu
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Keri M. Ramsey
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jeffrey M. Trent
- Genetic Basis of Human Disease Division, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Neurology Research, Barrow Neurological Institute, Phoenix, Arizona, United States of America
| | - Matthew J. Huentelman
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - David W. Craig
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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Schrauwen I, Barber RM, Schatzberg SJ, Siniard AL, Corneveaux JJ, Porter BF, Vernau KM, Keesler RI, Matiasek K, Flegel T, Miller AD, Southard T, Mariani CL, Johnson GC, Huentelman MJ. Identification of novel genetic risk loci in Maltese dogs with necrotizing meningoencephalitis and evidence of a shared genetic risk across toy dog breeds. PLoS One 2014; 9:e112755. [PMID: 25393235 PMCID: PMC4231098 DOI: 10.1371/journal.pone.0112755] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/14/2014] [Indexed: 12/02/2022] Open
Abstract
Necrotizing meningoencephalitis (NME) affects toy and small breed dogs causing progressive, often fatal, inflammation and necrosis in the brain. Genetic risk loci for NME previously were identified in pug dogs, particularly associated with the dog leukocyte antigen (DLA) class II complex on chromosome 12, but have not been investigated in other susceptible breeds. We sought to evaluate Maltese and Chihuahua dogs, in addition to pug dogs, to identify novel or shared genetic risk factors for NME development. Genome-wide association testing of single nucleotide polymorphisms (SNPs) in Maltese dogs with NME identified 2 regions of genome-wide significance on chromosomes 4 (chr4:74522353T>A, p = 8.1×10−7) and 15 (chr15:53338796A>G, p = 1.5×10−7). Haplotype analysis and fine-mapping suggests that ILR7 and FBXW7, respectively, both important for regulation of immune system function, could be the underlying associated genes. Further evaluation of these regions and the previously identified DLA II locus across all three breeds, revealed an enrichment of nominal significant SNPs associated with chromosome 15 in pug dogs and DLA II in Maltese and Chihuahua dogs. Meta-analysis confirmed effect sizes the same direction in all three breeds for both the chromosome 15 and DLA II loci (p = 8.6×10–11 and p = 2.5×10−7, respectively). This suggests a shared genetic background exists between all breeds and confers susceptibility to NME, but effect sizes might be different among breeds. In conclusion, we identified the first genetic risk factors for NME development in the Maltese, chromosome 4 and chromosome 15, and provide evidence for a shared genetic risk between breeds associated with chromosome 15 and DLA II. Last, DLA II and IL7R both have been implicated in human inflammatory diseases of the central nervous system such as multiple sclerosis, suggesting that similar pharmacotherapeutic targets across species should be investigated.
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Affiliation(s)
- Isabelle Schrauwen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Renee M. Barber
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Scott J. Schatzberg
- The Animal Neurology and Imaging Center, Algodones, New Mexico, United States of America
| | - Ashley L. Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jason J. Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Brian F. Porter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karen M. Vernau
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Rebekah I. Keesler
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Kaspar Matiasek
- Section of Clinical & Comparative Neuropathology, Ludwig Maximilians University Munich, Munich, Germany
| | - Thomas Flegel
- Department of Small Animal Medicine, University of Leipzig, Leipzig, Germany
| | - Andrew D. Miller
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Teresa Southard
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Christopher L. Mariani
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Gayle C. Johnson
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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16
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Beecham GW, Hamilton K, Naj AC, Martin ER, Huentelman M, Myers AJ, Corneveaux JJ, Hardy J, Vonsattel JP, Younkin SG, Bennett DA, De Jager PL, Larson EB, Crane PK, Kamboh MI, Kofler JK, Mash DC, Duque L, Gilbert JR, Gwirtsman H, Buxbaum JD, Kramer P, Dickson DW, Farrer LA, Frosch MP, Ghetti B, Haines JL, Hyman BT, Kukull WA, Mayeux RP, Pericak-Vance MA, Schneider JA, Trojanowski JQ, Reiman EM, Schellenberg GD, Montine TJ. Genome-wide association meta-analysis of neuropathologic features of Alzheimer's disease and related dementias. PLoS Genet 2014; 10:e1004606. [PMID: 25188341 PMCID: PMC4154667 DOI: 10.1371/journal.pgen.1004606] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 07/14/2014] [Indexed: 01/11/2023] Open
Abstract
Alzheimer's disease (AD) and related dementias are a major public health challenge and present a therapeutic imperative for which we need additional insight into molecular pathogenesis. We performed a genome-wide association study and analysis of known genetic risk loci for AD dementia using neuropathologic data from 4,914 brain autopsies. Neuropathologic data were used to define clinico-pathologic AD dementia or controls, assess core neuropathologic features of AD (neuritic plaques, NPs; neurofibrillary tangles, NFTs), and evaluate commonly co-morbid neuropathologic changes: cerebral amyloid angiopathy (CAA), Lewy body disease (LBD), hippocampal sclerosis of the elderly (HS), and vascular brain injury (VBI). Genome-wide significance was observed for clinico-pathologic AD dementia, NPs, NFTs, CAA, and LBD with a number of variants in and around the apolipoprotein E gene (APOE). GalNAc transferase 7 (GALNT7), ATP-Binding Cassette, Sub-Family G (WHITE), Member 1 (ABCG1), and an intergenic region on chromosome 9 were associated with NP score; and Potassium Large Conductance Calcium-Activated Channel, Subfamily M, Beta Member 2 (KCNMB2) was strongly associated with HS. Twelve of the 21 non-APOE genetic risk loci for clinically-defined AD dementia were confirmed in our clinico-pathologic sample: CR1, BIN1, CLU, MS4A6A, PICALM, ABCA7, CD33, PTK2B, SORL1, MEF2C, ZCWPW1, and CASS4 with 9 of these 12 loci showing larger odds ratio in the clinico-pathologic sample. Correlation of effect sizes for risk of AD dementia with effect size for NFTs or NPs showed positive correlation, while those for risk of VBI showed a moderate negative correlation. The other co-morbid neuropathologic features showed only nominal association with the known AD loci. Our results discovered new genetic associations with specific neuropathologic features and aligned known genetic risk for AD dementia with specific neuropathologic changes in the largest brain autopsy study of AD and related dementias. Alzheimer's disease (AD) and related dementias are a major public health challenge and present a therapeutic imperative for which we need additional insight into molecular pathogenesis. We performed a genome-wide association study (GWAS), as well as an analysis of known genetic risk loci for AD dementia, using data from 4,914 brain autopsies. Genome-wide significance was observed for 7 genes and pathologic features of AD and related diseases. Twelve of the 22 genetic risk loci for clinically-defined AD dementia were confirmed in our pathologic sample. Correlation of effect sizes for risk of AD dementia with effect size for hallmark pathologic features of AD were strongly positive and linear. Our study discovered new genetic associations with specific pathologic features and aligned known genetic risk for AD dementia with specific pathologic changes in a large brain autopsy study of AD and related dementias.
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Affiliation(s)
- Gary W. Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Kara Hamilton
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Adam C. Naj
- Division of Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Matt Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Amanda J. Myers
- Department of Psychiatry & Behavioral Sciences, University of Miami, Miami, Florida, United States of America
| | - Jason J. Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - John Hardy
- Department of Molecular Neuroscience, University College London, London, United Kingdom
| | - Jean-Paul Vonsattel
- New York Brain Bank, Columbia University, New York, New York, United States of America
| | - Steven G. Younkin
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida, United States of America
| | - David A. Bennett
- Department of Neurological Sciences, Rush University, Chicago, Illinois, United States of America
| | - Philip L. De Jager
- Department of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eric B. Larson
- Group Health Research Institute, Seattle, Washington, United States of America
| | - Paul K. Crane
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - M. Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Julia K. Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Deborah C. Mash
- Department of Neurology, University of Miami, Miami, Florida, United States of America
| | - Linda Duque
- Department of Neurology, University of Miami, Miami, Florida, United States of America
| | - John R. Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Harry Gwirtsman
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joseph D. Buxbaum
- Department of Psychiatry, Mount Sinai Hospital, New York, New York, United States of America
| | - Patricia Kramer
- Department of Neurology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida, United States of America
| | - Lindsay A. Farrer
- Biomedical Genetics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Matthew P. Frosch
- C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Bradley T. Hyman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Walter A. Kukull
- Department of Epidemiology, National Alzheimer's Coordinating Center, University of Washington, Seattle, Washington, United States of America
| | - Richard P. Mayeux
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, United States of America
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Julie A. Schneider
- Department of Neurological Sciences, Rush University, Chicago, Illinois, United States of America
- Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, Illinois, United States of America
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric M. Reiman
- Arizona Alzheimer's Consortium, Banner Alzheimer's Institute, Phoenix, Arizona, United States of America
- Department of Psychiatry, University of Arizona, Phoenix, Arizona, United States of America
| | | | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas J. Montine
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Hutchins ED, Markov GJ, Eckalbar WL, George RM, King JM, Tokuyama MA, Geiger LA, Emmert N, Ammar MJ, Allen AN, Siniard AL, Corneveaux JJ, Fisher RE, Wade J, DeNardo DF, Rawls JA, Huentelman MJ, Wilson-Rawls J, Kusumi K. Transcriptomic analysis of tail regeneration in the lizard Anolis carolinensis reveals activation of conserved vertebrate developmental and repair mechanisms. PLoS One 2014; 9:e105004. [PMID: 25140675 PMCID: PMC4139331 DOI: 10.1371/journal.pone.0105004] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/17/2014] [Indexed: 01/09/2023] Open
Abstract
Lizards, which are amniote vertebrates like humans, are able to lose and regenerate a functional tail. Understanding the molecular basis of this process would advance regenerative approaches in amniotes, including humans. We have carried out the first transcriptomic analysis of tail regeneration in a lizard, the green anole Anolis carolinensis, which revealed 326 differentially expressed genes activating multiple developmental and repair mechanisms. Specifically, genes involved in wound response, hormonal regulation, musculoskeletal development, and the Wnt and MAPK/FGF pathways were differentially expressed along the regenerating tail axis. Furthermore, we identified 2 microRNA precursor families, 22 unclassified non-coding RNAs, and 3 novel protein-coding genes significantly enriched in the regenerating tail. However, high levels of progenitor/stem cell markers were not observed in any region of the regenerating tail. Furthermore, we observed multiple tissue-type specific clusters of proliferating cells along the regenerating tail, not localized to the tail tip. These findings predict a different mechanism of regeneration in the lizard than the blastema model described in the salamander and the zebrafish, which are anamniote vertebrates. Thus, lizard tail regrowth involves the activation of conserved developmental and wound response pathways, which are potential targets for regenerative medical therapies.
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Affiliation(s)
- Elizabeth D. Hutchins
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Glenn J. Markov
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Walter L. Eckalbar
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Rajani M. George
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Jesse M. King
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Minami A. Tokuyama
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Lauren A. Geiger
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Nataliya Emmert
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Michael J. Ammar
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - April N. Allen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ashley L. Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jason J. Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Rebecca E. Fisher
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Department of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, United States of America
| | - Juli Wade
- Departments of Psychology and Zoology, Program in Neuroscience, Michigan State University, East Lansing, Michigan, United States of America
| | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - J. Alan Rawls
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jeanne Wilson-Rawls
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Department of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, United States of America
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18
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Zhang K, Huentelman MJ, Rao F, Sun EI, Corneveaux JJ, Schork AJ, Wei Z, Waalen J, Miramontes-Gonzalez JP, Hightower CM, Maihofer AX, Mahata M, Pastinen T, Ehret GB, Schork NJ, Eskin E, Nievergelt CM, Saier MH, O'Connor DT. Genetic implication of a novel thiamine transporter in human hypertension. J Am Coll Cardiol 2014; 63:1542-55. [PMID: 24509276 DOI: 10.1016/j.jacc.2014.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/29/2013] [Accepted: 01/07/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVES This study coupled 2 strategies-trait extremes and genome-wide pooling-to discover a novel blood pressure (BP) locus that encodes a previously uncharacterized thiamine transporter. BACKGROUND Hypertension is a heritable trait that remains the most potent and widespread cardiovascular risk factor, although details of its genetic determination are poorly understood. METHODS Representative genomic deoxyribonucleic acid (DNA) pools were created from male and female subjects in the highest- and lowest-fifth percentiles of BP in a primary care population of >50,000 patients. The peak associated single-nucleotide polymorphisms were typed in individual DNA samples, as well as in twins/siblings phenotyped for cardiovascular and autonomic traits. Biochemical properties of the associated transporter were evaluated in cellular assays. RESULTS After chip hybridization and calculation of relative allele scores, the peak associations were typed in individual samples, revealing an association between hypertension, systolic BP, and diastolic BP and the previously uncharacterized solute carrier SLC35F3. The BP genetic association at SLC35F3 was validated by meta-analysis in an independent sample from the original source population, as well as the International Consortium for Blood Pressure Genome-Wide Association Studies (across North America and western Europe). Sequence homology to a putative yeast thiamine (vitamin B1) transporter prompted us to express human SLC35F3 in Escherichia coli, which catalyzed [(3)H]-thiamine uptake. SLC35F3 risk-allele homozygotes (T/T) displayed decreased erythrocyte thiamine content on microbiological assay. In twin pairs, the SLC35F3 risk allele predicted heritable cardiovascular traits previously associated with thiamine deficiency, including elevated cardiac stroke volume with decreased vascular resistance, and elevated pressor responses to environmental (cold) stress. Allelic expression imbalance confirmed that cis variation at the human SLC35F3 locus influenced expression of that gene, and the allelic expression imbalance peak coincided with the hypertension peak. CONCLUSIONS Novel strategies were coupled to position a new hypertension-susceptibility locus, uncovering a previously unsuspected thiamine transporter whose genetic variants predicted several disturbances in cardiac and autonomic function. The results have implications for the pathogenesis and treatment of systemic hypertension.
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Affiliation(s)
- Kuixing Zhang
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Matthew J Huentelman
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Fangwen Rao
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Eric I Sun
- Department of Biology, UCSD, La Jolla, California
| | - Jason J Corneveaux
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Andrew J Schork
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Zhiyun Wei
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Jill Waalen
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | | | - C Makena Hightower
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Adam X Maihofer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California; Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Manjula Mahata
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Tomi Pastinen
- Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Georg B Ehret
- Center for Complex Disease Genomics, McKusick-Nathans, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Nicholas J Schork
- Department of Psychiatry, UCSD, La Jolla, California; Departments of Computer Science and Human Genetics, University of California at Los Angeles, Los Angeles, California
| | - Eleazar Eskin
- Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Caroline M Nievergelt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California; Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | | | - Daniel T O'Connor
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California; Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Pharmacology and the Institute for Genomic Medicine, UCSD, La Jolla, California.
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Macias MP, Gonzales AM, Siniard AL, Walker AW, Corneveaux JJ, Huentelman MJ, Sabbagh MN, Decourt B. A cellular model of amyloid precursor protein processing and amyloid-β peptide production. J Neurosci Methods 2013; 223:114-22. [PMID: 24333289 DOI: 10.1016/j.jneumeth.2013.11.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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: 08/11/2013] [Revised: 11/24/2013] [Accepted: 11/27/2013] [Indexed: 01/10/2023]
Abstract
BACKGROUND A hallmark pathologic feature of Alzheimer's disease (AD) is accumulation of neuritic senile plaques in the brain parenchyma. Neurotoxic plaque cores are composed predominantly of amyloid-β (Aβ) peptides of 40 and 42 amino acids in length, formed by sequential cleavage of amyloid precursor protein (APP) by β-, and γ-secretases. There is a great interest in approaches to modulate Aβ peptide production and develop therapeutic interventions to reduce Aβ levels to halt or slow the progression of neurodegeneration. NEW METHOD We characterized and present the BE(2)-M17 human neuroblastoma cell line as a novel in vitro model of the APP-cleavage cascade to support future (1) functional studies of molecular regulators in Aβ production, and (2) high-throughput screening assays of new pharmacotherapeutics. RESULTS In BE(2)-M17 cells, both RNA (i.e., RT-PCR, RNA sequencing) and protein analyses (i.e., Western blots, ELISA), show endogenous expression of critical components of the amyloidogenic pathway, APP-cleavage intermediates CTF83 and CTF99, and final cleavage products Aβ40 and Aβ42. We further report effects of retinoic acid-mediated differentiation on morphology and gene expression in this cell line. COMPARISON WITH EXISTING METHOD(S) In contrast to primary isolates or other cell lines reported in current literature, BE(2)-M17 not only sustains baseline expression of the full contingent of APP-processing components, but also remains stably adherent during culture, facilitating experimental manipulations. CONCLUSIONS Our evidence supports the use of BE(2)-M17 as a novel, human, cell-based model of the APP processing pathway that offers a potential streamlined approach to dissect molecular functions of endogenous regulatory pathways, and perform mechanistic studies to identify modulators of Aβ production.
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Affiliation(s)
- Mimi P Macias
- Haldeman Laboratory of Molecular Diagnostics and Therapeutics, Banner Sun Health Research Institute, 10515 W, Santa Fe Drive, Sun City, AZ 85351, USA.
| | - Amanda M Gonzales
- Haldeman Laboratory of Molecular Diagnostics and Therapeutics, Banner Sun Health Research Institute, 10515 W, Santa Fe Drive, Sun City, AZ 85351, USA.
| | - Ashley L Siniard
- Neurogenomics Division, The Translational Genomics Research Institute, 445N, Fifth Street, Phoenix, AZ 85004, USA.
| | - Aaron W Walker
- Haldeman Laboratory of Molecular Diagnostics and Therapeutics, Banner Sun Health Research Institute, 10515 W, Santa Fe Drive, Sun City, AZ 85351, USA.
| | - Jason J Corneveaux
- Neurogenomics Division, The Translational Genomics Research Institute, 445N, Fifth Street, Phoenix, AZ 85004, USA.
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, 445N, Fifth Street, Phoenix, AZ 85004, USA.
| | - Marwan N Sabbagh
- Haldeman Laboratory of Molecular Diagnostics and Therapeutics, Banner Sun Health Research Institute, 10515 W, Santa Fe Drive, Sun City, AZ 85351, USA.
| | - Boris Decourt
- Haldeman Laboratory of Molecular Diagnostics and Therapeutics, Banner Sun Health Research Institute, 10515 W, Santa Fe Drive, Sun City, AZ 85351, USA.
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Shulman JM, Chen K, Keenan BT, Chibnik LB, Fleisher A, Thiyyagura P, Roontiva A, McCabe C, Patsopoulos NA, Corneveaux JJ, Yu L, Huentelman MJ, Evans DA, Schneider JA, Reiman EM, De Jager PL, Bennett DA. Genetic susceptibility for Alzheimer disease neuritic plaque pathology. JAMA Neurol 2013; 70:1150-7. [PMID: 23836404 DOI: 10.1001/jamaneurol.2013.2815] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
IMPORTANCE While numerous genetic susceptibility loci have been identified for clinical Alzheimer disease (AD), it is important to establish whether these variants are risk factors for the underlying disease pathology, including neuritic plaques. OBJECTIVES To investigate whether AD susceptibility loci from genome-wide association studies affect neuritic plaque pathology and to additionally identify novel risk loci for this trait. DESIGN, SETTING, AND PARTICIPANTS Candidate analysis of single-nucleotide polymorphisms and genome-wide association study in a joint clinicopathologic cohort, including 725 deceased subjects from the Religious Orders Study and the Rush Memory and Aging Project (2 prospective, community-based studies), followed by targeted validation in an independent neuroimaging cohort, including 114 subjects from multiple clinical and research centers. MAIN OUTCOMES AND MEASURES A quantitative measure of neuritic plaque pathologic burden, based on assessments of silver-stained tissue averaged from multiple brain regions. Validation based on β-amyloid load by immunocytochemistry, and replication with fibrillar β-amyloid positron emission tomographic imaging with Pittsburgh Compound B or florbetapir. RESULTS Besides the previously reported APOE and CR1 loci, we found that the ABCA7 (rs3764650; P = .02) and CD2AP (rs9349407; P = .03) AD susceptibility loci are associated with neuritic plaque burden. In addition, among the top results of our genome-wide association study, we discovered a novel variant near the amyloid precursor protein gene (APP, rs2829887) that is associated with neuritic plaques (P = 3.3 × 10-6). This polymorphism was associated with postmortem β-amyloid load as well as fibrillar β-amyloid in 2 independent cohorts of adults with normal cognition. CONCLUSIONS AND RELEVANCE These findings enhance understanding of AD risk factors by relating validated susceptibility alleles to increased neuritic plaque pathology and implicate common genetic variation at the APP locus in the earliest, presymptomatic stages of AD.
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Affiliation(s)
- Joshua M Shulman
- Departments of Neurology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston
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Giraldo M, Lopera F, Siniard AL, Corneveaux JJ, Schrauwen I, Carvajal J, Muñoz C, Ramirez-Restrepo M, Gaiteri C, Myers AJ, Caselli RJ, Kosik KS, Reiman EM, Huentelman MJ. Variants in triggering receptor expressed on myeloid cells 2 are associated with both behavioral variant frontotemporal lobar degeneration and Alzheimer's disease. Neurobiol Aging 2013; 34:2077.e11-8. [PMID: 23582655 DOI: 10.1016/j.neurobiolaging.2013.02.016] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Recent evidence suggests that rare genetic variants within the TREM2 gene are associated with increased risk of Alzheimer's disease. TREM2 mutations are the genetic basis for a condition characterized by polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL) and an early-onset dementia syndrome. TREM2 is important in the phagocytosis of apoptotic neuronal cells by microglia in the brain. Loss of function might lead to an impaired clearance and to accumulation of necrotic debris and subsequent neurodegeneration. In this study, we investigated a consanguineous family segregating autosomal recessive behavioral variant FTLD from Antioquia, Colombia. Exome sequencing identified a nonsense mutation in TREM2 (p.Trp198X) segregating with disease. Next, using a cohort of clinically characterized and neuropathologically verified sporadic AD cases and controls, we report replication of the AD risk association at rs75932628 within TREM2 and demonstrate that TREM2 is significantly overexpressed in the brain tissue from AD cases. These data suggest that a mutational burden in TREM2 may serve as a risk factor for neurodegenerative disease in general, and that potentially this class of TREM2 variant carriers with dementia should be considered as having a molecularly distinct form of neurodegenerative disease.
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Affiliation(s)
- Margarita Giraldo
- Grupo de Neurociencias de Antioquia, Universidad de Antioquia, Medellin, Colombia
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22
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Napolioni V, Ober-Reynolds B, Szelinger S, Corneveaux JJ, Pawlowski T, Ober-Reynolds S, Kirwan J, Persico AM, Melmed RD, Craig DW, Smith CJ, Huentelman MJ. Plasma cytokine profiling in sibling pairs discordant for autism spectrum disorder. J Neuroinflammation 2013; 10:38. [PMID: 23497090 PMCID: PMC3616926 DOI: 10.1186/1742-2094-10-38] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 02/19/2013] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVE Converging lines of evidence point to the existence of immune dysfunction in autism spectrum disorder (ASD), which could directly affect several key neurodevelopmental processes. Previous studies have shown higher cytokine levels in patients with autism compared with matched controls or subjects with other developmental disorders. In the current study, we used plasma-cytokine profiling for 25 discordant sibling pairs to evaluate whether these alterations occur within families with ASD. METHODS Plasma-cytokine profiling was conducted using an array-based multiplex sandwich ELISA for simultaneous quantitative measurement of 40 unique targets. We also analyzed the correlations between cytokine levels and clinically relevant quantitative traits (Vineland Adaptive Behavior Scale in Autism (VABS) composite score, Social Responsiveness Scale (SRS) total T score, head circumference, and full intelligence quotient (IQ)). In addition, because of the high phenotypic heterogeneity of ASD, we defined four subgroups of subjects (those who were non-verbal, those with gastrointestinal issues, those with regressive autism, and those with a history of allergies), which encompass common and/or recurrent endophenotypes in ASD, and tested the cytokine levels in each group. RESULTS None of the measured parameters showed significant differences between children with ASD and their related typically developing siblings. However, specific target levels did correlate with quantitative clinical traits, and these were significantly different when the ASD subgroups were analyzed. It is notable that these differences seem to be attributable to a predisposing immunogenetic background, as no other significant differences were noticed between discordant sibling pairs. Interleukin-1β appears to be the cytokine most involved in quantitative traits and clinical subgroups of ASD. CONCLUSIONS In the present study, we found a lack of significant differences in plasma-cytokine levels between children with ASD and in their related non-autistic siblings. Thus, our results support the evidence that the immune profiles of children with autism do not differ from their typically developing siblings. However, the significant association of cytokine levels with the quantitative traits and the clinical subgroups analyzed suggests that altered immune responses may affect core feature of ASD.
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Affiliation(s)
- Valerio Napolioni
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), 445 N Fifth Street, Phoenix, AZ 85004, USA
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23
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Holton P, Ryten M, Nalls M, Trabzuni D, Weale ME, Hernandez D, Crehan H, Gibbs JR, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD, Ramirez-Restrepo M, Engel A, Myers AJ, Corneveaux JJ, Huentelman MJ, Dillman A, Cookson MR, Reiman EM, Singleton A, Hardy J, Guerreiro R. Initial assessment of the pathogenic mechanisms of the recently identified Alzheimer risk Loci. Ann Hum Genet 2013; 77:85-105. [PMID: 23360175 PMCID: PMC3578142 DOI: 10.1111/ahg.12000] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [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: 01/19/2012] [Accepted: 03/05/2012] [Indexed: 12/27/2022]
Abstract
Recent genome wide association studies have identified CLU, CR1, ABCA7 BIN1, PICALM and MS4A6A/MS4A6E in addition to the long established APOE, as loci for Alzheimer's disease. We have systematically examined each of these loci to assess whether common coding variability contributes to the risk of disease. We have also assessed the regional expression of all the genes in the brain and whether there is evidence of an eQTL explaining the risk. In agreement with other studies we find that coding variability may explain the ABCA7 association, but common coding variability does not explain any of the other loci. We were not able to show that any of the loci had eQTLs within the power of this study. Furthermore the regional expression of each of the loci did not match the pattern of brain regional distribution in Alzheimer pathology. Although these results are mainly negative, they allow us to start defining more realistic alternative approaches to determine the role of all the genetic loci involved in Alzheimer's disease.
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Affiliation(s)
- Patrick Holton
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Michael Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Daniah Trabzuni
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Michael E. Weale
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
| | - Dena Hernandez
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Helen Crehan
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - J. Raphael Gibbs
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Richard Mayeux
- Gertrude H. Sergievsky Center and Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics and Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Biostatistics, Ophthalmology, Epidemiology, and Neurology, Boston University Schools of Medicine and Public Health, Boston, MA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | - Manuel Ramirez-Restrepo
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, FL
| | - Anzhelika Engel
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, FL
| | - Amanda J. Myers
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, FL
| | - Jason J. Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute and Arizona Alzheimer's Consortium, Phoenix, AZ
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute and Arizona Alzheimer's Consortium, Phoenix, AZ
| | - Allissa Dillman
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Eric M. Reiman
- Neurogenomics Division, Translational Genomics Research Institute and Arizona Alzheimer's Consortium, Phoenix, AZ
- Banner Alzheimer's Institute and Department of Psychiatry, University of Arizona, Phoenix, AZ
- Department of Psychiatry, University of Arizona, Tucson, AZ
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Reta Lila Weston Laboratories and Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Rita Guerreiro
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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24
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Eckalbar WL, Hutchins ED, Markov GJ, Allen AN, Corneveaux JJ, Lindblad-Toh K, Di Palma F, Alföldi J, Huentelman MJ, Kusumi K. Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes. BMC Genomics 2013; 14:49. [PMID: 23343042 PMCID: PMC3561122 DOI: 10.1186/1471-2164-14-49] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 01/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies. RESULTS Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5' and 3' UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage. CONCLUSIONS Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.
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Affiliation(s)
- Walter L Eckalbar
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA
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25
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Swaminathan S, Huentelman MJ, Corneveaux JJ, Myers AJ, Faber KM, Foroud T, Mayeux R, Shen L, Kim S, Turk M, Hardy J, Reiman EM, Saykin AJ. Analysis of copy number variation in Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. PLoS One 2012; 7:e50640. [PMID: 23227193 PMCID: PMC3515604 DOI: 10.1371/journal.pone.0050640] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/23/2012] [Indexed: 11/22/2022] Open
Abstract
Copy number variations (CNVs) are genomic regions that have added (duplications) or deleted (deletions) genetic material. They may overlap genes affecting their function and have been shown to be associated with disease. We previously investigated the role of CNVs in late-onset Alzheimer's disease (AD) and mild cognitive impairment using Alzheimer’s Disease Neuroimaging Initiative (ADNI) and National Institute of Aging-Late Onset AD/National Cell Repository for AD (NIA-LOAD/NCRAD) Family Study participants, and identified a number of genes overlapped by CNV calls. To confirm the findings and identify other potential candidate regions, we analyzed array data from a unique cohort of 1617 Caucasian participants (1022 AD cases and 595 controls) who were clinically characterized and whose diagnosis was neuropathologically verified. All DNA samples were extracted from brain tissue. CNV calls were generated and subjected to quality control (QC). 728 cases and 438 controls who passed all QC measures were included in case/control association analyses including candidate gene and genome-wide approaches. Rates of deletions and duplications did not significantly differ between cases and controls. Case-control association identified a number of previously reported regions (CHRFAM7A, RELN and DOPEY2) as well as a new gene (HLA-DRA). Meta-analysis of CHRFAM7A indicated a significant association of the gene with AD and/or MCI risk (P = 0.006, odds ratio = 3.986 (95% confidence interval 1.490–10.667)). A novel APP gene duplication was observed in one case sample. Further investigation of the identified genes in independent and larger samples is warranted.
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Affiliation(s)
- Shanker Swaminathan
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Matthew J. Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- The Arizona Alzheimer's Consortium, Phoenix, Arizona, United States of America
| | - Jason J. Corneveaux
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- The Arizona Alzheimer's Consortium, Phoenix, Arizona, United States of America
| | - Amanda J. Myers
- Departments of Psychiatry and Behavioral Sciences, and Human Genetics and Genomics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, Florida, United States of America
| | - Kelley M. Faber
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Tatiana Foroud
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Richard Mayeux
- The Gertrude H. Sergievsky Center, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Li Shen
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Mari Turk
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- The Arizona Alzheimer's Consortium, Phoenix, Arizona, United States of America
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lila Research Laboratories, University College London Institute of Neurology, London, United Kingdom
| | - Eric M. Reiman
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- The Arizona Alzheimer's Consortium, Phoenix, Arizona, United States of America
- Banner Alzheimer’s Institute, Phoenix, Arizona, United States of America
| | - Andrew J. Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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26
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Schrauwen I, Sommen M, Corneveaux JJ, Reiman RA, Hackett NJ, Claes C, Claes K, Bitner-Glindzicz M, Coucke P, Van Camp G, Huentelman MJ. A sensitive and specific diagnostic test for hearing loss using a microdroplet PCR-based approach and next generation sequencing. Am J Med Genet A 2012. [PMID: 23208854 DOI: 10.1002/ajmg.a.35737] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Implementing DNA diagnostics in clinical practice for extremely heterogeneous diseases such as hearing loss is challenging, especially when attempting to reach high sensitivity and specificity in a cost-effective fashion. Next generation sequencing has enabled the development of such a test, but the most commonly used genomic target enrichment methods such as hybridization-based capture suffer from restrictions. In this study, we have adopted a new flexible approach using microdroplet PCR-based technology for target enrichment, in combination with massive parallel sequencing to develop a DNA diagnostic test for autosomal recessive hereditary hearing loss. This approach enabled us to identify the genetic basis of hearing loss in 9 of 24 patients, a success rate of 37.5%. Our method also proved to have high sensitivity and specificity. Currently, routine molecular genetic diagnostic testing for deafness is in most cases only performed for the GJB2 gene and a positive result is typically only obtained in 10-20% of deaf children. Individuals with mutations in GJB2 had already been excluded in our selected set of 24 patients. Therefore, we anticipate that our deafness test may lead to a genetic diagnosis in roughly 50% of unscreened autosomal recessive deafness cases. We propose that this diagnostic testing approach represents a significant improvement in clinical practice as a standard diagnostic tool for children with hearing loss.
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27
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Di Pietro F, Dato S, Carpi FM, Corneveaux JJ, Serfaustini S, Maoloni S, Mignini F, Huentelman MJ, Passarino G, Napolioni V. TP53*P72 allele influences negatively female life expectancy in a population of central Italy: cross-sectional study and genetic-demographic approach analysis. J Gerontol A Biol Sci Med Sci 2012; 68:539-45. [PMID: 23125046 DOI: 10.1093/gerona/gls223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The association of TP53 P72R (rs1042522) with longevity remains uncertain and varies with ethnicity. Here, we tested its association with longevity in a cross-sectional population of Central Italy (18-106 years, N = 1,072), by integrating demographic information and frequency data to account for the different survival rates between sexes through the application of a genetic-demographic approach. rs1042522 affects females longevity, showing significant associations in Comparison 2 (Age Class 3 [>91 years] vs Age Class 2 [73-91 years]) under both additive (odds ratio [OR] 0.574; p = .006) and dominant (OR 0.513; p = .006) models. The TP53*P72 allele is significantly underrepresented in Age Class 3 only in women (OR 0.575; p = .008). The genetic-demographic approach demonstrated that the frequency of female TP53*P72 carriers underwent a significant reduction after 82 years (OR 0.586; p = .002). The same analyses gave nonsignificant results in men. The discrepancies among the results obtained on rs1042522 for longevity could result from the pleiotropic effects of p53 and the potential ethnic variation of its functional variants.
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Affiliation(s)
- Fabio Di Pietro
- School of Biosciences and Biotechnologies, University of Camerino, Camerino, Italy
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Flores K, Wolschin F, Corneveaux JJ, Allen AN, Huentelman MJ, Amdam GV. Genome-wide association between DNA methylation and alternative splicing in an invertebrate. BMC Genomics 2012; 13:480. [PMID: 22978521 PMCID: PMC3526459 DOI: 10.1186/1471-2164-13-480] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 09/12/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data. RESULTS We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher's exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation. CONCLUSIONS This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively influencing exon inclusion during transcription. The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.
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Affiliation(s)
- Kevin Flores
- School of Life Sciences, Arizona State University, PO Box 874501, 85287, Tempe, AZ, USA.
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29
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Eckalbar WL, Lasku E, Infante CR, Elsey RM, Markov GJ, Allen AN, Corneveaux JJ, Losos JB, DeNardo DF, Huentelman MJ, Wilson-Rawls J, Rawls A, Kusumi K. Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock. Dev Biol 2012; 363:308-19. [DOI: 10.1016/j.ydbio.2011.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/22/2011] [Accepted: 11/29/2011] [Indexed: 12/11/2022]
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Keenan BT, Shulman JM, Chibnik LB, Raj T, Tran D, Sabuncu MR, Allen AN, Corneveaux JJ, Hardy JA, Huentelman MJ, Lemere CA, Myers AJ, Nicholson-Weller A, Reiman EM, Evans DA, Bennett DA, De Jager PL. A coding variant in CR1 interacts with APOE-ε4 to influence cognitive decline. Hum Mol Genet 2012; 21:2377-88. [PMID: 22343410 DOI: 10.1093/hmg/dds054] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Complement receptor 1 (CR1) is an Alzheimer's disease (AD) susceptibility locus that also influences AD-related traits such as episodic memory decline and neuritic amyloid plaque deposition. We implemented a functional fine-mapping approach, leveraging intermediate phenotypes to identify functional variant(s) within the CR1 locus. Using 1709 subjects (697 deceased) from the Religious Orders Study and the Rush Memory and Aging Project, we tested 41 single-nucleotide polymorphisms (SNPs) within the linkage disequilibrium block containing the published CR1 AD SNP (rs6656401) for associations with episodic memory decline, and then examined the functional consequences of the top result. We report that a coding variant in the LHR-D (long homologous repeat D) region of the CR1 gene, rs4844609 (Ser1610Thr, minor allele frequency = 0.02), is associated with episodic memory decline and accounts for the known effect of the index SNP rs6656401 (D' = 1, r(2)= 0.084) on this trait. Further, we demonstrate that the coding variant's effect is largely dependent on an interaction with APOE-ε4 and mediated by an increased burden of AD-related neuropathology. Finally, in our data, this coding variant is also associated with AD susceptibility (joint odds ratio = 1.4). Taken together, our analyses identify a CR1 coding variant that influences episodic memory decline; it is a variant known to alter the conformation of CR1 and points to LHR-D as the functional domain within the CR1 protein that mediates the effect on memory decline. We thus implicate C1q and MBL, which bind to LHR-D, as likely targets of the variant's effect and suggest that CR1 may be an important intermediate in the clearance of Aβ42 particles by C1q.
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Affiliation(s)
- Brendan T Keenan
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
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31
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Barber RM, Schatzberg SJ, Corneveaux JJ, Allen AN, Porter BF, Pruzin JJ, Platt SR, Kent M, Huentelman MJ. Identification of risk loci for necrotizing meningoencephalitis in Pug dogs. ACTA ACUST UNITED AC 2011; 102 Suppl 1:S40-6. [PMID: 21846746 DOI: 10.1093/jhered/esr048] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Due to their unique population structure, purebred dogs have emerged as a key model for the study of complex genetic disorders. To evaluate the utility of a newly available high-density canine whole-genome array with >170,000 single nucleotide polymorphisms (SNPs), genome-wide association was performed on a small number of case and control dogs to determine disease susceptibility loci in canine necrotizing meningoencephalitis (NME), a disorder with known non-Mendelian inheritance that shares clinical similarities with atypical variants of multiple sclerosis in humans. Genotyping of 30 NME-affected Pug dogs and 68 healthy control Pugs identified 2 loci associated with NME, including a region within dog leukocyte antigen class II on chromosome 12 that remained significant after Bonferroni correction. Our results support the utility of this high-density SNP array, confirm that dogs are a powerful model for mapping complex genetic disorders and provide important preliminary data to support in depth genetic analysis of NME in numerous affected breeds.
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Affiliation(s)
- Renee M Barber
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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De Jager PL, Shulman JM, Chibnik LB, Keenan BT, Raj T, Wilson RS, Yu L, Leurgans SE, Tran D, Aubin C, Anderson CD, Biffi A, Corneveaux JJ, Huentelman MJ, Rosand J, Daly MJ, Myers AJ, Reiman EM, Bennett DA, Evans DA. A genome-wide scan for common variants affecting the rate of age-related cognitive decline. Neurobiol Aging 2011; 33:1017.e1-15. [PMID: 22054870 DOI: 10.1016/j.neurobiolaging.2011.09.033] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/09/2011] [Accepted: 09/16/2011] [Indexed: 11/24/2022]
Abstract
Age-related cognitive decline is likely promoted by accumulated brain injury due to chronic conditions of aging, including neurodegenerative and vascular disease. Because common neuronal mechanisms may mediate the adaptation to diverse cerebral insults, we hypothesized that susceptibility for age-related cognitive decline may be due in part to a shared genetic network. We have therefore performed a genome-wide association study using a quantitative measure of global cognitive decline slope, based on repeated measures of 17 cognitive tests in 749 subjects from the Religious Orders Study. Top results were evaluated in 3 independent replication cohorts, consisting of 2279 additional subjects with repeated cognitive testing. As expected, we find that the Alzheimer's disease (AD) susceptibility locus, APOE, is strongly associated with rate of cognitive decline (P(DISC) = 5.6 × 10(-9); P(JOINT)= 3.7 × 10(-27)). We additionally discover a variant, rs10808746, which shows consistent effects in the replication cohorts and modestly improved evidence of association in the joint analysis (P(DISC) = 6.7 × 10(-5); P(REP) = 9.4 × 10(-3); P(JOINT) = 2.3 × 10(-5)). This variant influences the expression of 2 adjacent genes, PDE7A and MTFR1, which are potential regulators of inflammation and oxidative injury, respectively. Using aggregate measures of genetic risk, we find that known susceptibility loci for cardiovascular disease, type 2 diabetes, and inflammatory diseases are not significantly associated with cognitive decline in our cohort. Our results suggest that intermediate phenotypes, when coupled with larger sample sizes, may be a useful tool to dissect susceptibility loci for age-related cognitive decline and uncover shared molecular pathways with a role in neuronal injury.
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Affiliation(s)
- Philip L De Jager
- Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA.
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Valla J, Yaari R, Wolf AB, Kusne Y, Beach TG, Roher AE, Corneveaux JJ, Huentelman MJ, Caselli RJ, Reiman EM. Reduced posterior cingulate mitochondrial activity in expired young adult carriers of the APOE ε4 allele, the major late-onset Alzheimer's susceptibility gene. J Alzheimers Dis 2011; 22:307-13. [PMID: 20847408 DOI: 10.3233/jad-2010-100129] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In vivo PET imaging studies of young-adult carriers of the apolipoprotein E ε4 allele (APOEε4), the major Alzheimer's disease (AD) susceptibility gene, have demonstrated declines in glucose metabolism in brain areas later vulnerable to AD, such as posterior cingulate cortex, decades before the possible onset of symptoms. We have previously shown in postmortem studies that such metabolic declines in AD are associated with brain regional mitochondrial dysfunction. To determine whether young adult at-risk individuals demonstrate similar mitochondrial functional decline, we histochemically assessed postmortem tissues from the posterior cingulate cortex of young-adult carriers and noncarriers of APOEε4. At-risk ε4 carriers had lower mitochondrial cytochrome oxidase activity than noncarriers in posterior cingulate cortex, particularly within the superficial cortical lamina, a pattern similar to that seen in AD patients. Except for one 34 year-old ε4 homozygote, the ε4 carriers did not have increased soluble amyloid-β, histologic amyloid-β, or tau pathology in this same region. This functional biomarker may prove useful in early detection and tracking of AD and indicates that mitochondrial mechanisms may contribute to the predisposition to AD before any evidence of amyloid or tau pathology.
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Affiliation(s)
- Jon Valla
- Barrow Neurological Institute, St. Joseph's Hospital & Medical Center, Phoenix, AZ, USA.
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Chibnik LB, Shulman JM, Leurgans SE, Schneider JA, Wilson RS, Tran D, Aubin C, Buchman AS, Heward CB, Myers AJ, Hardy JA, Huentelman MJ, Corneveaux JJ, Reiman EM, Evans DA, Bennett DA, De Jager PL. CR1 is associated with amyloid plaque burden and age-related cognitive decline. Ann Neurol 2011; 69:560-9. [PMID: 21391232 DOI: 10.1002/ana.22277] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 09/03/2010] [Accepted: 09/17/2010] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Recently, genome-wide association studies have identified 3 new susceptibility loci for Alzheimer's disease (AD), CLU, CR1, and PICALM. We leveraged available neuropsychological and autopsy data from 2 cohort studies to investigate whether these loci are associated with cognitive decline and AD neuropathology. METHODS The Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP) are longitudinal studies that enroll nondemented subjects and include annual clinical evaluations and brain donation at death. We evaluated CR1 (rs6656401), CLU (rs11136000), and PICALM (rs7110631) in 1,666 subjects. We evaluated associations between genotypes and rate of change in cognitive function as well as AD-related pathology. Lastly, we used pathway analysis to determine whether relationships between single nucleotide polymorphisms and cognitive decline are mediated through AD pathology. RESULTS Among our study cohort, the mean years of follow-up were 7.8 for ROS and 4.3 for MAP. Only the CR1 locus was associated with both global cognitive decline (p = 0.011) and global AD pathology (p = 0.025). More specifically, the locus affects the deposition of neuritic amyloid plaque (p = 0.009). In a mediation analysis, controlling for amyloid pathology strongly attenuated the effect of the CR1 locus on cognitive decline. INTERPRETATION We found that common variation at the CR1 locus has a broad impact on cognition and that this effect is largely mediated by an individual's amyloid plaque burden. We therefore highlight 1 functional consequence of the CR1 susceptibility allele and generalize the role of this locus to cognitive aging in the general population.
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Affiliation(s)
- Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
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Liang WS, Chen K, Lee W, Sidhar K, Corneveaux JJ, Allen AN, Myers A, Villa S, Meechoovet B, Pruzin J, Bandy D, Fleisher AS, Langbaum JBS, Huentelman MJ, Jensen K, Dunckley T, Caselli RJ, Kaib S, Reiman EM. Association between GAB2 haplotype and higher glucose metabolism in Alzheimer's disease-affected brain regions in cognitively normal APOEε4 carriers. Neuroimage 2010; 54:1896-902. [PMID: 20888920 DOI: 10.1016/j.neuroimage.2010.09.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 09/02/2010] [Accepted: 09/24/2010] [Indexed: 10/19/2022] Open
Abstract
In a genome-wide association study (GWAS) of late-onset Alzheimer's disease (AD), we found an association between common haplotypes of the GAB2 gene and AD risk in carriers of the apolipoprotein E (APOE) ε4 allele, the major late-onset AD susceptibility gene. We previously proposed the use of fluorodeoxyglucose positron emission tomography (FDG-PET) measurements as a quantitative pre-symptomatic endophenotype, more closely related to disease risk than the clinical syndrome itself, to help evaluate putative genetic and non-genetic modifiers of AD risk. In this study, we examined the relationship between the presence or absence of the relatively protective GAB2 haplotype and PET measurements of regional-to-whole brain FDG uptake in several AD-affected brain regions in 158 cognitively normal late-middle-aged APOEε4 homozygotes, heterozygotes, and non-carriers. GAB2 haplotypes were characterized using Affymetrix Genome-Wide Human SNP 6.0 Array data from each of these subjects. As predicted, the possibly protective GAB2 haplotype was associated with higher regional-to-whole brain FDG uptake in AD-affected brain regions in APOEε4 carriers. While additional studies are needed, this study supports the association between the possibly protective GAB2 haplotype and the risk of late-onset AD in APOEε4 carriers. It also supports the use of brain-imaging endophenotypes to help assess possible modifiers of AD risk.
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Affiliation(s)
- Winnie S Liang
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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Langbaum JBS, Chen K, Caselli RJ, Lee W, Reschke C, Bandy D, Alexander GE, Burns CM, Kaszniak AW, Reeder SA, Corneveaux JJ, Allen AN, Pruzin J, Huentelman MJ, Fleisher AS, Reiman EM. Hypometabolism in Alzheimer-affected brain regions in cognitively healthy Latino individuals carrying the apolipoprotein E epsilon4 allele. ACTA ACUST UNITED AC 2010; 67:462-8. [PMID: 20385913 DOI: 10.1001/archneurol.2010.30] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
OBJECTIVE To investigate with fluorodeoxyglucose positron emission tomography whether regional reductions in the cerebral metabolic rate for glucose (CMRgl) previously found in cognitively healthy late-middle-aged apolipoprotein E (APOE) epsilon4 carriers extend to members of the Latino Mexican American community. DESIGN Prospective cohort study. SETTING Banner Alzheimer's Institute, Phoenix, Arizona. PATIENTS OR OTHER PARTICIPANTS Eleven APOE epsilon4 carriers and 16 noncarriers from Arizona's Latino community (mean [SD] age, 54.6 [6.4] years) matched for sex, mean age, and educational level and who were predominantly of self-designated Mexican origin. MAIN OUTCOME MEASURE A brain mapping algorithm was used to compare cross-sectional regional CMRgl in Latino APOE epsilon4 carriers vs noncarriers. RESULTS Participant groups had similar distributions for age, sex, education, family history of dementia, clinical ratings, and neuropsychological test scores. Latino APOE epsilon4 carriers had lower CMRgl than the noncarriers in the posterior cingulate, precuneus, and parietal regions previously found to be preferentially affected in patients with Alzheimer disease (AD) and cognitively healthy non-Latino APOE epsilon4 carriers. Additionally, the Latino APOE epsilon4 carriers had lower CMRgl in the middle and anterior cingulate cortex, hippocampus, and thalamus. CONCLUSIONS This study provides support for the relationship between APOE epsilon4 and risk of AD in Latino individuals. It illustrates the role of positron emission tomography as a presymptomatic endophenotype for the assessment of AD risk factors and supports the inclusion of Latino APOE epsilon4 carriers in proof-of-concept studies using fluorodeoxyglucose PET to evaluate promising presymptomatic treatments in cognitively healthy carriers of this common AD susceptibility gene.
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Yaari R, Langbaum JB, Corneveaux JJ, Huentelman MJ, Beach TG, Valla J, Roher AE, Reiman EM. P3‐010: Is there an increased risk of death from natural causes in young adult apolipoprotein E epsilon 4 carriers? Alzheimers Dement 2010. [DOI: 10.1016/j.jalz.2010.05.1503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Roy Yaari
- Banner Alzheimer's InstitutePhoenix AZ USA
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
| | - Jessica B. Langbaum
- Banner Alzheimer's InstitutePhoenix AZ USA
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
| | - Jason J. Corneveaux
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
- Translational Genomics InstitutePhoenix AZ USA
| | - Matthew J. Huentelman
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
- Translational Genomics Research InstitutePhoenix AZ USA
| | - Thomas G. Beach
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
- Banner Sun Health Research InstituteSun City AZ USA
| | - Jon Valla
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
- Barrow Neurological InstitutePhoenix AZ USA
| | - Alex E. Roher
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
- Banner Sun Health Research InstituteSun City AZ USA
| | - Eric M. Reiman
- Banner Alzheimer's InstitutePhoenix AZ USA
- Arizona Alzheimer's ConsortiumPhoenix AZ USA
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Corneveaux JJ, Myers AJ, Allen AN, Pruzin JJ, Ramirez M, Engel A, Nalls MA, Chen K, Lee W, Chewning K, Villa SE, Meechoovet HB, Gerber JD, Frost D, Benson HL, O'Reilly S, Chibnik LB, Shulman JM, Singleton AB, Craig DW, Van Keuren-Jensen KR, Dunckley T, Bennett DA, De Jager PL, Heward C, Hardy J, Reiman EM, Huentelman MJ. Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. Hum Mol Genet 2010; 19:3295-301. [PMID: 20534741 DOI: 10.1093/hmg/ddq221] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we assess 34 of the most replicated genetic associations for Alzheimer's disease (AD) using data generated on Affymetrix SNP 6.0 arrays and imputed at over 5.7 million markers from a unique cohort of over 1600 neuropathologically defined AD cases and controls (1019 cases and 591 controls). Testing the top genes from the AlzGene meta-analysis, we confirm the well-known association with APOE single nucleotide polymorphisms (SNPs), the CLU, PICALM and CR1 SNPs recently implicated in unusually large data sets, and previously implicated CST3 and ACE SNPs. In the cases of CLU, PICALM and CR1, as well as in APOE, the odds ratios we find are slightly larger than those previously reported in clinical samples, consistent with what we believe to be more accurate classification of disease in the clinically characterized and neuropathologically confirmed AD cases and controls.
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Affiliation(s)
- Jason J Corneveaux
- Neurogenomics Division, The Translational Genomics Research Institute (Gen, 445 N Fifth Street, Phoenix, AZ 85004, USA
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Stein JL, Hua X, Morra JH, Lee S, Hibar DP, Ho AJ, Leow AD, Toga AW, Sul JH, Kang HM, Eskin E, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen AN, Corneveaux JJ, Stephan DA, Webster J, DeChairo BM, Potkin SG, Jack CR, Weiner MW, Thompson PM. Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. Neuroimage 2010; 51:542-54. [PMID: 20197096 DOI: 10.1016/j.neuroimage.2010.02.068] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/15/2010] [Accepted: 02/22/2010] [Indexed: 12/16/2022] Open
Abstract
In a genome-wide association study of structural brain degeneration, we mapped the 3D profile of temporal lobe volume differences in 742 brain MRI scans of Alzheimer's disease patients, mildly impaired, and healthy elderly subjects. After searching 546,314 genomic markers, 2 single nucleotide polymorphisms (SNPs) were associated with bilateral temporal lobe volume (P<5 x 10(-7)). One SNP, rs10845840, is located in the GRIN2B gene which encodes the N-methyl-d-aspartate (NMDA) glutamate receptor NR2B subunit. This protein - involved in learning and memory, and excitotoxic cell death - has age-dependent prevalence in the synapse and is already a therapeutic target in Alzheimer's disease. Risk alleles for lower temporal lobe volume at this SNP were significantly over-represented in AD and MCI subjects vs. controls (odds ratio=1.273; P=0.039) and were associated with mini-mental state exam scores (MMSE; t=-2.114; P=0.035) demonstrating a negative effect on global cognitive function. Voxelwise maps of genetic association of this SNP with regional brain volumes, revealed intense temporal lobe effects (FDR correction at q=0.05; critical P=0.0257). This study uses large-scale brain mapping for gene discovery with implications for Alzheimer's disease.
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Affiliation(s)
- Jason L Stein
- Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Neuroscience Research Building 225E, 635 Charles Young Drive, Los Angeles, CA 90095-1769, USA
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40
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Stein JL, Hua X, Lee S, Ho AJ, Leow AD, Toga AW, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen AN, Corneveaux JJ, Dechairo BM, Potkin SG, Weiner MW, Thompson P. Voxelwise genome-wide association study (vGWAS). Neuroimage 2010; 53:1160-74. [PMID: 20171287 DOI: 10.1016/j.neuroimage.2010.02.032] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 01/21/2010] [Accepted: 02/11/2010] [Indexed: 01/23/2023] Open
Abstract
The structure of the human brain is highly heritable, and is thought to be influenced by many common genetic variants, many of which are currently unknown. Recent advances in neuroimaging and genetics have allowed collection of both highly detailed structural brain scans and genome-wide genotype information. This wealth of information presents a new opportunity to find the genes influencing brain structure. Here we explore the relation between 448,293 single nucleotide polymorphisms in each of 31,622 voxels of the entire brain across 740 elderly subjects (mean age+/-s.d.: 75.52+/-6.82 years; 438 male) including subjects with Alzheimer's disease, Mild Cognitive Impairment, and healthy elderly controls from the Alzheimer's Disease Neuroimaging Initiative (ADNI). We used tensor-based morphometry to measure individual differences in brain structure at the voxel level relative to a study-specific template based on healthy elderly subjects. We then conducted a genome-wide association at each voxel to identify genetic variants of interest. By studying only the most associated variant at each voxel, we developed a novel method to address the multiple comparisons problem and computational burden associated with the unprecedented amount of data. No variant survived the strict significance criterion, but several genes worthy of further exploration were identified, including CSMD2 and CADPS2. These genes have high relevance to brain structure. This is the first voxelwise genome wide association study to our knowledge, and offers a novel method to discover genetic influences on brain structure.
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Affiliation(s)
- Jason L Stein
- Laboratory of Neuro Imaging, Department of Neurology, University of California, Los Angeles School of Medicine, Neuroscience Research Building 225E, 635 Charles Young Drive, Los Angeles, CA 90095-1769, USA
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Engler-Chiurazzi E, Tsang C, Nonnenmacher S, Liang WS, Corneveaux JJ, Prokai L, Huentelman MJ, Bimonte-Nelson HA. Tonic Premarin dose-dependently enhances memory, affects neurotrophin protein levels and alters gene expression in middle-aged rats. Neurobiol Aging 2009; 32:680-97. [PMID: 19883953 DOI: 10.1016/j.neurobiolaging.2009.09.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 08/26/2009] [Accepted: 09/27/2009] [Indexed: 01/19/2023]
Abstract
Premarin™ is the most commonly prescribed estrogenic component of hormone therapy, given since 1942. The current study is the first examining cognitive effects of tonic Premarin treatment in an animal model. Middle-aged ovariectomized (Ovx) rats received vehicle or one of three doses of Premarin (12, 24 or 36μg daily). Rats were tested on a spatial working and reference memory maze battery. Both medium- and high-dose Premarin enhanced memory retention, while low-dose Premarin impaired learning and memory retention. Correlations with serum hormone levels showed that as the ratio of estrone:17β-estradiol increased, animals tended to show better working memory performance. Taken together with the dissociation of dose-specific estrogenic profiles, results suggest that higher levels of estrone, in the presence of 17β-estradiol concentrations higher than that of Ovx levels, may be beneficial for memory. Moreover, Premarin exerted dose and brain-region specific effects on BDNF and NGF protein levels, with most marked changes in cingulate and perirhinal cortices. Hippocampal gene expression profiling demonstrated significant Premarin-induced transcriptional changes in genes linked to plasticity and cognition. These findings indicate that Premarin can impact memory and the brain, and that dosing should be recognized as a clinically relevant factor possibly affecting the direction and efficacy of cognitive outcome.
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Huentelman MJ, Stephan DA, Talboom J, Corneveaux JJ, Reiman DM, Gerber JD, Barnes CA, Alexander GE, Reiman EM, Bimonte-Nelson HA. Peripheral delivery of a ROCK inhibitor improves learning and working memory. Behav Neurosci 2009; 123:218-23. [PMID: 19170447 DOI: 10.1037/a0014260] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Previously, utilizing a series of genome-wide association, brain imaging, and gene expression studies we implicated the KIBRA gene and the RhoA/ROCK pathway in hippocampal-mediated human memory. Here we show that peripheral administration of the ROCK inhibitor hydroxyfasudil improves spatial learning and working memory in the rodent model. This study supports the action of ROCK on learning and memory, suggests the potential value of ROCK inhibition for the promotion of cognition in humans, and highlights the powerful potential of unbiased genome-wide association studies to inform potential novel uses for existing pharmaceuticals.
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Affiliation(s)
- Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA.
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Schrauwen I, Ealy M, Huentelman MJ, Thys M, Homer N, Vanderstraeten K, Fransen E, Corneveaux JJ, Craig DW, Claustres M, Cremers CW, Dhooge I, Van de Heyning P, Vincent R, Offeciers E, Smith RJ, Van Camp G. A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis. Am J Hum Genet 2009; 84:328-38. [PMID: 19230858 DOI: 10.1016/j.ajhg.2009.01.023] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 01/12/2009] [Accepted: 01/30/2009] [Indexed: 11/25/2022] Open
Abstract
Otosclerosis is a common form of progressive hearing loss, characterized by abnormal bone remodeling in the otic capsule. The etiology of the disease is largely unknown, and both environmental and genetic factors have been implicated. To identify genetic factors involved in otosclerosis, we used a case-control discovery group to complete a genome-wide association (GWA) study with 555,000 single-nucleotide polymorphisms (SNPs), utilizing pooled DNA samples. By individual genotyping of the top 250 SNPs in a stepwise strategy, we were able to identify two highly associated SNPs that replicated in two additional independent populations. We then genotyped 79 tagSNPs to fine map the two genomic regions defined by the associated SNPs. The region with the strongest association signal, p(combined) = 6.23 x 10(-10), is on chromosome 7q22.1 and spans intron 1 to intron 4 of reelin (RELN), a gene known for its role in neuronal migration. Evidence for allelic heterogeneity was found in this region. Consistent with the GWA data, expression of RELN was confirmed in the inner ear and in stapes footplate specimens. In conclusion, we provide evidence that implicates RELN in the pathogenesis of otosclerosis.
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Friedman RA, Van Laer L, Huentelman MJ, Sheth SS, Van Eyken E, Corneveaux JJ, Tembe WD, Halperin RF, Thorburn AQ, Thys S, Bonneux S, Fransen E, Huyghe J, Pyykkö I, Cremers CWRJ, Kremer H, Dhooge I, Stephens D, Orzan E, Pfister M, Bille M, Parving A, Sorri M, Van de Heyning PH, Makmura L, Ohmen JD, Linthicum FH, Fayad JN, Pearson JV, Craig DW, Stephan DA, Van Camp G. GRM7 variants confer susceptibility to age-related hearing impairment. Hum Mol Genet 2009; 18:785-96. [PMID: 19047183 PMCID: PMC2638831 DOI: 10.1093/hmg/ddn402] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 11/20/2008] [Indexed: 01/22/2023] Open
Abstract
Age-related hearing impairment (ARHI), or presbycusis, is the most prevalent sensory impairment in the elderly. ARHI is a complex disease caused by an interaction between environmental and genetic factors. Here we describe the results of the first whole genome association study for ARHI. The study was performed using 846 cases and 846 controls selected from 3434 individuals collected by eight centers in six European countries. DNA pools for cases and controls were allelotyped on the Affymetrix 500K GeneChip for each center separately. The 252 top-ranked single nucleotide polymorphisms (SNPs) identified in a non-Finnish European sample group (1332 samples) and the 177 top-ranked SNPs from a Finnish sample group (360 samples) were confirmed using individual genotyping. Subsequently, the 23 most interesting SNPs were individually genotyped in an independent European replication group (138 samples). This resulted in the identification of a highly significant and replicated SNP located in GRM7, the gene encoding metabotropic glutamate receptor type 7. Also in the Finnish sample group, two GRM7 SNPs were significant, albeit in a different region of the gene. As the Finnish are genetically distinct from the rest of the European population, this may be due to allelic heterogeneity. We performed histochemical studies in human and mouse and showed that mGluR7 is expressed in hair cells and in spiral ganglion cells of the inner ear. Together these data indicate that common alleles of GRM7 contribute to an individual's risk of developing ARHI, possibly through a mechanism of altered susceptibility to glutamate excitotoxicity.
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Affiliation(s)
- Rick A Friedman
- House Ear Institute, Gonda Research Center for Cell and Molecular Biology, Los Angeles, CA, USA.
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Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, Homer N, Huentelman MJ. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 2008; 5:887-93. [PMID: 18794863 PMCID: PMC3171277 DOI: 10.1038/nmeth.1251] [Citation(s) in RCA: 231] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 08/22/2008] [Indexed: 01/01/2023]
Abstract
We developed a generalized framework for multiplexed resequencing of targeted regions of the human genome on the Illumina Genome Analyzer using degenerate indexed DNA sequence barcodes ligated to fragmented DNA prior to sequencing. Using this method, the DNA of multiple HapMap individuals was simultaneously sequenced at several ENCODE (ENCyclopedia of DNA Elements) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms from aligned sequenced reads. If we required that predicted polymorphisms be either previously identified by dbSNP or be visually evident upon reinspection of archived ENCODE traces, we observed a false-positive rate of 11.3% using strict thresholds (Ks>1,000) for predicting variants and 69.6% for lax thresholds (Ks>10). Conversely, false-negative rates ranged from 10.8% to 90.8%, with those at stricter cut-offs occurring at lower coverage (< 10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.
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Affiliation(s)
- David W Craig
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA.
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Corneveaux JJ, Liang WS, Reiman EM, Webster JA, Myers AJ, Zismann VL, Joshipura KD, Pearson JV, Hu-Lince D, Craig DW, Coon KD, Dunckley T, Bandy D, Lee W, Chen K, Beach TG, Mastroeni D, Grover A, Ravid R, Sando SB, Aasly JO, Heun R, Jessen F, Kölsch H, Rogers J, Hutton ML, Melquist S, Petersen RC, Alexander GE, Caselli RJ, Papassotiropoulos A, Stephan DA, Huentelman MJ. Evidence for an association between KIBRA and late-onset Alzheimer's disease. Neurobiol Aging 2008; 31:901-9. [PMID: 18789830 DOI: 10.1016/j.neurobiolaging.2008.07.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 07/19/2008] [Indexed: 12/29/2022]
Abstract
We recently reported evidence for an association between the individual variation in normal human episodic memory and a common variant of the KIBRA gene, KIBRA rs17070145 (T-allele). Since memory impairment is a cardinal clinical feature of Alzheimer's disease (AD), we investigated the possibility of an association between the KIBRA gene and AD using data from neuronal gene expression, brain imaging studies, and genetic association tests. KIBRA was significantly over-expressed and three of its four known binding partners under-expressed in AD-affected hippocampal, posterior cingulate and temporal cortex regions (P<0.010, corrected) in a study of laser-capture microdissected neurons. Using positron emission tomography in a cohort of cognitively normal, late-middle-aged persons genotyped for KIBRA rs17070145, KIBRA T non-carriers exhibited lower glucose metabolism than did carriers in posterior cingulate and precuneus brain regions (P<0.001, uncorrected). Lastly, non-carriers of the KIBRA rs17070145 T-allele had increased risk of late-onset AD in an association study of 702 neuropathologically verified expired subjects (P=0.034; OR=1.29) and in a combined analysis of 1026 additional living and expired subjects (P=0.039; OR=1.26). Our findings suggest that KIBRA is associated with both individual variation in normal episodic memory and predisposition to AD.
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Affiliation(s)
- Jason J Corneveaux
- Translational Genomics Research Institute (TGen), Neurogenomics Division, Phoenix, AZ 85004, USA
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Corneveaux JJ, Kruer MC, Hu-Lince D, Ramsey KE, Zismann VL, Stephan DA, Craig DW, Huentelman MJ. SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplification. Biotechniques 2007; 42:77-83. [PMID: 17269488 DOI: 10.2144/000112308] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Whole genome amplification by multiple displacement amplification (MDA) offers investigators using precious genomic DNA samples a high fidelity method for amplifying nanogram quantities of DNA several thousandfold. This becomes especially important for the modemrn day genomics researcher who more and more commonly is applying today's genome scanning technologies to patient cohort samples collected years ago that are irrecoverable and invariably in short supply. We present evidence here that MDA-prepared genomic DNA includes artifacts of chromosomal copy number that resemble copy number polymorphisms (CNPs) upon analysis of the DNA on the Affymetrix 10K GeneChip. The study of CNPs in both health and disease is a rapidly growing area of research, however our current understanding of the relevance of CNPs is incomplete. Our data indicate that utilization of whole genome-amplified samples for analysis heavily reliant on accurate copy number retention could be confounded if the genomic DNA sample was subjected to MDA. We recommend that small amounts of patient cohort DNA stocks be set aside and not subjected to whole genome amplification in order to facilitate the unbiased determination of chromosomal copy numbers when desired.
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Huentelman MJ, Craig DW, Shieh AD, Corneveaux JJ, Hu-Lince D, Pearson JV, Stephan DA. SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data. BMC Genomics 2005; 6:149. [PMID: 16262895 PMCID: PMC1280925 DOI: 10.1186/1471-2164-6-149] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 10/31/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High throughput microarray-based single nucleotide polymorphism (SNP) genotyping has revolutionized the way genome-wide linkage scans and association analyses are performed. One of the key features of the array-based GeneChip Mapping 10K Array from Affymetrix is the automated SNP calling algorithm. The Affymetrix algorithm was trained on a database of ethnically diverse DNA samples to create SNP call zones that are used as static models to make genotype calls for experimental data. We describe here the implementation of clustering algorithms on large training datasets resulting in improved SNP call rates on the 10K GeneChip. RESULTS A database of 948 individuals genotyped on the GeneChip Mapping 10K 2.0 Array was used to identify 822 SNPs that were called consistently less than 75% of the time. These SNPs represent on average 8.25% of the total SNPs on each chromosome with chromosome 19, the most gene-rich chromosome, containing the highest proportion of poor performers (18.7%). To remedy this, we created SNiPer, a new application which uses two clustering algorithms to yield increased call rates and equivalent concordance to Affymetrix called genotypes. We include a training set for these algorithms based on individual genotypes for 705 samples. SNiPer has the capability to be retrained for lab-specific training sets. SNiPer is freely available for download at http://www.tgen.org/neurogenomics/data. CONCLUSION The correct calling of poor performing SNPs may prove to be key in future linkage studies performed on the 10K GeneChip. It would prove particularly invaluable for those diseases that map to chromosome 19, known to contain a high proportion of poorly performing SNPs. Our results illustrate that SNiPer can be used to increase call rates on the 10K GeneChip without sacrificing accuracy, thereby increasing the amount of valid data generated.
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Affiliation(s)
- Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
| | - David W Craig
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
| | - Albert D Shieh
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
| | - Jason J Corneveaux
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
| | - Diane Hu-Lince
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
| | - John V Pearson
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
| | - Dietrich A Stephan
- Neurogenomics Division, The Translational Genomics Research Institute (TGen) Phoenix, Arizona 85004, USA
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