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Jansen E, Naymik M, Thapaliya G, Huentelman M, Beauchemin J, D'Sa V, Lewis CR, Deoni S, Carnell S. Parent-reported child appetite moderates relationships between child genetic obesity risk and parental feeding practices. Front Nutr 2023; 10:1174441. [PMID: 37324730 PMCID: PMC10266414 DOI: 10.3389/fnut.2023.1174441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
Background Food parenting practices are associated with child weight. Such associations may reflect the effects of parents' practices on children's food intake and weight. However, longitudinal, qualitative, and behavioral genetic evidence suggests these associations could, in some cases, reflect parents' response to children's genetic risk for obesity, an instance of gene-environment correlation. We tested for gene-environment correlations across multiple domains of food parenting practices and explored the role of parent-reported child appetite in these relationships. Materials and methods Data on relevant variables were available for N = 197 parent-child dyads (7.54 ± 2.67 years; 44.4% girls) participating in RESONANCE, an ongoing pediatric cohort study. Children's body mass index (BMI) polygenic risk score (PRS) were derived based on adult GWAS data. Parents reported on their feeding practices (Comprehensive Feeding Practices Questionnaire) and their child's eating behavior (Child Eating Behavior Questionnaire). Moderation effects of child eating behaviors on associations between child BMI PRS and parental feeding practices were examined, adjusting for relevant covariates. Results Of the 12 parental feeding practices, 2 were associated with child BMI PRS, namely, restriction for weight control (β = 0.182, p = 0.011) and teaching about nutrition (β = -0.217, p = 0.003). Moderation analyses demonstrated that when children had high genetic obesity risk and showed moderate/high (vs. low) food responsiveness, parents were more likely to restrict food intake to control weight. Conclusion Our results indicate that parents may adjust their feeding practices in response to a child's genetic propensity toward higher or lower bodyweight, and the adoption of food restriction to control weight may depend on parental perceptions of the child's appetite. Research using prospective data on child weight and appetite and food parenting from infancy is needed to further investigate how gene-environment relationships evolve through development.
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Affiliation(s)
- Elena Jansen
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Marcus Naymik
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Gita Thapaliya
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Matt Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Jennifer Beauchemin
- Advanced Baby Imaging Lab, Hasbro Children's Hospital, Rhode Island Hospital, Providence, RI, United States
| | - Viren D'Sa
- Advanced Baby Imaging Lab, Hasbro Children's Hospital, Rhode Island Hospital, Providence, RI, United States
| | - Candace R. Lewis
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
- School of Life Sciences, Arizona State University, Phoenix, AZ, United States
| | - Sean Deoni
- Advanced Baby Imaging Lab, Hasbro Children's Hospital, Rhode Island Hospital, Providence, RI, United States
- Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence, RI, United States
- Maternal, Newborn and Child Health Discovery and Tools, Bill and Melinda Gates Foundation, Seattle, WA, United States
| | - Susan Carnell
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
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Frankel E, Podder A, Sharifi M, Pillai R, Belnap N, Ramsey K, Dodson J, Venugopal P, Brzezinski M, Llaci L, Gerald B, Mills G, Sanchez-Castillo M, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Naymik M, Schrauwen I, Craig DW, Piras IS, Huentelman MJ, Schork NJ, Narayanan V, Rangasamy S. Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders. Cells 2023; 12:1437. [PMID: 37408271 DOI: 10.3390/cells12101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. A subset of patients who are recognized to have an overlapping neurological phenotype with RTT but are lacking a mutation in a gene that causes classical or atypical RTT can be described as having a 'Rett-syndrome-like phenotype (RTT-L). Here, we report eight patients from our cohort diagnosed as having RTT-L who carry mutations in genes unrelated to RTT. We annotated the list of genes associated with RTT-L from our patient cohort, considered them in the light of peer-reviewed articles on the genetics of RTT-L, and constructed an integrated protein-protein interaction network (PPIN) consisting of 2871 interactions connecting 2192 neighboring proteins among RTT- and RTT-L-associated genes. Functional enrichment analysis of RTT and RTT-L genes identified a number of intuitive biological processes. We also identified transcription factors (TFs) whose binding sites are common across the set of RTT and RTT-L genes and appear as important regulatory motifs for them. Investigation of the most significant over-represented pathway analysis suggests that HDAC1 and CHD4 likely play a central role in the interactome between RTT and RTT-L genes.
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Affiliation(s)
- Eric Frankel
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Avijit Podder
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Megan Sharifi
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Roshan Pillai
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Julius Dodson
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Pooja Venugopal
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Molly Brzezinski
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Lorida Llaci
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Brittany Gerald
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Gabrielle Mills
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Chris D Balak
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Szabolcs Szelinger
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ryan Richholt
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Nicholas J Schork
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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3
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Ramsey K, Belnap N, Bonfitto A, Jepsen W, Naymik M, Sanchez-Castillo M, Craig DW, Szelinger S, Huentelman MJ, Narayanan V, Rangasamy S. Progressive cerebellar atrophy caused by heterozygous TECPR2 mutations. Mol Genet Genomic Med 2022; 10:e1857. [PMID: 34994087 PMCID: PMC8830808 DOI: 10.1002/mgg3.1857] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/06/2022] Open
Affiliation(s)
- Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Newell Belnap
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Anna Bonfitto
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Wayne Jepsen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - David W Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
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4
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Windsor R, Stewart SD, Talboom J, Lewis C, Naymik M, Piras IS, Keller S, Borjesson DL, Clark G, Khanna C, Huentelman M. Leukocyte and cytokine variables in asymptomatic Pugs at genetic risk of necrotizing meningoencephalitis. J Vet Intern Med 2021; 35:2846-2852. [PMID: 34687084 PMCID: PMC8692191 DOI: 10.1111/jvim.16293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Necrotizing meningoencephalitis (NME, aka Pug dog encephalitis) is an inflammatory brain condition associated with advanced disease at initial presentation, rapid progression, and poor response to conventional immunomodulatory therapy. HYPOTHESIS/OBJECTIVES That genetic risk for NME, defined by a common germline DNA haplotype located on chromosome 12, is associated with altered blood cytokine concentrations and leukocyte subsets in asymptomatic Pugs. ANIMALS Forty Pug dogs asymptomatic for NME from a hospital sample. METHODS Prospective observational cohort study, including germline genome-wide genotyping, plasma cytokine determination by multiplexed profiling, and leukocyte subset characterization by flow cytometric analysis. RESULTS Seven (18%) dogs were high risk, 10 (25%) medium risk, and 23 (58%) low risk for NME, giving a risk haplotype frequency of 30%. High and medium risk Pugs had significantly lower proportion of CD4+ T cells (median 22% [range, 7.3%-38%] vs 29% [range, 16%-41%], P = .03) and higher plasma IL-10 concentrations than low-risk Pugs (median 14.11 pg/mL [range, 9.66-344.19 pg/mL] vs 12.21 pg/mL [range, 2.59-18.53 pg/mL], P = .001). No other variables were significantly associated with the NME haplotype-based risk. CONCLUSIONS AND CLINICAL IMPORTANCE These data suggest an immunological underpinning to NME and a biologic rationale for future clinical trials that investigate novel diagnostic, preventative, and therapeutic strategies for this disease.
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Affiliation(s)
- Rebecca Windsor
- Ethos Veterinary Health, Woburn, Massachusetts, USA.,Ethos Discovery (501c3), San Diego, California, USA
| | - Samuel D Stewart
- Ethos Veterinary Health, Woburn, Massachusetts, USA.,Ethos Discovery (501c3), San Diego, California, USA
| | - Joshua Talboom
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Candace Lewis
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Stefan Keller
- Department of Pathology, Microbiology, Immunology, University of California, Davis, Davis, California, USA
| | - Dori L Borjesson
- Department of Pathology, Microbiology, Immunology, University of California, Davis, Davis, California, USA
| | - Gary Clark
- Gary Clark Statistical Consulting LLC, Superior, Colorado, USA
| | - Chand Khanna
- Ethos Veterinary Health, Woburn, Massachusetts, USA.,Ethos Discovery (501c3), San Diego, California, USA
| | - Matthew Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
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5
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De La Vega FM, Chowdhury S, Moore B, Frise E, McCarthy J, Hernandez EJ, Wong T, James K, Guidugli L, Agrawal PB, Genetti CA, Brownstein CA, Beggs AH, Löscher BS, Franke A, Boone B, Levy SE, Õunap K, Pajusalu S, Huentelman M, Ramsey K, Naymik M, Narayanan V, Veeraraghavan N, Billings P, Reese MG, Yandell M, Kingsmore SF. Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. Genome Med 2021; 13:153. [PMID: 34645491 PMCID: PMC8515723 DOI: 10.1186/s13073-021-00965-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Clinical interpretation of genetic variants in the context of the patient's phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) holds promise to greatly simplify and speed genome interpretation by integrating predictive methods with the growing knowledge of genetic disease. Here we assess the diagnostic performance of Fabric GEM, a new, AI-based, clinical decision support tool for expediting genome interpretation. METHODS We benchmarked GEM in a retrospective cohort of 119 probands, mostly NICU infants, diagnosed with rare genetic diseases, who received whole-genome or whole-exome sequencing (WGS, WES). We replicated our analyses in a separate cohort of 60 cases collected from five academic medical centers. For comparison, we also analyzed these cases with current state-of-the-art variant prioritization tools. Included in the comparisons were trio, duo, and singleton cases. Variants underpinning diagnoses spanned diverse modes of inheritance and types, including structural variants (SVs). Patient phenotypes were extracted from clinical notes by two means: manually and using an automated clinical natural language processing (CNLP) tool. Finally, 14 previously unsolved cases were reanalyzed. RESULTS GEM ranked over 90% of the causal genes among the top or second candidate and prioritized for review a median of 3 candidate genes per case, using either manually curated or CNLP-derived phenotype descriptions. Ranking of trios and duos was unchanged when analyzed as singletons. In 17 of 20 cases with diagnostic SVs, GEM identified the causal SVs as the top candidate and in 19/20 within the top five, irrespective of whether SV calls were provided or inferred ab initio by GEM using its own internal SV detection algorithm. GEM showed similar performance in absence of parental genotypes. Analysis of 14 previously unsolved cases resulted in a novel finding for one case, candidates ultimately not advanced upon manual review for 3 cases, and no new findings for 10 cases. CONCLUSIONS GEM enabled diagnostic interpretation inclusive of all variant types through automated nomination of a very short list of candidate genes and disorders for final review and reporting. In combination with deep phenotyping by CNLP, GEM enables substantial automation of genetic disease diagnosis, potentially decreasing cost and expediting case review.
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Affiliation(s)
- Francisco M. De La Vega
- Fabric Genomics Inc., Oakland, CA USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA USA
- Current Address: Tempus Labs Inc., Redwood City, CA 94065 USA
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Barry Moore
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT USA
| | | | | | - Edgar Javier Hernandez
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT USA
| | - Terence Wong
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Kiely James
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Pankaj B. Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Catherine A. Brownstein
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Britt-Sabina Löscher
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Shawn E. Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Matt Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | | | | | | | - Mark Yandell
- Fabric Genomics Inc., Oakland, CA USA
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT USA
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Lewis CR, Bonham KS, McCann SH, Volpe AR, D’Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL, Klepac-Ceraj V. Family SES Is Associated with the Gut Microbiome in Infants and Children. Microorganisms 2021; 9:1608. [PMID: 34442687 PMCID: PMC8398307 DOI: 10.3390/microorganisms9081608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children. METHODS Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed. RESULTS Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001). CONCLUSIONS Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand.
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Affiliation(s)
- Candace R. Lewis
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Kevin S. Bonham
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
| | - Shelley Hoeft McCann
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
| | - Alexandra R. Volpe
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
| | - Viren D’Sa
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Matt D. De Both
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | | | - Sarah K. Highlander
- Pathogen and Microbiome Division, Translational Genomics Research Institute North (TGen), Flagstaff, AZ 86005, USA;
| | - Sean C. L. Deoni
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- MNCH D&T, Bill and Melinda Gates Foundation, Seattle, WA 98109, USA
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
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7
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Henderson AR, Wang Q, Meechoovet B, Siniard AL, Naymik M, De Both M, Huentelman MJ, Caselli RJ, Driver-Dunckley E, Dunckley T. DNA Methylation and Expression Profiles of Whole Blood in Parkinson's Disease. Front Genet 2021; 12:640266. [PMID: 33981329 PMCID: PMC8107387 DOI: 10.3389/fgene.2021.640266] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 12/11/2020] [Accepted: 03/16/2021] [Indexed: 12/20/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common age-related neurodegenerative disease. It is presently only accurately diagnosed at an advanced stage by a series of motor deficits, which are predated by a litany of non-motor symptoms manifesting over years or decades. Aberrant epigenetic modifications exist across a range of diseases and are non-invasively detectable in blood as potential markers of disease. We performed comparative analyses of the methylome and transcriptome in blood from PD patients and matched controls. Our aim was to characterize DNA methylation and gene expression patterns in whole blood from PD patients as a foundational step toward the future goal of identifying molecular markers that could predict, accurately diagnose, or track the progression of PD. We found that differentially expressed genes (DEGs) were involved in the processes of transcription and mitochondrial function and that PD methylation profiles were readily distinguishable from healthy controls, even in whole-blood DNA samples. Differentially methylated regions (DMRs) were functionally varied, including near transcription factor nuclear transcription factor Y subunit alpha (NFYA), receptor tyrosine kinase DDR1, RING finger ubiquitin ligase (RNF5), acetyltransferase AGPAT1, and vault RNA VTRNA2-1. Expression quantitative trait methylation sites were found at long non-coding RNA PAX8-AS1 and transcription regulator ZFP57 among others. Functional epigenetic modules were highlighted by IL18R1, PTPRC, and ITGB2. We identified patterns of altered disease-specific DNA methylation and associated gene expression in whole blood. Our combined analyses extended what we learned from the DEG or DMR results alone. These studies provide a foundation to support the characterization of larger sample cohorts, with the goal of building a thorough, accurate, and non-invasive molecular PD biomarker.
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Affiliation(s)
- Adrienne R Henderson
- Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Qi Wang
- Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Bessie Meechoovet
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Matthew De Both
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | | | - Travis Dunckley
- Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, United States
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8
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Jepsen WM, De Both M, Siniard AL, Ramsey K, Piras IS, Naymik M, Henderson A, Huentelman MJ. Adenosine triphosphate binding cassette subfamily C member 1 ( ABCC1) overexpression reduces APP processing and increases alpha- versus beta-secretase activity, in vitro. Biol Open 2021; 10:bio.054627. [PMID: 32878879 PMCID: PMC7860133 DOI: 10.1242/bio.054627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organic anion transporter Adenosine triphosphate binding cassette subfamily C member 1 (ABCC1), also known as MRP1, has been demonstrated in murine models of Alzheimer's disease (AD) to export amyloid beta (Abeta) from the endothelial cells of the blood–brain barrier to the periphery, and that pharmaceutical activation of ABCC1 can reduce amyloid plaque deposition in the brain. Here, we show that ABCC1 is not only capable of exporting Abeta from the cytoplasm of human cells, but also that its overexpression significantly reduces Abeta production and increases the ratio of alpha- versus beta-secretase mediated cleavage of the amyloid precursor protein (APP), likely via indirect modulation of alpha-, beta- and gamma-secretase activity. Summary:Adenosine triphosphate binding cassette subfamily C member 1 (ABCC1) overexpression skews APP processing towards the non-amyloidogenic pathway. Increasing ABCC1 expression or activity may prevent or attenuate Alzheimer's disease symptoms.
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Affiliation(s)
- Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA.,School of Life Sciences, Arizona State University, 427 E. Tyler Mall Tempe, AZ, 85281 USA.,Arizona Alzheimer's Consortium, 4745 N. 7th St., Ste. 105 Phoenix, AZ, 85014 USA
| | - Matthew De Both
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA
| | - Keri Ramsey
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Arizona Alzheimer's Consortium, 4745 N. 7th St., Ste. 105 Phoenix, AZ, 85014 USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA
| | - Adrienne Henderson
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA .,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA.,School of Life Sciences, Arizona State University, 427 E. Tyler Mall Tempe, AZ, 85281 USA.,Arizona Alzheimer's Consortium, 4745 N. 7th St., Ste. 105 Phoenix, AZ, 85014 USA
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9
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Llaci L, Ramsey K, Belnap N, Claasen AM, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Izat T, Naymik M, De Both M, Piras IS, Craig DW, Huentelman MJ, Narayanan V, Schrauwen I, Rangasamy S. Compound heterozygous mutations in SNAP29 is associated with Pelizaeus-Merzbacher-like disorder (PMLD). Hum Genet 2019; 138:1409-1417. [DOI: 10.1007/s00439-019-02077-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
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10
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Arboleda-Velasquez JF, Lopera F, O'Hare M, Delgado-Tirado S, Marino C, Chmielewska N, Saez-Torres KL, Amarnani D, Schultz AP, Sperling RA, Leyton-Cifuentes D, Chen K, Baena A, Aguillon D, Rios-Romenets S, Giraldo M, Guzmán-Vélez E, Norton DJ, Pardilla-Delgado E, Artola A, Sanchez JS, Acosta-Uribe J, Lalli M, Kosik KS, Huentelman MJ, Zetterberg H, Blennow K, Reiman RA, Luo J, Chen Y, Thiyyagura P, Su Y, Jun GR, Naymik M, Gai X, Bootwalla M, Ji J, Shen L, Miller JB, Kim LA, Tariot PN, Johnson KA, Reiman EM, Quiroz YT. Resistance to autosomal dominant Alzheimer's disease in an APOE3 Christchurch homozygote: a case report. Nat Med 2019; 25:1680-1683. [PMID: 31686034 PMCID: PMC6898984 DOI: 10.1038/s41591-019-0611-3] [Citation(s) in RCA: 279] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
We identified a PSEN1 mutation carrier from the world’s largest autosomal dominant Alzheimer’s disease kindred who did not develop mild cognitive impairment until her seventies, three decades after the expected age of clinical onset. She had two copies of the APOE3 Christchurch (R136S) mutation, unusually high brain amyloid, and limited tau/tangle and neurodegenerative measurements. Our findings have implications for APOE’s role in the pathogenesis, treatment, and prevention of Alzheimer’s disease.
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Affiliation(s)
- Joseph F Arboleda-Velasquez
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Michael O'Hare
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Santiago Delgado-Tirado
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Claudia Marino
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Natalia Chmielewska
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.,Boston College, Boston, MA, USA
| | - Kahira L Saez-Torres
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Dhanesh Amarnani
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Aaron P Schultz
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Reisa A Sperling
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital and the Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - David Leyton-Cifuentes
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.,Universidad Escuela de Ingenieria de Antioquia-EIA, Medellin, Colombia
| | - Kewei Chen
- The Banner Alzheimer's Institute, Phoenix, AZ, USA.,University of Arizona, Tucson, AZ, USA.,Arizona State University, Tempe, AZ, USA
| | - Ana Baena
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - David Aguillon
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Silvia Rios-Romenets
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Margarita Giraldo
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Edmarie Guzmán-Vélez
- Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Daniel J Norton
- Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA.,Department of Psychology, Gordon College, Wenham, MA, USA
| | | | - Arabiye Artola
- Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Justin S Sanchez
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Juliana Acosta-Uribe
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia.,Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Matthew Lalli
- Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden
| | - Rebecca A Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Ji Luo
- The Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Yinghua Chen
- The Banner Alzheimer's Institute, Phoenix, AZ, USA
| | | | - Yi Su
- The Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Gyungah R Jun
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Marcus Naymik
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Moiz Bootwalla
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - John B Miller
- Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Leo A Kim
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Pierre N Tariot
- The Banner Alzheimer's Institute, Phoenix, AZ, USA.,University of Arizona, Tucson, AZ, USA
| | - Keith A Johnson
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital and the Department of Neurology, Harvard Medical School, Boston, MA, USA.,Massachusetts General Hospital and Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Eric M Reiman
- The Banner Alzheimer's Institute, Phoenix, AZ, USA. .,University of Arizona, Tucson, AZ, USA. .,Arizona State University, Tempe, AZ, USA. .,Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Yakeel T Quiroz
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia. .,Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA. .,Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
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11
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Kari E, Llaci L, Go JL, Naymik M, Knowles JA, Leal SM, Rangasamy S, Huentelman MJ, Friedman RA, Schrauwen I. A de novo SIX1 variant in a patient with a rare nonsyndromic cochleovestibular nerve abnormality, cochlear hypoplasia, and bilateral sensorineural hearing loss. Mol Genet Genomic Med 2019; 7:e995. [PMID: 31595699 PMCID: PMC6900394 DOI: 10.1002/mgg3.995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 01/06/2023] Open
Abstract
Background Childhood hearing impairment affects language and cognitive development. Profound congenital sensorineural hearing impairment can be due to an abnormal cochleovestibular nerve (CVN) and cochleovestibular malformations, however, the etiology of these conditions remains unclear. Methods We used a trio‐based exome sequencing approach to unravel the underlying molecular etiology of a child with a rare nonsyndromic CVN abnormality and cochlear hypoplasia. Clinical and imaging data were also reviewed. Results We identified a de novo missense variant [p(Asn174Tyr)] in the DNA‐binding Homeodomain of SIX1, a gene which previously has been associated with autosomal dominant hearing loss (ADHL) and branchio‐oto‐renal or Branchio‐otic syndrome, a condition not seen in this patient. Conclusions SIX1 has an important function in otic vesicle patterning during embryogenesis, and mice show several abnormalities to their inner ear including loss of inner ear innervation. Previous reports on patients with SIX1 variants lack imaging data and nonsyndromic AD cases were reported to have no inner ear malformations. In conclusion, we show that a de novo variant in SIX1 in a patient with sensorineural hearing loss leads to cochleovestibular malformations and abnormalities of the CVN, without any other abnormalities. Without proper interventions, severe to profound hearing loss is devastating to both education and social integration. Choosing the correct intervention can be challenging and a molecular diagnosis may adjust intervention and improve outcomes, especially for rare cases.
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Affiliation(s)
- Elina Kari
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Lorida Llaci
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - John L Go
- Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marcus Naymik
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - James A Knowles
- Department of Cell Biology - MSC 5, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Sampath Rangasamy
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Matthew J Huentelman
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rick A Friedman
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Isabelle Schrauwen
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA.,Center for Statistical Genetics, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
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12
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Balak C, Benard M, Schaefer E, Iqbal S, Ramsey K, Ernoult-Lange M, Mattioli F, Llaci L, Geoffroy V, Courel M, Naymik M, Bachman KK, Pfundt R, Rump P, Ter Beest J, Wentzensen IM, Monaghan KG, McWalter K, Richholt R, Le Béchec A, Jepsen W, De Both M, Belnap N, Boland A, Piras IS, Deleuze JF, Szelinger S, Dollfus H, Chelly J, Muller J, Campbell A, Lal D, Rangasamy S, Mandel JL, Narayanan V, Huentelman M, Weil D, Piton A. Rare De Novo Missense Variants in RNA Helicase DDX6 Cause Intellectual Disability and Dysmorphic Features and Lead to P-Body Defects and RNA Dysregulation. Am J Hum Genet 2019; 105:509-525. [PMID: 31422817 PMCID: PMC6731366 DOI: 10.1016/j.ajhg.2019.07.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/17/2019] [Indexed: 01/13/2023] Open
Abstract
The human RNA helicase DDX6 is an essential component of membrane-less organelles called processing bodies (PBs). PBs are involved in mRNA metabolic processes including translational repression via coordinated storage of mRNAs. Previous studies in human cell lines have implicated altered DDX6 in molecular and cellular dysfunction, but clinical consequences and pathogenesis in humans have yet to be described. Here, we report the identification of five rare de novo missense variants in DDX6 in probands presenting with intellectual disability, developmental delay, and similar dysmorphic features including telecanthus, epicanthus, arched eyebrows, and low-set ears. All five missense variants (p.His372Arg, p.Arg373Gln, p.Cys390Arg, p.Thr391Ile, and p.Thr391Pro) are located in two conserved motifs of the RecA-2 domain of DDX6 involved in RNA binding, helicase activity, and protein-partner binding. We use functional studies to demonstrate that the first variants identified (p.Arg373Gln and p.Cys390Arg) cause significant defects in PB assembly in primary fibroblast and model human cell lines. These variants' interactions with several protein partners were also disrupted in immunoprecipitation assays. Further investigation via complementation assays included the additional variants p.Thr391Ile and p.Thr391Pro, both of which, similarly to p.Arg373Gln and p.Cys390Arg, demonstrated significant defects in P-body assembly. Complementing these molecular findings, modeling of the variants on solved protein structures showed distinct spatial clustering near known protein binding regions. Collectively, our clinical and molecular data describe a neurodevelopmental syndrome associated with pathogenic missense variants in DDX6. Additionally, we suggest DDX6 join the DExD/H-box genes DDX3X and DHX30 in an emerging class of neurodevelopmental disorders involving RNA helicases.
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Affiliation(s)
- Chris Balak
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA.
| | - Marianne Benard
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Elise Schaefer
- Medical Genetics Department, University Hospitals of Strasbourg, the Institute of Medical Genetics of Alsace, 67000 Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France
| | - Sumaiya Iqbal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Keri Ramsey
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Michèle Ernoult-Lange
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Francesca Mattioli
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France
| | - Lorida Llaci
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France
| | - Maité Courel
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Marcus Naymik
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | | | - Rolph Pfundt
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Patrick Rump
- Radboud University Nijmegen Medical Center, Department of Human Genetics, Division of Genome Diagnostics, 6525 GA Nijmegen, the Netherlands
| | - Johanna Ter Beest
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | | | | | | | - Ryan Richholt
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA
| | - Antony Le Béchec
- Medical Bioinformatics Unit, UF7363, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Wayne Jepsen
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Matt De Both
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Newell Belnap
- Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Ignazio S Piras
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Szabolcs Szelinger
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Hélène Dollfus
- Medical Genetics Department, University Hospitals of Strasbourg, the Institute of Medical Genetics of Alsace, 67000 Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France
| | - Jamel Chelly
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France; Molecular Genetics Unit, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France; Molecular Genetics Unit, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Arthur Campbell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dennis Lal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Sampathkumar Rangasamy
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Jean-Louis Mandel
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France; University of Strasbourg Institute of Advanced Studies, 67081 Strasbourg, France
| | - Vinodh Narayanan
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Matt Huentelman
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Amélie Piton
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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13
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Jepsen WM, Ramsey K, Szelinger S, Llaci L, Balak C, Belnap N, Bilagody C, De Both M, Gupta R, Naymik M, Pandey R, Piras IS, Sanchez-Castillo M, Rangasamy S, Narayanan V, Huentelman MJ. Two additional males with X-linked, syndromic mental retardation carry de novo mutations in HNRNPH2. Clin Genet 2019; 96:183-185. [PMID: 31236915 PMCID: PMC6852257 DOI: 10.1111/cge.13580] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Wayne M Jepsen
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona.,School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Keri Ramsey
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Szabolcs Szelinger
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Lorida Llaci
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Chris Balak
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Newell Belnap
- TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Cherae Bilagody
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Matthew De Both
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Raj Gupta
- Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Marcus Naymik
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Richa Pandey
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Ignazio S Piras
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Meredith Sanchez-Castillo
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Sampathkumar Rangasamy
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Vinodh Narayanan
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona
| | - Matthew J Huentelman
- Translational Genomics Research Institute (TGen), Phoenix, Arizona.,TGen's Center for Rare Childhood Disorders (C4RCD), Phoenix, Arizona.,School of Life Sciences, Arizona State University, Tempe, Arizona
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14
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Peter B, Dinu V, Liu L, Huentelman M, Naymik M, Lancaster H, Vose C, Schrauwen I. Exome Sequencing of Two Siblings with Sporadic Autism Spectrum Disorder and Severe Speech Sound Disorder Suggests Pleiotropic and Complex Effects. Behav Genet 2019; 49:399-414. [DOI: 10.1007/s10519-019-09957-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/18/2019] [Indexed: 12/19/2022]
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15
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Balak C, Belnap N, Ramsey K, Joss S, Devriendt K, Naymik M, Jepsen W, Siniard AL, Szelinger S, Parker ME, Richholt R, Izatt T, LaFleur M, Terraf P, Llaci L, De Both M, Piras IS, Rangasamy S, Schrauwen I, Craig DW, Huentelman M, Narayanan V. A novel
FBXO28
frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41‐q42 deletion phenotype. Am J Med Genet A 2018; 176:1549-1558. [DOI: 10.1002/ajmg.a.38712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Chris Balak
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Newell Belnap
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Keri Ramsey
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Shelagh Joss
- West of Scotland Genetics ServiceQueen Elizabeth University HospitalGlasgow United Kingdom
| | - Koen Devriendt
- Center for Human Genetics (Centrum Menselijke Erfelijkheid)University of LeuvenLeuven Belgium
| | - Marcus Naymik
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Wayne Jepsen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ashley L. Siniard
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Szabolcs Szelinger
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- UCLA Pathology & Laboratory MedicineUCLA Center for the Health SciencesLos Angeles California
| | - Mary E. Parker
- Department of Physical TherapyTexas State UniversitySan Marcos Texas
- U.R. Our Hope, Undiagnosed and Rare Disorder OrganizationAustin Texas
| | - Ryan Richholt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Tyler Izatt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Madison LaFleur
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Panieh Terraf
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Lorida Llaci
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Matt De Both
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ignazio S. Piras
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Isabelle Schrauwen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Molecular and Human Genetics, Center for Statistical GeneticsBaylor College of MedicineHouston Texas
| | - David W. Craig
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Translational GenomicsKeck School of Medicine of USCLos Angeles California
| | - Matt Huentelman
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Vinodh Narayanan
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
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16
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Schrauwen I, Kari E, Mattox J, Llaci L, Smeeton J, Naymik M, Raible DW, Knowles JA, Crump JG, Huentelman MJ, Friedman RA. De novo variants in GREB1L are associated with non-syndromic inner ear malformations and deafness. Hum Genet 2018; 137:459-470. [PMID: 29955957 PMCID: PMC6082420 DOI: 10.1007/s00439-018-1898-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 03/13/2018] [Accepted: 06/19/2018] [Indexed: 11/24/2022]
Abstract
Congenital inner ear malformations affecting both the osseous and membranous labyrinth can have a devastating impact on hearing and language development. With the exception of an enlarged vestibular aqueduct, non-syndromic inner ear malformations are rare, and their underlying molecular biology has thus far remained understudied. To identify molecular factors that might be important in the developing inner ear, we adopted a family-based trio exome sequencing approach in young unrelated subjects with severe inner ear malformations. We identified two previously unreported de novo loss-of-function variants in GREB1L [c.4368G>T;p.(Glu1410fs) and c.982C>T;p.(Arg328*)] in two affected subjects with absent cochleae and eighth cranial nerve malformations. The cochlear aplasia in these affected subjects suggests that a developmental arrest or problem at a very early stage of inner ear development exists, e.g., during the otic pit formation. Craniofacial Greb1l RNA expression peaks in mice during this time frame (E8.5). It also peaks in the developing inner ear during E13-E16, after which it decreases in adulthood. The crucial function of Greb1l in craniofacial development is also evidenced in knockout mice, which develop severe craniofacial abnormalities. In addition, we show that Greb1l-/- zebrafish exhibit a loss of abnormal sensory epithelia innervation. An important role for Greb1l in sensory epithelia innervation development is supported by the eighth cranial nerve deficiencies seen in both affected subjects. In conclusion, we demonstrate that GREB1L is a key player in early inner ear and eighth cranial nerve development. Abnormalities in cochleovestibular anatomy can provide challenges for cochlear implantation. Combining a molecular diagnosis with imaging techniques might aid the development of individually tailored therapeutic interventions in the future.
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Affiliation(s)
- Isabelle Schrauwen
- Molecular and Human Genetics Department, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA.
| | - Elina Kari
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
| | - Jacob Mattox
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, Keck University of Southern California School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Lorida Llaci
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Marcus Naymik
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - James A Knowles
- Department of Cell Biology-MSC 5, SUNY Downstate Medical Center, 450 Clarkson Avenue, BSB 2-5, Brooklyn, NY, 11203, USA
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Matthew J Huentelman
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Rick A Friedman
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
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17
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Piras IS, Mills G, Llaci L, Naymik M, Ramsey K, Belnap N, Balak CD, Jepsen WM, Szelinger S, Siniard AL, Lewis CR, LaFleur M, Richholt RF, De Both MD, Avela K, Rangasamy S, Craig DW, Narayanan V, Järvelä I, Huentelman MJ, Schrauwen I. Exploring genome-wide DNA methylation patterns in Aicardi syndrome. Epigenomics 2017; 9:1373-1386. [PMID: 28967789 DOI: 10.2217/epi-2017-0060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
AIM To explore differential DNA methylation (DNAm) in Aicardi syndrome (AIC), a severe neurodevelopmental disorder with largely unknown etiology. PATIENTS & METHODS We characterized DNAm in AIC female patients and parents using the Illumina 450 K array. Differential DNAm was assessed using the local outlier factor algorithm, and results were validated via qPCR in a larger set of AIC female patients, parents and unrelated young female controls. Functional epigenetic modules analysis was used to detect pathways integrating both genome-wide DNAm and RNA-seq data. RESULTS & CONCLUSION We detected differential methylation patterns in AIC patients in several neurodevelopmental and/or neuroimmunological networks. These networks may be part of the underlying pathogenic mechanisms involved in the disease.
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Affiliation(s)
- Ignazio S Piras
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Gabrielle Mills
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Lorida Llaci
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Newell Belnap
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Chris D Balak
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Wayne M Jepsen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Ashley L Siniard
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Candace R Lewis
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Madison LaFleur
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Ryan F Richholt
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Matt D De Both
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Hospital, Meilahdentie 2, FI-00029 Helsinki, Finland
| | - Sampathkumar Rangasamy
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - David W Craig
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,University of Southern California, Keck School of Medicine, Department of Translational Genomics, Los Angeles, NRT 1450 Biggy Street, CA 90033, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Haartmaninkatu 8, 00251 Helsinki, Finland
| | - Matthew J Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Center for Statistical Genetics, Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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18
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Kari E, Schrauwen I, Llaci L, Fisher LM, Go JL, Naymik M, Knowles JA, Huentelman MJ, Friedman RA. Compound heterozygous mutations in MASP1 in a deaf child with absent cochlear nerves. Neurol Genet 2017; 3:e153. [PMID: 28534045 PMCID: PMC5427666 DOI: 10.1212/nxg.0000000000000153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/27/2017] [Indexed: 11/15/2022]
Affiliation(s)
- Elina Kari
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - Isabelle Schrauwen
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - Lorida Llaci
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - Laurel M Fisher
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - John L Go
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - Marcus Naymik
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - James A Knowles
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - Matthew J Huentelman
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
| | - Rick A Friedman
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery (E.K., L.M.F., J.L.G., J.A.K., R.A.F.), Keck University of Southern California School of Medicine, Los Angeles; and TGen (I.S., L.L., M.N., M.J.H.), Translational Genomics Research Institute, Phoenix, AZ
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19
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Dickinson JM, D’Lugos AC, Naymik M, De Both M, Siniard A, Wolfe A, Curtis D, Gaesser GA, Huentelman MJ, Carroll CC. Transcriptional Signatures of Human Skeletal Muscle in Response to Aerobic and Resistance Exercise. Med Sci Sports Exerc 2017. [DOI: 10.1249/01.mss.0000517801.65200.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Banuelos E, Ramsey K, Belnap N, Krishnan M, Balak C, Szelinger S, Siniard AL, Russell M, Richholt R, De Both M, Piras I, Naymik M, Claasen AM, Rangasamy S, Huentelman MJ, Craig DW, Campeau PM, Narayanan V, Schrauwen I. Case Report: Novel mutations in TBC1D24 are associated with autosomal dominant tonic-clonic and myoclonic epilepsy and recessive Parkinsonism, psychosis, and intellectual disability. F1000Res 2017; 6:553. [PMID: 28663785 PMCID: PMC5473401 DOI: 10.12688/f1000research.10588.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2017] [Indexed: 12/27/2022] Open
Abstract
Mutations disrupting presynaptic protein TBC1D24 are associated with a variable neurological phenotype, including DOORS syndrome, myoclonic epilepsy, early-infantile epileptic encephalopathy, and non-syndromic hearing loss. In this report, we describe a family segregating autosomal dominant epilepsy, and a 37-year-old Caucasian female with a severe neurological phenotype including epilepsy, Parkinsonism, psychosis, visual and auditory hallucinations, gait ataxia and intellectual disability. Whole exome sequencing revealed two missense mutations in the TBC1D24 gene segregating within this family (c.1078C>T; p.Arg360Cys and c.404C>T; p.Pro135Leu). The female proband who presents with a severe neurological phenotype carries both of these mutations in a compound heterozygous state. The p.Pro135Leu variant, however, is present in the proband's mother and sibling as well, and is consistent with an autosomal dominant pattern linked to tonic-clonic and myoclonic epilepsy. In conclusion, we describe a single family in which TBC1D24 mutations cause expanded dominant and recessive phenotypes. In addition, we discuss and highlight that some variants in TBC1D24 might cause a dominant susceptibility to epilepsy.
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Affiliation(s)
- Erika Banuelos
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Newell Belnap
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Malavika Krishnan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Chris Balak
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Ashley L Siniard
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Megan Russell
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Ryan Richholt
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Matt De Both
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Ignazio Piras
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Ana M Claasen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Sampathkumar Rangasamy
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Matthew J Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - David W Craig
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine Research Center and University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
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