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Stefanski A, Pérez-Palma E, Brünger T, Montanucci L, Gati C, Klöckner C, Johannesen KM, Goodspeed K, Macnee M, Deng AT, Aledo-Serrano Á, Borovikov A, Kava M, Bouman AM, Hajianpour MJ, Pal DK, Engelen M, Hagebeuk EEO, Shinawi M, Heidlebaugh AR, Oetjens K, Hoffman TL, Striano P, Freed AS, Futtrup L, Balslev T, Abulí A, Danvoye L, Lederer D, Balci T, Nouri MN, Butler E, Drewes S, van Engelen K, Howell KB, Khoury J, May P, Trinidad M, Froelich S, Lemke JR, Tiller J, Freed AN, Kang JQ, Wuster A, Møller RS, Lal D. SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis. Brain 2023; 146:5198-5208. [PMID: 37647852 PMCID: PMC10689929 DOI: 10.1093/brain/awad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/05/2023] [Accepted: 07/08/2023] [Indexed: 09/01/2023] Open
Abstract
Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6 and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease versus non-severe disease (P = 2.9 × 10-3, 95% confidence interval: 1.5-15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 portal (https://slc6a1-portal.broadinstitute.org/).
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Affiliation(s)
- Arthur Stefanski
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Eduardo Pérez-Palma
- Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago de Chile 7610658, Chile
| | - Tobias Brünger
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, Cologne 50931, Germany
| | - Ludovica Montanucci
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cornelius Gati
- Department of Biological Sciences, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Genetics, University Hospital of Copenhagen, Rigshispitalet, Copenhagen 2100, Denmark
| | - Kimberly Goodspeed
- Children’s Health, Medical Center, Dallas, TX 75235, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marie Macnee
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, Cologne 50931, Germany
| | - Alexander T Deng
- Clinical Genetics, Guys and St Thomas NHS Trust, London SE19RT, UK
| | - Ángel Aledo-Serrano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid 28034, Spain
| | - Artem Borovikov
- Research and Counseling Department, Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Maina Kava
- Department of Neurology and Metabolic Medicine, Perth Children’s Hospital, Perth 6009, Australia
- School of Paediatrics and Child Health, UWA Medical School, University of Western Australia, Perth 6009, Australia
| | - Arjan M Bouman
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam 3015GD, The Netherlands
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics and Genomics, Albany Medical College, Albany Med Health System, Albany, NY 12208, USA
| | - Deb K Pal
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College, London SE58AF, UK
- Department of Basic and Clinical Neurosciences, King’s College Hospital, London SE59RS, UK
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam Public Health, Amsterdam University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Eveline E O Hagebeuk
- Department of Pediatric Neurology, Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede and Zwolle 2103SW, The Netherlands
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St.Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kathryn Oetjens
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA
| | - Trevor L Hoffman
- Department of Regional Genetics, Anaheim, Southern California Kaiser Permanente Medical Group, CA 92806, USA
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa 16147, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa 16132, Italy
| | - Amanda S Freed
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA 91101, USA
| | - Line Futtrup
- Department of Paediatrics, Regional Hospital of Central Jutland, Viborg 8800, Denmark
| | - Thomas Balslev
- Department of Paediatrics, Regional Hospital of Central Jutland, Viborg 8800, Denmark
- Centre for Educational Development, Aarhus University, Aarhus 8200, Denmark
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, University Hospital Vall d’Hebron, Barcelona 08035, Spain
| | - Leslie Danvoye
- Department of Neurology, Université catholique de Louvain, Cliniques universitaires Saint-Luc, Brussels 1200, Belgium
| | - Damien Lederer
- Centre for Human Genetics, Institute for Pathology and Genetics, Gosselies 6041, Belgium
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A3K7, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5A5, Canada
| | - Maryam Nabavi Nouri
- Department of Paediatrics, Division of Pediatric Neurology, London Health Sciences Centre, London, ON N6A5W9, Canada
| | | | - Sarah Drewes
- Department of Medical Genetics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Kalene van Engelen
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Katherine B Howell
- Department of Neurology, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Jean Khoury
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Marena Trinidad
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Steven Froelich
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig 04103, Germany
| | | | | | - Jing-Qiong Kang
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA
- Neuroscience Graduate Program, Vanderbilt University, Nashville, TN 37235, USA
- Department of Neurology, Vanderbilt Brain Institute, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Kennedy Center of Human Development, Nashville, TN 37203, USA
| | - Arthur Wuster
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark
| | - Dennis Lal
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
- Stanley Center of Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Neurology, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
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2
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Kim S, Stockwell A, Qin H, Gao SS, Sagolla M, Stoilov I, Wuster A, Lai P, Yaspan BL, Jeanne M. Rare CIDEC coding variants enriched in age-related macular degeneration patients with small low-luminance deficit cause lipid droplet and fat storage defects. PLoS One 2023; 18:e0280484. [PMID: 37079518 PMCID: PMC10118094 DOI: 10.1371/journal.pone.0280484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The basis of Age-related macular degeneration (AMD) genetic risk has been well documented; however, few studies have looked at genetic biomarkers of disease progression or treatment response within advanced AMD patients. Here we report the first genome-wide analysis of genetic determinants of low-luminance vision deficit (LLD), which is seen as predictive of visual acuity loss and anti-VEGF treatment response in neovascular AMD patients. METHODS AMD patients were separated into small- and large-LLD groups for comparison and whole genome sequencing was performed. Genetic determinants of LLD were assessed by common and rare variant genetic analysis. Follow-up functional analysis of rare coding variants identified by the burden test was then performed in vitro. RESULTS We identified four coding variants in the CIDEC gene. These rare variants were only present in patients with a small LLD, which has been previously shown to indicate better prognosis and better anti-VEGF treatment response. Our in vitro functional characterization of these CIDEC alleles revealed that all decrease the binding affinity between CIDEC and the lipid droplet fusion effectors PLIN1, RAB8A and AS160. The rare CIDEC alleles all cause a hypomorphic defect in lipid droplet fusion and enlargement, resulting in a decreased fat storage capability in adipocytes. CONCLUSIONS As we did not detect CIDEC expression in the ocular tissue affected by AMD, our results suggest that the CIDEC variants do not play a direct role in the eye and influence low-luminance vision deficit via an indirect and systemic effect related to fat storage capacity.
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Affiliation(s)
- Sehyun Kim
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
| | - Amy Stockwell
- Department of Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Han Qin
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
| | - Simon S Gao
- Department of Clinical Imaging, Genentech Inc., South San Francisco, California, United States of America
| | - Meredith Sagolla
- Department of Research Pathology, Genentech Inc., South San Francisco, California, United States of America
| | - Ivaylo Stoilov
- Medical Affairs Ophthalmology, Genentech Inc., South San Francisco, California, United States of America
| | - Arthur Wuster
- Department of Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Phillip Lai
- Early Clinical Development, Genentech Inc., South San Francisco, California, United States of America
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Marion Jeanne
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
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3
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Estrada K, Froelich S, Wuster A, Bauer CR, Sterling T, Clark WT, Ru Y, Trinidad M, Nguyen HP, Luu AR, Wendt DJ, Yogalingam G, Yu GK, LeBowitz JH, Cardon LR. Identifying therapeutic drug targets using bidirectional effect genes. Nat Commun 2021; 12:2224. [PMID: 33850126 PMCID: PMC8044152 DOI: 10.1038/s41467-021-21843-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/12/2021] [Indexed: 01/15/2023] Open
Abstract
Prioritizing genes for translation to therapeutics for common diseases has been challenging. Here, we propose an approach to identify drug targets with high probability of success by focusing on genes with both gain of function (GoF) and loss of function (LoF) mutations associated with opposing effects on phenotype (Bidirectional Effect Selected Targets, BEST). We find 98 BEST genes for a variety of indications. Drugs targeting those genes are 3.8-fold more likely to be approved than non-BEST genes. We focus on five genes (IGF1R, NPPC, NPR2, FGFR3, and SHOX) with evidence for bidirectional effects on stature. Rare protein-altering variants in those genes result in significantly increased risk for idiopathic short stature (ISS) (OR = 2.75, p = 3.99 × 10-8). Finally, using functional experiments, we demonstrate that adding an exogenous CNP analog (encoded by NPPC) rescues the phenotype, thus validating its potential as a therapeutic treatment for ISS. Our results show the value of looking for bidirectional effects to identify and validate drug targets.
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Affiliation(s)
| | | | | | | | | | | | - Yuanbin Ru
- BioMarin Pharmaceutical Inc., Novato, CA, USA
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4
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Simpfendorfer KR, Li W, Shih A, Wen H, Kothari HP, Einsidler EA, Wuster A, Hunkapiller J, Behrens TW, Graham RR, Townsend MJ, Behar DM, Hu R, Greenspan E, Gregersen PK. Influence of genetic copy number variants of the human GLUT3 glucose transporter gene SLC2A3 on protein expression, glycolysis and rheumatoid arthritis risk: A genetic replication study. Mol Genet Metab Rep 2019; 19:100470. [PMID: 30997344 PMCID: PMC6453668 DOI: 10.1016/j.ymgmr.2019.100470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 12/07/2018] [Revised: 03/18/2019] [Accepted: 03/30/2019] [Indexed: 12/20/2022] Open
Abstract
Objectives The gene encoding glucose transporter 3 (GLUT3, SLC2A3) is present in the human population at variable copy number. An overt disease phenotype of SLC2A3 copy number variants has not been reported; however, deletion of SLC2A3 has been previously reported to protect carriers from rheumatoid arthritis, implicating GLUT3 as a therapeutic target in rheumatoid arthritis. Here we aim to perform functional analysis of GLUT3 copy number variants in immune cells, and test the reported protective association of the GLUT3 copy number variants for rheumatoid arthritis in a genetic replication study. Methods Cells from genotyped healthy controls were analyzed for SLC2A3/GLUT3 expression and glycolysis capacity. We genotyped the SLC2A3 copy number variant in four independent cohorts of rheumatoid arthritis and controls and one cohort of multiple sclerosis and controls. Results Heterozygous deletion of SLC2A3 correlates directly with expression levels of GLUT3 and influences glycolysis rates in the human immune system. The frequency of the SLC2A3 copy number variant is not different between rheumatoid arthritis, multiple sclerosis and control groups. Conclusions Despite a robust SLC2A3 gene copy number dependent phenotype, our study of large groups of rheumatoid arthritis cases and controls provides no evidence for rheumatoid arthritis disease protection in deletion carriers. These data emphasize the importance of well powered replication studies to confirm or refute genetic associations, particularly for relatively rare variants. T cell and macrophage expression of SLC2A3/GLUT3 correlates to SLC2A3 gene copy number in a dose dependent manner. Glycolysis rates are reduced in individuals harboring a deletion of the GLUT3 gene SLC2A3 Deletion of SLC2A3 is not associated with protection from rheumatoid arthritis Deletion of SLC2A3 is not associated with risk for multiple sclerosis GLUT3 is not a viable therapeutic target for RA as previously proposed based on a protective association of SLC2A3 deletion.
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Affiliation(s)
- Kim R Simpfendorfer
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, USA
| | - Wentian Li
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA
| | - Andrew Shih
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA
| | - Hongxiu Wen
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA
| | - Harini P Kothari
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA
| | - Edward A Einsidler
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA
| | - Arthur Wuster
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Julie Hunkapiller
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Timothy W Behrens
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Robert R Graham
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Michael J Townsend
- Department of Biomarker Discovery OMNI, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Doron M Behar
- Gene by Gene, Genomic Research Center, Houston, TX, USA
| | - Rui Hu
- Gene by Gene, Genomic Research Center, Houston, TX, USA
| | | | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, the Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, USA
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5
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Skon-Hegg C, Zhang J, Wu X, Sagolla M, Ota N, Wuster A, Tom J, Doran E, Ramamoorthi N, Caplazi P, Monroe J, Lee WP, Behrens TW. LACC1 Regulates TNF and IL-17 in Mouse Models of Arthritis and Inflammation. J Immunol 2018; 202:183-193. [PMID: 30510070 DOI: 10.4049/jimmunol.1800636] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/16/2018] [Indexed: 12/29/2022]
Abstract
Both common and rare genetic variants of laccase domain-containing 1 (LACC1, previously C13orf31) are associated with inflammatory bowel disease, leprosy, Behcet disease, and systemic juvenile idiopathic arthritis. However, the functional relevance of these variants is unclear. In this study, we use LACC1-deficient mice to gain insight into the role of LACC1 in regulating inflammation. Following oral administration of Citrobacter rodentium, LACC1 knockout (KO) mice had more severe colon lesions compared with wildtype (WT) controls. Immunization with collagen II, a collagen-induced arthritis (CIA) model, resulted in an accelerated onset of arthritis and significantly worse arthritis and inflammation in LACC1 KO mice. Similar results were obtained in a mannan-induced arthritis model. Serum and local TNF in CIA paws and C. rodentium colons were significantly increased in LACC1 KO mice compared with WT controls. The percentage of IL-17A-producing CD4+ T cells was elevated in LACC1 KO mice undergoing CIA as well as aged mice compared with WT controls. Neutralization of IL-17, but not TNF, prevented enhanced mannan-induced arthritis in LACC1 KO mice. These data provide new mechanistic insight into the function of LACC1 in regulating TNF and IL-17 during inflammatory responses. We hypothesize that these effects contribute to immune-driven pathologies observed in individuals carrying LACC1 variants.
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Affiliation(s)
- Cara Skon-Hegg
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080; .,Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Juan Zhang
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Meredith Sagolla
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | - Naruhisa Ota
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Arthur Wuster
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080; and
| | - Jennifer Tom
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | - Emma Doran
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Nandhini Ramamoorthi
- Department of Biomarker Discovery, Genentech, Inc., South San Francisco, CA 94080
| | - Patrick Caplazi
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | - John Monroe
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Timothy W Behrens
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080
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6
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Rathore N, Ramani SR, Pantua H, Payandeh J, Bhangale T, Wuster A, Kapoor M, Sun Y, Kapadia SB, Gonzalez L, Zarrin AA, Goate A, Hansen DV, Behrens TW, Graham RR. Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer's disease. PLoS Genet 2018; 14:e1007427. [PMID: 30388101 PMCID: PMC6235402 DOI: 10.1371/journal.pgen.1007427] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 05/16/2018] [Revised: 11/14/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022] Open
Abstract
Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA) is a cell surface inhibitory receptor that recognizes specific O-glycosylated proteins and is expressed on various innate immune cell types including microglia. We show here that a common missense variant (G78R, rs1859788) of PILRA is the likely causal allele for the confirmed Alzheimer’s disease risk locus at 7q21 (rs1476679). The G78R variant alters the interaction of residues essential for sialic acid engagement, resulting in >50% reduced binding for several PILRA ligands including a novel ligand, complement component 4A, and herpes simplex virus 1 (HSV-1) glycoprotein B. PILRA is an entry receptor for HSV-1 via glycoprotein B, and macrophages derived from R78 homozygous donors showed significantly decreased levels of HSV-1 infection at several multiplicities of infection compared to homozygous G78 macrophages. We propose that PILRA G78R protects individuals from Alzheimer’s disease risk via reduced inhibitory signaling in microglia and reduced microglial infection during HSV-1 recurrence. Alzheimer’s disease (AD) is a devastating neurodegenerative disorder resulting from a complex interaction of environmental and genetic risk factors. Despite considerable progress in defining the genetic component of AD risk, understanding the biology of common variant associations is a challenge. We find that PILRA G78R (rs1859788) is the likely AD risk variant from the 7q21 locus (rs1476679) and PILRA G78R reduces PILRA endogenous and exogenous ligand binding. Our study highlights a new immune signaling axis in AD and suggests a role for exogenous ligands (HSV-1). Further, we have identified that reduced function of a negative regulator of microglia and neutrophils is protective from AD risk, providing a new candidate therapeutic target.
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Affiliation(s)
- Nisha Rathore
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Sree Ranjani Ramani
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, California, United States of America
| | - Homer Pantua
- Department of Immunology and Infectious Diseases, Genentech Inc., South San Francisco, California, United States of America
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Tushar Bhangale
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America.,Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Arthur Wuster
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America.,Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Manav Kapoor
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Yonglian Sun
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Sharookh B Kapadia
- Department of Immunology and Infectious Diseases, Genentech Inc., South San Francisco, California, United States of America
| | - Lino Gonzalez
- Department of Proteomics & Biological Resources, Genentech Inc., South San Francisco, California, United States of America
| | - Ali A Zarrin
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Alison Goate
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - David V Hansen
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
| | - Timothy W Behrens
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Robert R Graham
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America
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7
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Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 2018; 11:11/546/eaat6409. [PMID: 30181241 PMCID: PMC6130803 DOI: 10.1126/scisignal.aat6409] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions.
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Affiliation(s)
- Marc Torrent
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK. .,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia S de Groot
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arthur Wuster
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - M Madan Babu
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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8
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Manzanillo P, Mouchess M, Ota N, Dai B, Ichikawa R, Wuster A, Haley B, Alvarado G, Kwon Y, Caothien R, Roose-Girma M, Warming S, McKenzie BS, Keir ME, Scherl A, Ouyang W, Yi T. Inflammatory Bowel Disease Susceptibility Gene C1ORF106 Regulates Intestinal Epithelial Permeability. Immunohorizons 2018; 2:164-171. [PMID: 31022698 DOI: 10.4049/immunohorizons.1800027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/07/2018] [Indexed: 11/19/2022] Open
Abstract
Intestinal epithelial cells form a physical barrier that is tightly regulated to control intestinal permeability. Proinflammatory cytokines, such as TNF-α, increase epithelial permeability through disruption of epithelial junctions. The regulation of the epithelial barrier in inflammatory gastrointestinal disease remains to be fully characterized. In this article, we show that the human inflammatory bowel disease genetic susceptibility gene C1ORF106 plays a key role in regulating gut epithelial permeability. C1ORF106 directly interacts with cytohesins to maintain functional epithelial cell junctions. C1orf106-deficient mice are hypersensitive to TNF-α-induced increase in epithelial permeability, and this is associated with increased diarrhea. This study identifies C1ORF106 as an epithelial cell junction protein, and the loss of C1ORF106 augments TNF-α-induced intestinal epithelial leakage and diarrhea that may play a critical role in the development of inflammatory bowel disease.
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Affiliation(s)
- Paolo Manzanillo
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080;
| | - Maria Mouchess
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Naruhisa Ota
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Bingbing Dai
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Ryan Ichikawa
- Department of Biomarker Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Arthur Wuster
- Department of Human Genetics, Genentech Inc., South San Francisco, CA 94080
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Gabriela Alvarado
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Youngsu Kwon
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA 94080; and
| | - Roger Caothien
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Meron Roose-Girma
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Soren Warming
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Brent S McKenzie
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA 94080; and
| | - Mary E Keir
- Department of Biomarker Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Alexis Scherl
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080
| | - Wenjun Ouyang
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080;
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080;
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9
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Narasimhan VM, Rahbari R, Scally A, Wuster A, Mason D, Xue Y, Wright J, Trembath RC, Maher ER, van Heel DA, Auton A, Hurles ME, Tyler-Smith C, Durbin R. Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes. Nat Commun 2017; 8:303. [PMID: 28827725 PMCID: PMC5566399 DOI: 10.1038/s41467-017-00323-y] [Citation(s) in RCA: 63] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 06/20/2017] [Indexed: 11/08/2022] Open
Abstract
Heterozygous mutations within homozygous sequences descended from a recent common ancestor offer a way to ascertain de novo mutations across multiple generations. Using exome sequences from 3222 British-Pakistani individuals with high parental relatedness, we estimate a mutation rate of 1.45 ± 0.05 × 10-8 per base pair per generation in autosomal coding sequence, with a corresponding non-crossover gene conversion rate of 8.75 ± 0.05 × 10-6 per base pair per generation. This is at the lower end of exome mutation rates previously estimated in parent-offspring trios, suggesting that post-zygotic mutations contribute little to the human germ-line mutation rate. We find frequent recurrence of mutations at polymorphic CpG sites, and an increase in C to T mutations in a 5' CCG 3' to 5' CTG 3' context in the Pakistani population compared to Europeans, suggesting that mutational processes have evolved rapidly between human populations.Estimates of human mutation rates differ substantially based on the approach. Here, the authors present a multi-generational estimate from the autozygous segment in a non-European population that gives insight into the contribution of post-zygotic mutations and population-specific mutational processes.
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Affiliation(s)
| | - Raheleh Rahbari
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Arthur Wuster
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA UK
- Department of Human Genetics and Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA UK
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ UK
| | - Richard C. Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences and Medicine, King’s College, London, SE1 1UL UK
| | - Eamonn R. Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ UK
- Cambridge NIHR Biomedical Research Centre, Cambridge, CB2 0QQ UK
| | - David A. van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT UK
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | | | | | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA UK
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10
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Sitrin J, Suto E, Wuster A, Eastham-Anderson J, Kim JM, Austin CD, Lee WP, Behrens TW. The Ox40/Ox40 Ligand Pathway Promotes Pathogenic Th Cell Responses, Plasmablast Accumulation, and Lupus Nephritis in NZB/W F1 Mice. J Immunol 2017; 199:1238-1249. [PMID: 28696253 DOI: 10.4049/jimmunol.1700608] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/07/2017] [Indexed: 12/11/2022]
Abstract
Ox40 ligand (Ox40L) locus genetic variants are associated with the risk for systemic lupus erythematosus (SLE); however, it is unclear how Ox40L contributes to SLE pathogenesis. In this study, we evaluated the contribution of Ox40L and its cognate receptor, Ox40, using in vivo agonist and antagonist approaches in the NZB × NZW (NZB/W) F1 mouse model of SLE. Ox40 was highly expressed on several CD4 Th cell subsets in the spleen and kidney of diseased mice, and expression correlated with disease severity. Treatment of aged NZB/W F1 mice with agonist anti-Ox40 mAbs potently exacerbated renal disease, which was accompanied by activation of kidney-infiltrating T cells and cytokine production. The agonist mAbs also induced activation and inflammatory gene expression in splenic CD4 T cells, including IFN-regulated genes, increased the number of follicular helper T cells and plasmablasts in the spleen, and led to elevated levels of serum IgM and enhanced renal glomerular IgM deposition. In a type I IFN-accelerated lupus model, treatment with an antagonist Ox40:Fc fusion protein significantly delayed the onset of severe proteinuria and improved survival. These data support the hypothesis that the Ox40/Ox40L pathway drives cellular and humoral autoimmune responses during lupus nephritis in NZB/W F1 mice and emphasize the potential clinical value of targeting this pathway in human lupus.
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Affiliation(s)
- Jonathan Sitrin
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080;
| | - Eric Suto
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Arthur Wuster
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | | | - Jeong M Kim
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Cary D Austin
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080; and
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Timothy W Behrens
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080
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11
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Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell 2017; 168:830-842.e7. [PMID: 28235197 DOI: 10.1016/j.cell.2017.01.037] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 10/13/2016] [Accepted: 01/27/2017] [Indexed: 01/07/2023]
Abstract
De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities. We describe a multiple dnCNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional dnCNVs. These CNVs originate from independent formation incidences, are predominantly tandem duplications or complex gains, exhibit breakpoint junction features reminiscent of replicative repair, and show increased de novo point mutations flanking the rearrangement junctions. The active CNV mutation shower appears to be restricted to a transient perizygotic period. We propose that a defect in the CNV formation process is responsible for the "CNV-mutator state," and this state is dampened after early embryogenesis. The constitutional MdnCNV phenomenon resembles chromosomal instability in various cancers. Investigations of this phenomenon may provide unique access to understanding genomic disorders, structural variant mutagenesis, human evolution, and cancer biology.
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Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA.
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur Wuster
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Ling Zhang
- Collaborative Innovation Center of Genetics and Development, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zechen Chong
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Violet Gelowani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karin Writzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Marjorie Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Scull
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Zhang
- Collaborative Innovation Center of Genetics and Development, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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12
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Wuster A, Chang D, Behrens TW, Bhangale TR. geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation. Bioinformatics 2017; 33:599-600. [PMID: 28035029 PMCID: PMC5408921 DOI: 10.1093/bioinformatics/btw698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/02/2016] [Indexed: 11/25/2022] Open
Abstract
Motivation We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression quantitative trait loci (eQTL) or Hi-C genome conformation data and reports the most likely candidate genes. In the absence of annotation data, geneAttribution relies on the distances between the genes and the input variant. Availability and Implementation The package is freely available from http://www.bioconductor.org/. A quick-start vignette is included with the package.
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Affiliation(s)
- Arthur Wuster
- Department of Human Genetics.,Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, CA 94080, USA
| | | | | | - Tushar R Bhangale
- Department of Human Genetics.,Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, CA 94080, USA
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13
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Yang C, Hojer CD, Zhou M, Wu X, Wuster A, Lee WP, Yaspan BL, Chan AC. Regulation of T-cell receptor downmodulation by DENND1B in TH2 cells and allergic disease. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.192.1] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The DENN-domain is an evolutionary conserved protein module found in all eukaryotes and serves as an exchange factor for Rab-GTPases to regulate diverse cellular functions. Variants in DENND1B are associated with development of childhood asthma and other immune disorders. To understand how DENND1B may contribute to diseases, Dennd1b−/− mice were generated and exhibit hyper-allergic responses following antigen challenge. Dennd1b−/− TH2, but not other TH cells, exhibit delayed receptor-induced TCR downmodulation, enhanced TCR signaling, and increased production of effector cytokines. As DENND1B interacts with AP-2 and Rab35, TH2 cells deficient in AP-2 or Rab35 also exhibit enhanced TCR-mediated effector functions. Moreover, human TH2 cells carrying asthma-associated DENND1B variants express less DENND1B and phenocopy Dennd1b−/− TH2 cells. These results provide a molecular basis for how DENND1B, a previously unrecognized regulator of TCR downmodulation in TH2 cells, contributes to asthma pathogenesis and how DENN-domain containing proteins may contribute to other human disorders.
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14
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Wuster A, Behrens TW. Thinking differently about lupus. eLife 2016; 5. [PMID: 27023642 PMCID: PMC4821793 DOI: 10.7554/elife.15352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
A search for the genetic causes of an autoimmune disease called systemic lupus erythematosus reveals a new twist on an old story.
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15
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Yang CW, Hojer CD, Zhou M, Wu X, Wuster A, Lee WP, Yaspan BL, Chan AC. Regulation of T Cell Receptor Signaling by DENND1B in TH2 Cells and Allergic Disease. Cell 2016; 164:141-155. [PMID: 26774822 DOI: 10.1016/j.cell.2015.11.052] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/11/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
Abstract
The DENN domain is an evolutionary conserved protein module found in all eukaryotes and serves as an exchange factor for Rab-GTPases to regulate diverse cellular functions. Variants in DENND1B are associated with development of childhood asthma and other immune disorders. To understand how DENND1B may contribute to human disease, Dennd1b(-/-) mice were generated and exhibit hyper-allergic responses following antigen challenge. Dennd1b(-/-) TH2, but not other TH cells, exhibit delayed receptor-induced T cell receptor (TCR) downmodulation, enhanced TCR signaling, and increased production of effector cytokines. As DENND1B interacts with AP-2 and Rab35, TH2 cells deficient in AP-2 or Rab35 also exhibit enhanced TCR-mediated effector functions. Moreover, human TH2 cells carrying asthma-associated DENND1B variants express less DENND1B and phenocopy Dennd1b(-/-) TH2 cells. These results provide a molecular basis for how DENND1B, a previously unrecognized regulator of TCR downmodulation in TH2 cells, contributes to asthma pathogenesis and how DENN-domain-containing proteins may contribute to other human disorders.
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Affiliation(s)
- Chiao-Wen Yang
- Department of Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Caroline D Hojer
- Department of Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Meijuan Zhou
- Department of Translational Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Arthur Wuster
- Department of Human Genetics, Genentech, One DNA Way, South San Francisco, CA 94080, USA; Department of Bioinformatics and Computational Biology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Andrew C Chan
- Research, Genentech, One DNA Way, South San Francisco, CA 94080, USA.
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16
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Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B, Stratton MR, Hurles ME. Timing, rates and spectra of human germline mutation. Nat Genet 2015; 48:126-133. [PMID: 26656846 PMCID: PMC4731925 DOI: 10.1038/ng.3469] [Citation(s) in RCA: 361] [Impact Index Per Article: 40.1] [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: 06/04/2015] [Accepted: 11/20/2015] [Indexed: 12/15/2022]
Abstract
Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. Mutation rate increased with paternal age in all families, but the number of additional mutations per year differed more than two-fold between families. Meta-analysis of 6,570 mutations showed that germline methylation influences mutation rates. In contrast to somatic mutations, we found remarkable consistency of germline mutation spectra between the sexes and at different paternal ages. 3.8% of mutations were mosaic in the parental germline, resulting in 1.3% of mutations being shared between siblings. The number of these shared mutations varied significantly between families. Our data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells, but is reduced substantially during post-pubertal spermatogenesis. These findings have important consequences for the recurrence risks of disorders caused by de novo mutations.
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Affiliation(s)
- Raheleh Rahbari
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Arthur Wuster
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.,Department of Human Genetics and Department of Bioinformatics and Computational Biology, Genentech Inc, 1 DNA Way, CA 94080 South San Francisco, USA
| | - Sarah J Lindsay
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Saeed Al Turki
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Anna Dominiczak
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew Morris
- Medical Research Institute, University of Dundee, Dundee, United Kingdom
| | - David Porteous
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Blair Smith
- Medical Research Institute, University of Dundee, Dundee, United Kingdom
| | | | | | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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17
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Abstract
Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences. Availability:http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html Contact:ajv@mrc-lmb.cam.ac.uk
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Affiliation(s)
- Arthur Wuster
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK
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18
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Abstract
Quorum sensing is a process of intercellular communication. It allows individual cells to assess population density and to co-ordinate behaviour by secreting and sensing communication molecules. In the yeast Saccharomyces cerevisiae, the communication molecules are the aromatic alcohols tryptophol and phenylethanol, and quorum sensing regulates the transition between the solitary yeast form and the filamentous form. Though it is known that addition of these communication molecules to yeast cultures causes large changes in gene expression, how these changes are orchestrated and whether this system is conserved in related fungal species is still unknown. In this work, by employing an integrated computational approach that makes use of large-scale genomics datasets, such as ChIP-ChIP and expression analysis upon deletion and over-expression of transcriptional factors, we predict CAT8 and MIG1 as key transcriptional regulators that control the differential expression of the genes affected by aromatic alcohol communication. In addition, through a comparative genomic analysis involving 31 fungal species, we show that the S. cerevisiae quorum sensing system is a recent evolutionary innovation and that the genes which are differentially expressed upon treatment with these molecules are distributed across the genome in a highly non-random manner. The identified transcription factors will aid in further unravelling the molecular mechanisms of S. cerevisiae quorum sensing and may facilitate the engineering of regulatory circuits for applications such as the expression of heterologous proteins via aromatic alcohols.
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19
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Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 2009; 5:294. [PMID: 19690563 PMCID: PMC2736650 DOI: 10.1038/msb.2009.52] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 06/07/2009] [Indexed: 12/14/2022] Open
Abstract
Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome-scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we show that transcription factor (TF) dynamics and regulatory network organization are tightly linked. By classifying TFs in the yeast regulatory network into three hierarchical layers (top, core, and bottom) and integrating diverse genome-scale datasets, we find that the TFs have static and dynamic properties that are similar within a layer and different across layers. At the protein level, the top-layer TFs are relatively abundant, long-lived, and noisy compared with the core- and bottom-layer TFs. Although variability in expression of top-layer TFs might confer a selective advantage, as this permits at least some members in a clonal cell population to initiate a response to changing conditions, tight regulation of the core- and bottom-layer TFs may minimize noise propagation and ensure fidelity in regulation. We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population.
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Affiliation(s)
- Raja Jothi
- Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
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Abstract
A robust knowledge of the interactions between small molecules and specific proteins aids the development of new biotechnological tools and the identification of new drug targets, and can lead to specific biological insights. Such knowledge can be obtained through chemogenomic screens. In these screens, each small molecule from a chemical library is applied to each cell type from a library of cells, and the resulting phenotypes are recorded. Chemogenomic screens have recently become very common and will continue to generate large amounts of data. The interpretation of this data will occupy biologists and chemists alike for some time to come. This review discusses methods for the acquisition and interpretation of chemogenomic data, in addition to possible applications of chemogenomics in biotechnology.
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Affiliation(s)
- Arthur Wuster
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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