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Jurgens JA, Barry BJ, Chan WM, MacKinnon S, Whitman MC, Matos Ruiz PM, Pratt BM, England EM, Pais L, Lemire G, Groopman E, Glaze C, Russell KA, Singer-Berk M, Di Gioia SA, Lee AS, Andrews C, Shaaban S, Wirth MM, Bekele S, Toffoloni M, Bradford VR, Foster EE, Berube L, Rivera-Quiles C, Mensching FM, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Wilson MW, Weisburd B, Lek M, Brand H, Talkowski ME, MacArthur DG, O’Donnell-Luria A, Robson CD, Hunter DG, Engle EC. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders. medRxiv 2024:2024.03.22.24304594. [PMID: 38585811 PMCID: PMC10996726 DOI: 10.1101/2024.03.22.24304594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Purpose To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs). Methods We coupled phenotyping with exome or genome sequencing of 467 pedigrees with genetically unsolved oCCDDs, integrating analyses of pedigrees, human and animal model phenotypes, and de novo variants to identify rare candidate single nucleotide variants, insertion/deletions, and structural variants disrupting protein-coding regions. Prioritized variants were classified for pathogenicity and evaluated for genotype/phenotype correlations. Results Analyses elucidated phenotypic subgroups, identified pathogenic/likely pathogenic variant(s) in 43/467 probands (9.2%), and prioritized variants of uncertain significance in 70/467 additional probands (15.0%). These included known and novel variants in established oCCDD genes, genes associated with syndromes that sometimes include oCCDDs (e.g., MYH10, KIF21B, TGFBR2, TUBB6), genes that fit the syndromic component of the phenotype but had no prior oCCDD association (e.g., CDK13, TGFB2), genes with no reported association with oCCDDs or the syndromic phenotypes (e.g., TUBA4A, KIF5C, CTNNA1, KLB, FGF21), and genes associated with oCCDD phenocopies that had resulted in misdiagnoses. Conclusion This study suggests that unsolved oCCDDs are clinically and genetically heterogeneous disorders often overlapping other Mendelian conditions and nominates many candidates for future replication and functional studies.
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Affiliation(s)
- Julie A. Jurgens
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brenda J. Barry
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Mary C. Whitman
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | | | - Brandon M. Pratt
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Eleina M. England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynn Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Carmen Glaze
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn A. Russell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvio Alessandro Di Gioia
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, 10591, USA
| | - Arthur S. Lee
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline Andrews
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Sherin Shaaban
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Megan M. Wirth
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Sarah Bekele
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Melissa Toffoloni
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | | | - Emma E. Foster
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Lindsay Berube
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | | | | | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack M. Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E. Talkowski
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline D. Robson
- Division of Neuroradiology, Department of Radiology, Boston Children’s Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - David G. Hunter
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth C. Engle
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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Babadi M, Fu JM, Lee SK, Smirnov AN, Gauthier LD, Walker M, Benjamin DI, Zhao X, Karczewski KJ, Wong I, Collins RL, Sanchis-Juan A, Brand H, Banks E, Talkowski ME. Author Correction: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data. Nat Genet 2024; 56:553. [PMID: 38263447 DOI: 10.1038/s41588-024-01663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Affiliation(s)
- Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jack M Fu
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrey N Smirnov
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura D Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Walker
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David I Benjamin
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric Banks
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. medRxiv 2023:2023.12.22.23300468. [PMID: 38234731 PMCID: PMC10793524 DOI: 10.1101/2023.12.22.23300468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generated single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. Seventy-five percent of elements (44 of 59) validated in an in vivo transgenic reporter assay, demonstrating that single cell accessibility is a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieved significant reduction in our variant search space and nominated candidate variants predicted to regulate known CCDD disease genes MAFB, PHOX2A, CHN1, and EBF3 - as well as new candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work provides novel non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.
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Affiliation(s)
- Arthur S Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Lauren J Ayers
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Lydia N Fozo
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Brandon M Pratt
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Thomas E Collins
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Boxun Zhao
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Matthew F Rose
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Pathology, Boston Children's Hospital, Boston, MA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Medical Genetics Training Program, Harvard Medical School, Boston, MA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Alan P Tenney
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cassia Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Harvard College, Cambridge, MA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Brenda J Barry
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Victoria R Bradford
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Eunjung Alice Lee
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
- Medical Genetics Training Program, Harvard Medical School, Boston, MA
- Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, MA
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Babadi M, Fu JM, Lee SK, Smirnov AN, Gauthier LD, Walker M, Benjamin DI, Zhao X, Karczewski KJ, Wong I, Collins RL, Sanchis-Juan A, Brand H, Banks E, Talkowski ME. GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data. Nat Genet 2023; 55:1589-1597. [PMID: 37604963 PMCID: PMC10904014 DOI: 10.1038/s41588-023-01449-0] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/16/2023] [Indexed: 08/23/2023]
Abstract
Copy number variants (CNVs) are major contributors to genetic diversity and disease. While standardized methods, such as the genome analysis toolkit (GATK), exist for detecting short variants, technical challenges have confounded uniform large-scale CNV analyses from whole-exome sequencing (WES) data. Given the profound impact of rare and de novo coding CNVs on genome organization and human disease, we developed GATK-gCNV, a flexible algorithm to discover rare CNVs from sequencing read-depth information, complete with open-source distribution via GATK. We benchmarked GATK-gCNV in 7,962 exomes from individuals in quartet families with matched genome sequencing and microarray data, finding up to 95% recall of rare coding CNVs at a resolution of more than two exons. We used GATK-gCNV to generate a reference catalog of rare coding CNVs in WES data from 197,306 individuals in the UK Biobank, and observed strong correlations between per-gene CNV rates and measures of mutational constraint, as well as rare CNV associations with multiple traits. In summary, GATK-gCNV is a tunable approach for sensitive and specific CNV discovery in WES data, with broad applications.
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Affiliation(s)
- Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jack M Fu
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrey N Smirnov
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura D Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Walker
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David I Benjamin
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric Banks
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Liao C, Moyses-Oliveira M, De Esch CE, Bhavsar R, Nuttle X, Li A, Yu A, Burt ND, Erdin S, Fu JM, Wang M, Morley T, Han L, Dion PA, Rouleau GA, Zhang B, Brennand KJ, Talkowski ME, Ruderfer DM. Convergent coexpression of autism-associated genes suggests some novel risk genes may not be detectable in large-scale genetic studies. Cell Genomics 2023; 3:100277. [PMID: 37082147 PMCID: PMC10112287 DOI: 10.1016/j.xgen.2023.100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/01/2022] [Accepted: 02/10/2023] [Indexed: 03/21/2023]
Abstract
Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder characterized by deficits in social interactions and communication. Protein-altering variants in many genes have been shown to contribute to ASD; however, understanding the convergence across many genes remains a challenge. We demonstrate that coexpression patterns from 993 human postmortem brains are significantly correlated with the transcriptional consequences of CRISPR perturbations in human neurons. Across 71 ASD risk genes, there was significant tissue-specific convergence implicating synaptic pathways. Tissue-specific convergence was further demonstrated across schizophrenia and atrial fibrillation risk genes. The degree of ASD convergence was significantly correlated with ASD association from rare variation and differential expression in ASD brains. Positively convergent genes showed intolerance to functional mutations and had shorter coding lengths than known risk genes even after removing association with ASD. These results indicate that convergent coexpression can identify potentially novel genes that are unlikely to be discovered by sequencing studies.
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Weiner DJ, Ling E, Erdin S, Tai DJC, Yadav R, Grove J, Fu JM, Nadig A, Carey CE, Baya N, Bybjerg-Grauholm J, Berretta S, Macosko EZ, Sebat J, O'Connor LJ, Hougaard DM, Børglum AD, Talkowski ME, McCarroll SA, Robinson EB. Statistical and functional convergence of common and rare genetic influences on autism at chromosome 16p. Nat Genet 2022; 54:1630-1639. [PMID: 36280734 PMCID: PMC9649437 DOI: 10.1038/s41588-022-01203-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022]
Abstract
The canonical paradigm for converting genetic association to mechanism involves iteratively mapping individual associations to the proximal genes through which they act. In contrast, in the present study we demonstrate the feasibility of extracting biological insights from a very large region of the genome and leverage this strategy to study the genetic influences on autism. Using a new statistical approach, we identified the 33-Mb p-arm of chromosome 16 (16p) as harboring the greatest excess of autism's common polygenic influences. The region also includes the mechanistically cryptic and autism-associated 16p11.2 copy number variant. Analysis of RNA-sequencing data revealed that both the common polygenic influences within 16p and the 16p11.2 deletion were associated with decreased average gene expression across 16p. The transcriptional effects of the rare deletion and diffuse common variation were correlated at the level of individual genes and analysis of Hi-C data revealed patterns of chromatin contact that may explain this transcriptional convergence. These results reflect a new approach for extracting biological insight from genetic association data and suggest convergence of common and rare genetic influences on autism at 16p.
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Affiliation(s)
- Daniel J Weiner
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Emi Ling
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Serkan Erdin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek J C Tai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Rachita Yadav
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jakob Grove
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Jack M Fu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ajay Nadig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Caitlin E Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nikolas Baya
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sabina Berretta
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Evan Z Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Luke J O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Anders D Børglum
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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7
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Kuo SS, van der Merwe C, Fu JM, Carey CE, Talkowski ME, Bishop SL, Robinson EB. Developmental Variability in Autism Across 17 000 Autistic Individuals and 4000 Siblings Without an Autism Diagnosis: Comparisons by Cohort, Intellectual Disability, Genetic Etiology, and Age at Diagnosis. JAMA Pediatr 2022; 176:915-923. [PMID: 35849387 PMCID: PMC9295026 DOI: 10.1001/jamapediatrics.2022.2423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/14/2022] [Indexed: 01/02/2023]
Abstract
Importance Presence of developmental delays in autism is well established, yet few studies have characterized variability in developmental milestone attainment in this population. Objective To characterize variability in the age at which autistic individuals attain key developmental milestones based on co-occurring intellectual disability (ID), presence of a rare disruptive genetic variant associated with neurodevelopmental disorders (NDD), age at autism diagnosis, and research cohort membership. Design The study team harmonized data from 4 cross-sectional autism cohorts: the Autism Genetics Research Exchange (n = 3284; 1997-2015), The Autism Simplex Collection (n = 694; 2008-2011), the Simons Simplex Collection (n = 2753; 2008-2011), and the Simons Foundation Powering Autism Research for Knowledge (n = 10 367; 2016-present). The last sample further included 4145 siblings without an autism diagnosis or ID. Participants Convenience sample of 21 243 autistic individuals or their siblings without an autism diagnosis aged 4 to 17 years. Main Outcomes and Measures Parents reported ages at which participants attained key milestones including smiling, sitting upright, crawling, walking, spoon-feeding self, speaking words, speaking phrases, and acquiring bladder and bowel control. A total of 5295 autistic individuals, and their biological parents, were genetically characterized to identify de novo variants in NDD-associated genes. The study team conducted time-to-event analyses to estimate and compare percentiles in time with milestone attainment across autistic individuals, subgroups of autistic individuals, and the sibling sample. Results Seventeen thousand ninety-eight autistic individuals (mean age, 9.15 years; 80.8% male) compared with 4145 siblings without autism or ID (mean age, 10.2 years; 50.2% female) showed delays in milestone attainment, with median (IQR) delays ranging from 0.7 (0.3-1.6) to 19.7 (11.4-32.2) months. More severe and more variable delays in autism were associated with the presence of co-occurring ID, carrying an NDD-associated rare genetic variant, and being diagnosed with autism by age 5 years. More severe and more variable delays were also associated with membership in earlier study cohorts, consistent with autism's diagnostic and ascertainment expansion over the last 30 years. Conclusions and Relevance As the largest summary to date of developmental milestone attainment in autism, to our knowledge, this study demonstrates substantial developmental variability across different conditions and provides important context for understanding the phenotypic and etiological heterogeneity of autism.
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Affiliation(s)
- Susan S. Kuo
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Celia van der Merwe
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Jack M. Fu
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Caitlin E. Carey
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Somer L. Bishop
- Department of Psychiatry, University of California, San Francisco
| | - Elise B. Robinson
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston
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8
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Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, Dong S, Wamsley B, Klei L, Wang L, Hao SP, Stevens CR, Cusick C, Babadi M, Banks E, Collins B, Dodge S, Gabriel SB, Gauthier L, Lee SK, Liang L, Ljungdahl A, Mahjani B, Sloofman L, Smirnov AN, Barbosa M, Betancur C, Brusco A, Chung BHY, Cook EH, Cuccaro ML, Domenici E, Ferrero GB, Gargus JJ, Herman GE, Hertz-Picciotto I, Maciel P, Manoach DS, Passos-Bueno MR, Persico AM, Renieri A, Sutcliffe JS, Tassone F, Trabetti E, Campos G, Cardaropoli S, Carli D, Chan MCY, Fallerini C, Giorgio E, Girardi AC, Hansen-Kiss E, Lee SL, Lintas C, Ludena Y, Nguyen R, Pavinato L, Pericak-Vance M, Pessah IN, Schmidt RJ, Smith M, Costa CIS, Trajkova S, Wang JYT, Yu MHC, Cutler DJ, De Rubeis S, Buxbaum JD, Daly MJ, Devlin B, Roeder K, Sanders SJ, Talkowski ME. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat Genet 2022; 54:1320-1331. [PMID: 35982160 PMCID: PMC9653013 DOI: 10.1038/s41588-022-01104-0] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023]
Abstract
Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
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Affiliation(s)
- Jack M Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Minshi Peng
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lily Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Christine R Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline Cusick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett Collins
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Gauthier
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lindsay Liang
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrey N Smirnov
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mafalda Barbosa
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, 'Città della Salute e della Scienza' University Hospital, Turin, Italy
| | - Brian H Y Chung
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael L Cuccaro
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology, , University of Trento, Trento, Italy
| | | | - J Jay Gargus
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Gail E Herman
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Irva Hertz-Picciotto
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Patricia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
| | - Dara S Manoach
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio M Persico
- Interdepartmental Program 'Autism 0-90', 'Gaetano Martino' University Hospital, University of Messina, Messina, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - James S Sutcliffe
- Department of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Flora Tassone
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
| | - Gabriele Campos
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Marcus C Y Chan
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Ana Cristina Girardi
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Emily Hansen-Kiss
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
| | - So Lun Lee
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Carla Lintas
- Service for Neurodevelopmental Disorders, University Campus Bio-medico of Rome, Rome, Italy
| | - Yunin Ludena
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Margaret Pericak-Vance
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Isaac N Pessah
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Moyra Smith
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Claudia I S Costa
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Jaqueline Y T Wang
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mullin H C Yu
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mark J Daly
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
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9
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Wigdor EM, Weiner DJ, Grove J, Fu JM, Thompson WK, Carey CE, Baya N, van der Merwe C, Walters RK, Satterstrom FK, Palmer DS, Rosengren A, Bybjerg-Grauholm J, Hougaard DM, Mortensen PB, Daly MJ, Talkowski ME, Sanders SJ, Bishop SL, Børglum AD, Robinson EB. The female protective effect against autism spectrum disorder. Cell Genom 2022; 2:100134. [PMID: 36778135 PMCID: PMC9903803 DOI: 10.1016/j.xgen.2022.100134] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/26/2022] [Accepted: 04/27/2022] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is diagnosed three to four times more frequently in males than in females. Genetic studies of rare variants support a female protective effect (FPE) against ASD. However, sex differences in common inherited genetic risk for ASD are less studied, particularly within families. Leveraging the Danish iPSYCH resource, we found siblings of female ASD cases (n = 1,707) had higher rates of ASD than siblings of male ASD cases (n = 6,270; p < 1.0 × 10-10). In the Simons Simplex and SPARK collections, mothers of ASD cases (n = 7,436) carried more polygenic risk for ASD than fathers of ASD cases (n = 5,926; 0.08 polygenic risk score [PRS] SD; p = 7.0 × 10-7). Further, male unaffected siblings under-inherited polygenic risk (n = 1,519; p = 0.03). Using both epidemiologic and genetic approaches, our findings strongly support an FPE against ASD's common inherited influences.
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Affiliation(s)
- Emilie M. Wigdor
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Daniel J. Weiner
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jakob Grove
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, 8000 Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Jack M. Fu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Caitlin E. Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nikolas Baya
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Celia van der Merwe
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Raymond K. Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - F. Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Duncan S. Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, 4000 Roskilde, Denmark
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark
| | | | - David M. Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Preben Bo Mortensen
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, 8000 Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, 4000 Roskilde, Denmark
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus, Denmark
- Center for Integrated Register-based Research, Aarhus University, 8210 Aarhus, Denmark
| | - Mark J. Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Finnish Institute for Molecular Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephan J. Sanders
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Somer L. Bishop
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anders D. Børglum
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, 8000 Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, 4000 Roskilde, Denmark
| | - Elise B. Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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10
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Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK. Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut 2021; 70:285-296. [PMID: 32651235 PMCID: PMC7815889 DOI: 10.1136/gutjnl-2019-319706] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/08/2020] [Accepted: 04/20/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD. DESIGN To evaluate the impact of host genetics on the gut microbiota of patients with IBD, we combined whole exome sequencing of the host genome and whole genome shotgun sequencing of 1464 faecal samples from 525 patients with IBD and 939 population-based controls. We followed a four-step analysis: (1) exome-wide microbial quantitative trait loci (mbQTL) analyses, (2) a targeted approach focusing on IBD-associated genomic regions and protein truncating variants (PTVs, minor allele frequency (MAF) >5%), (3) gene-based burden tests on PTVs with MAF <5% and exome copy number variations (CNVs) with site frequency <1%, (4) joint analysis of both cohorts to identify the interactions between disease and host genetics. RESULTS We identified 12 mbQTLs, including variants in the IBD-associated genes IL17REL, MYRF, SEC16A and WDR78. For example, the decrease of the pathway acetyl-coenzyme A biosynthesis, which is involved in short chain fatty acids production, was associated with variants in the gene MYRF (false discovery rate <0.05). Changes in functional pathways involved in the metabolic potential were also observed in participants carrying rare PTVs or CNVs in CYP2D6, GPR151 and CD160 genes. These genes are known for their function in the immune system. Moreover, interaction analyses confirmed previously known IBD disease-specific mbQTLs in TNFSF15. CONCLUSION This study highlights that both common and rare genetic variants affecting the immune system are key factors in shaping the gut microbiota in the context of IBD and pinpoints towards potential mechanisms for disease treatment.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Christine Stevens
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Laura Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Hendrik van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora A Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutic, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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11
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Fu JM, Leslie EJ, Scott AF, Murray JC, Marazita ML, Beaty TH, Scharpf RB, Ruczinski I. Detection of de novo copy number deletions from targeted sequencing of trios. Bioinformatics 2019; 35:571-578. [PMID: 30084993 PMCID: PMC6378941 DOI: 10.1093/bioinformatics/bty677] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 11/25/2022] Open
Abstract
MOTIVATION De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. RESULTS We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. AVAILABILITY AND IMPLEMENTATION MDTS is freely available as open source software from the Bioconductor repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jack M Fu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Alan F Scott
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L Marazita
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Robert B Scharpf
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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12
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Ramachandran KV, Fu JM, Schaffer TB, Na CH, Delannoy M, Margolis SS. Activity-Dependent Degradation of the Nascentome by the Neuronal Membrane Proteasome. Mol Cell 2018; 71:169-177.e6. [PMID: 29979964 PMCID: PMC6070390 DOI: 10.1016/j.molcel.2018.06.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/12/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022]
Abstract
Activity-dependent changes in neuronal function require coordinated regulation of the protein synthesis and protein degradation machinery to maintain protein homeostasis, critical for proper neuronal function. However, the biochemical evidence for this balance and coordination is largely lacking. Leveraging our recent discovery of a neuronal-specific 20S membrane proteasome complex (NMP), we began exploring how neuronal activity regulates its function. Here, we found that the NMP degrades exclusively a large fraction of ribosome-associated nascent polypeptides that are being newly synthesized during neuronal stimulation. Using deep-coverage and global mass spectrometry, we identified the nascent protein substrates of the NMP, which included products encoding immediate-early genes, such as c-Fos and Npas4. Intriguingly, we found that turnover of nascent polypeptides and not full-length proteins through the NMP occurred independent of canonical ubiquitylation pathways. We propose that these findings generally define a neuronal activity-induced protein homeostasis program of coordinated protein synthesis and degradation through the NMP.
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Affiliation(s)
- Kapil V Ramachandran
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Jack M Fu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Thomas B Schaffer
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael Delannoy
- The Johns Hopkins University School of Medicine Microscope Facility, Baltimore, MD 21205, USA
| | - Seth S Margolis
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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13
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Hu T, Zhang XZ, Sun JM, Li HY, Fu JM. Leaf functional trait variation associated with salt tolerance in perennial ryegrass. Plant Biol (Stuttg) 2014; 16:107-116. [PMID: 23590346 DOI: 10.1111/plb.12012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/05/2013] [Indexed: 06/02/2023]
Abstract
Salinity is one of major environmental stresses that dramatically threaten plant growth, and variations in genetic structure and functional traits have important effects on the salt tolerance of perennial ryegrass (Lolium perenne L.). The objectives of this study were to: (i) assess the inter-clonal variation of functional traits of accessions among geographic groups or between wild and commercial groups in response to salt stress; (ii) develop a mathematical model to effectively assess salt tolerance of perennial ryegrass accessions originating from different geographic populations; and (iii) determine the relation between spatial genetic structure and salt tolerance in perennial ryegrass. Wide variations were found among the accessions for seven functional traits. One regression model (F = 0.49 × F1 + 0.303 × F2 + 0.207 × F3) was established to ascertain salt tolerance of each accession. The highest variation of the traits and salt tolerance were obtained for accessions from the European group. Wild accessions exhibited more variation in functional traits and salt tolerance than commercial cultivars. Both molecular marker techniques and functional traits were used to conduct phylogenetic analysis, and the majority of accessions from the same or adjacent regions were clustered into the same group or subgroup. The perennial ryegrass accessions with similar salt tolerance had a close phylogenetic background. The patterns in functional trait variations associated with salt tolerance might allow acceleration of the process for improving salt stress resistance in perennial ryegrass.
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Affiliation(s)
- T Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, China
| | - X Z Zhang
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - J M Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, China
| | - H Y Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, China
| | - J M Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, China
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14
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Deng WJ, Zheng JS, Bi XH, Fu JM, Wong MH. Distribution of PBDEs in air particles from an electronic waste recycling site compared with Guangzhou and Hong Kong, South China. Environ Int 2007; 33:1063-9. [PMID: 17631964 DOI: 10.1016/j.envint.2007.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 05/14/2007] [Accepted: 06/01/2007] [Indexed: 05/16/2023]
Abstract
Air samples of total suspended particles (TSP, particles less than 30-60 microm), and particles with aerodynamic diameter smaller than 2.5 microm (PM(2.5)) were collected simultaneously at Guiyu (an electronic waste recycling site), three urban sites in Hong Kong and two urban sites in Guangzhou, South China from 16 August to 17 September 2004. Twenty-two PBDE congeners (BDE-3, -7, -15, -17, -28, -49, -71, -47, -66, -77, -100, -119, -99, -85, -126, -154, -153, -138, -156, -184, -183, -191) in TSP and PM(2.5) were measured. The results showed that the overall average concentrations of TSP and PM(2.5) collected at Guiyu were 124 and 62.1 microg m(-3), respectively. The monthly concentrations of the sum of 22 BDE congeners contained in TSP and PM(2.5) at Guiyu were 21.5 and 16.6 ng m(-3), with 74.5 and 84.3%, contributed by nine congeners (BDE-28, -47, -66, -100, -99, -154, -153, -183 and -191 respectively). This pattern was similar to Tsuen Wan site of Hong Kong. Two urban sites of Guangzhou had the same congener pattern, but were different from Yuen Long and Hok Tsui sites of Hong Kong. The results also showed that the amount of mono to penta brominated congeners, which are more toxic, accounted for 79.4-95.6% of Sigma(22)PBDEs from all sites. All congeners tested in Guiyu were up to 58-691 times higher than the other urban sites and more than 100 times higher than other studies reported elsewhere. The higher concentration in the air was due to heating or opening burning of electronic waste since PBDEs are formed when plastics containing brominated flame retardants are heated.
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Affiliation(s)
- W J Deng
- Croucher Institute for Environmental Sciences and Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
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15
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Tang XL, Bi XH, Sheng GY, Tan JH, Fu JM. Seasonal variation of the particle size distribution of n-alkanes and polycyclic aromatic hydrocarbons (PAHs) in urban aerosol of Guangzhou, China. Environ Monit Assess 2006; 117:193-213. [PMID: 16917707 DOI: 10.1007/s10661-006-0440-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 06/30/2005] [Indexed: 05/11/2023]
Abstract
Seasonal aerosol samples have been collected by Andersen Hi-Vol pumping system equipped with a five stage cascade impactor and a backup filter (size range: 10-7.2 microm, 7.2-3.0 microm, 3.0-1.5 microm, 1.5-0.95 microm, 0.95-0.49 microm, <or=0.49 microm) in the Liwan district, Guangzhou. n-Alkanes were measured using gas chromatography and PAHs were measured using gas chromatography/mass spectrometry analysis. The bimodal log-normal distributions of n-alkanes and semi-volatile PAHs were found, while for non-volatile PAHs that was unimodal, so much as the mode of semi-volatile PAHs was similar with that of the particles. The n-alkanes and PAHs were preferably associated with fine particles. C (max) (carbon number maximum) (C(22)-C(26)), CPI (carbon preference index) (1.12-1.21), U/R (unresolved to resolved components ratio) (7.42-10.7), wax% (0.9-3.12%) and the diagnostic ratios for PAHs revealed that vehicular emission was the major source of these organic compounds during the study periods, while the contribution of epicuticular waxes emitted by terrestrial plants was minor. CPI(2) (values for petrogenic hydrocarbons), CPI(3) (values for biogenic n-alkanes) and wax% revealed that the natural preferentially accumulated in the larger aerosol while the anthropogenic in the smaller. In addition, the different MMDs (mass median diameters) for n-alkanes and PAHs were observed in different seasons. The MMDs for n-alkanes and PAHs were higher in autumn/winter than those in spring/summer. The seasonal effect was related to the hydrocarbon content in the individual particulate fractions, showing a preferential association of n-alkanes and PAHs with larger particles in the autumn/winter season.
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Affiliation(s)
- X L Tang
- State Key Laboratory of Organic Geochemistry, Guangdong Key Laboratory of Environment and Resources, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, PR China
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16
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Yu YX, Wen S, Feng YL, Bi XH, Wang XM, Peng PA, Sheng GY, Fu JM. Development of a Compound-Specific Carbon Isotope Analysis Method for Atmospheric Formaldehyde via NaHSO3 and Cysteamine Derivatization. Anal Chem 2005; 78:1206-11. [PMID: 16478113 DOI: 10.1021/ac051616f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel method has been developed for the compound-specific carbon isotope analysis of atmospheric formaldehyde using gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). The method allows the determination of the delta13C value for atmospheric formaldehyde at nanogram levels with higher precision and lower detection limit. In the present work, atmospheric formaldehyde was collected using NaHSO3-coated Sep-Pak silica gel cartridges, washed out by water, then derivatized by cysteamine of known delta13C value, and the delta13C value of its derivative (thiazolidine) determined by GC/C/IRMS. Finally, the delta13C value of atmospheric formaldehyde could be calculated by a simple mass balance equation between formaldehyde, cysteamine, and thiazolidine. Using three formaldehydes with different delta13C values, calibration experiments were carried out over large ranges of formaldehyde concentrations. The carbon isotope analysis method achieved excellent reproducibility and high accuracy. There was no carbon isotopic fractionation throughout the derivatization processes. The differences in the carbon isotopic compositions of thiazolidine between the measured and predicted values were always <0.5 per thousand, within the specifications of the GC/C/IRMS system. The present method was also compared with the previous 2,4-dinitrophenylhydrazine derivatization method, and this method could be performed with lower analytical error and detection limit. Using this method, four 6-h ambient atmospheric formaldehyde samples were consecutively collected from 8 to 9 March 2005. The results showed that the delta13C values of atmospheric formaldehyde were different during the daytime and nighttime. This method proved suitable for the routine operation and may provide additional insight on sources and sinks of atmospheric formaldehyde.
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Affiliation(s)
- Y X Yu
- Research Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200072, P. R. China
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17
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Li XD, Mai BX, Zhang G, Sheng GY, Fu JM, Pan SM, Wai OW, Li YS. Distribution of organochlorine pesticides in a sediment profile of the Pearl River estuary. Bull Environ Contam Toxicol 2001; 67:871-880. [PMID: 11692203 DOI: 10.1007/s001280203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2000] [Accepted: 08/07/2001] [Indexed: 05/23/2023]
Affiliation(s)
- X D Li
- Department of Civil and Structural Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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18
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Yu ZQ, Peng PA, Fu JM, Sheng GY. [The determination of porphyrin carbon isotope composition by gas chromatography-isotope ratio monitoring mass spectrometry technique]. Se Pu 2001; 19:97-100. [PMID: 12541647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
The porphyrin carbon isotope composition can be used to explore the precursor of porphyrin, oil-oil and oil-source rock correction and calculation of paleo P CO2. The conventional method is limited because of its time consuming and large sample size (several mg of individual porphyrin) required. Therefore, it hampers the application of porphyrin carbon isotope composition into the chemistry and geoscience. The present paper describes a quantification method to prepare bis-(tert-butyldimethylsiloxy) silicon (IV) [(TBDMSO)2Si(IV)] porphyrin which is sufficiently volatile at 300 degrees C and can be used for GC-IRMS analysis. The analysis of carbon isotope composition of aetio I as the form of free base, nickel, demetalization derivative, silicon(IV) and (TBDMSO)2Si(IV) have shown that aetio I porphyrin has no obvious isotope fractionation in the whole synthesis procedure for (TBDMSO)2Si(IV) porphyrin. The carbon isotope study on the porphyrin mixtures of aetio I and OEP indicates that isotope exchange between porphyrins during the synthesis of (TBDMSO)2Si(IV) porphyrin is absent. The method can be applied to the determination of porphyrin carbon isotope compositions. The advantages of the method are time saving, less sample size and lower standard deviation.
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Affiliation(s)
- Z Q Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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19
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Lao BS, Sheng GY, Fu JM, Wen KW, Zhang G, Min YS. [A study on the contents of fat and fatty acids in five shellfishes]. Se Pu 2001; 19:137-40. [PMID: 12541656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
The contents of fat and fatty acids in Callista erycina (Linnaeus), Paphia (Paratapes) undulata (Born), Meretrix meretrix (Linnaeus), Chlamys farreri (Jones et Preston) and Patinopecten yessoensis (Jay) were studied. Fat was extracted with Bligh & Dyer (B&D) method. The lipid classes were transesterified with potassium hydroxide in methanol. Fatty acid methyl esters (FAMEs) were assayed with GC-MS and polar capillary column (HP-INNOWax 30 m x 0.25 mm i.d. x 0.25 micron). GC injector temperature was 220 degrees C. The column temperature was programmed from 150 degrees C (1 min) to 200 degrees C at 10 degrees C/min and then from 200 degrees C to 250 degrees C at 2 degrees C/min. FAMEs were identified by MS library, and part by their standards. Total identified fatty acids were over 99% for all samples. Fat contents of them were all over 1% by wet samples. And ratios between omega-3PUFA and omega-6PUFA were above 2 by and large. Patinopecten yessoensis (Jay) contains more fat and the valuable fatty acids, EPA and DHA. It is suitable to use it as the source of EPA and DHA.
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Affiliation(s)
- B S Lao
- State Key Laboratory of Organic Geochemistry & Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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Abstract
The association of pollutants (nutrients, heavy metals and organic compounds) with colloidal and suspended particle matter (SPM) plays a dominant role in determining their transport, fate, biogeochemistry, bioavailability and toxicity in natural waters. A scheme for the fractionation and composition of colloidal and SPM from river waters has been tested. All four separation methods, i.e. sieving, continuous flow centrifugation, tangential flow filtration, sedimentation field-flow fractionation, were for the first time used to separate five size particulate fractions from river. Significant (gram) amounts of colloidal material (<1 microm) in three size ranges, nominally 1-0.2, 0.2-0.006 and 0.006-0.003 microm were obtained. The separation scheme was able to process large samples (100 l), within reasonable times (1 day) and the apparatus was portable. The aquatic colloid size was also characterized with high resolution by using sedimentation field-flow fractionation technique. The mass-based particle size distribution for the water sample showed a broad size distribution between 0.05 and 0.4 microm with the maximum around 0.14 microm. There was a systematic increase in the content of organic carbon (estimated by loss on ignition), Mg, Ca, Na, Cu and Zn with decreasing particle size, highlighting the importance of the colloidal (<1 microm) fraction. It was concluded that the colloidal Cu and Zn concentrations in rivers might be much higher than those reported before.
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Affiliation(s)
- Y Ran
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, People's Republic of China
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Lao BS, Sheng GY, Fu JM, Wen KW, Zhang G, Min YS, Li KC. [Stability of fatty acids in stored oyster]. Se Pu 2000; 18:340-2. [PMID: 12541513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
The contents of twenty-three kinds of fatty acids in the lyophilized oyster that stored for 0, 15, 30, 45, 60, 75, 90 days were studied. Oyster fat was extracted from the powder by means of SFE. The extraction was performed for 40 min at a pressure of 37 MPa and a temperature of 50 degrees C with supercritical carbon dioxide containing 8% (V/V) ethanol at a flow-rate of 2 mL/min as liquid carbon dioxide, and the recovery of oyster fat by extraction was over 99%. After being extracted, fat was esterified with potassium hydroxide and methanol. Methyl esters of fatty acid were separated and determined by 30 m x 0.25 mm i.d. x 0.25 micron HP-INNOWax capillary column and MS detector. The injector temperature was 220 degrees C. The column temperature was programmed from 150 degrees C (1 min) to 200 degrees C at 10 degrees C/min and then from 200 degrees C to 250 degrees C at 2 degrees C/min. Twenty-three peaks were identified with gas chromatography/mass spectrometry, and quantified with area normalization method. The variations of contents of them were shown. During storage, the contents of saturated fatty acids and mono-unsaturated fatty acids were getting higher, and those of polyunsaturated fatty acids were getting lower. The decrease of them was gradual, and there was no special period of stability. And the stability of fatty acids in oyster related to the degree of unsaturation of them. The higher the unsaturation the lower the stable it was. After being stored for 90 days, the content of EPA decreased from 16.94% to 5.43% and that of DHA from 9.25% to 2.86%.
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Affiliation(s)
- B S Lao
- Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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22
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Campbell RM, Cartwright C, Chen W, Chen Y, Duzic E, Fu JM, Loveland M, Manning R, McKibben B, Pleiman CM, Silverman L, Trueheart J, Webb DR, Wilkinson V, Witter DJ, Xie X, Castelhano AL. Selective A1-adenosine receptor antagonists identified using yeast Saccharomyces cerevisiae functional assays. Bioorg Med Chem Lett 1999; 9:2413-8. [PMID: 10476879 DOI: 10.1016/s0960-894x(99)00398-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Evaluation of a biased "library" of pyrrolo[2,3-d]pyrimidines using yeast-based functional assays expressing human A1- and A2a-adenosine receptors, led to the A1 selective antagonist 4b. A direct correlation between yeast functional activity and binding data was established. Practical compounds with polar residues at C-4 of the pyrrolopyrimidine system required H-bond donor functionality for high potency.
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Affiliation(s)
- R M Campbell
- Cadus Pharmaceutical Corporation, Tarrytown, NY 10591, USA
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23
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Abstract
A novel pyridone-based tyrosine analog, 6, has been designed to mimic the binding interaction of SH2 domains with phosphotyrosine (pTyr) containing peptides. Synthesis of 6 features a key Pd catalyzed coupling of beta-iodoalanine with phosphonomethyl 4-pyridone triflate.
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Affiliation(s)
- J M Fu
- Cadus Pharmaceutical Corporation, Tarrytown, NY 10591, USA
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24
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Abstract
Clozapine is associated with a high incidence of agranulocytosis. We had previously found that it is oxidized by granulocytes, or simply HOCl, to a reactive metabolite that irreversibly binds to the cells, and we proposed that this reactive metabolite is responsible for clozapine-induced agranulocytosis. The reactive metabolite appeared to be a nitrenium ion formed by chlorination of the nitrogen bridge between the two aromatic rings. If this is correct, analogs that contain this structural feature should also be oxidized to a reactive intermediate while those not possessing this feature would, at least, not form the same type of reactive intermediate and, therefore, may not induce agranulocytosis. We tested the first part of this hypothesis with three clozapine analogs that do contain a nitrogen bridge and three that do not. Consistent with the hypothesis, the three analogs that do contain the nitrogen bridge formed reactive intermediates that could be trapped with glutathione when oxidized by HOCl, myeloperoxidase or activated neutrophils. In contrast, we found no evidence of a reactive intermediate on oxidation of analogs that contained an oxygen or sulfur bridge rather than a nitrogen bridge. If such reactive metabolites are responsible for drug-induced agranulocytosis, it should be possible to use such a simple screening method to test drugs at an early stage in their development for the potential to induce agranulocytosis.
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Affiliation(s)
- J Uetrecht
- Faculty of Pharmacy and Medicine, University of Toronto, Canada.
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25
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Shi JH, Cao JR, Fu JM. [Clinical study on action of artificial respiration produced by pressing in massage under anesthesia for lumbar intervertebral disc prolapse]. Zhongguo Zhong Xi Yi Jie He Za Zhi 1997; 17:79-80. [PMID: 9812661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
OBJECTIVE To observe whether the gas exchange is sufficient for the requirement of body when the patient was prone in position and pressed in the course of massage under intravenous anesthesia with sodium pentothal (SP) for the treatment of lumbar intervertebral disc prolapse. METHODS The oxygen would not be given to the patients whose heart and lung functions were good during the course of anesthesia and massage, respiratory function and blood gas analysis were studied on 20 patients selected randomly. RESULTS Tidal volume was smaller and respiratory rate was faster than normal respiration. Saturation pulse oxygen was still normal in all patients. There were no significant changes in blood gas analysis before spinal injection and after massage (P > 0.05). CONCLUSION The pressing could attain the action of artificial respiration. The respiration pattern was similar to high frequency positive pressure ventilation. The action of vibration and diffusion had normal respiratory effect.
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Affiliation(s)
- J H Shi
- Guanganmen Hospital, China Academy of Traditional Chinese Medicine, Beijing
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26
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Schroeder SA, Roongta V, Fu JM, Jones CR, Gorenstein DG. Sequence-dependent variations in the 31P NMR spectra and backbone torsional angles of wild-type and mutant Lac operator fragments. Biochemistry 1989; 28:8292-303. [PMID: 2605186 DOI: 10.1021/bi00447a006] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assignment of the 31P resonances of a series of six sequenced-related tetradecamer DNA duplexes, d(TGTGAGCGCTCACA)2, d(TATGAGCGCTCATA)2, d(TCTGAGCGCTCAGA)2, d(TGTGTGCGCACACA)2, d(TGTGACGCGTCACA)2 and d(CACAGTATACTGTG)2, related to the lac operator DNA sequence was determined either by site-specific 17O labeling of the phosphoryl groups or by two-dimensional 1H-31P pure absorption phase constant time (PAC) heteronuclear correlation spectroscopy. J(H3'-P) coupling constants for each of the phosphates of the tetradecamers were obtained from 1H-31P J-resolved selective proton flip 2D spectra. By use of a modified Karplus relationship the C4'-C3'-O3'-P torsional angles (epsilon) were obtained. Comparison of the 31P chemical shifts and J(H3'-P) coupling constants of these sequences has allowed greater insight into those various factors responsible for 31P chemical shift variations in oligonucleotides and provided an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These sequence-specific variations in the conformation of the DNA sugar phosphate backbone of various lac operator DNA sequences can possibly explain the sequence-specific recognition of DNA by DNA binding proteins, as mediated through direct contacts between the phosphates and the protein.
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Affiliation(s)
- S A Schroeder
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
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27
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Fu JM. [Effects of platelet activating factor on blood platelets]. Sheng Li Ke Xue Jin Zhan 1989; 20:40-4. [PMID: 2549618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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28
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Gorenstein DG, Schroeder SA, Fu JM, Metz JT, Roongta V, Jones CR. Assignments of 31P NMR resonances in oligodeoxyribonucleotides: origin of sequence-specific variations in the deoxyribose phosphate backbone conformation and the 31P chemical shifts of double-helical nucleic acids. Biochemistry 1988; 27:7223-37. [PMID: 3207672 DOI: 10.1021/bi00419a009] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
It is now possible to unambiguously assign all 31P resonances in the 31P NMR spectra of oligonucleotides by either two-dimensional NMR techniques or site-specific 17O labeling of the phosphoryl groups. Assignment of 31P signals in tetradecamer duplexes, (dTGTGAGCGCTCACA)2, (dTAT-GAGCGCTCATA)2, (dTCTGAGCGCTCAGA)2, and (dTGTGTGCGCACACA)2, and the dodecamer duplex d(CGTGAATTCGCG)2 containing one base-pair mismatch, combined with additional assignments in the literature, has allowed an analysis of the origin of the sequence-specific variation in 31P chemical shifts of DNA. The 31P chemical shifts of duplex B-DNA phosphates correlate reasonably well with some aspects of the Dickerson/Calladine sum function for variation in the helical twist of the oligonucleotides. Correlations between experimentally measured P-O and C-O torsional angles and results from molecular mechanics energy minimization calculations show that these results are consistent with the hypothesis that sequence-specific variations in 31P chemical shifts are attributable to sequence-specific changes in the deoxyribose phosphate backbone. The major structural variation responsible for these 31P shift perturbations appears to be P-O and C-O backbone torsional angles which respond to changes in the local helical structure. Furthermore, 31P chemical shifts and JH3'-P coupling constants both indicate that these backbone torsional angle variations are more permissive at the ends of the double helix than in the middle. Thus 31P NMR spectroscopy and molecular mechanics energy minimization calculations appear to be able to support sequence-specific structural variations along the backbone of the DNA in solution.
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Affiliation(s)
- D G Gorenstein
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
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29
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Schroeder SA, Fu JM, Jones CR, Gorenstein DG. Assignment of phosphorus-31 and nonexchangeable proton resonances in a symmetrical 14 base pair lac pseudooperator DNA fragment. Biochemistry 1987; 26:3812-21. [PMID: 2820476 DOI: 10.1021/bi00387a012] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 31P chemical shifts of all 13 phosphates and the chemical shifts of nearly all of the non-exchangeable protons of a symmetrical 14 base pair lac pseudooperator DNA fragment have been assigned by regiospecific labeling with oxygen-17 and two-dimensional NMR techniques. At 22 degrees C, 8 of the 13 phosphorus resonances can distinctly be resolved while the remaining 5 resonances occur in two separate overlapping regions. The 31P chemical shifts of this particular 14 base pair oligonucleotide do not follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence the more upfield the 31P resonance occurs, as shown from other 31P assignment studies. Failure of this general rule is believed to be a result of helical distortions that occur along the oligonucleotide double helix, on the basis of the analysis of Callidine [Callidine, C.R. (1982) J. Mol. Biol. 161, 343-352]. Notable exceptions to the phosphate position relationship are 5'-Py-Pu-3' dinucleotide sequences, which resonate at a lower field strength than expected in agreement with similar results as reported by Ott and Eckstein [Ott, J., & Eckstein, F. (1985) Biochemistry 24, 253]. A reasonable correlation exists between 31P chemical shifts values of the 14-mer and the helical twist sum function of Calladine. The most unusual 31P resonance occurs most upfield in the 31P spectrum, which has been assigned to the second phosphate position (5'-GpT-3') from the 5' end. This unusual chemical shift may be the result of the predicted large helical twist angle that occurs at this position in the 14-mer sequence. Further, it is believed that the large helical twist represents a unique structural feature responsible for optimum binding contact between lac repressor protein and this 14-mer lac pseudooperator segment. Assignments of proton resonances were made from two-dimensional 1H-1H nuclear Overhauser effect (NOESY) connectivities in a sequential manner applicable to right-handed B-DNA, in conjunction with two-dimensional homonuclear and heteronuclear J-correlated spectroscopies (1H-1H COSY and 31P-1H HETCOR). Most nonexchangeable base proton and deoxyribose proton (except for some unresolved H4', H5', and H5" protons) resonances were assigned.
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Affiliation(s)
- S A Schroeder
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
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