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Pak CM, Gilmore MJ, Bulkley JE, Chakraborty P, Dagan-Rosenfeld O, Foreman AKM, Gollob MH, Jenkins CL, Katz AE, Lee K, Meeks N, O'Daniel JM, Posey JE, Rego SM, Shah N, Steiner RD, Stergachis AB, Subramanian SL, Trotter T, Wallace K, Williams MS, Goddard KAB, Buchanan AH, Manickam K, Powell B, Ezzell Hunter J. Implementing Evidence-Based Assertions of Clinical Actionability in the Context of Secondary Findings: Updates from the ClinGen Actionability Working Group. Genet Med 2024:101164. [PMID: 38757444 DOI: 10.1016/j.gim.2024.101164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
PURPOSE The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions. METHODS Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs. RESULTS The resulting rubric has a four-point scale (limited, moderate, strong, definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, pre-defined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs. CONCLUSION The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.
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Affiliation(s)
- Christine M Pak
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon.
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, and Division of Metabolics University of Ottawa, Ottawa, Ontario
| | - Orit Dagan-Rosenfeld
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | | | - Charisma L Jenkins
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Alexander E Katz
- Division of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kristy Lee
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Naomi Meeks
- Section of Genetics, Department of Pediatrics, University of Colorado, Aurora, Colorado
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Jennifer E Posey
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas
| | - Shannon M Rego
- Institute for Human Genetics, University of California, San Francisco, California
| | - Neethu Shah
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas
| | - Robert D Steiner
- University of Wisconsin and Marshfield Clinic, Marshfield and Madison, Wisconsin
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Sai Lakshmi Subramanian
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, and Roche Diagnostics, Santa Clara, California
| | - Tracy Trotter
- Department of Pediatrics, John Muir Health, Walnut Creek, California
| | - Kathleen Wallace
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Marc S Williams
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Adam H Buchanan
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | - Kandamurugu Manickam
- Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, Ohio
| | - Bradford Powell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Jessica Ezzell Hunter
- Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat Struct Mol Biol 2024; 31:568-577. [PMID: 38347148 DOI: 10.1038/s41594-024-01225-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.
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Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Katja G Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Tullius TW, Isaac RS, Ranchalis J, Dubocanin D, Churchman LS, Stergachis AB. RNA polymerases reshape chromatin and coordinate transcription on individual fibers. bioRxiv 2023:2023.12.22.573133. [PMID: 38187631 PMCID: PMC10769320 DOI: 10.1101/2023.12.22.573133] [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: 01/09/2024]
Abstract
During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address these limitations, we employed long-read chromatin fiber sequencing (Fiber-seq) to visualize RNA polymerases within their native chromatin context at single-molecule and near single-nucleotide resolution along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of single-molecule RNA Polymerase (Pol) II and III transcription associated footprints, which, in aggregate, mirror bulk short-read sequencing-based measurements of transcription. We show that Pol II pausing destabilizes downstream nucleosomes, with frequently paused genes maintaining a short-term memory of these destabilized nucleosomes. Furthermore, we demonstrate pervasive direct coordination and anti-coordination between nearby Pol II genes, Pol III genes, transcribed enhancers, and insulator elements. This coordination is largely limited to spatially organized elements within 5 kb of each other, implicating short-range chromatin environments as a predominant determinant of coordinated polymerase initiation. Overall, transcription initiation reshapes surrounding nucleosome architecture and coordinates nearby transcriptional machinery along individual chromatin fibers.
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Affiliation(s)
- Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jane Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
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Ma JG, O’Neill MJ, Richardson E, Thomson KL, Ingles J, Muhammad A, Solus JF, Davogustto G, Anderson KC, Benjamin Shoemaker M, Stergachis AB, Floyd BJ, Dunn K, Parikh VN, Chubb H, Perrin MJ, Roden DM, Vandenberg JI, Ng CA, Glazer AM. Multi-site validation of a functional assay to adjudicate SCN5A Brugada Syndrome-associated variants. medRxiv 2023:2023.12.19.23299592. [PMID: 38196587 PMCID: PMC10775332 DOI: 10.1101/2023.12.19.23299592] [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: 01/11/2024]
Abstract
Brugada Syndrome (BrS) is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in the cardiac sodium channel gene, SCN5A. Interpreting the pathogenicity of SCN5A missense variants is challenging and ~79% of SCN5A missense variants in ClinVar are currently classified as Variants of Uncertain Significance (VUS). An in vitro SCN5A-BrS automated patch clamp assay was generated for high-throughput functional studies of NaV1.5. The assay was independently studied at two separate research sites - Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute - revealing strong correlations, including peak INa density (R2=0.86). The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. The assay accurately distinguished benign controls (24/25) from pathogenic controls (23/24). Odds of Pathogenicity values derived from the experimental results yielded 0.042 for normal function (BS3 criterion) and 24.0 for abnormal function (PS3 criterion), resulting in up to strong evidence for both ACMG criteria. The calibrated assay was then used to study SCN5A VUS observed in four families with BrS and other arrhythmia phenotypes associated with SCN5A loss-of-function. The assay revealed loss-of-function for three of four variants, enabling reclassification to likely pathogenic. This validated APC assay provides clinical-grade functional evidence for the reclassification of current VUS and will aid future SCN5A-BrS variant classification.
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Affiliation(s)
- Joanne G. Ma
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | | | - Ebony Richardson
- Clinical Genomics Laboratory, Centre for Population Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia and Murdoch Children Research Institute, Melbourne, Australia
| | - Kate L. Thomson
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Jodie Ingles
- Clinical Genomics Laboratory, Centre for Population Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia and Murdoch Children Research Institute, Melbourne, Australia
| | - Ayesha Muhammad
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joseph F. Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Giovanni Davogustto
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Katherine C. Anderson
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Benjamin Shoemaker
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Brendan J. Floyd
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyla Dunn
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Victoria N. Parikh
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Henry Chubb
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark J. Perrin
- Department of Genomic Medicine, Royal Melbourne Hospital, Victoria, Australia
| | - Dan M. Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Andrew M. Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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6
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Jha A, Bohaczuk SC, Mao Y, Ranchalis J, Mallory BJ, Min AT, Hamm MO, Swanson E, Dubocanin D, Finkbeiner C, Li T, Whittington D, Noble WS, Stergachis AB, Vollger MR. DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. bioRxiv 2023:2023.04.20.537673. [PMID: 37131601 PMCID: PMC10153250 DOI: 10.1101/2023.04.20.537673] [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: 05/04/2023]
Abstract
Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as co-processing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools. Here, we introduce fibertools, a state-of-the-art toolkit that features a semi-supervised convolutional neural network for fast and accurate identification of m6A-marked bases using PacBio single-molecule long-read sequencing, as well as the co-processing of long-read genetic and epigenetic data produced using either PacBio or Oxford Nanopore sequencing platforms. We demonstrate accurate DNA-m6A identification (>90% precision and recall) along >20 kilobase long DNA molecules with a ~1,000-fold improvement in speed. In addition, we demonstrate that fibertools can readily integrate genetic and epigenetic data at single-molecule resolution, including the seamless conversion between molecular and reference coordinate systems, allowing for accurate genetic and epigenetic analyses of long-read data within structurally and somatically variable genomic regions.
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Affiliation(s)
- Anupama Jha
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C. Bohaczuk
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Yizi Mao
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Jane Ranchalis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Alan T. Min
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Morgan O. Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Elliott Swanson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Danilo Dubocanin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Connor Finkbeiner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dale Whittington
- Department of Medical Chemistry, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Andrew B. Stergachis
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Mitchell R. Vollger
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
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7
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Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind WH, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener MH, Byers PHH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. Full-length Isoform Sequencing for Resolving the Molecular Basis of Charcot-Marie-Tooth 2A. Neurol Genet 2023; 9:e200090. [PMID: 37560121 PMCID: PMC10409571 DOI: 10.1212/nxg.0000000000200090] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
Objectives Transcript sequencing of patient-derived samples has been shown to improve the diagnostic yield for solving cases of suspected Mendelian conditions, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. Methods We applied short-read and full-length transcript sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. Results We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts the branch point critical for intron 6 splicing. Full-length long-read isoform complementary DNA (cDNA) sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates 5 distinct altered splicing transcripts. All 5 altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). Discussion This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.
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Affiliation(s)
- Andrew B Stergachis
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Elizabeth E Blue
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Madelyn A Gillentine
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Lee-Kai Wang
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Ulrike Schwarze
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Adriana Sedeño Cortés
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Jane Ranchalis
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Aimee Allworth
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Austin E Bland
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Sirisak Chanprasert
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Jingheng Chen
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Daniel Doherty
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Andrew B Folta
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Ian Glass
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Martha Horike-Pyne
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Alden Y Huang
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Alyna T Khan
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Kathleen A Leppig
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Danny E Miller
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Ghayda Mirzaa
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Azma Parhin
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Wendy H Raskind
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Elisabeth A Rosenthal
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Sam Sheppeard
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Samuel Strohbehn
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Virginia P Sybert
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Thao T Tran
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Mark H Wener
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Peter H H Byers
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Stanley F Nelson
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Michael J Bamshad
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Katrina M Dipple
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Gail P Jarvik
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Suzanne Hoppins
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Fuki M Hisama
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
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Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YHH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv 2023:2023.09.26.559521. [PMID: 37808736 PMCID: PMC10557686 DOI: 10.1101/2023.09.26.559521] [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: 10/10/2023]
Abstract
Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.
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Affiliation(s)
- Mitchell R. Vollger
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kiara C. Eldred
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Elliott Swanson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | - Yong-Han H. Cheng
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Yizi Mao
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elizabeth E. Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Katherine M. Munson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | | | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kathleen A. Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | | | | | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Stephanie M. Sherman
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Amy L. Yuen
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | - Thomas A. Reh
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Peter H. Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Fuki M. Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gail P. Jarvik
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Yasemin Sancak
- University of Washington School of Medicine, Department of Pharmacology, Seattle, WA, USA
| | - Katrina M. Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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9
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Pujol‐Giménez J, Mirzaa G, Blue EE, Albano G, Miller DE, Allworth A, Bennett JT, Byers PH, Chanprasert S, Chen J, Doherty D, Folta AB, Gillentine MA, Glass I, Hing A, Horike‐Pyne M, Leppig KA, Parhin A, Ranchalis J, Raskind WH, Rosenthal EA, Schwarze U, Sheppeard S, Strohbehn S, Sybert VP, Timms A, Wener M, Bamshad MJ, Hisama FM, Jarvik GP, Dipple KM, Hediger MA, Stergachis AB. Dominant-negative variant in SLC1A4 causes an autosomal dominant epilepsy syndrome. Ann Clin Transl Neurol 2023; 10:1046-1053. [PMID: 37194416 PMCID: PMC10270265 DOI: 10.1002/acn3.51786] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 04/15/2023] [Indexed: 05/18/2023] Open
Abstract
SLC1A4 is a trimeric neutral amino acid transporter essential for shuttling L-serine from astrocytes into neurons. Individuals with biallelic variants in SLC1A4 are known to have spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM) syndrome, but individuals with heterozygous variants are not thought to have disease. We identify an 8-year-old patient with global developmental delay, spasticity, epilepsy, and microcephaly who has a de novo heterozygous three amino acid duplication in SLC1A4 (L86_M88dup). We demonstrate that L86_M88dup causes a dominant-negative N-glycosylation defect of SLC1A4, which in turn reduces the plasma membrane localization of SLC1A4 and the transport rate of SLC1A4 for L-serine.
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Affiliation(s)
- Jonai Pujol‐Giménez
- Department of Nephrology and HypertensionUniversity Hospital Bern, InselspitalBernSwitzerland
- Department of Biomedical ResearchUniversity of BernBernSwitzerland
| | - Ghayda Mirzaa
- Center for Integrative Brain ResearchSeattle Children's Research InstituteSeattleWashingtonUSA
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Elizabeth E. Blue
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
- Department of Laboratory Medicine and PathologyUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Giuseppe Albano
- Department of Nephrology and HypertensionUniversity Hospital Bern, InselspitalBernSwitzerland
- Department of Biomedical ResearchUniversity of BernBernSwitzerland
| | - Danny E. Miller
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- Department of MedicineUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Aimee Allworth
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - James T. Bennett
- Center for Integrative Brain ResearchSeattle Children's Research InstituteSeattleWashingtonUSA
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- Center for Developmental Biology and Regenerative MedicineSeattle Children's Research InstituteSeattleWashingtonUSA
| | - Peter H. Byers
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
- Department of MedicineUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Sirisak Chanprasert
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Jingheng Chen
- Department of Laboratory Medicine and PathologyUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Daniel Doherty
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Andrew B. Folta
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | | | - Ian Glass
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Anne Hing
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Martha Horike‐Pyne
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Kathleen A. Leppig
- Group Health CooperativeKaiser Permanente WashingtonSeattleWashingtonUSA
| | - Azma Parhin
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Jane Ranchalis
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Wendy H. Raskind
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | | | - Ulrike Schwarze
- Department of MedicineUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Sam Sheppeard
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Samuel Strohbehn
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Virginia P. Sybert
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Andrew Timms
- Center for Developmental Biology and Regenerative MedicineSeattle Children's Research InstituteSeattleWashingtonUSA
| | - Mark Wener
- Department of MedicineUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Michael J. Bamshad
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Fuki M. Hisama
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
| | - Gail P. Jarvik
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
- Genome SciencesUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Katrina M. Dipple
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Matthias A. Hediger
- Department of Nephrology and HypertensionUniversity Hospital Bern, InselspitalBernSwitzerland
- Department of Biomedical ResearchUniversity of BernBernSwitzerland
| | - Andrew B. Stergachis
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- University of Washington, Institute of Public Health GeneticsSeattleWashingtonUSA
- Genome SciencesUniversity of Washington School of MedicineSeattleWashingtonUSA
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10
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Debo BM, Mallory BJ, Stergachis AB. Evaluation of N 6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes. Genome Res 2023; 33:427-434. [PMID: 36788024 PMCID: PMC10078290 DOI: 10.1101/gr.276696.122] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Abstract
Low-level DNA N 6-methyldeoxyadenosine (DNA-m6A) has recently been reported across various eukaryotes. Although anti-m6A antibody-based approaches are commonly used to measure DNA-m6A levels, this approach is known to be confounded by DNA secondary structures, RNA contamination, and bacterial contamination. To evaluate for these confounding features, we introduce an approach for systematically validating the selectivity of antibody-based DNA-m6A methods and use a highly selective anti-DNA-m6A antibody to reexamine patterns of DNA-m6A in C. reinhardtii, A. thaliana, and D. melanogaster Our findings raise caution about the use of antibody-based methods for endogenous m6A quantification and mapping in eukaryotes.
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Affiliation(s)
- Brian M Debo
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin J Mallory
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195-7720, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington 98195, USA
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11
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Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind W, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener M, Byers PH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A. bioRxiv 2023:2023.02.07.526487. [PMID: 36798371 PMCID: PMC9934537 DOI: 10.1101/2023.02.07.526487] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Objectives Transcript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. Methods We applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. Results We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). Discussion This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.
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Affiliation(s)
- Andrew B Stergachis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Elizabeth E Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Institute of Public Health Genetics, Seattle, WA, USA
| | | | - Lee-Kai Wang
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Adriana Sedeño Cortés
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Austin E Bland
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Jingheng Chen
- University of Washington, Institute of Public Health Genetics, Seattle, WA, USA
| | - Daniel Doherty
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B Folta
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Alyna T Khan
- University of Washington, Institute of Public Health Genetics, Seattle, WA, USA
- University of Washington, Department of Biostatistics, Seattle, WA, USA
| | - Kathleen A Leppig
- Group Health Cooperative, Kaiser Permanente Washington, Seattle, WA, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Ghayda Mirzaa
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
| | - Azma Parhin
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Wendy Raskind
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elisabeth A Rosenthal
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Virginia P Sybert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Thao T Tran
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Mark Wener
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Peter H Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Stanley F Nelson
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Katrina M Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Gail P Jarvik
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Suzanne Hoppins
- University of Washington School of Medicine, Department of Biochemistry, Seattle, WA, USA
| | - Fuki M Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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12
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Girskis KM, Stergachis AB, DeGennaro EM, Doan RN, Qian X, Johnson MB, Wang PP, Sejourne GM, Nagy MA, Pollina EA, Sousa AMM, Shin T, Kenny CJ, Scotellaro JL, Debo BM, Gonzalez DM, Rento LM, Yeh RC, Song JHT, Beaudin M, Fan J, Kharchenko PV, Sestan N, Greenberg ME, Walsh CA. Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions. Neuron 2021; 109:3239-3251.e7. [PMID: 34478631 DOI: 10.1016/j.neuron.2021.08.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/02/2021] [Accepted: 08/06/2021] [Indexed: 01/21/2023]
Abstract
Human accelerated regions (HARs) are the fastest-evolving regions of the human genome, and many are hypothesized to function as regulatory elements that drive human-specific gene regulatory programs. We interrogate the in vitro enhancer activity and in vivo epigenetic landscape of more than 3,100 HARs during human neurodevelopment, demonstrating that many HARs appear to act as neurodevelopmental enhancers and that sequence divergence at HARs has largely augmented their neuronal enhancer activity. Furthermore, we demonstrate PPP1R17 to be a putative HAR-regulated gene that has undergone remarkable rewiring of its cell type and developmental expression patterns between non-primates and primates and between non-human primates and humans. Finally, we show that PPP1R17 slows neural progenitor cell cycle progression, paralleling the cell cycle length increase seen predominantly in primate and especially human neurodevelopment. Our findings establish HARs as key components in rewiring human-specific neurodevelopmental gene regulatory programs and provide an integrated resource to study enhancer activity of specific HARs.
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Affiliation(s)
- Kelly M Girskis
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ellen M DeGennaro
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew B Johnson
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Peter P Wang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabrielle M Sejourne
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Aurel Nagy
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Pollina
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston MA, USA
| | - Connor J Kenny
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia L Scotellaro
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian M Debo
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lariza M Rento
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca C Yeh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Janet H T Song
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Nenad Sestan
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Michael E Greenberg
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
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13
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Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M. Single cell biology-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:74-97. [PMID: 34605044 DOI: 10.1111/nyas.14692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
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Affiliation(s)
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California
| | - Ana I Domingos
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, United Kingdom.,The Howard Hughes Medical Institute, New York, New York
| | - Naomi Habib
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts.,Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Homaira Hamidzada
- Toronto General Hospital Research Institute, University Health Network; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, New York
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Jessica Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron Streets
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, Berkeley, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington; and Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, and Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Uri Alon
- Faculty of Sciences, Department of Human Biology, University of Haifa, Haifa, Israel
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Pfau
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts
| | - Arjun Raj
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, California.,Department of Bioengineering, Stanford University, Stanford, California.,Department of Applied Physics, Stanford University, Stanford, California
| | - Nancy R Zhang
- Graduate Group in Genomics and Computational Biology and Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine; and Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | | | | | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hernan G Garcia
- Department of Physics; Biophysics Graduate Group; Department of Molecular and Cell Biology; and Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California
| | | | - Federico Gaiti
- New York Genome Center and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, and Center for Systems Biology Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Allon M Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Samantha A Morris
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri.,Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Merrit Romeike
- Max Perutz Laboratories Vienna, University of Vienna, Vienna, Austria
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14
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Stergachis AB, Krier JB, Merugumala SK, Berry GT, Lin AP. Clinical utility of brain MRS imaging of patients with adult-onset non-cirrhotic hyperammonemia. Mol Genet Metab Rep 2021; 27:100742. [PMID: 33763331 PMCID: PMC7973242 DOI: 10.1016/j.ymgmr.2021.100742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 11/15/2022] Open
Abstract
Adult-onset non-cirrhotic hyperammonemia (NCH) is a rare, but often fatal condition that can result in both reversible and irreversible neurological defects. Here we present five cases of adult-onset non-cirrhotic hyperammonemia wherein brain magnetic resonance spectroscopy (MRS) scans for cerebral glutamine (Gln) and myo-inositol (mI) levels helped guide clinical management. Specifically, we demonstrate that when combined with traditional brain magnetic resonance imaging (MRI) scans, cerebral Gln and mI MRS can help disentangle the reversible from irreversible neurological defects associated with hyperammonemic crisis. Specifically, we demonstrate that whereas an elevated brain MRS Gln level is associated with reversible neurological defects, markedly low mI levels are associated with a risk for irreversible neurological defects such as central pontine myelinolysis. Overall, our findings indicate the utility of brain MRS in guiding clinical care and prognosis in patients with adult-onset non-cirrhotic hyperammonemia.
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Affiliation(s)
- Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Joel B Krier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sai K Merugumala
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander P Lin
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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15
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Stergachis AB, Mogensen KM, Khoury CC, Lin AP, Peake RW, Baker JJ, Barkoudah E, Sahai I, Sweetser DA, Berry GT, Krier JB. A retrospective study of adult patients with noncirrhotic hyperammonemia. J Inherit Metab Dis 2020; 43:1165-1172. [PMID: 32713002 DOI: 10.1002/jimd.12292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/03/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Adult-onset noncirrhotic hyperammonemia (NCH) is poorly understood and has a high morbidity and mortality. To elucidate the etiology and management of NCH, we performed a retrospective analysis of 23 adults (median age 51) with NCH treated between 2014 and 2020 at two academic medical centers. Hyperammonemia was diagnosed in all cases during the evaluation of altered mental status, with 22% presenting with seizures. Peak ammonia levels were >200 μmol/L in 70% of cases. Defects in ammonia metabolism were assessed using urea cycle biochemical testing, germline genetic testing, and testing for urease-producing infectious agents. Ammonia metabolism defects in these cases appear attributable to four major sources: (a) infection with urease-producing organism (n = 5); (b) previously undiagnosed inborn errors of metabolism (IEMs) (n = 4); (c) clinical exposures causing acquired urea cycle dysfunction (n = 6); and (d) unexplained acquired urea cycle dysfunction (uaUCD) (n = 8), as evidenced by biochemical signatures of urea cycle dysfunction without a genetic or clinical exposure. Severe protein malnutrition appeared to be a reversible risk factor for uaUCD. Overall, 13% of our cohort died prior to resolution of hyperammonemia, 26% died after hyperammonemia resolution, 57% survived after having reversible neurological changes, and 4% survived with irreversible neurological changes. Renal replacement therapy for ammonia clearance was often utilized for patients with an ammonia level above 250 μmol/L and patients were frequently empirically treated with antibiotics targeting urea-splitting organisms. Our study demonstrates that acquired urea cycle dysfunction, IEMs and urease-producing infections are major sources of adult-onset NCH and highlights successful management strategies for adult-onset NCH.
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Affiliation(s)
- Andrew B Stergachis
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kris M Mogensen
- Department of Nutrition, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Charbel C Khoury
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander P Lin
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Roy Wa Peake
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua J Baker
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ebrahim Barkoudah
- Hospital Medicine Unit, Division of General Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Inderneel Sahai
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David A Sweetser
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joel B Krier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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16
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Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 2020; 368:1449-1454. [PMID: 32587015 DOI: 10.1126/science.aaz1646] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 01/12/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing of chromatin stencils enabled nucleotide-resolution readout of the primary architecture of multikilobase chromatin fibers (Fiber-seq). Fiber-seq exposed widespread plasticity in the linear organization of individual chromatin fibers and illuminated principles guiding regulatory DNA actuation, the coordinated actuation of neighboring regulatory elements, single-molecule nucleosome positioning, and single-molecule transcription factor occupancy. Our approach and results open new vistas on the primary architecture of gene regulation.
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Affiliation(s)
- Andrew B Stergachis
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Brian M Debo
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA. .,Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
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17
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Boueiz A, Pham B, Chase R, Lamb A, Lee S, Naing ZZC, Cho MH, Parker MM, Sakornsakolpat P, Hersh CP, Crapo JD, Stergachis AB, Tal-Singer R, DeMeo DL, Silverman EK, Zhou X, Castaldi PJ. Integrative Genomics Analysis Identifies ACVR1B as a Candidate Causal Gene of Emphysema Distribution. Am J Respir Cell Mol Biol 2019; 60:388-398. [PMID: 30335480 DOI: 10.1165/rcmb.2018-0110oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple associations with emphysema apicobasal distribution (EABD), but the biological functions of these variants are unknown. To characterize the functions of EABD-associated variants, we integrated GWAS results with 1) expression quantitative trait loci (eQTL) from the Genotype Tissue Expression (GTEx) project and subjects in the COPDGene (Genetic Epidemiology of COPD) study and 2) cell type epigenomic marks from the Roadmap Epigenomics project. On the basis of these analyses, we selected a variant near ACVR1B (activin A receptor type 1B) for functional validation. SNPs from 168 loci with P values less than 5 × 10-5 in the largest GWAS meta-analysis of EABD were analyzed. Eighty-four loci overlapped eQTL, with 12 of these loci showing greater than 80% likelihood of harboring a single, shared GWAS and eQTL causal variant. Seventeen cell types were enriched for overlap between EABD loci and Roadmap Epigenomics marks (permutation P < 0.05), with the strongest enrichment observed in CD4+, CD8+, and regulatory T cells. We selected a putative causal variant, rs7962469, associated with ACVR1B expression in lung tissue for additional functional investigation, and reporter assays confirmed allele-specific regulatory activity for this variant in human bronchial epithelial and Jurkat immune cell lines. ACVR1B expression levels exhibit a nominally significant association with emphysema distribution. EABD-associated loci are preferentially enriched in regulatory elements of multiple cell types, most notably T-cell subsets. Multiple EABD loci colocalize to regulatory elements that are active across multiple tissues and cell types, and functional analyses confirm the presence of an EABD-associated functional variant that regulates ACVR1B expression, indicating that transforming growth factor-β signaling plays a role in the EABD phenotype. Clinical trial registered with www.clinicaltrials.gov (NCT00608764).
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Affiliation(s)
- Adel Boueiz
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine
| | | | | | | | - Sool Lee
- 1 Channing Division of Network Medicine
| | | | - Michael H Cho
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine
| | | | | | - Craig P Hersh
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine
| | - James D Crapo
- 3 Pulmonary Medicine, National Jewish Health, Denver, Colorado; and
| | | | | | - Dawn L DeMeo
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine
| | - Edwin K Silverman
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine
| | - Xiaobo Zhou
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine
| | - Peter J Castaldi
- 1 Channing Division of Network Medicine.,6 Division of General Medicine and Primary Care, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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18
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Li GZ, Tio MC, Pak LM, Krier J, Tullius SG, Riella LV, Malek SK, Stergachis AB, Stergachis AB. Noncirrhotic hyperammonemia after deceased donor kidney transplantation: A case report. Am J Transplant 2019; 19:3197-3201. [PMID: 31347272 PMCID: PMC6864227 DOI: 10.1111/ajt.15545] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/27/2019] [Accepted: 07/20/2019] [Indexed: 01/25/2023]
Abstract
A 72-year-old woman with end-stage kidney disease due to recurrent urinary tract infections and obstructive uropathy of a solitary kidney presented to our hospital for renal transplantation. She underwent successful transplantation of a deceased donor allograft, but developed acute mental status deterioration on the fifth postoperative day. Her serum ammonia was found to be markedly elevated to 447 μmol/L in the setting of normal hepatic function. She was treated with emergent dialysis and empiric antibiotics targeting urea-splitting organisms, and ultimately made a full neurologic recovery with stable renal allograft function. Noncirrhotic hyperammonemia (NCH) is an exceedingly rare clinical entity but seems to have a predilection for patients who have undergone solid organ transplantation. This report emphasizes the importance of rapid diagnosis and initiation of treatment for NCH, which is associated with a high rate of mortality and irreversible neurological morbidity. We outline the successful workup and management approach for this patient.
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Affiliation(s)
- George Z. Li
- Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Maria C. Tio
- Department of Medicine, Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Linda M. Pak
- Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Joel Krier
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Stefan G. Tullius
- Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Leonardo V. Riella
- Department of Medicine, Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Sayeed K. Malek
- Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Andrew B. Stergachis
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Andrew B Stergachis
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
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19
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Stergachis AB, Pujol-Giménez J, Gyimesi G, Fuster D, Albano G, Troxler M, Picker J, Rosenberg PA, Bergin A, Peters J, El Achkar CM, Harini C, Manzi S, Rotenberg A, Hediger MA, Rodan LH. Recurrent SLC1A2 variants cause epilepsy via a dominant negative mechanism. Ann Neurol 2019; 85:921-926. [PMID: 30937933 DOI: 10.1002/ana.25477] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 03/31/2019] [Indexed: 12/20/2022]
Abstract
SLC1A2 is a trimeric transporter essential for clearing glutamate from neuronal synapses. Recurrent de novo SLC1A2 missense variants cause a severe, early onset developmental and epileptic encephalopathy via an unclear mechanism. We demonstrate that all 3 variants implicated in this condition localize to the trimerization domain of SLC1A2, and that the Leu85Pro variant acts via a dominant negative mechanism to reduce, but not eliminate, wild-type SLC1A2 protein localization and function. Finally, we demonstrate that treatment of a 20-month-old SLC1A2-related epilepsy patient with the SLC1A2-modulating agent ceftriaxone did not result in a significant change in daily spasm count. ANN NEUROL 2019;85:921-926.
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Affiliation(s)
- Andrew B Stergachis
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jonai Pujol-Giménez
- Department of Nephrology and Hypertension, University Hospital Bern, Inselspital, Bern, Switzerland.,Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Gergely Gyimesi
- Department of Nephrology and Hypertension, University Hospital Bern, Inselspital, Bern, Switzerland.,Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Daniel Fuster
- Department of Nephrology and Hypertension, University Hospital Bern, Inselspital, Bern, Switzerland.,Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Giusppe Albano
- Department of Nephrology and Hypertension, University Hospital Bern, Inselspital, Bern, Switzerland.,Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Marina Troxler
- Department of Nephrology and Hypertension, University Hospital Bern, Inselspital, Bern, Switzerland.,Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Jonathan Picker
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Paul A Rosenberg
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ann Bergin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Jurriaan Peters
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | | | - Chellamani Harini
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Shannon Manzi
- Department of Pharmacy, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Alexander Rotenberg
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Matthias A Hediger
- Department of Nephrology and Hypertension, University Hospital Bern, Inselspital, Bern, Switzerland.,Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
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20
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Stouffs K, Stergachis AB, Vanderhasselt T, Dica A, Janssens S, Vandervore L, Gheldof A, Bodamer O, Keymolen K, Seneca S, Liebaers I, Jayaraman D, Hill HE, Partlow JN, Walsh CA, Jansen AC. Expanding the clinical spectrum of biallelic ZNF335 variants. Clin Genet 2018; 94:246-251. [PMID: 29652087 DOI: 10.1111/cge.13260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/25/2018] [Accepted: 03/28/2018] [Indexed: 11/28/2022]
Abstract
ZNF335 plays an essential role in neurogenesis and biallelic variants in ZNF335 have been identified as the cause of severe primary autosomal recessive microcephaly in 2 unrelated families. We describe, herein, 2 additional affected individuals with biallelic ZNF335 variants, 1 individual with a homozygous c.1399 T > C, p.(Cys467Arg) variant, and a second individual with compound heterozygous c.2171_2173delTCT, p.(Phe724del) and c.3998A > G, p.(Glu1333Gly) variants with the latter variant predicted to affect splicing. Whereas the first case presented with early death and a severe phenotype characterized by anterior agyria with prominent extra-axial spaces, absent basal ganglia, and hypoplasia of the brainstem and cerebellum, the second case had a milder clinical presentation with hypomyelination and otherwise preserved brain structures on MRI. Our findings expand the clinical spectrum of ZNF335-associated microcephaly.
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Affiliation(s)
- K Stouffs
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium.,Neurogenetics Research Unit, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - A B Stergachis
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - A Dica
- Pediatric Neurology Clinic, Alexandru Obregia Hospital, Bucharest, Romania
| | - S Janssens
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - L Vandervore
- Neurogenetics Research Unit, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - A Gheldof
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium.,Neurogenetics Research Unit, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - O Bodamer
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - K Keymolen
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium.,Neurogenetics Research Unit, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - S Seneca
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium.,Neurogenetics Research Unit, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - I Liebaers
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - D Jayaraman
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - H E Hill
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - J N Partlow
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts
| | - C A Walsh
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts
| | - A C Jansen
- Neurogenetics Research Unit, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium.,Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
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21
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Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ. Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards. Methods Mol Biol 2016; 1410:207-21. [PMID: 26867746 DOI: 10.1007/978-1-4939-3524-6_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In targeted proteomics, the development of robust methodologies is dependent upon the selection of a set of optimal peptides for each protein-of-interest. Unfortunately, predicting which peptides and respective product ion transitions provide the greatest signal-to-noise ratio in a particular assay matrix is complicated. Using in vitro synthesized proteins as analytical standards, we report here an empirically driven method for the selection of said peptides in a human plasma assay matrix.
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Affiliation(s)
- James G Bollinger
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Foege Building S-113B, 3720 15th Avenue, NE, 355065, Seattle, WA, 98195-5065, USA.
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22
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Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ. Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Mol Cell Proteomics 2015; 14:2331-40. [PMID: 26100116 DOI: 10.1074/mcp.m115.051300] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 11/06/2022] Open
Abstract
Targeted mass spectrometry is an essential tool for detecting quantitative changes in low abundant proteins throughout the proteome. Although selected reaction monitoring (SRM) is the preferred method for quantifying peptides in complex samples, the process of designing SRM assays is laborious. Peptides have widely varying signal responses dictated by sequence-specific physiochemical properties; one major challenge is in selecting representative peptides to target as a proxy for protein abundance. Here we present PREGO, a software tool that predicts high-responding peptides for SRM experiments. PREGO predicts peptide responses with an artificial neural network trained using 11 minimally redundant, maximally relevant properties. Crucial to its success, PREGO is trained using fragment ion intensities of equimolar synthetic peptides extracted from data independent acquisition experiments. Because of similarities in instrumentation and the nature of data collection, relative peptide responses from data independent acquisition experiments are a suitable substitute for SRM experiments because they both make quantitative measurements from integrated fragment ion chromatograms. Using an SRM experiment containing 12,973 peptides from 724 synthetic proteins, PREGO exhibits a 40-85% improvement over previously published approaches at selecting high-responding peptides. These results also represent a dramatic improvement over the rules-based peptide selection approaches commonly used in the literature.
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Affiliation(s)
- Brian C Searle
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington 98195; §Proteome Software Inc., Portland, OR 97219
| | - Jarrett D Egertson
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - James G Bollinger
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Andrew B Stergachis
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Michael J MacCoss
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington 98195;
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23
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Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA. Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature 2015; 515:365-70. [PMID: 25409825 PMCID: PMC4405208 DOI: 10.1038/nature13972] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 10/15/2014] [Indexed: 12/27/2022]
Abstract
The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here we show that mouse TF footprints conjointly encode a regulatory lexicon that is ∼95% similar with that derived from human TF footprints. However, only ∼20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Furthermore, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results indicate that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry, enabling and potentiating cis-regulatory plasticity. Mouse genomic footprinting reveals conservation of transcription factor (TF) recognition repertoires and trans-regulatory circuitry despite massive turnover of DNA elements that contact TFs in vivo. Having generated genomic DNase I footprinting data of the mouse genome across 25 cell and tissue types, these authors use these data to quantify cis-versus-trans regulatory contributions to mammalian regulatory evolution. They describe more than 600 motifs that collectively are over 95% similar to that recognized in vivo by human transcription factors (TFs). Despite substantial turnover of the cis-regulatory landscape around each TF gene, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Conservation between mouse and human TF regulatory networks is particularly similar at the highest organization level. The work was performed as part of the mouse ENCODE project.
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Affiliation(s)
- Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alex P Reynolds
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Miaohua Zhang
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Rachel Byron
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Sandra Stelhing-Sun
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R Scott Hansen
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Audra K Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Piper M Treuting
- Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Rajinder Kaul
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Mark Groudine
- 1] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA [2] Division of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA
| | - M A Bender
- 1] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA [2] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Elhanan Borenstein
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98102, USA [3] Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - John A Stamatoyannopoulos
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Medicine, University of Washington, Seattle, Washington 98195, USA
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24
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Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep 2014; 8:2015-2030. [PMID: 25220462 DOI: 10.1016/j.celrep.2014.08.019] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 05/20/2014] [Accepted: 08/07/2014] [Indexed: 01/23/2023] Open
Abstract
Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. We mapped DNase I hypersensitive sites (DHSs) in A. thaliana seedlings and used genomic footprinting to delineate ∼ 700,000 sites of in vivo transcription factor (TF) occupancy at nucleotide resolution. We show that variation associated with 72 diverse quantitative phenotypes localizes within DHSs. TF footprints encode an extensive cis-regulatory lexicon subject to recent evolutionary pressures, and widespread TF binding within exons may have shaped codon usage patterns. The architecture of A. thaliana TF regulatory networks is strikingly similar to that of animals in spite of diverged regulatory repertoires. We analyzed regulatory landscape dynamics during heat shock and photomorphogenesis, disclosing thousands of environmentally sensitive elements and enabling mapping of key TF regulatory circuits underlying these fundamental responses. Our results provide an extensive resource for the study of A. thaliana gene regulation and functional biology.
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Affiliation(s)
| | - Andrej A Arsovski
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Janne Lempe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex P Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Audra K Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Shawn T Sullivan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Agnieszka Thompson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Fidencio V Neri
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sanie Mnaimneh
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Ally Yang
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Timothy R Hughes
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada; Canadian Institute for Advanced Research (CIFAR) Program in Genetic Networks, Toronto ON M5G 1Z8, Canada
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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25
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Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B. Panorama: a targeted proteomics knowledge base. J Proteome Res 2014; 13:4205-10. [PMID: 25102069 PMCID: PMC4156235 DOI: 10.1021/pr5006636] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Panorama
is a web application for storing, sharing, analyzing,
and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software
tool for targeted proteomics experiments. Panorama allows laboratories
to store and organize curated results contained in Skyline documents
with fine-grained permissions, which facilitates distributed collaboration
and secure sharing of published and unpublished data via a web-browser
interface. It is fully integrated with the Skyline workflow and supports
publishing a document directly to a Panorama server from the Skyline
user interface. Panorama captures the complete Skyline document information
content in a relational database schema. Curated results published
to Panorama can be aggregated and exported as chromatogram libraries.
These libraries can be used in Skyline to pick optimal targets in
new experiments and to validate peak identification of target peptides.
Panorama is open-source and freely available. It is distributed as
part of LabKey Server,2 an open source
biomedical research data management system. Laboratories and organizations
can set up Panorama locally by downloading and installing the software
on their own servers. They can also request freely hosted projects
on https://panoramaweb.org, a Panorama server maintained
by the Department of Genome Sciences at the University of Washington.
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Affiliation(s)
- Vagisha Sharma
- University of Washington , Seattle, Washington 98195, United States
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26
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Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA. Exonic transcription factor binding directs codon choice and affects protein evolution. Science 2013; 342:1367-72. [PMID: 24337295 DOI: 10.1126/science.1243490] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.
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Affiliation(s)
- Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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27
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Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 2013; 154:888-903. [PMID: 23953118 DOI: 10.1016/j.cell.2013.07.020] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/16/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Cellular-state information between generations of developing cells may be propagated via regulatory regions. We report consistent patterns of gain and loss of DNase I-hypersensitive sites (DHSs) as cells progress from embryonic stem cells (ESCs) to terminal fates. DHS patterns alone convey rich information about cell fate and lineage relationships distinct from information conveyed by gene expression. Developing cells share a proportion of their DHS landscapes with ESCs; that proportion decreases continuously in each cell type as differentiation progresses, providing a quantitative benchmark of developmental maturity. Developmentally stable DHSs densely encode binding sites for transcription factors involved in autoregulatory feedback circuits. In contrast to normal cells, cancer cells extensively reactivate silenced ESC DHSs and those from developmental programs external to the cell lineage from which the malignancy derives. Our results point to changes in regulatory DNA landscapes as quantitative indicators of cell-fate transitions, lineage relationships, and dysfunction.
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Affiliation(s)
- Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Alex Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Brady Miller
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.,Department of Medicine, Division of Hematology University of Washington, Seattle, WA 98195, USA
| | - Sharon L Paige
- Department of Pathology, University of Washington, Seattle, WA 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, CA 94143, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Shelly Heimfeld
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Charles E Murry
- Department of Pathology, University of Washington, Seattle, WA 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.,Department of Bioengineering, University of Washington, Seattle, WA 98109, USA.,Department of Medicine, Division of Cardiology University of Washington, Seattle, WA 98195, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.,Department of Medicine, Division of Oncology University of Washington, Seattle, WA 98195, USA
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28
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Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM. Personal and population genomics of human regulatory variation. Genome Res 2013; 22:1689-97. [PMID: 22955981 PMCID: PMC3431486 DOI: 10.1101/gr.134890.111] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The characteristics and evolutionary forces acting on regulatory variation in humans remains elusive because of the difficulty in defining functionally important noncoding DNA. Here, we combine genome-scale maps of regulatory DNA marked by DNase I hypersensitive sites (DHSs) from 138 cell and tissue types with whole-genome sequences of 53 geographically diverse individuals in order to better delimit the patterns of regulatory variation in humans. We estimate that individuals likely harbor many more functionally important variants in regulatory DNA compared with protein-coding regions, although they are likely to have, on average, smaller effect sizes. Moreover, we demonstrate that there is significant heterogeneity in the level of functional constraint in regulatory DNA among different cell types. We also find marked variability in functional constraint among transcription factor motifs in regulatory DNA, with sequence motifs for major developmental regulators, such as HOX proteins, exhibiting levels of constraint comparable to protein-coding regions. Finally, we perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipocytokine signaling. These data and results provide new insights into patterns of regulatory variation in individuals and populations and demonstrate that a large proportion of functionally important variation lies beyond the exome.
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Affiliation(s)
- Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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29
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Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, Sandstrom R, Bates D, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Harding L, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature 2012; 489:75-82. [PMID: 22955617 PMCID: PMC3721348 DOI: 10.1038/nature11232] [Citation(s) in RCA: 1898] [Impact Index Per Article: 158.2] [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: 12/15/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.
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Affiliation(s)
- Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | | | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Kavita Garg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Abigail K. Ebersol
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tristan Frum
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Lisa Harding
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ericka M. Johnson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Bryan Lajoie
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Bum-Kyu Lee
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Darin London
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Dimitra Lotakis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric D. Nguyen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexias Safi
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Minerva E. Sanchez
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Amartya Sanyal
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Anthony Shafer
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeremy M. Simon
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Lingyun Song
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Zhancheng Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Zhuzhu Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Boris Lenhard
- Bergen Center for Computational Science, University of Bergen, Bergen, Norway
| | - Muneesh Tewari
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael O. Dorschner
- Dept. of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - R. Scott Hansen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Patrick A. Navas
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | | | - Vishwanath R. Iyer
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Jason D. Lieb
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Shamil R. Sunyaev
- Dept. of Medicine, Division of Genetics, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Peter J. Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Rajinder Kaul
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Terrence S. Furey
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Job Dekker
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | | | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA
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30
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Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender M, Groudine M, Kaul R, Stamatoyannopoulos JA. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012; 489:83-90. [PMID: 22955618 PMCID: PMC3736582 DOI: 10.1038/nature11212] [Citation(s) in RCA: 566] [Impact Index Per Article: 47.2] [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] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 05/10/2012] [Indexed: 01/04/2023]
Abstract
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.
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Affiliation(s)
- Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Matthew T. Maurano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jun Neri
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Anthony Schafer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - R. Scott Hansen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Peter Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Miaohua Zhang
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | | | - Rachel Byron
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Michael Bender
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Mark Groudine
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195
| | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Oncology, Deparment of Medicine, University of Washington, Seattle, WA 98195
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31
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Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. Circuitry and dynamics of human transcription factor regulatory networks. Cell 2012; 150:1274-86. [PMID: 22959076 DOI: 10.1016/j.cell.2012.04.040] [Citation(s) in RCA: 373] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/19/2012] [Accepted: 04/23/2012] [Indexed: 12/20/2022]
Abstract
The combinatorial cross-regulation of hundreds of sequence-specific transcription factors (TFs) defines a regulatory network that underlies cellular identity and function. Here we use genome-wide maps of in vivo DNaseI footprints to assemble an extensive core human regulatory network comprising connections among 475 sequence-specific TFs and to analyze the dynamics of these connections across 41 diverse cell and tissue types. We find that human TF networks are highly cell selective and are driven by cohorts of factors that include regulators with previously unrecognized roles in control of cellular identity. Moreover, we identify many widely expressed factors that impact transcriptional regulatory networks in a cell-selective manner. Strikingly, in spite of their inherent diversity, all cell-type regulatory networks independently converge on a common architecture that closely resembles the topology of living neuronal networks. Together, our results provide an extensive description of the circuitry, dynamics, and organizing principles of the human TF regulatory network.
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Affiliation(s)
- Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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32
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Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ. Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods 2011; 8:1041-3. [PMID: 22056677 PMCID: PMC3227787 DOI: 10.1038/nmeth.1770] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/11/2011] [Indexed: 11/16/2022]
Abstract
We report a method for high-throughput, cost-efficient empirical discovery of optimal proteotypic peptides and fragment ions for targeted proteomics applications using in vitro-synthesized proteins. We demonstrate the approach using human transcription factors – which are typically difficult, low-abundance – targets with an overall success rate of 98%. We show further that targeted proteomic assays developed using our approach facilitate robust in vivo quantification of human transcription factors.
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Affiliation(s)
- Andrew B Stergachis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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