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Yin JZ, Keszei AFA, Houliston S, Filandr F, Beenstock J, Daou S, Kitaygorodsky J, Schriemer DC, Mazhab-Jafari MT, Gingras AC, Sicheri F. The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA. Structure 2024:S0969-2126(24)00081-9. [PMID: 38531363 DOI: 10.1016/j.str.2024.02.021] [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: 06/22/2023] [Revised: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.
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Affiliation(s)
- Jay Z Yin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jonah Beenstock
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Salima Daou
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Julia Kitaygorodsky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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2
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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3
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Mishra V, Sharma K, Bose A, Maisonneuve P, Visweswariah SS. The evolutionary divergence of receptor guanylyl cyclase C has implications for preclinical models for receptor-directed therapeutics. J Biol Chem 2024; 300:105505. [PMID: 38029963 PMCID: PMC7615481 DOI: 10.1016/j.jbc.2023.105505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Mutations in receptor guanylyl cyclase C (GC-C) cause severe gastrointestinal disease, including meconium ileus, early onset acute diarrhea, and pediatric inflammatory bowel disease that continues into adulthood. Agonists of GC-C are US Food and Drug Administration-approved drugs for the treatment of constipation and irritable bowel syndrome. Therapeutic strategies targeting GC-C are tested in preclinical mouse models, assuming that murine GC-C mimics human GC-C in its biochemical properties and downstream signaling events. Here, we reveal important differences in ligand-binding affinity and GC activity between mouse GC-C and human GC-C. We generated a series of chimeric constructs of various domains of human and mouse GC-C to show that the extracellular domain of mouse GC-C contributed to log-orders lower affinity of mouse GC-C for ligands than human GC-C. Further, the Vmax of the murine GC domain was lower than that of human GC-C, and allosteric regulation of the receptor by ATP binding to the intracellular kinase-homology domain also differed. These altered properties are reflected in the high concentrations of ligands required to elicit signaling responses in the mouse gut in preclinical models and the specificity of a GC inhibitor towards human GC-C. Therefore, our studies identify considerations in using the murine model to test molecules for therapeutic purposes that work as either agonists or antagonists of GC-C, and vaccines for the bacterial heat-stable enterotoxin that causes watery diarrhea in humans.
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Affiliation(s)
- Vishwas Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Kritica Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Avipsa Bose
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Pierre Maisonneuve
- UMR 5248 - Chemistry & Biology of Membranes and Nano-Objects, CNRS - Université de Bordeaux, Institut Européen de Chimie et Biologie, Pessac, France
| | - Sandhya S Visweswariah
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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4
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Guichard A, Lu S, Kanca O, Bressan D, Huang Y, Ma M, Sanz Juste S, Andrews JC, Jay KL, Sneider M, Schwartz R, Huang MC, Bei D, Pan H, Ma L, Lin WW, Auradkar A, Bhagwat P, Park S, Wan KH, Ohsako T, Takano-Shimizu T, Celniker SE, Wangler MF, Yamamoto S, Bellen HJ, Bier E. A comprehensive Drosophila resource to identify key functional interactions between SARS-CoV-2 factors and host proteins. Cell Rep 2023; 42:112842. [PMID: 37480566 PMCID: PMC10962759 DOI: 10.1016/j.celrep.2023.112842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/18/2023] [Accepted: 07/05/2023] [Indexed: 07/24/2023] Open
Abstract
Development of effective therapies against SARS-CoV-2 infections relies on mechanistic knowledge of virus-host interface. Abundant physical interactions between viral and host proteins have been identified, but few have been functionally characterized. Harnessing the power of fly genetics, we develop a comprehensive Drosophila COVID-19 resource (DCR) consisting of publicly available strains for conditional tissue-specific expression of all SARS-CoV-2 encoded proteins, UAS-human cDNA transgenic lines encoding established host-viral interacting factors, and GAL4 insertion lines disrupting fly homologs of SARS-CoV-2 human interacting proteins. We demonstrate the utility of the DCR to functionally assess SARS-CoV-2 genes and candidate human binding partners. We show that NSP8 engages in strong genetic interactions with several human candidates, most prominently with the ATE1 arginyltransferase to induce actin arginylation and cytoskeletal disorganization, and that two ATE1 inhibitors can reverse NSP8 phenotypes. The DCR enables parallel global-scale functional analysis of SARS-CoV-2 components in a prime genetic model system.
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Affiliation(s)
- Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel Bressan
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Department of Epigenetics & Molecular Carcinogenesis at MD Anderson, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan C Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Kristy L Jay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Marketta Sneider
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Ruth Schwartz
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Liwen Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Pranjali Bhagwat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Soo Park
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kenneth H Wan
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Takashi Ohsako
- Advanced Technology Center, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Toshiyuki Takano-Shimizu
- Kyoto Drosophila Stock Center and Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 616-8354, Japan
| | - Susan E Celniker
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Tata Institute for Genetics and Society - UCSD, La Jolla, CA 92093, USA.
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5
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Hao B, Kovács IA. A positive statistical benchmark to assess network agreement. Nat Commun 2023; 14:2988. [PMID: 37225699 DOI: 10.1038/s41467-023-38625-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Current computational methods for validating experimental network datasets compare overlap, i.e., shared links, with a reference network using a negative benchmark. However, this fails to quantify the level of agreement between the two networks. To address this, we propose a positive statistical benchmark to determine the maximum possible overlap between networks. Our approach can efficiently generate this benchmark in a maximum entropy framework and provides a way to assess whether the observed overlap is significantly different from the best-case scenario. We introduce a normalized overlap score, Normlap, to enhance comparisons between experimental networks. As an application, we compare molecular and functional networks, resulting in an agreement network of human as well as yeast network datasets. The Normlap score can improve the comparison between experimental networks by providing a computational alternative to network thresholding and validation.
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Affiliation(s)
- Bingjie Hao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, 60208, USA
| | - István A Kovács
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, 60208, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, 60208, USA.
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6
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Abdullah M, Greco BM, Laurent JM, Garge RK, Boutz DR, Vandeloo M, Marcotte EM, Kachroo AH. Rapid, scalable, combinatorial genome engineering by marker-less enrichment and recombination of genetically engineered loci in yeast. Cell Rep Methods 2023; 3:100464. [PMID: 37323580 PMCID: PMC10261898 DOI: 10.1016/j.crmeth.2023.100464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/30/2023] [Accepted: 04/12/2023] [Indexed: 06/17/2023]
Abstract
A major challenge to rationally building multi-gene processes in yeast arises due to the combinatorics of combining all of the individual edits into the same strain. Here, we present a precise and multi-site genome editing approach that combines all edits without selection markers using CRISPR-Cas9. We demonstrate a highly efficient gene drive that selectively eliminates specific loci by integrating CRISPR-Cas9-mediated double-strand break (DSB) generation and homology-directed recombination with yeast sexual assortment. The method enables marker-less enrichment and recombination of genetically engineered loci (MERGE). We show that MERGE converts single heterologous loci to homozygous loci at ∼100% efficiency, independent of chromosomal location. Furthermore, MERGE is equally efficient at converting and combining multiple loci, thus identifying compatible genotypes. Finally, we establish MERGE proficiency by engineering a fungal carotenoid biosynthesis pathway and most of the human α-proteasome core into yeast. Therefore, MERGE lays the foundation for scalable, combinatorial genome editing in yeast.
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Affiliation(s)
- Mudabir Abdullah
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Brittany M. Greco
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Jon M. Laurent
- Institute of Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Riddhiman K. Garge
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R. Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michelle Vandeloo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Aashiq H. Kachroo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
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7
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Alnasir JJ, Shanahan HP. Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq. J Comput Biol 2023; 30:131-148. [PMID: 36689201 DOI: 10.1089/cmb.2021.0476] [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] [Indexed: 01/24/2023] Open
Abstract
Given the wide variability in the quality of next-generation sequencing data submitted to public repositories, it is essential to identify methods that can perform quality control on these data sets when additional quality control data, such as mean tile data, are missing from public repositories. In this study, we present evidence that correlating counts of reads corresponding to pairs of motifs separated over specific distances on individual exons can be used as a proxy mean tile data in the data sets we analyzed and hence could be used when mean tile data are not available. As test data sets we use the Homo sapiens in vitro transcribed (IVT) data set, and a Drosophila melanogaster data set comprising wild and mutant types. We find that a FastQC analysis of the available parts of these data sets demonstrates that the per-tile sequencing quality is good for all the data sets apart from the mutant-type data where the mutant-r3 data are worse than the mutant-r2 data. Correspondingly, intra-exon motif correlations are reasonably large for all data sets except this latter case where the mutant-r2 correlations are low and the mutant-r3 correlations close to zero. We propose that these extremely low correlations are indicative of bias of technical origin, such as flowcell errors. In addition to this, the intra-exon motif correlations as a function of both guanosine-cytosine (GC) content parameters are somewhat higher and less dependent on the GC content parameters in the IVT-Plasmids messenger RNA (mRNA) selection free RNA-Seq sample (control) than in the other RNA-Seq samples that did undergo mRNA selection: both ribosomal depletion (IVT-Only) and PolyA selection (IVT-PolyA, wild type, and mutant).
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Affiliation(s)
- Jamie J Alnasir
- Department of Computing, Imperial College, London, United Kingdom
| | - Hugh P Shanahan
- Department of Computer Science, Royal Holloway, University of London, Egham, United Kingdom
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8
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Sommer MJ, Cha S, Varabyou A, Rincon N, Park S, Minkin I, Pertea M, Steinegger M, Salzberg SL. Structure-guided isoform identification for the human transcriptome. eLife 2022; 11:e82556. [PMID: 36519529 PMCID: PMC9812405 DOI: 10.7554/elife.82556] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Recently developed methods to predict three-dimensional protein structure with high accuracy have opened new avenues for genome and proteome research. We explore a new hypothesis in genome annotation, namely whether computationally predicted structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by protein structure predictions, we evaluated over 230,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues. From this set of assembled transcripts, we identified hundreds of isoforms with more confidently predicted structure and potentially superior function in comparison to canonical isoforms in the latest human gene database. We illustrate our new method with examples where structure provides a guide to function in combination with expression and evolutionary evidence. Additionally, we provide the complete set of structures as a resource to better understand the function of human genes and their isoforms. These results demonstrate the promise of protein structure prediction as a genome annotation tool, allowing us to refine even the most highly curated catalog of human proteins. More generally we demonstrate a practical, structure-guided approach that can be used to enhance the annotation of any genome.
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Affiliation(s)
- Markus J Sommer
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of EngineeringBaltimoreUnited States
- Center for Computational Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sooyoung Cha
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
- Artificial Intelligence Institute, Seoul National UniversitySeoulRepublic of Korea
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Natalia Rincon
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of EngineeringBaltimoreUnited States
- Center for Computational Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sukhwan Park
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
- Artificial Intelligence Institute, Seoul National UniversitySeoulRepublic of Korea
| | - Ilia Minkin
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of EngineeringBaltimoreUnited States
- Center for Computational Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of EngineeringBaltimoreUnited States
- Center for Computational Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Martin Steinegger
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
- Artificial Intelligence Institute, Seoul National UniversitySeoulRepublic of Korea
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of EngineeringBaltimoreUnited States
- Center for Computational Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
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9
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Premzl M. Revised eutherian gene collections. BMC Genom Data 2022; 23:56. [PMID: 35870891 PMCID: PMC9308196 DOI: 10.1186/s12863-022-01071-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/13/2022] [Indexed: 11/24/2022] Open
Abstract
Objectives The most recent research projects in scientific field of eutherian comparative genomics included intentions to sequence every extant eutherian species genome in foreseeable future, so that future revisions and updates of eutherian gene data sets were expected. Data description Using 35 public eutherian reference genomic sequence assemblies and free available software, the eutherian comparative genomic analysis protocol RRID:SCR_014401 was published as guidance against potential genomic sequence errors. The protocol curated 14 eutherian third-party data gene data sets, including, in aggregate, 2615 complete coding sequences that were deposited in European Nucleotide Archive. The published eutherian gene collections were used in revisions and updates of eutherian gene data set classifications and nomenclatures that included gene annotations, phylogenetic analyses and protein molecular evolution analyses.
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10
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Ni P, Moe J, Su Z. Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice. BMC Biol 2022; 20:221. [PMID: 36199141 PMCID: PMC9535988 DOI: 10.1186/s12915-022-01426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Predicting cis-regulatory modules (CRMs) in a genome and their functional states in various cell/tissue types of the organism are two related challenging computational tasks. Most current methods attempt to simultaneously achieve both using data of multiple epigenetic marks in a cell/tissue type. Though conceptually attractive, they suffer high false discovery rates and limited applications. To fill the gaps, we proposed a two-step strategy to first predict a map of CRMs in the genome, and then predict functional states of all the CRMs in various cell/tissue types of the organism. We have recently developed an algorithm for the first step that was able to more accurately and completely predict CRMs in a genome than existing methods by integrating numerous transcription factor ChIP-seq datasets in the organism. Here, we presented machine-learning methods for the second step. RESULTS We showed that functional states in a cell/tissue type of all the CRMs in the genome could be accurately predicted using data of only 1~4 epigenetic marks by a variety of machine-learning classifiers. Our predictions are substantially more accurate than the best achieved so far. Interestingly, a model trained on a cell/tissue type in humans can accurately predict functional states of CRMs in different cell/tissue types of humans as well as of mice, and vice versa. Therefore, epigenetic code that defines functional states of CRMs in various cell/tissue types is universal at least in humans and mice. Moreover, we found that from tens to hundreds of thousands of CRMs were active in a human and mouse cell/tissue type, and up to 99.98% of them were reutilized in different cell/tissue types, while as small as 0.02% of them were unique to a cell/tissue type that might define the cell/tissue type. CONCLUSIONS Our two-step approach can accurately predict functional states in any cell/tissue type of all the CRMs in the genome using data of only 1~4 epigenetic marks. Our approach is also more cost-effective than existing methods that typically use data of more epigenetic marks. Our results suggest common epigenetic rules for defining functional states of CRMs in various cell/tissue types in humans and mice.
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Affiliation(s)
- Pengyu Ni
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Joshua Moe
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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11
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Banani SF, Afeyan LK, Hawken SW, Henninger JE, Dall'Agnese A, Clark VE, Platt JM, Oksuz O, Hannett NM, Sagi I, Lee TI, Young RA. Genetic variation associated with condensate dysregulation in disease. Dev Cell 2022; 57:1776-1788.e8. [PMID: 35809564 PMCID: PMC9339523 DOI: 10.1016/j.devcel.2022.06.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 03/30/2021] [Revised: 03/11/2022] [Accepted: 06/14/2022] [Indexed: 12/18/2022]
Abstract
A multitude of cellular processes involve biomolecular condensates, which has led to the suggestion that diverse pathogenic mutations may dysregulate condensates. Although proof-of-concept studies have identified specific mutations that cause condensate dysregulation, the full scope of the pathological genetic variation that affects condensates is not yet known. Here, we comprehensively map pathogenic mutations to condensate-promoting protein features in putative condensate-forming proteins and find over 36,000 pathogenic mutations that plausibly contribute to condensate dysregulation in over 1,200 Mendelian diseases and 550 cancers. This resource captures mutations presently known to dysregulate condensates, and experimental tests confirm that additional pathological mutations do indeed affect condensate properties in cells. These findings suggest that condensate dysregulation may be a pervasive pathogenic mechanism underlying a broad spectrum of human diseases, provide a strategy to identify proteins and mutations involved in pathologically altered condensates, and serve as a foundation for mechanistic insights into disease and therapeutic hypotheses.
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Affiliation(s)
- Salman F Banani
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Susana W Hawken
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Program of Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Victoria E Clark
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jesse M Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ido Sagi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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12
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Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. Res Sq 2022:rs.3.rs-1354127. [PMID: 35677070 PMCID: PMC9176654 DOI: 10.21203/rs.3.rs-1354127/v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Physical interactions between viral and host proteins are responsible for almost all aspects of the viral life cycle and the host's immune response. Studying viral-host protein-protein interactions is thus crucial for identifying strategies for treatment and prevention of viral infection. Here, we use high-throughput yeast two-hybrid and affinity purification followed by mass spectrometry to generate a comprehensive SARS-CoV-2-human protein-protein interactome network consisting of both binary and co-complex interactions. We report a total of 739 high-confidence interactions, showing the highest overlap of interaction partners among published datasets as well as the highest overlap with genes differentially expressed in samples (such as upper airway and bronchial epithelial cells) from patients with SARS-CoV-2 infection. Showcasing the utility of our network, we describe a novel interaction between the viral accessory protein ORF3a and the host zinc finger transcription factor ZNF579 to illustrate a SARS-CoV-2 factor mediating a direct impact on host transcription. Leveraging our interactome, we performed network-based drug screens for over 2,900 FDA-approved/investigational drugs and obtained a curated list of 23 drugs that had significant network proximities to SARS-CoV-2 host factors, one of which, carvedilol, showed promising antiviral properties. We performed electronic health record-based validation using two independent large-scale, longitudinal COVID-19 patient databases and found that carvedilol usage was associated with a significantly lowered probability (17%-20%, P < 0.001) of obtaining a SARS-CoV-2 positive test after adjusting various confounding factors. Carvedilol additionally showed anti-viral activity against SARS-CoV-2 in a human lung epithelial cell line [half maximal effective concentration (EC 50 ) value of 4.1 µM], suggesting a mechanism for its beneficial effect in COVID-19. Our study demonstrates the value of large-scale network systems biology approaches for extracting biological insight from complex biological processes.
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Yuan Liu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
| | - Shagun Gupta
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, US
| | - Mauricio I. Paramo
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Chengsheng Mao
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, US
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, US
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Shayne Wierbowski
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, US
| | - Marta Bertolotti
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
| | - Mriganka Nerkar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, US
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, US
| | - Haley Gula
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, US
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, US
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, US
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Serpil C. Erzurum
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, US
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, US
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, US
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13
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Abstract
For decades, budding yeast, a single-cellular eukaryote, has provided remarkable insights into human biology. Yeast and humans share several thousand genes despite morphological and cellular differences and over a billion years of separate evolution. These genes encode critical cellular processes, the failure of which in humans results in disease. Although recent developments in genome engineering of mammalian cells permit genetic assays in human cell lines, there is still a need to develop biological reagents to study human disease variants in a high-throughput manner. Many protein-coding human genes can successfully substitute for their yeast equivalents and sustain yeast growth, thus opening up doors for developing direct assays of human gene function in a tractable system referred to as 'humanized yeast'. Humanized yeast permits the discovery of new human biology by measuring human protein activity in a simplified organismal context. This Review summarizes recent developments showing how humanized yeast can directly assay human gene function and explore variant effects at scale. Thus, by extending the 'awesome power of yeast genetics' to study human biology, humanizing yeast reinforces the high relevance of evolutionarily distant model organisms to explore human gene evolution, function and disease.
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14
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Smith E, Campbell S, Wilson AN, Shumate J, Baillargeon P, Scampavia L, Kamenecka TM, Spicer TP, Solt LA. High throughput screening for compounds to the orphan nuclear receptor NR2F6. SLAS Discov 2022; 27:242-8. [PMID: 35331960 DOI: 10.1016/j.slasd.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/24/2022]
Abstract
NR2F6 is considered an orphan nuclear receptor since its endogenous ligand has yet to be identified. Recently, NR2F6 has emerged as a novel cancer therapeutic target. NR2F6 has been demonstrated to be upregulated or overexpressed in several cancers. Importantly, Nr2f6-/- mice spontaneously reject tumors and develop host-protective immunological memory, a consequence of NR2F6 acting as an immune checkpoint in effector T cells. Collectively, these data suggest that modulation of NR2F6 activity may have important clinical applications in the fight against cancer. The nuclear receptor superfamily of ligand-regulated transcription factors has proven to be an excellent source of targets for therapeutic intervention of a broad range of diseases. Approximately 15% of FDA approved drugs target NRs, demonstrating their clinical efficacy. To identify small molecule regulators of NR2F6 activity, with the overall goal of immuno-oncology, we developed and initiated a high-throughput cell-based assay that specifically measures the transcriptional activity of NR2F6. We completed automated screening of approximately 666,000 compounds and identified 5,008 initial hits. Further screening efforts, including counterscreening assays, confirmed 128 of these hits, most of which had IC50s of equal to or less than 5μM potencies. Here, we report, for the first time, the identification of several small molecule compounds to the orphan nuclear receptor, NR2F6.
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15
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Marcogliese PC, Deal SL, Andrews J, Harnish JM, Bhavana VH, Graves HK, Jangam S, Luo X, Liu N, Bei D, Chao YH, Hull B, Lee PT, Pan H, Bhadane P, Huang MC, Longley CM, Chao HT, Chung HL, Haelterman NA, Kanca O, Manivannan SN, Rossetti LZ, German RJ, Gerard A, Schwaibold EMC, Fehr S, Guerrini R, Vetro A, England E, Murali CN, Barakat TS, van Dooren MF, Wilke M, van Slegtenhorst M, Lesca G, Sabatier I, Chatron N, Brownstein CA, Madden JA, Agrawal PB, Keren B, Courtin T, Perrin L, Brugger M, Roser T, Leiz S, Mau-Them FT, Delanne J, Sukarova-Angelovska E, Trajkova S, Rosenhahn E, Strehlow V, Platzer K, Keller R, Pavinato L, Brusco A, Rosenfeld JA, Marom R, Wangler MF, Yamamoto S. Drosophila functional screening of de novo variants in autism uncovers damaging variants and facilitates discovery of rare neurodevelopmental diseases. Cell Rep 2022; 38:110517. [PMID: 35294868 PMCID: PMC8983390 DOI: 10.1016/j.celrep.2022.110517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 02/02/2021] [Revised: 09/23/2021] [Accepted: 02/18/2022] [Indexed: 12/30/2022] Open
Abstract
Individuals with autism spectrum disorder (ASD) exhibit an increased burden of de novo mutations (DNMs) in a broadening range of genes. While these studies have implicated hundreds of genes in ASD pathogenesis, which DNMs cause functional consequences in vivo remains unclear. We functionally test the effects of ASD missense DNMs using Drosophila through "humanization" rescue and overexpression-based strategies. We examine 79 ASD variants in 74 genes identified in the Simons Simplex Collection and find 38% of them to cause functional alterations. Moreover, we identify GLRA2 as the cause of a spectrum of neurodevelopmental phenotypes beyond ASD in 13 previously undiagnosed subjects. Functional characterization of variants in ASD candidate genes points to conserved neurobiological mechanisms and facilitates gene discovery for rare neurodevelopmental diseases.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Samantha L Deal
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Jonathan Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - V Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Hematology/Oncology, BCM, Houston, TX 77030, USA
| | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Yu-Hsin Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Brooke Hull
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pradnya Bhadane
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Colleen M Longley
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Nele A Haelterman
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sathiya N Manivannan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Linda Z Rossetti
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | | | - Sarah Fehr
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Annalisa Vetro
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Eleina England
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Isabelle Sabatier
- Department of Pediatric Neurology, Lyon University Hospitals, Lyon, France
| | - Nicolas Chatron
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Thomas Courtin
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Laurence Perrin
- Genetic Department, Robert Debré Hospital, APHP.Nord-Université de Paris, Paris 75019, France
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Timo Roser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Lindwurmstraße 4, 80337 Munich, Germany
| | - Steffen Leiz
- Department of Pediatrics and Adolescent Medicine, Hospital Dritter Orden, Munich, Germany
| | - Frederic Tran Mau-Them
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France; Laboratoire de Génétique, Innovation en Diagnostic Génomique des Maladies Rares UF6254, Plateau Technique de Biologie, CHU Dijon, 14 Rue Paul Gaffarel, BP 77908, 21079 Dijon, France
| | - Julian Delanne
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, Republic of Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Erik Rosenhahn
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Roberto Keller
- Adult Autism Center, Mental Health Department, Health Unit ASL Città di Torino, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy; Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, Turin, Italy
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
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16
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Ivanov IP, Saba JA, Fan CM, Wang J, Firth AE, Cao C, Green R, Dever TE. Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency. Proc Natl Acad Sci U S A 2022; 119:e2117226119. [PMID: 35217614 DOI: 10.1073/pnas.2117226119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 01/15/2023] Open
Abstract
Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of mammalian genes, we identified five homeobox (Hox) gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. An analysis of published cap analysis of gene expression sequencing (CAGE-seq) data and generated CAGE-seq data for messenger RNAs (mRNAs) from mouse somites revealed that the 5' leaders of Hox mRNAs of interest contain conserved uORFs, are generally much shorter than reported, and lack previously proposed internal ribosome entry site elements. We show that the conserved uORFs inhibit Hox reporter expression and that altering the stringency of start codon selection by overexpressing eIF1 or eIF5 modulates the expression of Hox reporters. We also show that modifying ribosome homeostasis by depleting a large ribosomal subunit protein or treating cells with sublethal concentrations of puromycin leads to lower stringency of start codon selection. Thus, altering global translation can confer gene-specific effects through altered start codon selection stringency.
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17
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Desai J, Francis C, Longo K, Hoss A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3128-3141. [PMID: 35286381 PMCID: PMC8989546 DOI: 10.1093/nar/gkac155] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/14/2022] [Accepted: 02/26/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is frequently involved in the diversification of protein function and can also be modulated for therapeutic purposes. Here we develop a predictive model, called Exon ByPASS (predicting Exon skipping Based on Protein amino acid SequenceS), to assess the criticality of exon inclusion based solely on information contained in the amino acid sequence upstream and downstream of the exon junctions. By focusing on protein sequence, Exon ByPASS predicts exon skipping independent of tissue and species in the absence of any intronic information. We validate model predictions using transcriptomic and proteomic data and show that the model can capture exon skipping in different tissues and species. Additionally, we reveal potential therapeutic opportunities by predicting synthetically skippable exons and neo-junctions arising in cancer cells.
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Affiliation(s)
- Jigar Desai
- To whom correspondence should be addressed. Tel: +1 704 214 7914;
| | | | | | - Andrew Hoss
- Wave Life Sciences, Cambridge, MA 02138, USA
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18
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Stieglitz JT, Potts KA, Van Deventer JA. Broadening the Toolkit for Quantitatively Evaluating Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2021; 10:3094-3104. [PMID: 34730946 DOI: 10.1021/acssynbio.1c00370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic code expansion is a powerful approach for advancing critical fields such as biological therapeutic discovery. However, the machinery for genetically encoding noncanonical amino acids (ncAAs) is only available in limited plasmid formats, constraining potential applications. In extreme cases, the introduction of two separate plasmids, one containing an orthogonal translation system (OTS) to facilitate ncAA incorporation and a second for expressing a ncAA-containing protein of interest, is not possible due to a lack of the available selection markers. One strategy to circumvent this challenge is to express the OTS and protein of interest from a single vector. For what we believe is the first time in yeast, we describe here several sets of single plasmid systems (SPSs) for performing genetic code manipulation and compare the ncAA incorporation capabilities of these plasmids against the capabilities of previously described dual plasmid systems (DPSs). For both dual fluorescent protein reporters and yeast display reporters tested with multiple OTSs and ncAAs, measured ncAA incorporation efficiencies with SPSs were determined to be equal to efficiencies determined with DPSs. Click chemistry on yeast cells displaying ncAA-containing proteins was also shown to be feasible in both formats, although differences in reactivity between formats suggest the need for caution when using such approaches. Additionally, we investigated whether these reporters would support the separation of yeast strains known to exhibit distinct ncAA incorporation efficiencies. Model sorts conducted with mixtures of two strains transformed with the same SPS or DPS both led to the enrichment of a strain known to support a higher efficiency ncAA incorporation, suggesting that these reporters will be suitable for conducting screens for strains exhibiting enhanced ncAA incorporation efficiencies. Overall, our results confirm that SPSs are well behaved in yeast and provide a convenient alternative to DPSs. SPSs are expected to be invaluable for conducting high-throughput investigations of the effects of genetic or genomic changes on ncAA incorporation efficiency and, more fundamentally, the eukaryotic translation apparatus.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Kelly A. Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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19
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Singh P, Fragoza R, Blengini CS, Tran TN, Pannafino G, Al-Sweel N, Schimenti KJ, Schindler K, Alani EA, Yu H, Schimenti JC. Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging. Nat Commun 2021; 12:5005. [PMID: 34408140 PMCID: PMC8373927 DOI: 10.1038/s41467-021-25028-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/20/2021] [Indexed: 01/12/2023] Open
Abstract
Embryonic aneuploidy from mis-segregation of chromosomes during meiosis causes pregnancy loss. Proper disjunction of homologous chromosomes requires the mismatch repair (MMR) genes MLH1 and MLH3, essential in mice for fertility. Variants in these genes can increase colorectal cancer risk, yet the reproductive impacts are unclear. To determine if MLH1/3 single nucleotide polymorphisms (SNPs) in human populations could cause reproductive abnormalities, we use computational predictions, yeast two-hybrid assays, and MMR and recombination assays in yeast, selecting nine MLH1 and MLH3 variants to model in mice via genome editing. We identify seven alleles causing reproductive defects in mice including female subfertility and male infertility. Remarkably, in females these alleles cause age-dependent decreases in litter size and increased embryo resorption, likely a consequence of fewer chiasmata that increase univalents at meiotic metaphase I. Our data suggest that hypomorphic alleles of meiotic recombination genes can predispose females to increased incidence of pregnancy loss from gamete aneuploidy. Proper meiotic chromosome segregation requires mismatch repair genes MLH1 and MLH3, of which variants occur in the human population. Here, the authors use computational predictions and yeast assays to select human MLH1/3 variants for modelling in mice, observing reproductive defects from abnormal levels of crossing over.
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Affiliation(s)
- Priti Singh
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA.,Preclinical Modeling Core Lab, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert Fragoza
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Tina N Tran
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Najla Al-Sweel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Kerry J Schimenti
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | - Eric A Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.,Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA. .,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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20
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Guo Y, Zhou D, Li W, Cao J, Nie R, Xiong L, Ruan X. Identifying polyadenylation signals with biological embedding via self-attentive gated convolutional highway networks. Appl Soft Comput 2021. [DOI: 10.1016/j.asoc.2021.107133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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22
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Moparthi L, Koch S. A uniform expression library for the exploration of FOX transcription factor biology. Differentiation 2020; 115:30-36. [PMID: 32858261 DOI: 10.1016/j.diff.2020.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 12/29/2022]
Abstract
Forkhead box (FOX) family transcription factors play essential roles in development, tissue homeostasis, and disease. Although the biology of several FOX proteins has been studied in depth, it is unclear to what extent these findings apply to even closely related family members, which frequently exert overlapping but non-redundant functions. To help address this question, we have generated a uniform, ready-to-use expression library of all 44 human FOX transcription factors with a convenient peptide tag for parallel screening assays. In addition, we have generated multiple universal forkhead box reporter plasmids, which can be used to monitor the transcriptional activity of most FOX proteins with high fidelity. As a proof-of-principle, we use our plasmid library to identify the DNA repair protein XRCC6/Ku70 as a selective FOX interaction partner and regulator of FOX transcriptional activity. We believe that these tools, which we make available via the Addgene plasmid repository, will considerably expedite the investigation of FOX protein biology.
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Affiliation(s)
- Lavanya Moparthi
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Linköping University, Linköping, Sweden.
| | - Stefan Koch
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Linköping University, Linköping, Sweden.
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23
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Strezoska Ž, Dickerson SM, Maksimova E, Chou E, Gross MM, Hemphill K, Hardcastle T, Perkett M, Stombaugh J, Miller GW, Anderson EM, Vermeulen A, Smith AVB. CRISPR-mediated transcriptional activation with synthetic guide RNA. J Biotechnol 2020; 319:25-35. [PMID: 32470463 DOI: 10.1016/j.jbiotec.2020.05.005] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 04/03/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
Abstract
The CRISPR-Cas9 system has been adapted for transcriptional activation (CRISPRa) and several second-generation CRISPRa systems (including VPR, SunTag, and SAM) have been developed to recruit different transcriptional activators to a deactivated Cas9, which is guided to a transcriptional start site via base complementarity with a target guide RNA. Multiple studies have shown the benefit of CRISPRa using plasmid or lentiviral expressed guide RNA, but the use of synthetic guide RNA has not been reported. Here we demonstrate the effective use of synthetic guide RNA for gene activation via CRISPRa. CRISPRa crRNA may be used with a canonical tracrRNA using the VPR or SunTag activation systems or with an extended tracrRNA containing an aptamer sequence for the SAM system. Transcriptional activation with synthetic crRNA:tracrRNA is comparable to activation achieved with expression vectors and combining several crRNA sequences targeting the same gene can enhance transcriptional activation. The use of synthetic crRNA is also ideal for simultaneous activation of multiple genes or use with dCas9-VPR mRNA when viral transduction is not feasible. Here, we perform a proof-of-principle arrayed screen using a CRISPRa crRNA library consisting of 153 cytokine receptor targets to identify regulators of IL-6 cytokine secretion. Together, these results demonstrate the suitability of synthetic CRISPRa guide RNA for high throughput, arrayed screening applications which allow for more complex phenotypic readouts to complement viability and drug resistance assays typically used in a pooled screening format.
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Affiliation(s)
| | | | | | - Eldon Chou
- Horizon Discovery, Lafayette 80026, United States
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24
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Garge RK, Laurent JM, Kachroo AH, Marcotte EM. Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes. Genetics 2020; 215:1153-1169. [PMID: 32522745 PMCID: PMC7404242 DOI: 10.1534/genetics.120.303378] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
Many gene families have been expanded by gene duplications along the human lineage, relative to ancestral opisthokonts, but the extent to which the duplicated genes function similarly is understudied. Here, we focused on structural cytoskeletal genes involved in critical cellular processes, including chromosome segregation, macromolecular transport, and cell shape maintenance. To determine functional redundancy and divergence of duplicated human genes, we systematically humanized the yeast actin, myosin, tubulin, and septin genes, testing ∼81% of human cytoskeletal genes across seven gene families for their ability to complement a growth defect induced by inactivation or deletion of the corresponding yeast ortholog. In five of seven families-all but α-tubulin and light myosin, we found at least one human gene capable of complementing loss of the yeast gene. Despite rescuing growth defects, we observed differential abilities of human genes to rescue cell morphology, meiosis, and mating defects. By comparing phenotypes of humanized strains with deletion phenotypes of their interaction partners, we identify instances of human genes in the actin and septin families capable of carrying out essential functions, but failing to fully complement the cytoskeletal roles of their yeast orthologs, thus leading to abnormal cell morphologies. Overall, we show that duplicated human cytoskeletal genes appear to have diverged such that only a few human genes within each family are capable of replacing the essential roles of their yeast orthologs. The resulting yeast strains with humanized cytoskeletal components now provide surrogate platforms to characterize human genes in simplified eukaryotic contexts.
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Affiliation(s)
- Riddhiman K Garge
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Jon M Laurent
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Aashiq H Kachroo
- The Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montreal, H4B 1R6 Quebec, Canada
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
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25
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Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS Discov 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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26
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Laurent JM, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM. Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PLoS Biol 2020; 18:e3000627. [PMID: 32421706 PMCID: PMC7259792 DOI: 10.1371/journal.pbio.3000627] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 05/29/2020] [Accepted: 04/14/2020] [Indexed: 01/17/2023] Open
Abstract
Despite over a billion years of evolutionary divergence, several thousand human genes possess clearly identifiable orthologs in yeast, and many have undergone lineage-specific duplications in one or both lineages. These duplicated genes may have been free to diverge in function since their expansion, and it is unclear how or at what rate ancestral functions are retained or partitioned among co-orthologs between species and within gene families. Thus, in order to investigate how ancestral functions are retained or lost post-duplication, we systematically replaced hundreds of essential yeast genes with their human orthologs from gene families that have undergone lineage-specific duplications, including those with single duplications (1 yeast gene to 2 human genes, 1:2) or higher-order expansions (1:>2) in the human lineage. We observe a variable pattern of replaceability across different ortholog classes, with an obvious trend toward differential replaceability inside gene families, and rarely observe replaceability by all members of a family. We quantify the ability of various properties of the orthologs to predict replaceability, showing that in the case of 1:2 orthologs, replaceability is predicted largely by the divergence and tissue-specific expression of the human co-orthologs, i.e., the human proteins that are less diverged from their yeast counterpart and more ubiquitously expressed across human tissues more often replace their single yeast ortholog. These trends were consistent with in silico simulations demonstrating that when only one ortholog can replace its corresponding yeast equivalent, it tends to be the least diverged of the pair. Replaceability of yeast genes having more than 2 human co-orthologs was marked by retention of orthologous interactions in functional or protein networks as well as by more ancestral subcellular localization. Overall, we performed >400 human gene replaceability assays, revealing 50 new human-yeast complementation pairs, thus opening up avenues to further functionally characterize these human genes in a simplified organismal context.
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Affiliation(s)
- Jon M. Laurent
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Systems Genetics, NYU Langone Health, New York, New York, United States of America
| | - Riddhiman K. Garge
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ashley I. Teufel
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Claus O. Wilke
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Aashiq H. Kachroo
- The Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montreal, Quebec, Canada
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
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27
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Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, Keinan A, Schimenti JC, Clark AG, Yu H. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nat Commun 2019; 10:4141. [PMID: 31515488 PMCID: PMC6742646 DOI: 10.1038/s41467-019-11959-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [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: 01/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022] Open
Abstract
Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at > 1% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual's genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.
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Affiliation(s)
- Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shayne D Wierbowski
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jin Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tina N Tran
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Juan F Beltran
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Christen A Rivera-Erick
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kaixiong Ye
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Li Yao
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Xiaomu Wei
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alon Keinan
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - John C Schimenti
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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28
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Abstract
Advances in sequencing technology have made whole-genome and whole-exome datasets more accessible for both clinical diagnosis and cutting-edge human genetics research. Although a number of in silico algorithms have been developed to predict the pathogenicity of variants identified in these datasets, functional studies are critical to determining how specific genomic variants affect protein function, especially for missense variants. In the Undiagnosed Diseases Network (UDN) and other rare disease research consortia, model organisms (MO) including Drosophila, C. elegans, zebrafish, and mice are actively used to assess the function of putative human disease-causing variants. This protocol describes a method for the functional assessment of rare human variants used in the Model Organisms Screening Center Drosophila Core of the UDN. The workflow begins with gathering human and MO information from multiple public databases, using the MARRVEL web resource to assess whether the variant is likely to contribute to a patient's condition as well as design effective experiments based on available knowledge and resources. Next, genetic tools (e.g., T2A-GAL4 and UAS-human cDNA lines) are generated to assess the functions of variants of interest in Drosophila. Upon development of these reagents, two-pronged functional assays based on rescue and overexpression experiments can be performed to assess variant function. In the rescue branch, the endogenous fly genes are "humanized" by replacing the orthologous Drosophila gene with reference or variant human transgenes. In the overexpression branch, the reference and variant human proteins are exogenously driven in a variety of tissues. In both cases, any scorable phenotype (e.g., lethality, eye morphology, electrophysiology) can be used as a read-out, irrespective of the disease of interest. Differences observed between reference and variant alleles suggest a variant-specific effect, and thus likely pathogenicity. This protocol allows rapid, in vivo assessments of putative human disease-causing variants of genes with known and unknown functions.
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Affiliation(s)
- J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine
| | - Samantha L Deal
- Program in Developmental Biology, Baylor College of Medicine
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Neuroscience, Baylor College of Medicine
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine; Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine; Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Neuroscience, Baylor College of Medicine;
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29
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Wood L, Wright GJ. Approaches to identify extracellular receptor–ligand interactions. Curr Opin Struct Biol 2019; 56:28-36. [DOI: 10.1016/j.sbi.2018.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
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30
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Abstract
While the genome sequencing revolution has led to the sequencing and assembly of many thousands of new genomes, genome annotation still uses very nearly the same technology that we have used for the past two decades. The sheer number of genomes necessitates the use of fully automated procedures for annotation, but errors in annotation are just as prevalent as they were in the past, if not more so. How are we to solve this growing problem?
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Affiliation(s)
- Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA.
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31
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Huang R, Grishagin I, Wang Y, Zhao T, Greene J, Obenauer JC, Ngan D, Nguyen DT, Guha R, Jadhav A, Southall N, Simeonov A, Austin CP. The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics. Front Pharmacol 2019; 10:445. [PMID: 31133849 PMCID: PMC6524730 DOI: 10.3389/fphar.2019.00445] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/08/2019] [Indexed: 12/16/2022] Open
Abstract
Chemical genomics aims to comprehensively define, and ultimately predict, the effects of small molecule compounds on biological systems. Chemical activity profiling approaches must consider chemical effects on all pathways operative in mammalian cells. To enable a strategic and maximally efficient chemical profiling of pathway space, we have created the NCATS BioPlanet, a comprehensive integrated pathway resource that incorporates the universe of 1,658 human pathways sourced from publicly available, manually curated sources, which have been subjected to thorough redundancy and consistency cross-evaluation. BioPlanet supports interactive browsing, retrieval, and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of corresponding bioactivity assay, as well as visualization of pathways on a 3-dimensional globe, in which the distance between any two pathways is proportional to their degree of gene component overlap. Using this resource, we propose a strategy to identify a minimal set of 362 biological assays that can interrogate the universe of human pathways. The NCATS BioPlanet is a public resource, which will be continually expanded and updated, for systems biology, toxicology, and chemical genomics, available at http://tripod.nih.gov/bioplanet/.
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Affiliation(s)
- Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | | | - Yuhong Wang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Tongan Zhao
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Jon Greene
- Rancho BioSciences, San Diego, CA, United States
| | | | - Deborah Ngan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Dac-Trung Nguyen
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Rajarshi Guha
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Ajit Jadhav
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Noel Southall
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Anton Simeonov
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Christopher P Austin
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
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32
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Abstract
The Open Material Transfer Agreement is a material-transfer agreement that enables broader sharing and use of biological materials by biotechnology practitioners working within the practical realities of technology transfer.
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Affiliation(s)
- Linda Kahl
- BioBricks Foundation, San Francisco, California, USA
| | - Jennifer Molloy
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | | | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - David Grewal
- BioBricks Foundation, San Francisco, California, USA.,Yale Law School, New Haven, Connecticut, USA
| | - Richard Johnson
- BioBricks Foundation, San Francisco, California, USA.,Global Helix, Washington, DC, USA
| | - Drew Endy
- BioBricks Foundation, San Francisco, California, USA.,Department of Bioengineering, Stanford University, Stanford, California, USA
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33
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Kalkatawi M, Magana-Mora A, Jankovic B, Bajic VB. DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions. Bioinformatics 2019; 35:1125-1132. [PMID: 30184052 PMCID: PMC6449759 DOI: 10.1093/bioinformatics/bty752] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/15/2018] [Accepted: 08/31/2018] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Recognition of different genomic signals and regions (GSRs) in DNA is crucial for understanding genome organization, gene regulation, and gene function, which in turn generate better genome and gene annotations. Although many methods have been developed to recognize GSRs, their pure computational identification remains challenging. Moreover, various GSRs usually require a specialized set of features for developing robust recognition models. Recently, deep-learning (DL) methods have been shown to generate more accurate prediction models than 'shallow' methods without the need to develop specialized features for the problems in question. Here, we explore the potential use of DL for the recognition of GSRs. RESULTS We developed DeepGSR, an optimized DL architecture for the prediction of different types of GSRs. The performance of the DeepGSR structure is evaluated on the recognition of polyadenylation signals (PAS) and translation initiation sites (TIS) of different organisms: human, mouse, bovine and fruit fly. The results show that DeepGSR outperformed the state-of-the-art methods, reducing the classification error rate of the PAS and TIS prediction in the human genome by up to 29% and 86%, respectively. Moreover, the cross-organisms and genome-wide analyses we performed, confirmed the robustness of DeepGSR and provided new insights into the conservation of examined GSRs across species. AVAILABILITY AND IMPLEMENTATION DeepGSR is implemented in Python using Keras API; it is available as open-source software and can be obtained at https://doi.org/10.5281/zenodo.1117159. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Manal Kalkatawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arturo Magana-Mora
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Drilling Technology Team, EXPEC-ARC, Saudi Aramco, Dhahran, Saudi Arabia
| | - Boris Jankovic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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34
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Stefanidis L, Fusco ND, Cooper SE, Smith-Carpenter JE, Alper BJ. Molecular Determinants of Substrate Specificity in Human Insulin-Degrading Enzyme. Biochemistry 2018; 57:4903-4914. [PMID: 30004674 DOI: 10.1021/acs.biochem.8b00474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Insulin-degrading enzyme (IDE) is a 110 kDa chambered zinc metalloendopeptidase that degrades insulin, amyloid β, and other intermediate-sized aggregation prone peptides that adopt β-structures. Structural studies of IDE in complex with multiple physiological substrates have suggested a role for hydrophobic and aromatic residues of the IDE active site in substrate binding and catalysis. Here, we examine functional requirements for conserved hydrophobic and aromatic IDE active site residues that are positioned within 4.5 Å of IDE-bound insulin B chain and amyloid β peptides in the reported crystal structures for the respective enzyme-substrate complexes. Charge, size, hydrophobicity, aromaticity, and other functional group requirements for substrate binding IDE active site residues were examined through mutational analysis of the recombinant human enzyme and enzyme kinetic studies conducted using native and fluorogenic derivatives of human insulin and amyloid β peptides. A functional requirement for IDE active site residues F115, A140, F141, Y150, W199, F202, F820, and Y831 was established, and specific contributions of residue charge, size, and hydrophobicity to substrate binding, specificity, and proteolysis were demonstrated. IDE mutant alleles that exhibited enhanced or diminished proteolytic activity toward insulin or amyloid β peptides and derivative substrates were identified.
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Affiliation(s)
- Lazaros Stefanidis
- Department of Chemistry , Sacred Heart University , Fairfield , Connecticut 06825 , United States
| | - Nicholas D Fusco
- Department of Chemistry , Sacred Heart University , Fairfield , Connecticut 06825 , United States
| | - Samantha E Cooper
- Department of Chemistry and Biochemistry , Fairfield University , Fairfield , Connecticut 06824 , United States
| | - Jillian E Smith-Carpenter
- Department of Chemistry and Biochemistry , Fairfield University , Fairfield , Connecticut 06824 , United States
| | - Benjamin J Alper
- Department of Chemistry , Sacred Heart University , Fairfield , Connecticut 06825 , United States
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35
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Niu M, Tabari E, Ni P, Su Z. Towards a map of cis-regulatory sequences in the human genome. Nucleic Acids Res 2018; 46:5395-5409. [PMID: 29733395 PMCID: PMC6009671 DOI: 10.1093/nar/gky338] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 01/17/2018] [Revised: 04/14/2018] [Accepted: 04/19/2018] [Indexed: 01/10/2023] Open
Abstract
Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs. Here, we integrated 620 TF ChIP-seq datasets produced by the ENCODE project for 168 TFs in 79 different cell/tissue types and predicted an unprecedentedly completely map of CREs in CRMs in the human genome at single nucleotide resolution. The map includes 305 912 CRMs containing a total of 1 178 913 CREs belonging to 736 unique TF binding motifs. The predicted CREs and CRMs tend to be subject to either purifying selection or positive selection, thus are likely to be functional. Based on the results, we also examined the status of available ChIP-seq datasets for predicting the entire regulatory genome of humans.
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Affiliation(s)
- Meng Niu
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Ehsan Tabari
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Pengyu Ni
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
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36
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Smith‐Carpenter JE, Alper BJ. Functional requirement for human pitrilysin metallopeptidase 1 arginine 183, mutated in amyloidogenic neuropathy. Protein Sci 2018; 27:861-873. [PMID: 29383861 PMCID: PMC5866943 DOI: 10.1002/pro.3380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 01/01/2023]
Abstract
Here we report the enzymologic characterization of recombinant human pitrilysin metallopeptidase 1 (Pitrm1) and derivative mutants including the arginine-to-glutamine substitution mutant Pitrm1 R183Q, which has been implicated in inherited amyloidogenic neuropathy. Recombinant Pitrm1 R183Q was readily expressed in and purified from Escherichia coli, but was less active than the recombinant wild-type enzyme against recombinant amyloid beta-peptide (Aβ 1-40). A novel fluorogenic substrate derived from the reported Aβ 1-40 core peptide cleavage sequence, Mca-KLVFFAEDK-(Dnp)-OH, was synthesized and applied to real-time kinetic study of Pitrm1 and derivative mutants including Pitrm1 R183Q. The Pitrm1 R183Q mutant exhibited significantly decreased rate of fluorogenic peptide hydrolysis, yet retained similar binding affinity by comparison with the wild-type enzyme. Targeted mutagenic analysis revealed a functional requirement for uncharged or electropositive residues in place of Pitrm1 R183. Residue R183 is positioned within an N-terminal strand-loop-strand motif that is conserved among M16C, but not M16A or M16B family metallopeptidases. Truncation analysis revealed that this strand-loop-strand motif inclusive of residue R183 is essential Pitrm1 function. A requirement for charged residues within 4.5 Å of residue R183 was demonstrated, and Pitrm1 R183Q was found to exhibit increased sensitivity to heat inactivation. Our findings indicate that charge sharing in the vicinity of Pitrm1 R183 is critical to enzyme activity, providing potential insight into a molecular basis of Pitrm1 dysfunction.
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Affiliation(s)
| | - Benjamin J. Alper
- Department of ChemistrySacred Heart UniversityFairfieldConnecticut06825
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37
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Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB. Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function. J Cell Sci 2018; 131:jcs.206565. [PMID: 29180514 DOI: 10.1242/jcs.206565] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/20/2017] [Indexed: 12/23/2022] Open
Abstract
Multiciliated cells (MCCs) drive fluid flow in diverse tubular organs and are essential for the development and homeostasis of the vertebrate central nervous system, airway and reproductive tracts. These cells are characterized by dozens or hundreds of motile cilia that beat in a coordinated and polarized manner. In recent years, genomic studies have not only elucidated the transcriptional hierarchy for MCC specification but also identified myriad new proteins that govern MCC ciliogenesis, cilia beating and cilia polarization. Interestingly, this burst of genomic data has also highlighted that proteins with no obvious role in cilia do, in fact, have important ciliary functions. Understanding the function of proteins with little prior history of study presents a special challenge, especially when faced with large numbers of such proteins. Here, we define the subcellular localization in MCCs of ∼200 proteins not previously implicated in cilia biology. Functional analyses arising from the screen provide novel links between actin cytoskeleton and MCC ciliogenesis.
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Affiliation(s)
- Fan Tu
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jakub Sedzinski
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,The Danish Stem Cell Centre (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yun Ma
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,The Otorhinolaryngology Hospital, First Affiliated Hospital of Sun Yat-sen University, SunYat-sen University, Guangzhou, P.R. China
| | - Edward M Marcotte
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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38
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39
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King J, Foster J, Davison JM, Rawls JF, Breton G. Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. Zebrafish 2017; 15:202-205. [PMID: 29173090 DOI: 10.1089/zeb.2017.1486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 11/12/2022] Open
Abstract
The completion of the zebrafish genome sequence and advances in miniaturization and multiplexing were essential to the creation of techniques such as RNA-seq, ChIP-seq, and high-throughput behavioral and chemical screens. Multiplexing was also instrumental in the recent enhancement of the classic yeast one-hybrid interaction techniques to provide unprecedented discovery capabilities for protein-DNA interactions. Unfortunately its use for zebrafish research is currently hampered by the lack of an open reading frame (ORF) clone collection. As a first step toward a complete collection, we describe a small library of transcriptional regulatory proteins comprising 142 ORFs and its potential applications.
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Affiliation(s)
- Justin King
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - Justin Foster
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - James M Davison
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - John F Rawls
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - Ghislain Breton
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
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40
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Wangler MF, Yamamoto S, Chao HT, Posey JE, Westerfield M, Postlethwait J, Hieter P, Boycott KM, Campeau PM, Bellen HJ. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics 2017; 207:9-27. [PMID: 28874452 PMCID: PMC5586389 DOI: 10.1534/genetics.117.203067] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [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: 04/14/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Hsiao-Tuan Chao
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4C, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario K1H 8L1, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Quebec H3T 1C5, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
- Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, Texas 77030
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41
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Liu T, Jia P, Ma H, Reed SA, Luo X, Larman HB, Schultz PG. Construction and Screening of a Lentiviral Secretome Library. Cell Chem Biol 2017; 24:767-771.e3. [PMID: 28602759 DOI: 10.1016/j.chembiol.2017.05.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 12/31/2016] [Revised: 04/11/2017] [Accepted: 05/15/2017] [Indexed: 12/22/2022]
Abstract
Over 2,000 human proteins are predicted to be secreted, but the biological function of the many of these proteins is still unknown. Moreover, a number of these proteins may act as new therapeutic agents or be targets for the development of therapeutic antibodies. To further explore the extracellular proteome, we have developed a secretome-enriched open reading frame (ORF) library that can be readily screened for autocrine activity in cell-based phenotypic or reporter assays. Next-generation sequencing (NGS) and database analysis predict that the library contains approximately 900 ORFs encoding known secreted proteins (accounting for 77.8% of the library), as well as genes encoding potentially unknown secreted proteins. In a proof-of-principle study, human TF-1 cells were screened for proliferative factors, and the known cytokine GMCSF was identified as a dominant hit. This library offers a relatively low-cost and straightforward approach for functional autocrine screens of secreted proteins.
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Affiliation(s)
- Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Panpan Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Huailei Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Sean A Reed
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhou Luo
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - H Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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42
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Yang F, Sun S, Tan G, Costanzo M, Hill DE, Vidal M, Andrews BJ, Boone C, Roth FP. Identifying pathogenicity of human variants via paralog-based yeast complementation. PLoS Genet 2017; 13:e1006779. [PMID: 28542158 PMCID: PMC5466341 DOI: 10.1371/journal.pgen.1006779] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/09/2017] [Accepted: 04/25/2017] [Indexed: 11/21/2022] Open
Abstract
To better understand the health implications of personal genomes, we now face a largely unmet challenge to identify functional variants within disease-associated genes. Functional variants can be identified by trans-species complementation, e.g., by failure to rescue a yeast strain bearing a mutation in an orthologous human gene. Although orthologous complementation assays are powerful predictors of pathogenic variation, they are available for only a few percent of human disease genes. Here we systematically examine the question of whether complementation assays based on paralogy relationships can expand the number of human disease genes with functional variant detection assays. We tested over 1,000 paralogous human-yeast gene pairs for complementation, yielding 34 complementation relationships, of which 33 (97%) were novel. We found that paralog-based assays identified disease variants with success on par with that of orthology-based assays. Combining all homology-based assay results, we found that complementation can often identify pathogenic variants outside the homologous sequence region, presumably because of global effects on protein folding or stability. Within our search space, paralogy-based complementation more than doubled the number of human disease genes with a yeast-based complementation assay for disease variation. Functional complementation assays of human disease-associated gene variants can reveal many more human disease variants at high confidence than current computational approaches, even using highly-diverged model organisms. However, this has generally only been possible for a minority of human disease genes for which orthologous complementation is known in the relevant model organism, so that alternative assays are urgently needed. Here we show that complementation relationships can be found for many additional human disease genes by exploiting paralogous human-yeast gene relationships, and that disease variant identification using paralogy-based assays performs on par with orthology-based assays.
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Affiliation(s)
- Fan Yang
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Song Sun
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Guihong Tan
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Costanzo
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - David E. Hill
- Center for Cancer Systems Biology (CCSB), Dana- Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana- Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brenda J. Andrews
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Frederick P. Roth
- Donnelly Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Center for Cancer Systems Biology (CCSB), Dana- Farber Cancer Institute, Boston, Massachusetts, United States of America
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- * E-mail:
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43
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Lu H, Villafane N, Dogruluk T, Grzeskowiak CL, Kong K, Tsang YH, Zagorodna O, Pantazi A, Yang L, Neill NJ, Kim YW, Creighton CJ, Verhaak RG, Mills GB, Park PJ, Kucherlapati R, Scott KL. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. Cancer Res 2017; 77:3502-3512. [PMID: 28512244 DOI: 10.1158/0008-5472.can-16-2745] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Oncogenic gene fusions drive many human cancers, but tools to more quickly unravel their functional contributions are needed. Here we describe methodology permitting fusion gene construction for functional evaluation. Using this strategy, we engineered the known fusion oncogenes, BCR-ABL1, EML4-ALK, and ETV6-NTRK3, as well as 20 previously uncharacterized fusion genes identified in The Cancer Genome Atlas datasets. In addition to confirming oncogenic activity of the known fusion oncogenes engineered by our construction strategy, we validated five novel fusion genes involving MET, NTRK2, and BRAF kinases that exhibited potent transforming activity and conferred sensitivity to FDA-approved kinase inhibitors. Our fusion construction strategy also enabled domain-function studies of BRAF fusion genes. Our results confirmed other reports that the transforming activity of BRAF fusions results from truncation-mediated loss of inhibitory domains within the N-terminus of the BRAF protein. BRAF mutations residing within this inhibitory region may provide a means for BRAF activation in cancer, therefore we leveraged the modular design of our fusion gene construction methodology to screen N-terminal domain mutations discovered in tumors that are wild-type at the BRAF mutation hotspot, V600. We identified an oncogenic mutation, F247L, whose expression robustly activated the MAPK pathway and sensitized cells to BRAF and MEK inhibitors. When applied broadly, these tools will facilitate rapid fusion gene construction for subsequent functional characterization and translation into personalized treatment strategies. Cancer Res; 77(13); 3502-12. ©2017 AACR.
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Affiliation(s)
- Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Nicole Villafane
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angeliki Pantazi
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lixing Yang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Young Won Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Roel G Verhaak
- The Jackson Laboratory, Genomic Medicine, Farmington, Connecticut
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Raju Kucherlapati
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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44
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Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ. Interactome disassembly during apoptosis occurs independent of caspase cleavage. Mol Syst Biol 2017; 13:906. [PMID: 28082348 PMCID: PMC5293159 DOI: 10.15252/msb.20167067] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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] [Indexed: 12/18/2022] Open
Abstract
Protein-protein interaction networks (interactomes) define the functionality of all biological systems. In apoptosis, proteolysis by caspases is thought to initiate disassembly of protein complexes and cell death. Here we used a quantitative proteomics approach, protein correlation profiling (PCP), to explore changes in cytoplasmic and mitochondrial interactomes in response to apoptosis initiation as a function of caspase activity. We measured the response to initiation of Fas-mediated apoptosis in 17,991 interactions among 2,779 proteins, comprising the largest dynamic interactome to date. The majority of interactions were unaffected early in apoptosis, but multiple complexes containing known caspase targets were disassembled. Nonetheless, proteome-wide analysis of proteolytic processing by terminal amine isotopic labeling of substrates (TAILS) revealed little correlation between proteolytic and interactome changes. Our findings show that, in apoptosis, significant interactome alterations occur before and independently of caspase activity. Thus, apoptosis initiation includes a tight program of interactome rearrangement, leading to disassembly of relatively few, select complexes. These early interactome alterations occur independently of cleavage of these protein by caspases.
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Affiliation(s)
- Nichollas E Scott
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Lindsay D Rogers
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Nat F Brown
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Nikolaus Fortelny
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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45
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Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biol 2016; 17:266. [PMID: 28038678 PMCID: PMC5203714 DOI: 10.1186/s13059-016-1118-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [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: 06/13/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. RESULTS We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data. CONCLUSIONS Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.
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Affiliation(s)
- Abhinav Nellore
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jean-Philippe Fortin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - José Alquicira-Hernández
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Undergraduate Program in Genome Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Leonardo Collado-Torres
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Siruo Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Mathematics and Computer Science, Centre College, Danville, KY, USA
| | - Robert A Phillips
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biological Sciences, Salisbury University, Salisbury, MD, USA
| | - Nishika Karbhari
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
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46
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Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT. Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation. Proc Natl Acad Sci U S A 2016; 113:E3892-900. [PMID: 27325776 DOI: 10.1073/pnas.1600582113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Targeted transcriptional regulation is a powerful tool to study genetic mediators of cellular behavior. Here, we show that catalytically dead Cas9 (dCas9) targeted to genomic regions upstream or downstream of the transcription start site allows for specific and sustainable gene-expression level alterations in tumor cells in vitro and in syngeneic immune-competent mouse models. We used this approach for a high-coverage pooled gene-activation screen in vivo and discovered previously unidentified modulators of tumor growth and therapeutic response. Moreover, by using dCas9 linked to an activation domain, we can either enhance or suppress target gene expression simply by changing the genetic location of dCas9 binding relative to the transcription start site. We demonstrate that these directed changes in gene-transcription levels occur with minimal off-target effects. Our findings highlight the use of dCas9-mediated transcriptional regulation as a versatile tool to reproducibly interrogate tumor phenotypes in vivo.
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47
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Masser DR, Stanford DR, Hadad N, Giles CB, Wren JD, Sonntag WE, Richardson A, Freeman WM. Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation. Age (Dordr) 2016; 38:49. [PMID: 27091453 PMCID: PMC5005917 DOI: 10.1007/s11357-016-9914-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
Epigenetic regulation through DNA methylation (5mC) plays an important role in development, aging, and a variety of diseases. Genome-wide studies of base- and strand-specific 5mC are limited by the extensive sequencing required. Targeting bisulfite sequencing to specific genomic regions through sequence capture with complimentary oligonucleotide probes retains the advantages of bisulfite sequencing while focusing sequencing reads on regions of interest, enables analysis of more samples by decreasing the amount of sequence required per sample, and provides base- and strand-specific absolute quantitation of CG and non-CG methylation levels. As an example, an oligonucleotide capture set to interrogate 5mC levels in all rat RefSeq gene promoter regions (18,814) and CG islands, shores, and shelves (18,411) was generated. Validation using whole-genome methylation standards and biological samples demonstrates enrichment of the targeted regions and accurate base-specific quantitation of CG and non-CG methylation for both forward and reverse genomic strands. A total of 170 Mb of the rat genome is covered including 6.6 million CGs and over 67 million non-CG sites, while reducing the amount of sequencing required by ~85 % as compared to existing whole-genome sequencing methods. This oligonucleotide capture targeting approach and quantitative validation workflow can also be applied to any genome of interest.
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Affiliation(s)
- Dustin R. Masser
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Harold Hamm Diabetes Center, Oklahoma City, OK USA
| | - David R. Stanford
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Harold Hamm Diabetes Center, Oklahoma City, OK USA
- Oklahoma Nathan Shock Center of Excellence in Basic Biology of Aging, Oklahoma City, OK USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Oklahoma Center for Neuroscience, Oklahoma City, OK USA
| | - Cory B. Giles
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Jonathan D. Wren
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Oklahoma Nathan Shock Center of Excellence in Basic Biology of Aging, Oklahoma City, OK USA
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - William E. Sonntag
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Oklahoma Nathan Shock Center of Excellence in Basic Biology of Aging, Oklahoma City, OK USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Arlan Richardson
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Oklahoma Nathan Shock Center of Excellence in Basic Biology of Aging, Oklahoma City, OK USA
- Oklahoma City VA Medical Center, Oklahoma City, OK USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Willard M. Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Reynolds Oklahoma Center on Aging, Oklahoma City, OK USA
- Harold Hamm Diabetes Center, Oklahoma City, OK USA
- Oklahoma Nathan Shock Center of Excellence in Basic Biology of Aging, Oklahoma City, OK USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Department of Physiology OUHSC, BSMB 653, P.O. Box 26901, Oklahoma City, OK 73126 USA
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48
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Abstract
Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their evolutionary profiles against a diverse set of phenotypes recently annotated across multiple mammalian species. We identify 2,759 compelling associations between human CNEs and a diverse set of mammalian phenotypes. We discuss multiple CNEs, including a predicted ear element near BMP7, a pelvic CNE in FBN1, a brain morphology element in UBE4B, and an aquatic adaptation forelimb CNE near EGR2, and provide a full list of our predictions. As more genomes are sequenced and more traits are annotated across species, we expect our method to facilitate the interpretation of noncoding mutations in human disease and expedite the discovery of individual CNEs that play key roles in human evolution and development.
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Affiliation(s)
- Amir Marcovitz
- Department of Developmental Biology, Stanford University
| | - Robin Jia
- Department of Computer Science, Stanford University
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University Department of Computer Science, Stanford University Department of Pediatrics, Stanford University
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49
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Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Mol Syst Biol 2016; 12:863. [PMID: 27107012 PMCID: PMC4848762 DOI: 10.15252/msb.20156660] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [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] [Indexed: 12/22/2022] Open
Abstract
High‐throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome‐scale interaction mapping. Here, we report Barcode Fusion Genetics‐Yeast Two‐Hybrid (BFG‐Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG‐Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein‐pair barcodes that can be quantified via next‐generation sequencing. We applied BFG‐Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG‐Y2H increases the efficiency of protein matrix screening, with quality that is on par with state‐of‐the‐art Y2H methods.
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Affiliation(s)
- Nozomu Yachie
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Synthetic Biology Division, Research Center for Advanced Science and Technology The University of Tokyo, Tokyo, Japan Institute for Advanced Bioscience, Keio University, Tsuruoka, Yamagata, Japan PRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Evangelia Petsalaki
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Joseph C Mellor
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN Institut Pasteur, Paris, France
| | - Marta Verby
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Sedide B Ozturk
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Siyang Li
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Atina G Cote
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Roberto Mosca
- Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Jennifer J Knapp
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Minjeong Ko
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Analyn Yu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Nidhi Sahni
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Song Yi
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Tanya Tyagi
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cassandra Wong
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Louai Musa
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Yi-Chun Liu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Pascal Braun
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Plant Systems Biology, Technische Universität München Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Aloy
- Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Canadian Institute for Advanced Research, Toronto, ON, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell 2016; 164:805-17. [PMID: 26871637 PMCID: PMC4882190 DOI: 10.1016/j.cell.2016.01.029] [Citation(s) in RCA: 340] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/12/2015] [Accepted: 01/20/2016] [Indexed: 12/11/2022]
Abstract
While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms").
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Affiliation(s)
- Xinping Yang
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | | | - Shuli Kang
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gloria M. Sheynkman
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tong Hao
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron Richardson
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Song Sun
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada,Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Fan Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yun A. Shen
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan R. Murray
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kerstin Spirohn
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bridget E. Begg
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Miquel Duran-Frigola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Andrew MacWilliams
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel J. Pevzner
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Boston University School of Medicine, Boston, MA 02118, USA
| | - Quan Zhong
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shelly A. Trigg
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley Tam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nidhi Sahni
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Song Yi
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Maria D. Rodriguez
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dawit Balcha
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Guihong Tan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Brenda Andrews
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Xianghong J. Zhou
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kourosh Salehi-Ashtiani
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Benoit Charloteaux
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alyce A. Chen
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A. Calderwood
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Catalonia, Spain
| | - Frederick P. Roth
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada,Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - David E. Hill
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA,Correspondence: (M.V.), (Y.X.), (L.M.I.)
| | - Yu Xia
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.
| | - Marc Vidal
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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