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Sternberg PW, Van Auken K, Wang Q, Wright A, Yook K, Zarowiecki M, Arnaboldi V, Becerra A, Brown S, Cain S, Chan J, Chen WJ, Cho J, Davis P, Diamantakis S, Dyer S, Grigoriadis D, Grove CA, Harris T, Howe K, Kishore R, Lee R, Longden I, Luypaert M, Müller HM, Nuin P, Quinton-Tulloch M, Raciti D, Schedl T, Schindelman G, Stein L. WormBase 2024: status and transitioning to Alliance infrastructure. Genetics 2024; 227:iyae050. [PMID: 38573366 PMCID: PMC11075546 DOI: 10.1093/genetics/iyae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
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Affiliation(s)
- Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Adam Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magdalena Zarowiecki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stephanie Brown
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | | | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ian Longden
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Hans-Michael Müller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
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Wheeler DW, Kopsick JD, Sutton N, Tecuatl C, Komendantov AO, Nadella K, Ascoli GA. Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. eLife 2024; 12:RP90597. [PMID: 38345923 PMCID: PMC10942544 DOI: 10.7554/elife.90597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Previously, Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression (Wheeler et al., 2015). Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
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Affiliation(s)
- Diek W Wheeler
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Jeffrey D Kopsick
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason UniversityFairfaxUnited States
| | - Nate Sutton
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Carolina Tecuatl
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Alexander O Komendantov
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Kasturi Nadella
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason UniversityFairfaxUnited States
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3
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Wheeler DW, Kopsick JD, Sutton N, Tecuatl C, Komendantov AO, Nadella K, Ascoli GA. Hippocampome.org v2.0: a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.12.540597. [PMID: 37425693 PMCID: PMC10327012 DOI: 10.1101/2023.05.12.540597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression. Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
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Affiliation(s)
- Diek W. Wheeler
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Jeffrey D. Kopsick
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Interdisciplinary Program in Neuroscience; College of Science; George Mason University, Fairfax, VA, USA
| | - Nate Sutton
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Carolina Tecuatl
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Alexander O. Komendantov
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Kasturi Nadella
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Interdisciplinary Program in Neuroscience; College of Science; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
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Barranco D, Cabo-Ruiz V, Risco R. Use of fine capillaries for cryopreservation of Caenorhabditis elegans by vitrification. Cryobiology 2023; 113:104585. [PMID: 37690502 DOI: 10.1016/j.cryobiol.2023.104585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Caenorhabditis elegans is an exceptional model organism. More than twenty thousand different strains have been developed, increasing knowledge on countless topics. However, the traditional method to cryopreserve this nematode, based on slow freezing, usually reaches recovery rates of around 35% for the L1 and L2 larval stages. Here, we propose two alternative methods to cryopreserve this nematode based on vitrification that are applicable in common laboratories and allow the selective individual cryopreservation of this organism. These new methods require ultra-high warming rates, which are achieved by employing very thin capillaries as the nematode container, and a very low final concentration of cryoprotectants, which, as compared to slow freezing, reduce toxicity damage. The recovery rate was 98.5% for larvae (L1 - L4) and 84.3% for adults. Given these results, our procedures offer an alternative to cryopreserve this nematode (larvae and adults) with higher recovery rates, avoiding expensive requirements. Indeed, it only needed a container with liquid nitrogen and a warming bath for water at 37 °C. The high performance of this approach has been revealed by preserving the long-term memory and, probably, the connectome of this nematode.
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Affiliation(s)
- Daniel Barranco
- Escuela Superior de Ingeniería, University of Seville, Spain; Faculty of Education and Psychology, University of Atlantico Medio, Spain.
| | | | - Ramón Risco
- Escuela Superior de Ingeniería, University of Seville, Spain; National Accelerators Centre-US, JA, CSIC, Seville, Spain.
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5
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Balasubramaniam B, Topalidou I, Kelley M, Meadows SM, Funk O, Ailion M, Fay DS. Effectors of anterior morphogenesis in C. elegans embryos. Biol Open 2023; 12:bio059982. [PMID: 37345480 PMCID: PMC10339035 DOI: 10.1242/bio.059982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 06/23/2023] Open
Abstract
During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. At present, the factors that contribute to aECM function are mostly unknown, including the aECM components themselves, their posttranslational regulators, and the pathways required for their secretion. Here we showed that two proteins previously linked to aECM function, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function in a complex. Proteomics experiments also suggested potential roles for SYM-3/FAM102A and SYM-4/WDR44 family proteins in intracellular trafficking. Nonetheless, we found no evidence to support a critical function for SYM-3 or SYM-4 in the apical deposition of two aECM components, NOAH-1 and FBN-1. Moreover, loss of a key splicing regulator of fbn-1, MEC-8/RBPMS2, had surprisingly little effect on the abundance or deposition of FBN-1. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. We also characterized morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a similar phenotype to mec-8; sym double mutants. Collectively, these findings add to our knowledge of factors controlling embryonic morphogenesis.
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Affiliation(s)
- Boopathi Balasubramaniam
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle 98195-7350, WA, USA
| | - Melissa Kelley
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Sarina M. Meadows
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Owen Funk
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle 98195-7350, WA, USA
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
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6
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Moreno A, Taffet A, Tjahjono E, Anderson QL, Kirienko NV. Examining Sporadic Cancer Mutations Uncovers a Set of Genes Involved in Mitochondrial Maintenance. Genes (Basel) 2023; 14:1009. [PMID: 37239369 PMCID: PMC10218105 DOI: 10.3390/genes14051009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondria are key organelles for cellular health and metabolism and the activation of programmed cell death processes. Although pathways for regulating and re-establishing mitochondrial homeostasis have been identified over the past twenty years, the consequences of disrupting genes that regulate other cellular processes, such as division and proliferation, on affecting mitochondrial function remain unclear. In this study, we leveraged insights about increased sensitivity to mitochondrial damage in certain cancers, or genes that are frequently mutated in multiple cancer types, to compile a list of candidates for study. RNAi was used to disrupt orthologous genes in the model organism Caenorhabditis elegans, and a series of assays were used to evaluate these genes' importance for mitochondrial health. Iterative screening of ~1000 genes yielded a set of 139 genes predicted to play roles in mitochondrial maintenance or function. Bioinformatic analyses indicated that these genes are statistically interrelated. Functional validation of a sample of genes from this set indicated that disruption of each gene caused at least one phenotype consistent with mitochondrial dysfunction, including increased fragmentation of the mitochondrial network, abnormal steady-state levels of NADH or ROS, or altered oxygen consumption. Interestingly, RNAi-mediated knockdown of these genes often also exacerbated α-synuclein aggregation in a C. elegans model of Parkinson's disease. Additionally, human orthologs of the gene set showed enrichment for roles in human disorders. This gene set provides a foundation for identifying new mechanisms that support mitochondrial and cellular homeostasis.
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Affiliation(s)
| | | | | | | | - Natalia V. Kirienko
- Department of BioSciences, Rice University, 6100 Main St, MS140, Houston, TX 77005, USA; (A.M.); (A.T.); (E.T.); (Q.L.A.)
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7
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Boopathi B, Topalidou I, Kelley M, Meadows SM, Funk O, Ailion M, Fay DS. Pathways that affect anterior morphogenesis in C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.537986. [PMID: 37163004 PMCID: PMC10168279 DOI: 10.1101/2023.04.23.537986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. We showed that two conserved proteins linked to this process, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function together in a complex. Proteomics data also suggested potential roles for FAM102A and WDR44 family proteins in intracellular trafficking, consistent with their localization patterns. Nonetheless, we found no evidence to support a clear function for SYM-3 or SYM-4 in the apical deposition of two aECM components, FBN-1 and NOAH. Surprisingly, loss of MEC-8/RBPMS2, a conserved splicing factor and regulator of fbn-1 , had little effect on the abundance or deposition of FBN-1 to the aECM. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. Lastly, we examined morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a related embryonic phenotype to mec-8; sym double mutants. Collectively, our findings add to our knowledge of pathways controlling embryonic morphogenesis. SUMMARY STATEMENT We identify new proteins in apical ECM biology in C. elegans and provide evidence that SYM-3/FAM102A and SYM-4/WDR44 function together in trafficking but do not regulate apical ECM protein deposition.
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Affiliation(s)
- Balasubramaniam Boopathi
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, United States of America
| | - Melissa Kelley
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sarina M Meadows
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Owen Funk
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, United States of America
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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8
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Roadmap to the study of gene and protein phylogeny and evolution-A practical guide. PLoS One 2023; 18:e0279597. [PMID: 36827278 PMCID: PMC9955684 DOI: 10.1371/journal.pone.0279597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 12/12/2022] [Indexed: 02/25/2023] Open
Abstract
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.
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9
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Schmauder L, Sima S, Hadj AB, Cesar R, Richter K. Binding of the HSF-1 DNA-binding domain to multimeric C. elegans consensus HSEs is guided by cooperative interactions. Sci Rep 2022; 12:8984. [PMID: 35643773 PMCID: PMC9148306 DOI: 10.1038/s41598-022-12736-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
The protein HSF-1 is the controlling transcription factor of the heat-shock response (HSR). Its binding to the heat-shock elements (HSEs) induces the strong upregulation of conserved heat-shock proteins, including Hsp70s, Hsp40s and small HSPs. Next to these commonly known HSPs, more than 4000 other HSEs are found in the promoter regions of C. elegans genes. In microarray experiments, few of the HSE-containing genes are specifically upregulated during the heat-shock response. Most of the 4000 HSE-containing genes instead are unaffected by elevated temperatures and coexpress with genes unrelated to the HSR. This is also the case for several genes related to the HSP chaperone system, like dnj-12, dnj-13, and hsp-1. Interestingly, several promoters of the dedicated HSR-genes, like F44E5.4p, hsp-16.48p or hsp-16.2p, contain extended HSEs in their promoter region, composed of four or five HSE-elements instead of the common trimeric HSEs. We here aim at understanding how HSF-1 interacts with the different promoter regions. To this end we purify the nematode HSF-1 DBD and investigate the interaction with DNA sequences containing these regions. EMSA assays suggest that the HSF-1 DBD interacts with most of these HSE-containing dsDNAs, but with different characteristics. We employ sedimentation analytical ultracentrifugation (SV-AUC) to determine stoichiometry, affinity, and cooperativity of HSF-1 DBD binding to these HSEs. Interestingly, most HSEs show cooperative binding of the HSF-1 DBD with up to five DBDs being bound. In most cases binding to the HSEs of inducible promoters is stronger, even though the consensus scores are not always higher. The observed high affinity of HSF-1 DBD to the non-inducible HSEs of dnj-12, suggests that constitutive expression may be supported from some promoter regions, a fact that is evident for this transcription factor, that is essential also under non-stress conditions.
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Abstract
Over the past 50 years, the nematode worm Caenorhabditis elegans has become established as one of the most powerful and widely used model organisms. This article explores the origins and subsequent history of a generally accepted system for gene naming and genetic nomenclature in C. elegans.
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Affiliation(s)
- Jonathan Hodgkin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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11
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van Sluijs L, Bosman KJ, Pankok F, Blokhina T, Wilten JIHA, te Molder DM, Riksen JAG, Snoek BL, Pijlman GP, Kammenga JE, Sterken MG. Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. Front Cell Infect Microbiol 2022; 11:758331. [PMID: 35174100 PMCID: PMC8841876 DOI: 10.3389/fcimb.2021.758331] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Kobus J. Bosman
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Frederik Pankok
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Tatiana Blokhina
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Jop I. H. A. Wilten
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Dennie M. te Molder
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Mark G. Sterken
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mark G. Sterken,
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12
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Brayton CF. Laboratory Codes in Nomenclature and Scientific Communication (Advancing Organism Nomenclature in Scientific Communication to Improve Research Reporting and Reproducibility). ILAR J 2021; 62:295-309. [PMID: 36528817 DOI: 10.1093/ilar/ilac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/23/2022] [Indexed: 12/23/2022] Open
Abstract
Laboratory registration codes, also known as laboratory codes or lab codes, are a key element in standardized laboratory animal and genetic nomenclature. As such they are critical to accurate scientific communication and to research reproducibility and integrity. The original committee on Mouse Genetic Nomenclature published nomenclature conventions for mice genetics in 1940, and then conventions for inbred strains in 1952. Unique designations were needed, and have been in use since the 1950s, for the sources of animals and substrains, for the laboratories that identified new alleles or mutations, and then for developers of transgenes and induced mutations. Current laboratory codes are typically a 2- to 4-letter acronym for an institution or an investigator. Unique codes are assigned from the International Laboratory Code Registry, which was developed and is maintained by ILAR in the National Academies (National Academies of Sciences Engineering and Medicine and previously National Academy of Sciences). As a resource for the global research community, the registry has been online since 1997. Since 2003 mouse and rat genetic and strain nomenclature rules have been reviewed and updated annually as a joint effort of the International Committee on Standardized Genetic Nomenclature for Mice and the Rat Genome and Nomenclature Committee. The current nomenclature conventions (particularly conventions for non-inbred animals) are applicable beyond rodents, although not widely adopted. Ongoing recognition, since at least the 1930s, of the research relevance of genetic backgrounds and origins of animals, and of spontaneous and induced genetic variants speaks to the need for broader application of standardized nomenclature for animals in research, particularly given the increasing numbers and complexities of genetically modified swine, nonhuman primates, fish, and other species.
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Affiliation(s)
- Cory F Brayton
- Johns Hopkins Medicine, Molecular and Comparative Pathobiology, Baltimore, Maryland, USA
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13
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Chen T, Luo S, Wang X, Zhou Y, Dai Y, Zhou L, Feng S, Yuan M, Ding C. Polyphenols from Blumea laciniata Extended the Lifespan and Enhanced Resistance to Stress in Caenorhabditis elegans via the Insulin Signaling Pathway. Antioxidants (Basel) 2021; 10:antiox10111744. [PMID: 34829615 PMCID: PMC8614712 DOI: 10.3390/antiox10111744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
Blumea laciniata is widely used as a folk medicine in Asia, but relevant literature on it is rarely reported. We confirmed that polyphenol extract (containing chlorogenic acid, rutin, and luteolin-4-O-glucoside) from B. laciniata (EBL) showed strong antioxidant ability in vitro. Hence, in this work, we applied Caenorhabditis elegans to further investigate the antioxidant and anti-ageing abilities of EBL in vivo. The results showed that EBL enhanced the survival of C. elegans under thermal stress by 12.62% and sharply reduced the reactive oxygen species level as well as the content of malonaldehyde. Moreover, EBL increased the activities of antioxidant enzymes such as catalase and superoxide dismutase. Additionally, EBL promoted DAF-16, a transcription factor, into the nucleus. Besides, EBL extended the lifespan of C. elegans by 17.39%, showing an anti-ageing effect. Different mutants indicated that the insulin/IGF-1 signaling pathway participated in the antioxidant and anti-ageing effect of EBL on C. elegans.
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14
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Udayakumar P, Das R, Kannadasan A. Significance of probiotics in remodeling the gut consortium to enhance the immunity of Caenorhabditis elegans. Genesis 2021; 59:e23454. [PMID: 34664387 DOI: 10.1002/dvg.23454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/10/2022]
Abstract
In the recent past, Caenorhabditis elegans has emerged as one of the leading nematode models for studying host-microbe interactions on molecular, cellular, or organismal levels. In general, morphological and functional similarities of the gut of C. elegans with respect to that of human has brought in speculations on the study of the intestinal microbiota. On the other hand, probiotics have proved their efficacy in metabolism, development, and pathogenesis thereby inducing an immune response in C. elegans. Nurturing C. elegans with probiotics has led to immunomodulatory effects in the intestinal microbiota, proposing C. elegans as one of the in vivo screening criteria to select potential probiotic bacteria for host health-promoting factors. The major prospect of these probiotics is to exert longevity toward the host in diverse environmental conditions. The extent of research on probiotic metabolism has shed light on mechanisms of the immunomodulatory effect exerted by the nematode model. This review discusses various aspects of the effects of probiotics in improving the health and mechanisms involved in conferring immunity in C. elegans.
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Affiliation(s)
- Prithika Udayakumar
- Dr. APJ Abdul Kalam Centre for Excellence in Innovation and Entrepreneurship, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Reena Das
- Dr. APJ Abdul Kalam Centre for Excellence in Innovation and Entrepreneurship, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Anandbabu Kannadasan
- Dr. APJ Abdul Kalam Centre for Excellence in Innovation and Entrepreneurship, Dr. M.G.R. Educational and Research Institute, Chennai, India
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15
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Chandler R, Cogo S, Lewis P, Kevei E. Modelling the functional genomics of Parkinson's disease in Caenorhabditis elegans: LRRK2 and beyond. Biosci Rep 2021; 41:BSR20203672. [PMID: 34397087 PMCID: PMC8415217 DOI: 10.1042/bsr20203672] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
For decades, Parkinson's disease (PD) cases have been genetically categorised into familial, when caused by mutations in single genes with a clear inheritance pattern in affected families, or idiopathic, in the absence of an evident monogenic determinant. Recently, genome-wide association studies (GWAS) have revealed how common genetic variability can explain up to 36% of PD heritability and that PD manifestation is often determined by multiple variants at different genetic loci. Thus, one of the current challenges in PD research stands in modelling the complex genetic architecture of this condition and translating this into functional studies. Caenorhabditis elegans provide a profound advantage as a reductionist, economical model for PD research, with a short lifecycle, straightforward genome engineering and high conservation of PD relevant neural, cellular and molecular pathways. Functional models of PD genes utilising C. elegans show many phenotypes recapitulating pathologies observed in PD. When contrasted with mammalian in vivo and in vitro models, these are frequently validated, suggesting relevance of C. elegans in the development of novel PD functional models. This review will discuss how the nematode C. elegans PD models have contributed to the uncovering of molecular and cellular mechanisms of disease, with a focus on the genes most commonly found as causative in familial PD and risk factors in idiopathic PD. Specifically, we will examine the current knowledge on a central player in both familial and idiopathic PD, Leucine-rich repeat kinase 2 (LRRK2) and how it connects to multiple PD associated GWAS candidates and Mendelian disease-causing genes.
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Affiliation(s)
| | - Susanna Cogo
- School of Biological Sciences, University of Reading, Reading, RG6 6AH, U.K
- Department of Biology, University of Padova, Padova, Via Ugo Bassi 58/B, 35121, Italy
| | - Patrick A. Lewis
- Royal Veterinary College, University of London, London, NW1 0TU, U.K
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, U.K
| | - Eva Kevei
- School of Biological Sciences, University of Reading, Reading, RG6 6AH, U.K
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16
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17
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Emmons SW, Yemini E, Zimmer M. Methods for analyzing neuronal structure and activity in Caenorhabditis elegans. Genetics 2021; 218:6303616. [PMID: 34151952 DOI: 10.1093/genetics/iyab072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
The model research animal Caenorhabditis elegans has unique properties making it particularly advantageous for studies of the nervous system. The nervous system is composed of a stereotyped complement of neurons connected in a consistent manner. Here, we describe methods for studying nervous system structure and function. The transparency of the animal makes it possible to visualize and identify neurons in living animals with fluorescent probes. These methods have been recently enhanced for the efficient use of neuron-specific reporter genes. Because of its simple structure, for a number of years, C. elegans has been at the forefront of connectomic studies defining synaptic connectivity by electron microscopy. This field is burgeoning with new, more powerful techniques, and recommended up-to-date methods are here described that encourage the possibility of new work in C. elegans. Fluorescent probes for single synapses and synaptic connections have allowed verification of the EM reconstructions and for experimental approaches to synapse formation. Advances in microscopy and in fluorescent reporters sensitive to Ca2+ levels have opened the way to observing activity within single neurons across the entire nervous system.
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Affiliation(s)
- Scott W Emmons
- Department of Genetics and Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 1041, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Manuel Zimmer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria and.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
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18
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Wang Y, Luo S, Xu Z, Liu L, Feng S, Chen T, Zhou L, Yuan M, Huang Y, Ding CB. The potential antioxidant ability of hydroxytyrosol on Caenorhabditis elegans against oxidative damage via the insulin signaling pathway. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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19
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Kim E, Kim J, Kim C, Lee J. Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level. Nucleic Acids Res 2021; 49:3338-3353. [PMID: 33693840 PMCID: PMC8034613 DOI: 10.1093/nar/gkab141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/28/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Karyotype change and subsequent evolution is triggered by chromosome fusion and rearrangement events, which often occur when telomeres become dysfunctional. Telomeres protect linear chromosome ends from DNA damage responses (DDRs), and telomere dysfunction may result in genome instability. However, the complex chromosome end structures and the other possible consequences of telomere dysfunction have rarely been resolved at the nucleotide level due to the lack of the high-throughput methods needed to analyse these highly repetitive regions. Here we applied long-read sequencing technology to Caenorhabditis elegans survivor lines that emerged after telomere dysfunction. The survivors have preserved traces of DDRs in their genomes and our data revealed that variants generated by telomere dysfunction are accumulated along all chromosomes. The reconstruction of the chromosome end structures through de novo genome assemblies revealed diverse types of telomere damage processing at the nucleotide level. When telomeric repeats were totally eroded by telomere dysfunction, DDRs were mostly terminated by chromosome fusion events. We also partially reconstructed the most complex end structure and its DDR signatures, which would have been accumulated via multiple cell divisions. These finely resolved chromosome end structures suggest possible mechanisms regarding the repair processes after telomere dysfunction, providing insights into chromosome evolution in nature.
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Affiliation(s)
- Eunkyeong Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Chuna Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon 34141, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
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20
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Choi CP, Tay RJ, Starostik MR, Feng S, Moresco JJ, Montgomery BE, Xu E, Hammonds MA, Schatz MC, Montgomery TA, Yates JR, Jacobsen SE, Kim JK. SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. eLife 2021; 10:e60681. [PMID: 33587037 PMCID: PMC7884074 DOI: 10.7554/elife.60681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/02/2021] [Indexed: 12/29/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) play essential roles in silencing repetitive elements to promote fertility in metazoans. Studies in worms, flies, and mammals reveal that piRNAs are expressed in a sex-specific manner. However, the mechanisms underlying this sex-specific regulation are unknown. Here we identify SNPC-1.3, a male germline-enriched variant of a conserved subunit of the small nuclear RNA-activating protein complex, as a male-specific piRNA transcription factor in Caenorhabditis elegans. SNPC-1.3 colocalizes with the core piRNA transcription factor, SNPC-4, in nuclear foci of the male germline. Binding of SNPC-1.3 at male piRNA loci drives spermatogenic piRNA transcription and requires SNPC-4. Loss of snpc-1.3 leads to depletion of male piRNAs and defects in male-dependent fertility. Furthermore, TRA-1, a master regulator of sex determination, binds to the snpc-1.3 promoter and represses its expression during oogenesis. Loss of TRA-1 targeting causes ectopic expression of snpc-1.3 and male piRNAs during oogenesis. Thus, sexually dimorphic regulation of snpc-1.3 expression coordinates male and female piRNA expression during germline development.
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Affiliation(s)
- Charlotte P Choi
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Rebecca J Tay
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los AngelesLos AngelesUnited States
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical CenterDallasUnited States
| | | | - Emily Xu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Maya A Hammonds
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Michael C Schatz
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | | | - John R Yates
- Department of Molecular Medicine, The Scripps Research InstituteLa JollaUnited States
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
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21
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Hutchison LAD, Berger B, Kohane IS. Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. Bioinformatics 2020; 36:4047-4057. [PMID: 31860066 PMCID: PMC7332571 DOI: 10.1093/bioinformatics/btz864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/23/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION The advent of in vivo automated techniques for single-cell lineaging, sequencing and analysis of gene expression has begun to dramatically increase our understanding of organismal development. We applied novel meta-analysis and visualization techniques to the EPIC single-cell-resolution developmental gene expression dataset for Caenorhabditis elegans from Bao, Murray, Waterston et al. to gain insights into regulatory mechanisms governing the timing of development. RESULTS Our meta-analysis of the EPIC dataset revealed that a simple linear combination of the expression levels of the developmental genes is strongly correlated with the developmental age of the organism, irrespective of the cell division rate of different cell lineages. We uncovered a pattern of collective sinusoidal oscillation in gene activation, in multiple dominant frequencies and in multiple orthogonal axes of gene expression, pointing to the existence of a coordinated, multi-frequency global timing mechanism. We developed a novel method based on Fisher's Discriminant Analysis to identify gene expression weightings that maximally separate traits of interest, and found that remarkably, simple linear gene expression weightings are capable of producing sinusoidal oscillations of any frequency and phase, adding to the growing body of evidence that oscillatory mechanisms likely play an important role in the timing of development. We cross-linked EPIC with gene ontology and anatomy ontology terms, employing Fisher's Discriminant Analysis methods to identify previously unknown positive and negative genetic contributions to developmental processes and cell phenotypes. This meta-analysis demonstrates new evidence for direct linear and/or sinusoidal mechanisms regulating the timing of development. We uncovered a number of previously unknown positive and negative correlations between developmental genes and developmental processes or cell phenotypes. Our results highlight both the continued relevance of the EPIC technique, and the value of meta-analysis of previously published results. The presented analysis and visualization techniques are broadly applicable across developmental and systems biology. AVAILABILITY AND IMPLEMENTATION Analysis software available upon request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Bonnie Berger
- MIT Computer Science and AI Lab, Cambridge, MA 02139, USA
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22
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Chowanadisai W, Hart MD, Strong MD, Graham DM, Rucker RB, Smith BJ, Keen CL, Messerli MA. Genetic and Genomic Advances in Developmental Models: Applications for Nutrition Research. Adv Nutr 2020; 11:971-978. [PMID: 32135011 PMCID: PMC7360451 DOI: 10.1093/advances/nmaa022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/22/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
There is increasing appreciation that dietary components influence and interact with genes important to metabolism. How such influences impact developmental regulation and programming or risks of chronic diseases remains unclear. Nutrition is recognized to affect development and chronic diseases, but our understanding about how genes essential to nutrient metabolism regulate development and impact risks of these diseases remains unclear. Historically, mammalian models, especially rodents such as rats and mice, have been the primary models used for nutrition and developmental nutrition science, although their complexity and relatively slow rate of development often compromise rapid progress in resolving fundamental, genetic-related questions. Accordingly, the objective of this review is to highlight the opportunities for developmental models in the context of uncovering the function of gene products that are relevant to human nutrition and provide the scientific bases for these opportunities. We present recent studies in zebrafish related to obesity as applications of developmental models in nutritional science. Although the control of external factors and dependent variables, such as nutrition, can be a challenge, suggestions for standardizations related to diet are made to improve consistency in findings between laboratories. The review also highlights the need for standardized diets across different developmental models, which could improve consistency in findings across laboratories. Alternative and developmental animal models have advantages and largely untapped potential for the advancement of nutrigenomics and nutritionally relevant research areas.
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Affiliation(s)
| | - Matthew D Hart
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Morgan D Strong
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - David M Graham
- Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Robert B Rucker
- Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Brenda J Smith
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Carl L Keen
- Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Mark A Messerli
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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23
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Partridge FA, Forman R, Bataille CJR, Wynne GM, Nick M, Russell AJ, Else KJ, Sattelle DB. Anthelmintic drug discovery: target identification, screening methods and the role of open science. Beilstein J Org Chem 2020; 16:1203-1224. [PMID: 32550933 PMCID: PMC7277699 DOI: 10.3762/bjoc.16.105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Helminths, including cestodes, nematodes and trematodes, are a huge global health burden, infecting hundreds of millions of people. In many cases, existing drugs such as benzimidazoles, diethylcarbamazine, ivermectin and praziquantel are insufficiently efficacious, contraindicated in some populations, or at risk of the development of resistance, thereby impeding progress towards World Health Organization goals to control or eliminate these neglected tropical diseases. However, there has been limited recent progress in developing new drugs for these diseases due to lack of commercial attractiveness, leading to the introduction of novel, more efficient models for drug innovation that attempt to reduce the cost of research and development. Open science aims to achieve this by encouraging collaboration and the sharing of data and resources between organisations. In this review we discuss how open science has been applied to anthelmintic drug discovery. Open resources, including genomic information from many parasites, are enabling the identification of targets for new antiparasitic agents. Phenotypic screening remains important, and there has been much progress in open-source systems for compound screening with parasites, including motility assays but also high content assays with more detailed investigation of helminth physiology. Distributed open science compound screening programs, such as the Medicines for Malaria Venture Pathogen Box, have been successful at facilitating screening in diverse assays against many different parasite pathogens and models. Of the compounds identified so far in these screens, tolfenpyrad, a repurposed insecticide, shows significant promise and there has been much progress in creating more potent and selective derivatives. This work exemplifies how open science approaches can catalyse drug discovery against neglected diseases.
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Affiliation(s)
- Frederick A Partridge
- Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Ruth Forman
- The Lydia Becker Institute for Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Carole J R Bataille
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA United Kingdom
| | - Graham M Wynne
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA United Kingdom
| | - Marina Nick
- Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Angela J Russell
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA United Kingdom
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, United Kingdom
| | - Kathryn J Else
- The Lydia Becker Institute for Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - David B Sattelle
- Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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24
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Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Cho J, Davis P, Gao S, Grove CA, Kishore R, Lee RYN, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers FH, Russell M, Schindelman G, Auken KV, Wang Q, Williams G, Wright AJ, Yook K, Howe KL, Schedl T, Stein L, Sternberg PW. WormBase: a modern Model Organism Information Resource. Nucleic Acids Res 2020; 48:D762-D767. [PMID: 31642470 PMCID: PMC7145598 DOI: 10.1093/nar/gkz920] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 01/16/2023] Open
Abstract
WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.
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Affiliation(s)
- Todd W Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sibyl Gao
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Christian A Grove
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Raymond Y N Lee
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cecilia Nakamura
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Faye H Rodgers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gary Schindelman
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kimberly V Auken
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qinghua Wang
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam J Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
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25
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Abstract
The root-knot nematodes of the genus Meloidogyne are important and damaging parasites capable of infecting most flowering plants. Within this genus, several species of the Meloidogyne incognita group show evidence of paleopolyploidy in their genomes. We used our software tool POInT, the Polyploidy Orthology Inference Tool, to phylogenetically model the gene losses that followed that polyploidy. These models, and simulations based on them, show that three of these species (M. incognita, M. arenaria and M. javanica) descend from a single common hybridization event that yielded triplicated genomes with three distinguishable subgenomes. While one of the three subgenomes shows elevated gene loss rates relative to the other two, this subgenome does not show elevated sequence divergence. In all three species, ancestral loci where two of the three gene copies have been lost are less likely to have orthologs in Caenorhabditis elegans that are lethal when knocked down than are ancestral loci with surviving duplicate copies.
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26
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The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting. Genome Res 2019; 29:2104-2116. [PMID: 31744903 PMCID: PMC6886508 DOI: 10.1101/gr.254839.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022]
Abstract
3′ Untranslated regions (3′ UTRs) of mRNAs emerged as central regulators of cellular function because they contain important but poorly characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode Caenorhabditis elegans is ideal to study these interactions because it possesses a well-defined 3′ UTRome. To improve its annotation, we have used a genome-wide bioinformatics approach to download raw transcriptome data for 1088 transcriptome data sets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3′-UTR data at ultradeep coverage. Here, we describe and release to the community the updated version of the worm 3′ UTRome, which we named 3′ UTRome v2. This resource contains high-quality 3′-UTR data mapped at single-base ultraresolution for 23,084 3′-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this data set to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3′ UTRome v2 represents the most comprehensive and high-resolution 3′-UTR data set available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3′-UTR biology, and miRNA targeting in a living organism.
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27
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Holmer R, van Velzen R, Geurts R, Bisseling T, de Ridder D, Smit S. GeneNoteBook, a collaborative notebook for comparative genomics. Bioinformatics 2019; 35:4779-4781. [PMID: 31199463 PMCID: PMC6853645 DOI: 10.1093/bioinformatics/btz491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 05/03/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms. AVAILABILITY AND IMPLEMENTATION GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rens Holmer
- Laboratory of Molecular Biology, 6708PB Wageningen, The Netherlands.,Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, 6708PB Wageningen, The Netherlands
| | - Rene Geurts
- Laboratory of Molecular Biology, 6708PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, 6708PB Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
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28
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Nomoto Y, Kubota Y, Ohnishi Y, Kasahara K, Tomita A, Oshime T, Yamashita H, Fahmi M, Ito M. Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. PLoS One 2019; 14:e0215187. [PMID: 31504044 PMCID: PMC6736238 DOI: 10.1371/journal.pone.0215187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/06/2019] [Indexed: 11/24/2022] Open
Abstract
Obtaining a comprehensive understanding of the gene regulatory networks, or gene cascades, involved in cell fate determination and cell lineage segregation in Caenorhabditis elegans is a long-standing challenge. Although RNA-sequencing (RNA-Seq) is a promising technique to resolve these questions, the bioinformatics tools to identify associated gene cascades from RNA-Seq data remain inadequate. To overcome these limitations, we developed Gene Cascade Finder (GCF) as a novel tool for building gene cascades by comparison of mutant and wild-type RNA-Seq data along with integrated information of protein-protein interactions, expression timing, and domains. Application of GCF to RNA-Seq data confirmed that SPN-4 and MEX-3 regulate the canonical Wnt pathway during embryonic development. Moreover, lin-35, hsp-3, and gpa-12 were found to be involved in MEX-1-dependent neurogenesis, and MEX-3 was found to control the gene cascade promoting neurogenesis through lin-35 and apl-1. Thus, GCF could be a useful tool for building gene cascades from RNA-Seq data.
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Affiliation(s)
- Yusuke Nomoto
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Yukihiro Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Yuto Ohnishi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Kota Kasahara
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Aimi Tomita
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takehiro Oshime
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Hiroki Yamashita
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Muhamad Fahmi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
- * E-mail:
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29
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Abstract
In recent years, tremendous advances have been made in our ability to characterize complex microbial communities such as the gut microbiota, and numerous surveys of the human gut microbiota have identified countless associations between different compositional attributes of the gut microbiota and adverse health conditions. However, most of these findings in humans are purely correlative and animal models are required for prospective evaluation of such changes as causative factors in disease initiation or progression. As in most fields of biomedical research, microbiota-focused studies are predominantly performed in mouse or rat models. Depending on the field of research and experimental question or objective, non-rodent models may be preferable due to better translatability or an inability to use rodents for various reasons. The following review describes the utility and limitations of several non-rodent model species for research on the microbiota and its influence on host physiology and disease. In an effort to balance the breadth of potential model species with the amount of detail provided, four model species are discussed: zebrafish, dogs, pigs, and rabbits.
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Affiliation(s)
- Aaron C Ericsson
- Department of Veterinary Pathobiology, University of Missouri, United States of America
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30
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Brady SC, Zdraljevic S, Bisaga KW, Tanny RE, Cook DE, Lee D, Wang Y, Andersen EC. A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans. Genetics 2019; 212:1453-1468. [PMID: 31171655 PMCID: PMC6707474 DOI: 10.1534/genetics.119.302286] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines, and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene (scb-1) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance.
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Affiliation(s)
- Shannon C Brady
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208
| | - Stefan Zdraljevic
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208
| | - Karol W Bisaga
- Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois 60208
| | - Robyn E Tanny
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | | | - Daehan Lee
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Ye Wang
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611
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31
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Sheikh MO, Tayyari F, Zhang S, Judge MT, Weatherly DB, Ponce FV, Wells L, Edison AS. Correlations Between LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in Caenorhabditis elegans Development. Front Mol Biosci 2019; 6:49. [PMID: 31316996 PMCID: PMC6611444 DOI: 10.3389/fmolb.2019.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/11/2019] [Indexed: 01/19/2023] Open
Abstract
This study examined the relationship between glycans, metabolites, and development in C. elegans. Samples of N2 animals were synchronized and grown to five different time points ranging from L1 to a mixed population of adults, gravid adults, and offspring. Each time point was replicated seven times. The samples were each assayed by a large particle flow cytometer (Biosorter) for size distribution data, LC-MS/MS for targeted N- and O-linked glycans, and NMR for metabolites. The same samples were utilized for all measurements, which allowed for statistical correlations between the data. A new protocol was developed to correlate Biosorter developmental data with LC-MS/MS data to obtain stage-specific information of glycans. From the five time points, four distinct sizes of worms were observed from the Biosorter distributions, ranging from the smallest corresponding to L1 to adult animals. A network model was constructed using the four binned sizes of worms as starting nodes and adding glycans and metabolites that had correlations with r ≥ 0.5 to those nodes. The emerging structure of the network showed distinct patterns of N- and O-linked glycans that were consistent with previous studies. Furthermore, some metabolites that were correlated to these glycans and worm sizes showed interesting interactions. Of note, UDP-GlcNAc had strong positive correlations with many O-glycans that were expressed in the largest animals. Similarly, phosphorylcholine correlated with many N-glycans that were expressed in L1 animals.
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Affiliation(s)
- M Osman Sheikh
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Fariba Tayyari
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Sicong Zhang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Michael T Judge
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States.,Department of Genetics, University of Georgia, Athens, GA, United States
| | - D Brent Weatherly
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Francesca V Ponce
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Arthur S Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States.,Department of Genetics, University of Georgia, Athens, GA, United States.,Institute of Bioinformatics, University of Georgia, Athens, GA, United States
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32
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An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features. Comput Struct Biotechnol J 2019; 17:785-796. [PMID: 31312416 PMCID: PMC6607062 DOI: 10.1016/j.csbj.2019.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/23/2019] [Accepted: 05/26/2019] [Indexed: 12/23/2022] Open
Abstract
The availability of whole-genome sequences and associated multi-omics data sets, combined with advances in gene knockout and knockdown methods, has enabled large-scale annotation and exploration of gene and protein functions in eukaryotes. Knowing which genes are essential for the survival of eukaryotic organisms is paramount for an understanding of the basic mechanisms of life, and could assist in identifying intervention targets in eukaryotic pathogens and cancer. Here, we studied essential gene orthologs among selected species of eukaryotes, and then employed a systematic machine-learning approach, using protein sequence-derived features and selection procedures, to investigate essential gene predictions within and among species. We showed that the numbers of essential gene orthologs comprise small fractions when compared with the total number of orthologs among the eukaryotic species studied. In addition, we demonstrated that machine-learning models trained with subsets of essentiality-related data performed better than random guessing of gene essentiality for a particular species. Consistent with our gene ortholog analysis, the predictions of essential genes among multiple (including distantly-related) species is possible, yet challenging, suggesting that most essential genes are unique to a species. The present work provides a foundation for the expansion of genome-wide essentiality investigations in eukaryotes using machine learning approaches.
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Key Words
- CRISPR, Clustered regularly interspaced short palindromic repeats
- Essential genes
- Essentiality prediction
- Eukaryotes
- GBM, Gradient boosting method
- GI, Genetic interaction
- GLM, Generalised linear model
- GO, Gene ontology
- ML, Machine-learning
- Machine-learning
- NN, Artificial neural network
- OGEE, Online GEne essentiality database
- PPI, Protein-protein interaction
- PR-AUC, Area under the precision-recall curve
- RF, Random Forest
- RNAi, RNA interference
- ROC-AUC, Area under the receiver operating characteristic curve
- SPLS, Sparse partial least squares
- SVM, Support-Vector machine
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33
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Comparative Genomic Analysis of Trichinella spiralis Reveals Potential Mechanisms of Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2948973. [PMID: 31240209 PMCID: PMC6556364 DOI: 10.1155/2019/2948973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
Trichinellosis caused by parasitic nematodes of the genus Trichinella may result in human morbidity and mortality worldwide. Deciphering processes that drive species diversity and adaptation are key to understanding parasitism and developing effective control strategies. Our goal was to identify genes that are under positive selection and possible mechanisms of adaptive evolution of Trichinella spiralis genes using a comparative genomic analysis with the genomes of Brugia malayi, Trichuris suis, Ancylostoma ceylanicum, and Caenorhabditis elegans. The CODEML program derived from the PAML package was used to deduce the most probable dN/dS ratio, a measurement to detect genes/proteins undergoing adaptation. For each pair of sequences, those with a dN/dS ratio > 1 were considered positively selected genes (PSGs). Altogether, 986 genes were positively selected (p-value < 0.01). Genes involved in metabolic pathways, signaling pathways, and cytosolic DNA-sensing pathways were significantly enriched among the PSGs. Several PSGs are associated with exploitation of the host: modification of the host's metabolism, creation of new parasite-specific morphological structures between T. spiralis and the host interface, xenobiotic metabolism to combat low oxygen concentrations and host toxicity, muscle cell transformation, cell cycle arrest, DNA repair processes during nurse cell formation, antiapoptotic factors, immunomodulation, and regulation of epigenetic processes. Some of the T. spiralis PSGs have C. elegans orthologs that confer severe or lethal RNAi phenotypes. Fifty-seven PSGs in T. spiralis were analyzed to encode differentially expressed proteins. The present study utilized an overall comparative genomic analysis to discover PSGs within T. spiralis and their relationships with biological function and organism fitness. This analysis adds to our understanding of the possible mechanism that contributes to T. spiralis parasitism and biological adaptation within the host, and thus these identified genes may be potential targets for drug and vaccine development.
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34
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Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans. SCIENCE CHINA-LIFE SCIENCES 2019; 62:579-593. [DOI: 10.1007/s11427-019-9482-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 12/31/2022]
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35
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Abstract
WormBase is an open-access model-organism database that provides current and accurate genetic information of C. elegans and related nematodes. Users can search WormBase by several fields, including a gene or human disease. A special feature of the database is the inclusion of micropublications, peer-reviewed data that may go unpublished in traditional venues.
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Affiliation(s)
| | - Daryl D Hurd
- a St. John Fisher College , Rochester , New York , USA
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36
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Berrios DC, Beheshti A, Costes SV. FAIRness and Usability for Open-access Omics Data Systems. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2018:232-241. [PMID: 30815061 PMCID: PMC6371294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the "FAIRness" of NASA's GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility.
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Affiliation(s)
- Daniel C Berrios
- Universities Space Research Association
- NASA Ames Research Center, Moffett Field, CA
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37
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Maxson Jones K, Ankeny RA, Cook-Deegan R. The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project. JOURNAL OF THE HISTORY OF BIOLOGY 2018; 51:693-805. [PMID: 30390178 PMCID: PMC7307446 DOI: 10.1007/s10739-018-9538-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the "community" of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner's proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.
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Affiliation(s)
- Kathryn Maxson Jones
- Department of History, Princeton University, Princeton, NJ, USA.
- MBL McDonnell Foundation Scholar, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Rachel A Ankeny
- School of Humanities, The University of Adelaide, Adelaide, Australia
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, Consortium for Science, Policy & Outcomes, Arizona State University, Barrett & O'Connor Washington Center, Washington, D.C., USA
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Dong X, Chaisiri K, Xia D, Armstrong SD, Fang Y, Donnelly MJ, Kadowaki T, McGarry JW, Darby AC, Makepeace BL. Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism. Gigascience 2018; 7:5160133. [PMID: 30445460 PMCID: PMC6275457 DOI: 10.1093/gigascience/giy127] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
Background Trombidid mites have a unique life cycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea ("chiggers"), the larvae feed preferentially on vertebrates, including humans. Species in the genus Leptotrombidium are vectors of a potentially fatal bacterial infection, scrub typhus, that affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger, Leptotrombidium deliense, and for a velvet mite, Dinothrombium tinctorium. Results Sequencing was performed using Illumina technology. A 180 Mb draft assembly for D. tinctorium was generated from two paired-end and one mate-pair library using a single adult specimen. For L. deliense, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in the L. deliense genome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae. Conclusions Trombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.,Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.,School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China.,Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom
| | - Kittipong Chaisiri
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom.,Faculty of Tropical Medicine, Mahidol University, Ratchathewi Bangkok 10400, Thailand
| | - Dong Xia
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom.,The Royal Veterinary College, London NW1 0TU, United Kingdom
| | - Stuart D Armstrong
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom
| | - Yongxiang Fang
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - John W McGarry
- Institute of Veterinary Science, University of Liverpool, Liverpool L3 5RP, United Kingdom
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Benjamin L Makepeace
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom
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Bouzaglo D, Chasida I, Ezra Tsur E. Distributed retrieval engine for the development of cloud-deployed biological databases. BioData Min 2018; 11:26. [PMID: 30459848 PMCID: PMC6233384 DOI: 10.1186/s13040-018-0185-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/12/2018] [Indexed: 11/10/2022] Open
Abstract
The integration of cloud resources with federated data retrieval has the potential of improving the maintenance, accessibility and performance of specialized databases in the biomedical field. However, such an integrative approach requires technical expertise in cloud computing, usage of a data retrieval engine and development of a unified data-model, which can encapsulate the heterogeneity of biological data. Here, a framework for the development of cloud-based biological specialized databases is proposed. It is powered by a distributed biodata retrieval system, able to interface with different data formats, as well as provides an integrated way for data exploration. The proposed framework was implemented using Java as the development environment, and MongoDB as the database manager. Syntactic analysis was based on BSON, jsoup, Apache Commons and w3c.dom open libraries. Framework is available in: http://nbel-lab.com and is distributed under the creative common agreement.
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Affiliation(s)
- David Bouzaglo
- Neuro-biomorphic Engineering Lab, Faculty of Engineering, Jerusalem College of Technology, Jerusalem, Israel
| | - Israel Chasida
- Neuro-biomorphic Engineering Lab, Faculty of Engineering, Jerusalem College of Technology, Jerusalem, Israel
| | - Elishai Ezra Tsur
- Neuro-biomorphic Engineering Lab, Faculty of Engineering, Jerusalem College of Technology, Jerusalem, Israel
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Hahnel SR, Zdraljevic S, Rodriguez BC, Zhao Y, McGrath PT, Andersen EC. Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles. PLoS Pathog 2018; 14:e1007226. [PMID: 30372484 PMCID: PMC6224181 DOI: 10.1371/journal.ppat.1007226] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/08/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Benzimidazoles (BZ) are essential components of the limited chemotherapeutic arsenal available to control the global burden of parasitic nematodes. The emerging threat of BZ resistance among multiple nematode species necessitates the development of novel strategies to identify genetic and molecular mechanisms underlying this resistance. All detection of parasitic helminth resistance to BZ is focused on the genotyping of three variant sites in the orthologs of the β-tubulin gene found to confer resistance in the free-living nematode Caenorhabditis elegans. Because of the limitations of laboratory and field experiments in parasitic nematodes, it is difficult to look beyond these three sites to identify additional mechanisms that might contribute to BZ resistance in the field. Here, we took an unbiased genome-wide mapping approach in the free-living nematode species C. elegans to identify the genetic underpinnings of natural resistance to the commonly used BZ, albendazole (ABZ). We found a wide range of natural variation in ABZ resistance in natural C. elegans populations. In agreement with known mechanisms of BZ resistance in parasites, we found that a majority of the variation in ABZ resistance among wild C. elegans strains is caused by variation in the β-tubulin gene ben-1. This result shows empirically that resistance to ABZ naturally exists and segregates within the C. elegans population, suggesting that selection in natural niches could enrich for resistant alleles. We identified 25 distinct ben-1 alleles that are segregating at low frequencies within the C. elegans population, including many novel molecular variants. Population genetic analyses indicate that ben-1 variation arose multiple times during the evolutionary history of C. elegans and provide evidence that these alleles likely occurred recently because of local selective pressures. Additionally, we find purifying selection at all five β-tubulin genes, despite predicted loss-of-function variants in ben-1, indicating that BZ resistance in natural niches is a stronger selective pressure than loss of one β-tubulin gene. Furthermore, we used genome-editing to show that the most common parasitic nematode β-tubulin allele that confers BZ resistance, F200Y, confers resistance in C. elegans. Importantly, we identified a novel genomic region that is correlated with ABZ resistance in the C. elegans population but independent of ben-1 and the other β-tubulin loci, suggesting that there are multiple mechanisms underlying BZ resistance. Taken together, our results establish a population-level resource of nematode natural diversity as an important model for the study of mechanisms that give rise to BZ resistance.
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Affiliation(s)
- Steffen R. Hahnel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States of America
| | - Briana C. Rodriguez
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
| | - Yuehui Zhao
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Patrick T. McGrath
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States of America
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, United States of America
- * E-mail:
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Yague-Sanz C, Hermand D. SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data. Gigascience 2018; 7:5052207. [PMID: 30010768 PMCID: PMC6055573 DOI: 10.1093/gigascience/giy084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/04/2018] [Accepted: 07/01/2018] [Indexed: 11/13/2022] Open
Abstract
Background The spliceosomal transfer of a short spliced leader (SL) RNA to an independent pre-mRNA molecule is called SL trans-splicing and is widespread in the nematode Caenorhabditis elegans. While RNA-sequencing (RNA-seq) data contain information on such events, properly documented methods to extract them are lacking. Findings To address this, we developed SL-quant, a fast and flexible pipeline that adapts to paired-end and single-end RNA-seq data and accurately quantifies SL trans-splicing events. It is designed to work downstream of read mapping and uses the reads left unmapped as primary input. Briefly, the SL sequences are identified with high specificity and are trimmed from the input reads, which are then remapped on the reference genome and quantified at the nucleotide position level (SL trans-splice sites) or at the gene level. Conclusions SL-quant completes within 10 minutes on a basic desktop computer for typical C. elegans RNA-seq datasets and can be applied to other species as well. Validating the method, the SL trans-splice sites identified display the expected consensus sequence, and the results of the gene-level quantification are predictive of the gene position within operons. We also compared SL-quant to a recently published SL-containing read identification strategy that was found to be more sensitive but less specific than SL-quant. Both methods are implemented as a bash script available under the MIT license [1]. Full instructions for its installation, usage, and adaptation to other organisms are provided.
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Affiliation(s)
- Carlo Yague-Sanz
- URPhyM-GEMO, The University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Damien Hermand
- URPhyM-GEMO, The University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium
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Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res 2018; 28:1029-1038. [PMID: 29884752 PMCID: PMC6028123 DOI: 10.1101/gr.233460.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/03/2018] [Indexed: 01/13/2023]
Abstract
The recent introductions of low-cost, long-read, and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de novo sequence assembly a realistic proposition. The result is an explosion of new, ultracontiguous genome assemblies. To compare these genomes, we need robust methods for genome annotation. We describe the fully open source Comparative Annotation Toolkit (CAT), which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. We demonstrate the resulting discovery of novel genes, isoforms, and structural variants-even in genomes as well studied as rat and the great apes-and how these annotations improve cross-species RNA expression experiments.
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Affiliation(s)
- Ian T Fiddes
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA.,10x Genomics, Pleasanton, California 94566, USA
| | - Joel Armstrong
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA
| | - Stefanie Nachtweide
- Institute of Mathematics and Computer Science, University of Greifswald, 17489 Greifswald, Germany
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Pacific Biosciences of California, Incorporated, Menlo Park, California 94025, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Dent Earl
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA
| | - Thomas Keane
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, 17489 Greifswald, Germany
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA
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Saavedra-García P, Nichols K, Mahmud Z, Fan LYN, Lam EWF. Unravelling the role of fatty acid metabolism in cancer through the FOXO3-FOXM1 axis. Mol Cell Endocrinol 2018; 462:82-92. [PMID: 28087388 DOI: 10.1016/j.mce.2017.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/06/2016] [Accepted: 01/09/2017] [Indexed: 02/07/2023]
Abstract
Obesity and cachexia represent divergent states of nutritional and metabolic imbalance but both are intimately linked to cancer. There is an extensive overlap in their signalling pathways and molecular components involved such as fatty acids (FAs), which likely play a crucial role in cancer. Forkhead box (FOX) proteins are responsible of a wide range of transcriptional programmes during normal development, and the FOXO3-FOXM1 axis is associated with cancer initiation, progression and drug resistance. Free fatty acids (FFAs), FA synthesis and β-oxidation are associated with cancer development and progression. Meanwhile, insulin and some adipokines, that are up-regulated by FAs, are also involved in cancer development and poor prognosis. In this review, we discuss the role of FA metabolism in cancer and how FA metabolism integrates with the FOXO3-FOXM1 axis. These new insights may provide leads to better cancer diagnostics as well as strategies for tackling cancer development, progression and drug resistance.
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Affiliation(s)
- Paula Saavedra-García
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Katie Nichols
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Zimam Mahmud
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Lavender Yuen-Nam Fan
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK.
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Wang M, Ogé L, Perez-Garcia MD, Hamama L, Sakr S. The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation. Int J Mol Sci 2018; 19:ijms19020410. [PMID: 29385744 PMCID: PMC5855632 DOI: 10.3390/ijms19020410] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a crucial role in many processes. In cells, it is mediated by diverse RNA-binding proteins. These proteins can influence mRNA stability, translation, and localization. The PUF protein family (Pumilio and FBF) is composed of RNA-binding proteins highly conserved among most eukaryotic organisms. Previous investigations indicated that they could be involved in many processes by binding corresponding motifs in the 3′UTR or by interacting with other proteins. To date, most of the investigations on PUF proteins have been focused on Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae, while only a few have been conducted on Arabidopsis thaliana. The present article provides an overview of the PUF protein family. It addresses their RNA-binding motifs, biological functions, and post-transcriptional control mechanisms in Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, and Arabidopsis thaliana. These items of knowledge open onto new investigations into the relevance of PUF proteins in specific plant developmental processes.
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Affiliation(s)
- Ming Wang
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | | | - Latifa Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Soulaiman Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
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46
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Singh KD, Zheng X, Milstein S, Keller M, Roschitzki B, Grossmann J, Hengartner MO. Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PLoS One 2017; 12:e0182270. [PMID: 28759574 PMCID: PMC5536308 DOI: 10.1371/journal.pone.0182270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/14/2017] [Indexed: 11/21/2022] Open
Abstract
Cytoplasmic polyadenylation element binding (CPEB) proteins are evolutionary conserved RNA-binding proteins that control mRNA polyadenylation and translation. Orthologs in humans and other vertebrates are mainly involved in oogenesis. This is also the case for the C. elegans CPEB family member CPB-3, whereas two further CPEB proteins (CPB-1 and FOG-1) are involved in spermatogenesis. Here we describe the characterisation of a new missense allele of cpb-3 and show that loss of cpb-3 function leads to an increase in physiological germ cell death. To better understand the interaction and effect of C. elegans CPEB proteins on processes such as physiological apoptosis, germ cell differentiation, and regulation of gene expression, we characterised changes in the transcriptome and proteome of C. elegans CPEB mutants. Our results show that, despite their sequence similarities CPEB family members tend to have distinct overall effects on gene expression (both at the transcript and protein levels). This observation is consistent with the distinct phenotypes observed in the various CPEB family mutants.
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Affiliation(s)
- Kapil Dev Singh
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stuart Milstein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Martin Keller
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Michael O. Hengartner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
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47
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Lehmann S, Bass JJ, Barratt TF, Ali MZ, Szewczyk NJ. Functional phosphatome requirement for protein homeostasis, networked mitochondria, and sarcomere structure in C. elegans muscle. J Cachexia Sarcopenia Muscle 2017; 8:660-672. [PMID: 28508547 PMCID: PMC5566650 DOI: 10.1002/jcsm.12196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 12/08/2016] [Accepted: 01/26/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Skeletal muscle is central to locomotion and metabolic homeostasis. The laboratory worm Caenorhabditis elegans has been developed into a genomic model for assessing the genes and signals that regulate muscle development and protein degradation. Past work has identified a receptor tyrosine kinase signalling network that combinatorially controls autophagy, nerve signal to muscle to oppose proteasome-based degradation, and extracellular matrix-based signals that control calpain and caspase activation. The last two discoveries were enabled by following up results from a functional genomic screen of known regulators of muscle. Recently, a screen of the kinome requirement for muscle homeostasis identified roughly 40% of kinases as required for C. elegans muscle health; 80 have identified human orthologues and 53 are known to be expressed in skeletal muscle. To complement this kinome screen, here, we screen most of the phosphatases in C. elegans. METHODS RNA interference was used to knockdown phosphatase-encoding genes. Knockdown was first conducted during development with positive results also knocked down only in fully developed adult muscle. Protein homeostasis, mitochondrial structure, and sarcomere structure were assessed using transgenic reporter proteins. Genes identified as being required to prevent protein degradation were also knocked down in conditions that blocked proteasome or autophagic degradation. Genes identified as being required to prevent autophagic degradation were also assessed for autophagic vesicle accumulation using another transgenic reporter. Lastly, bioinformatics were used to look for overlap between kinases and phosphatases required for muscle homeostasis, and the prediction that one phosphatase was required to prevent mitogen-activated protein kinase activation was assessed by western blot. RESULTS A little over half of all phosphatases are each required to prevent abnormal development or maintenance of muscle. Eighty-six of these phosphatases have known human orthologues, 57 of which are known to be expressed in human skeletal muscle. Of the phosphatases required to prevent abnormal muscle protein degradation, roughly half are required to prevent increased autophagy. CONCLUSIONS A significant portion of both the kinome and phosphatome are required for establishing and maintaining C. elegans muscle health. Autophagy appears to be the most commonly triggered form of protein degradation in response to disruption of phosphorylation-based signalling. The results from these screens provide measurable phenotypes for analysing the combined contribution of kinases and phosphatases in a multi-cellular organism and suggest new potential regulators of human skeletal muscle for further analysis.
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Affiliation(s)
- Susann Lehmann
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Joseph J Bass
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Thomas F Barratt
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Mohammed Z Ali
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Nathaniel J Szewczyk
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
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Dong X, Armstrong SD, Xia D, Makepeace BL, Darby AC, Kadowaki T. Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history. Gigascience 2017; 6:1-17. [PMID: 28327890 PMCID: PMC5467014 DOI: 10.1093/gigascience/gix008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/01/2017] [Indexed: 01/09/2023] Open
Abstract
The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. We sequenced the genome of Tropilaelaps mercedesae, the prevalent ectoparasitic mite infesting honey bees in Asia, and predicted 15 190 protein-coding genes that were well supported by the mite transcriptomes and proteomic data. Although amino acid substitutions have been accelerated within the conserved core genes of two mites, T. mercedesae and Metaseiulus occidentalis, T. mercedesae has undergone the least gene family expansion and contraction between the seven arthropods we tested. The number of sensory system genes has been dramatically reduced, but T. mercedesae contains all gene sets required to detoxify xenobiotics. T. mercedesae is closely associated with a symbiotic bacterium (Rickettsiella grylli-like) and Deformed Wing Virus, the most prevalent honey bee virus. T. mercedesae has a very specialized life history and habitat as the ectoparasitic mite strictly depends on the honey bee inside a stable colony. Thus, comparison of the genome and transcriptome sequences with those of a tick and free-living mites has revealed the specific features of the genome shaped by interaction with the honey bee and colony environment. Genome and transcriptome sequences of T. mercedesae, as well as Varroa destructor (another globally prevalent ectoparasitic mite of honey bee), not only provide insights into the mite biology, but may also help to develop measures to control the most serious pests of the honey bee.
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Affiliation(s)
- Xiaofeng Dong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Dushu Lake Higher Education Town, Jiangsu Province 215123, China
| | - Stuart D Armstrong
- Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Dong Xia
- Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Benjamin L Makepeace
- Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Dushu Lake Higher Education Town, Jiangsu Province 215123, China
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Blazie SM, Geissel HC, Wilky H, Joshi R, Newbern J, Mangone M. Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues. Genetics 2017; 206:757-774. [PMID: 28348061 PMCID: PMC5499184 DOI: 10.1534/genetics.116.196774] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023] Open
Abstract
mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3'untranslated region (3'UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3'UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3'UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis.
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Affiliation(s)
- Stephen M Blazie
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281
| | - Heather C Geissel
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281
| | - Henry Wilky
- Barrett Honors College, Arizona State University, Tempe, Arizona 85281
| | - Rajan Joshi
- College of Letters and Sciences, Interdisciplinary Studies, Biological Sciences and Informatics, Arizona State University, Tempe, Arizona 85281
| | - Jason Newbern
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Barrett Honors College, Arizona State University, Tempe, Arizona 85281
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281
- Barrett Honors College, Arizona State University, Tempe, Arizona 85281
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50
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Vahdati Nia B, Kang C, Tran MG, Lee D, Murakami S. Meta Analysis of Human AlzGene Database: Benefits and Limitations of Using C. elegans for the Study of Alzheimer's Disease and Co-morbid Conditions. Front Genet 2017; 8:55. [PMID: 28553317 PMCID: PMC5427079 DOI: 10.3389/fgene.2017.00055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/19/2017] [Indexed: 11/21/2022] Open
Abstract
Human genome-wide association studies (GWAS) and linkage studies have identified 695 genes associated with Alzheimer's disease (AD), the vast majority of which are associated with late-onset AD. Although orthologs of these AD genes have been studied in several model species, orthologs in the nematode, Caenorhabditis elegans, remain incompletely identified, with orthologs to only 17 AD-related genes identified in the C. elegans database, WormBase. Therefore, we performed a comprehensive search for additional C. elegans orthologs of AD genes using well-established programs, including OrthoList, which utilizes four ontology prediction programs. We also validated 680 of the AD genes as a unique gene from the AlzGene database, including 431 genes (63%) that are predicted to have orthologs in C. elegans. Another 178 human AD genes (26%) were associated with one or more other neurological diseases, including amyotrophic lateral sclerosis, multiple sclerosis, Parkinson's disease, and schizophrenia. Of these, there were 105 genes (59%) with orthologs in C. elegans. Interestingly, three AD genes (ACE, TNF, and MTHFR) were associated with all four of the other neurological diseases. The human AD genes were enriched in three major ontology pathway groups, including lipoprotein metabolism, hemostasis, and extracellular matrix organizations, as well as in pathways that are amyloid related (NOTCH signaling) and associated with neural (neurotransmitter clearance) and immune (advanced glycation end-product receptor signaling and TRAF6-NF-kappaB) systems. Thus, the results from this study provide a potentially useful system for assessing comorbidities that may be associated with late-onset AD and other neurological conditions. The technical advantages and limitations of the ortholog searches are further discussed.
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Affiliation(s)
- Behrad Vahdati Nia
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Christine Kang
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Michelle G Tran
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Deborah Lee
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Shin Murakami
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
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