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Xu G, Liu H, Xia D, Zhao Y, Qian Y, Han H, Pan J, Jiang H, Jiang Y, Sun G. Time-course transcriptome analysis of lungs from mice infected with inhaled aerosolized Stenotrophomonas maltophilia. J Thorac Dis 2023; 15:4987-5005. [PMID: 37868883 PMCID: PMC10587000 DOI: 10.21037/jtd-23-1138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023]
Abstract
Background Stenotrophomonas maltophilia (SMA) has emerged as an important pathogen capable of causing an opportunistic and nosocomial infection. We performed RNA sequencing (RNA-seq) of lung tissues from mice with pulmonary SMA infection over time via aerosolized intratracheal inhalation to investigate transcription profile changes in SMA-infected lungs. Methods A mouse model of acute lethal SMA pneumonia was established in this study using aerosolized intratracheal inhalation, laying the groundwork for future SMA research. RNA-seq was then used to create a transcriptional profile of the lungs of the model mice at 0, 4, 12, 24, 48, and 72 hours post-infection (hpi). Mfuzz time clustering, weighted gene coexpression network analysis (WGCNA), and Immune Cell Abundance Identifier for mouse (ImmuCellAI-mouse) were used to analyze RNA-seq data. Results A gradual change in the lung transcriptional profile was observed, which was consistent with the expected disease progression. At 4 hpi, the expression of genes related to the acute phase inflammatory response increased, as predicted abundance of innate immune cells. At this stage, an increased demand for energy was also observed, including an increase in the expression of genes involved in circulation, muscle function and mitochondrial respiratory chain function. The expression of genes associated with endoplasmic reticulum stress (ERS) and autophagy increased at 24 hpi. Unlike the number of natural killer (NK) cells following most bacterial lung infections, the abundance of NK cells decreased following infection with SMA. The expression levels of Cxcl10, Cd14, Gbp5, Cxcr2, Tnip1, Zc3h12a, Egr1, Sell and Gbp2 were high and previously unreported in SMA pneumonia, and they may be important targets for future studies. Conclusions To our knowledge, this is the first study to investigate the pulmonary transcriptional response to SMA infection. The findings shed light on the molecular mechanisms underlying the pathogenesis of SMA pneumonia, which may aid in the development of therapies to reduce the occurrence of SMA pulmonary infection.
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Affiliation(s)
- Guangyang Xu
- The First Clinical College of Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Respiratory and Critical Care Medicine, Taizhou Second People’s Hospital, Taizhou, China
| | - Hui Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Dunling Xia
- The First Clinical College of Anhui Medical University, Hefei, China
| | - Yan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yao Qian
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hongyan Han
- Department of Respiratory and Critical Care Medicine, Taizhou Second People’s Hospital, Taizhou, China
| | - Jiahua Pan
- Department of Respiratory and Critical Care Medicine, Taizhou Second People’s Hospital, Taizhou, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Gengyun Sun
- The First Clinical College of Anhui Medical University, Hefei, China
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, China
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2
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Cummings MJ, Bakamutumaho B, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Jain K, Postler TS, Muwanga M, Nsereko C, Nayiga I, Kyebambe S, Che X, Sameroff S, Tokarz R, Shah SS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. HIV infection drives pro-inflammatory immunothrombotic pathway activation and organ dysfunction among adults with sepsis in Uganda. AIDS 2023; 37:233-245. [PMID: 36355913 PMCID: PMC9780191 DOI: 10.1097/qad.0000000000003410] [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: 11/12/2022]
Abstract
BACKGROUND The global burden of sepsis is concentrated in high HIV-burden settings in sub-Saharan Africa (SSA). Despite this, little is known about the immunopathology of sepsis in persons with HIV (PWH) in the region. We sought to determine the influence of HIV on host immune responses and organ dysfunction among adults hospitalized with suspected sepsis in Uganda. DESIGN Prospective cohort study. METHODS We compared organ dysfunction and 30-day outcome profiles of PWH and those without HIV. We quantified 14 soluble immune mediators, reflective of key domains of sepsis immunopathology, and performed whole-blood RNA-sequencing on samples from a subset of patients. We used propensity score methods to match PWH and those without HIV by demographics, illness duration, and clinical severity, and compared immune mediator concentrations and gene expression profiles across propensity score-matched groups. RESULTS Among 299 patients, 157 (52.5%) were PWH (clinical stage 3 or 4 in 80.3%, 67.7% with known HIV on antiretroviral therapy). PWH presented with more severe physiologic derangement and shock, and had higher 30-day mortality (34.5% vs. 10.2%; P < 0.001). Across propensity score-matched groups, PWH exhibited greater pro-inflammatory immune activation, including upregulation of interleukin (IL)-6, IL-8, IL-15, IL-17 and HMGB1 signaling, with concomitant T-cell exhaustion, prothrombotic pathway activation, and angiopoeitin-2-related endothelial dysfunction. CONCLUSIONS Sepsis-related organ dysfunction and mortality in Uganda disproportionately affect PWH, who demonstrate exaggerated activation of multiple immunothrombotic and metabolic pathways implicated in sepsis pathogenesis. Further investigations are needed to refine understanding of sepsis immunopathology in PWH, particularly mechanisms amenable to therapeutic manipulation.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Irene Nayiga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Kyebambe
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Shivang S. Shah
- Division of Infectious Diseases, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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3
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Lamer A, Fruchart M, Paris N, Popoff B, Payen A, Balcaen T, Gacquer W, Bouzille G, Cuggia M, Doutreligne M, Chazard E. Enhancing Data Reuse: Standardized Description of the Feature Extraction Process to Transform Raw Data into Meaningful Information (Preprint). JMIR Med Inform 2022; 10:e38936. [DOI: 10.2196/38936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/19/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
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4
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Cummings MJ, Bakamutumaho B, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Sameroff S, Tokarz R, Wong W, Shah SS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. Multidimensional analysis of the host response reveals prognostic and pathogen-driven immune subtypes among adults with sepsis in Uganda. Crit Care 2022; 26:36. [PMID: 35130948 PMCID: PMC8822787 DOI: 10.1186/s13054-022-03907-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background The global burden of sepsis is concentrated in sub-Saharan Africa, where severe infections disproportionately affect young, HIV-infected adults and high-burden pathogens are unique. In this context, poor understanding of sepsis immunopathology represents a crucial barrier to development of locally-effective treatment strategies. We sought to determine inter-individual immunologic heterogeneity among adults hospitalized with sepsis in a sub-Saharan African setting, and characterize associations between immune subtypes, infecting pathogens, and clinical outcomes. Methods Among a prospective observational cohort of 288 adults hospitalized with suspected sepsis in Uganda, we applied machine learning methods to 14 soluble host immune mediators, reflective of key domains of sepsis immunopathology (innate and adaptive immune activation, endothelial dysfunction, fibrinolysis), to identify immune subtypes in randomly-split discovery (N = 201) and internal validation (N = 87) sub-cohorts. In parallel, we applied similar methods to whole-blood RNA-sequencing data from a consecutive subset of patients (N = 128) to identify transcriptional subtypes, which we characterized using biological pathway and immune cell-type deconvolution analyses. Results Unsupervised clustering consistently identified two immune subtypes defined by differential activation of pro-inflammatory innate and adaptive immune pathways, with transcriptional evidence of concomitant CD56(-)/CD16( +) NK-cell expansion, T-cell exhaustion, and oxidative-stress and hypoxia-induced metabolic and cell-cycle reprogramming in the hyperinflammatory subtype. Immune subtypes defined by greater pro-inflammatory immune activation, T-cell exhaustion, and metabolic reprogramming were consistently associated with a high-prevalence of severe and often disseminated HIV-associated tuberculosis, as well as more extensive organ dysfunction, worse functional outcomes, and higher 30-day mortality. Conclusions Our results highlight unique host- and pathogen-driven features of sepsis immunopathology in sub-Saharan Africa, including the importance of severe HIV-associated tuberculosis, and reinforce the need to develop more biologically-informed treatment strategies in the region, particularly those incorporating immunomodulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13054-022-03907-3.
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5
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Kariyawasam H, Su S, Voogd O, Ritchie ME, Law CW. Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0. NAR Genom Bioinform 2022; 3:lqab116. [PMID: 34988439 PMCID: PMC8693569 DOI: 10.1093/nargab/lqab116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Glimma 1.0 introduced intuitive, point-and-click interactive graphics for differential gene expression analysis. Here, we present a major update to Glimma that brings improved interactivity and reproducibility using high-level visualization frameworks for R and JavaScript. Glimma 2.0 plots are now readily embeddable in R Markdown, thus allowing users to create reproducible reports containing interactive graphics. The revamped multidimensional scaling plot features dashboard-style controls allowing the user to dynamically change the colour, shape and size of sample points according to different experimental conditions. Interactivity was enhanced in the MA-style plot for comparing differences to average expression, which now supports selecting multiple genes, export options to PNG, SVG or CSV formats and includes a new volcano plot function. Feature-rich and user-friendly, Glimma makes exploring data for gene expression analysis more accessible and intuitive and is available on Bioconductor and GitHub.
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Affiliation(s)
- Hasaru Kariyawasam
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Oliver Voogd
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Charity W Law
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
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6
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Woodhouse MR, Sen S, Schott D, Portwood JL, Freeling M, Walley JW, Andorf CM, Schnable JC. qTeller: a tool for comparative multi-genomic gene expression analysis. Bioinformatics 2021; 38:236-242. [PMID: 34406385 DOI: 10.1093/bioinformatics/btab604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/23/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. RESULTS To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms' databases. AVAILABILITY AND IMPLEMENTATION The source code for qTeller is open-source and available through GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - David Schott
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Michael Freeling
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin W Walley
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.,Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Ji DX, Witt KC, Kotov DI, Margolis SR, Louie A, Chevée V, Chen KJ, Gaidt MM, Dhaliwal HS, Lee AY, Nishimura SL, Zamboni DS, Kramnik I, Portnoy DA, Darwin KH, Vance RE. Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons. eLife 2021; 10:67290. [PMID: 34151776 PMCID: PMC8248984 DOI: 10.7554/elife.67290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/20/2021] [Indexed: 12/18/2022] Open
Abstract
Type I interferons (IFNs) are essential for anti-viral immunity, but often impair protective immune responses during bacterial infections. An important question is how type I IFNs are strongly induced during viral infections, and yet are appropriately restrained during bacterial infections. The Super susceptibility to tuberculosis 1 (Sst1) locus in mice confers resistance to diverse bacterial infections. Here we provide evidence that Sp140 is a gene encoded within the Sst1 locus that represses type I IFN transcription during bacterial infections. We generated Sp140–/– mice and found that they are susceptible to infection by Legionella pneumophila and Mycobacterium tuberculosis. Susceptibility of Sp140–/– mice to bacterial infection was rescued by crosses to mice lacking the type I IFN receptor (Ifnar–/–). Our results implicate Sp140 as an important negative regulator of type I IFNs that is essential for resistance to bacterial infections.
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Affiliation(s)
- Daisy X Ji
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kristen C Witt
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Dmitri I Kotov
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Shally R Margolis
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Alexander Louie
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Victoria Chevée
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Katherine J Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Moritz M Gaidt
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Harmandeep S Dhaliwal
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Angus Y Lee
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Stephen L Nishimura
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Dario S Zamboni
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratory, Department of Medicine (Pulmonary Center), and Department of Microbiology, Boston University School of Medicine, Boston, United States
| | - Daniel A Portnoy
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - K Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, United States
| | - Russell E Vance
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
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8
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Clark BS, Miesfeld JB, Flinn MA, Collery RF, Link BA. Dynamic Polarization of Rab11a Modulates Crb2a Localization and Impacts Signaling to Regulate Retinal Neurogenesis. Front Cell Dev Biol 2021; 8:608112. [PMID: 33634099 PMCID: PMC7900515 DOI: 10.3389/fcell.2020.608112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/28/2020] [Indexed: 01/31/2023] Open
Abstract
Interkinetic nuclear migration (IKNM) is the process in which pseudostratified epithelial nuclei oscillate from the apical to basal surface and in phase with the mitotic cycle. In the zebrafish retina, neuroepithelial retinal progenitor cells (RPCs) increase Notch activity with apical movement of the nuclei, and the depth of nuclear migration correlates with the probability that the next cell division will be neurogenic. This study focuses on the mechanisms underlying the relationships between IKNM, cell signaling, and neurogenesis. In particular, we have explored the role IKNM has on endosome biology within RPCs. Through genetic manipulation and live imaging in zebrafish, we find that early (Rab5-positive) and recycling (Rab11a-positive) endosomes polarize in a dynamic fashion within RPCs and with reference to nuclear position. Functional analyses suggest that dynamic polarization of recycling endosomes and their activity within the neuroepithelia modulates the subcellular localization of Crb2a, consequently affecting multiple signaling pathways that impact neurogenesis including Notch, Hippo, and Wnt activities. As nuclear migration is heterogenous and asynchronous among RPCs, Rab11a-affected signaling within the neuroepithelia is modulated in a differential manner, providing mechanistic insight to the correlation of IKNM and selection of RPCs to undergo neurogenesis.
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Affiliation(s)
- Brian S Clark
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Joel B Miesfeld
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael A Flinn
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ross F Collery
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin Eye Institute, Milwaukee, WI, United States
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
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9
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Marini F, Linke J, Binder H. ideal: an R/Bioconductor package for interactive differential expression analysis. BMC Bioinformatics 2020; 21:565. [PMID: 33297942 PMCID: PMC7724894 DOI: 10.1186/s12859-020-03819-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking. RESULTS We developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis workflow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility. CONCLUSION ideal is distributed as an R package in the Bioconductor project ( http://bioconductor.org/packages/ideal/ ), and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make the ideal use of the data at hand.
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Affiliation(s)
- Federico Marini
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, 55131 Mainz, Germany
| | - Jan Linke
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, 55131 Mainz, Germany
| | - Harald Binder
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany
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10
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Singh U, Hur M, Dorman K, Wurtele ES. MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. Nucleic Acids Res 2020; 48:e23. [PMID: 31956905 PMCID: PMC7039010 DOI: 10.1093/nar/gkz1209] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The diverse and growing omics data in public domains provide researchers with tremendous opportunity to extract hidden, yet undiscovered, knowledge. However, the vast majority of archived data remain unused. Here, we present MetaOmGraph (MOG), a free, open-source, standalone software for exploratory analysis of massive datasets. Researchers, without coding, can interactively visualize and evaluate data in the context of its metadata, honing-in on groups of samples or genes based on attributes such as expression values, statistical associations, metadata terms and ontology annotations. Interaction with data is easy via interactive visualizations such as line charts, box plots, scatter plots, histograms and volcano plots. Statistical analyses include co-expression analysis, differential expression analysis and differential correlation analysis, with significance tests. Researchers can send data subsets to R for additional analyses. Multithreading and indexing enable efficient big data analysis. A researcher can create new MOG projects from any numerical data; or explore an existing MOG project. MOG projects, with history of explorations, can be saved and shared. We illustrate MOG by case studies of large curated datasets from human cancer RNA-Seq, where we identify novel putative biomarker genes in different tumors, and microarray and metabolomics data from Arabidopsis thaliana. MOG executable and code: http://metnetweb.gdcb.iastate.edu/ and https://github.com/urmi-21/MetaOmGraph/.
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Affiliation(s)
- Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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11
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Price A, Okumura A, Haddock E, Feldmann F, Meade-White K, Sharma P, Artami M, Lipkin WI, Threadgill DW, Feldmann H, Rasmussen AL. Transcriptional Correlates of Tolerance and Lethality in Mice Predict Ebola Virus Disease Patient Outcomes. Cell Rep 2020; 30:1702-1713.e6. [PMID: 32049004 PMCID: PMC11062563 DOI: 10.1016/j.celrep.2020.01.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 11/07/2019] [Accepted: 01/07/2020] [Indexed: 01/26/2023] Open
Abstract
Host response to infection is a major determinant of disease severity in Ebola virus disease (EVD), but gene expression programs associated with outcome are poorly characterized. Collaborative Cross (CC) mice develop strain-dependent EVD phenotypes of differential severity, ranging from tolerance to lethality. We screen 10 CC lines and identify clinical, virologic, and transcriptomic features that distinguish tolerant from lethal outcomes. Tolerance is associated with tightly regulated induction of immune and inflammatory responses shortly following infection, as well as reduced inflammatory macrophages and increased antigen-presenting cells, B-1 cells, and γδ T cells. Lethal disease is characterized by suppressed early gene expression and reduced lymphocytes, followed by uncontrolled inflammatory signaling, leading to death. We apply machine learning to predict outcomes with 99% accuracy in mice using transcriptomic profiles. This signature predicts outcomes in a cohort of EVD patients from western Africa with 75% accuracy, demonstrating potential clinical utility.
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Affiliation(s)
- Adam Price
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - Atsushi Okumura
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA; Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Elaine Haddock
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pryanka Sharma
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - Methinee Artami
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Heinz Feldmann
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA.
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