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Ngo TB, Josyula A, DeStefano S, Fertil D, Faust M, Lokwani R, Sadtler K. Intersection of Immunity, Metabolism, and Muscle Regeneration in an Autoimmune-Prone MRL Mouse Model. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306961. [PMID: 38192168 PMCID: PMC10953568 DOI: 10.1002/advs.202306961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/07/2023] [Indexed: 01/10/2024]
Abstract
Due to the limited capacity of mammals to regenerate complex tissues, researchers have worked to understand the mechanisms of tissue regeneration in organisms that maintain that capacity. One example is the MRL/MpJ mouse strain with unique regenerative capacity in ear pinnae that is absent from other strains, such as the common C57BL/6 strain. The MRL/MpJ mouse has also been associated with an autoimmune phenotype even in the absence of the mutant Fas gene described in its parent strain MRL/lpr. Due to these findings, the differences between the responses of MRL/MpJ versus C57BL/6 strain are evaluated in volumetric muscle injury and subsequent material implantation. One salient feature of the MRL/MpJ response to injury is robust adipogenesis within the muscle. This is associated with a decrease in M2-like polarization in response to biologically derived extracellular matrix scaffolds. In pro-fibrotic materials, such as polyethylene, there are fewer foreign body giant cells in the MRL/MpJ mice. As there are reports of both positive and negative influences of adipose tissue and adipogenesis on wound healing, this model can provide an important lens to investigate the interplay between stem cells, adipose tissue, and immune responses in trauma and material implantation.
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Affiliation(s)
- Tran B. Ngo
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
| | - Aditya Josyula
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
| | - Sabrina DeStefano
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
| | - Daphna Fertil
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
| | - Mondreakest Faust
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
| | - Ravi Lokwani
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
| | - Kaitlyn Sadtler
- Section on ImmunoengineeringCenter for Biomedical Engineering and Technology AccelerationNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20814USA
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Ngo TB, Josyula A, DeStefano S, Fertil D, Faust M, Lokwani R, Sadtler K. Ectopic adipogenesis in response to injury and material implantation in an autoimmune mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561105. [PMID: 37986843 PMCID: PMC10659416 DOI: 10.1101/2023.10.05.561105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Due to the limited capacity of mammals to regenerate complex tissues, researchers have worked to understand the mechanisms of tissue regeneration in organisms that maintain that capacity. One example is the MRL/MpJ mouse strain with unique regenerative capacity in ear pinnae that is absent from other strains, such as the common C57BL/6 strain. The MRL/MpJ mouse has also been associated with an autoimmune phenotype even in the absence of the mutant Fas gene described in its parent strain MRL/lpr. Due to these findings, we evaluated the differences between the responses of MRL/MpJ versus C57BL/6 strain in traumatic muscle injury and subsequent material implantation. One salient feature of the MRL/MpJ response to injury was a robust adipogenesis within the muscle. This was associated with a decrease in M2-like polarization in response to biologically derived extracellular matrix scaffolds. In pro-fibrotic materials, such as polyethylene, there were fewer foreign body giant cells in the MRL/MpJ mice. As there are reports of both positive and negative influences of adipose tissue and adipogenesis on wound healing, this model could provide an important lens to investigate the interplay between stem cells, adipose tissue, and immune responses in trauma and materials implantation.
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Affiliation(s)
- Tran B. Ngo
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
| | - Aditya Josyula
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
| | - Sabrina DeStefano
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
| | - Daphna Fertil
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
| | - Mondreakest Faust
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
| | - Ravi Lokwani
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
| | - Kaitlyn Sadtler
- Section on Immunoengineering, Center for Biomedical Engineering and Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20814
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Kim A, Choi SJ, Song GG, Kim JH, Jung JH. Characterization of virus-mediated autoimmunity and the consequences for pathological process in patients with systemic lupus erythematosus. Clin Rheumatol 2023; 42:2799-2809. [PMID: 37369873 DOI: 10.1007/s10067-023-06597-6] [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: 08/31/2022] [Revised: 04/01/2023] [Accepted: 04/07/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION/OBJECTIVES This study aimed to identify differentially expressed genes (DEGs) of systemic lupus erythematosus (SLE) using gene expression-based computational methodologies to analyze disease-immune interactions, which affect the development and progression of SLE. METHOD Twenty-six patients with SLE and 46 healthy controls were selected from the Gene Expression Omnibus (GEO) database. The significantly enriched immune and virus-related gene lists were computed and visualized by using the DEGs from the gene set enrichment analysis (GSEA). Quantification of 38 immune cells was performed in determining the impact of immune cells on the virus mediated immunity in SLE by using ImmQuant algorithm. RESULTS Thirty-nine upregulated and 57 downregulated were identified in SLE patient compared to the healthy controls. Upregulated genes were significantly implicated in Gene Ontology gene sets as cytokine mediated signaling, secretion, and exocytosis in immune response pathways in 26 female SLE patients. In addition, these genes were enriched in hepatitis C, influenza A, measles, Epstein-Barr virus, and herpes simplex virus 1 infection in Kyoto Encyclopedia of Genes and Genomes pathways. Especially, FCGR1A, IRF7, OAS2, CAMP, MX1, OAS3, OAS1, DEFA3, ISG15, and RSAD2 were involved in virus mediated SLE mechanism, and the expression for OAS1, OAS2, and IRF7 was closely associated with the quantities of colony forming unit-monocyte and colony forming unit-granulocyte. CONCLUSIONS Identifying virus-mediated SLE genes and quantifies of immune cells were used to understand the pathological process and perform early diagnosis of female SLE, and will lead to clinical tools for treating SLE in patients. Key Points • Using gene expression-based computational methodologies, the 57 immune and viral genes were significantly upregulated in 26 SLE patients. • The identified three key viral genes such as OAS1, OAS2, and IF7 were closely associated with colony-forming unit-monocytes and colony-forming unit-granulocytes, which affect the virus mediated immunity in SLE. • The viral genes and quantifies of immune cells are useful in understanding pathogenesis of SLE, and this will provide clinical strategies of potential treatment choices in SLE patients.
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Affiliation(s)
- Ahreum Kim
- Department of Education and Training, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | - Sung Jae Choi
- Department of Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Division of Rheumatology, Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Gwan Gyu Song
- Department of Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Division of Rheumatology, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Joo-Hang Kim
- Department of Education and Training, CHA Bundang Medical Center, Seongnam, Republic of Korea.
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea.
| | - Jae Hyun Jung
- Department of Medicine, Korea University College of Medicine, Seoul, Republic of Korea.
- Division of Rheumatology, Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Republic of Korea.
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Liang J, Fang D, Yao F, Chen L, Zou Z, Tang X, Feng L, Zhuang Y, Xie T, Wei P, Li P, Zheng H, Zhang S. Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration. Front Neurosci 2023; 17:1259622. [PMID: 37811327 PMCID: PMC10552924 DOI: 10.3389/fnins.2023.1259622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Photoreceptor degenerative diseases are characterized by the progressive death of photoreceptor cells, resulting in irreversible visual impairment. However, the role of competing endogenous RNA (ceRNA) in photoreceptor degeneration is unclear. We aimed to explore the shared ceRNA regulation network and potential molecular mechanisms between primary and secondary photoreceptor degenerations. Methods We established animal models for both types of photoreceptor degenerations and conducted retina RNA sequencing to identify shared differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). Using ceRNA regulatory principles, we constructed a shared ceRNA network and performed function enrichment and protein-protein interaction (PPI) analyses to identify hub genes and key pathways. Immune cell infiltration and drug-gene interaction analyses were conducted, and hub gene expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Results We identified 37 shared differentially expressed lncRNAs, 34 miRNAs, and 247 mRNAs and constructed a ceRNA network consisting of 3 lncRNAs, 5 miRNAs, and 109 mRNAs. Furthermore, we examined 109 common differentially expressed genes (DEGs) through functional annotation, PPI analysis, and regulatory network analysis. We discovered that these diseases shared the complement and coagulation cascades pathway. Eight hub genes were identified and enriched in the immune system process. Immune infiltration analysis revealed increased T cells and decreased B cells in both photoreceptor degenerations. The expression of hub genes was closely associated with the quantities of immune cell types. Additionally, we identified 7 immune therapeutical drugs that target the hub genes. Discussion Our findings provide new insights and directions for understanding the common mechanisms underlying the development of photoreceptor degeneration. The hub genes and related ceRNA networks we identified may offer new perspectives for elucidating the mechanisms and hold promise for the development of innovative treatment strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Shaochong Zhang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, Guangdong, China
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De Cauwer A, Pichot A, Molitor A, Stemmelen T, Carapito R, Bahram S, Georgel P. Measuring the transcriptome-wide effects of aging on murine adipocytes using RNAseq. STAR Protoc 2023; 4:102397. [PMID: 37393615 PMCID: PMC10328976 DOI: 10.1016/j.xpro.2023.102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/13/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Adipose tissue plays a central role in age-related diseases. While RNAseq protocols exist for many tissues, few data have been generated with this technology to explore gene expression in adipocytes, particularly during aging. Here, we present a protocol to analyze the transcriptional changes that occur in adipose tissue during normal and accelerated aging in mouse models. We describe steps for genotyping, diet control, euthanasia, and dissection. We then detail RNA purification and genome-wide data generation and analysis. For complete details on the use and execution of this protocol, please refer to De Cauwer et al. (2022) iScience. Sep 16;25(10):105149.
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Affiliation(s)
- Aurore De Cauwer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France.
| | - Angélique Pichot
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France
| | - Anne Molitor
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France
| | - Tristan Stemmelen
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France; Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, 67000 Strasbourg, France
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France; Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, 67000 Strasbourg, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France; Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, 67000 Strasbourg, France
| | - Philippe Georgel
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67085 Strasbourg, France.
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Dicer1 deficient mice exhibit premature aging and metabolic perturbations in adipocytes. iScience 2022; 25:105149. [PMID: 36185376 PMCID: PMC9523393 DOI: 10.1016/j.isci.2022.105149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/12/2022] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
Age-related diseases are major concern in developed countries. To avoid disabilities that accompany increased lifespan, pharmaceutical approaches are considered. Therefore, appropriate animal models are required for a better understanding of aging processes and potential in vivo assays to evaluate the impact of molecules that may delay the occurrence of age-related diseases. Few mouse models exhibiting pathological aging exist, but currently, none of them reproducibly mimics human diseases like osteoporosis, cognitive dysfunctions or sarcopenia that can be seen in some, but not all, elders. Here, we describe the premature aging phenotypes of Dicer-deficient mature animals, which exhibit an overall deterioration of many organs and tissues (skin, heart, and adipose tissue) ultimately leading to a significant reduction of their lifespan. Molecular characterization of transcriptional responses focused on the adipose tissue suggested that both canonical and non-canonical functions of DICER are involved in this process and highlight potential actionable pathways to revert it. Dicer1-deficient mice have a reduced lifespan with early age-related symptoms Mutant mice are resistant to high fat diet-induced disorders Myokines FGF21 and GDF15 are likely key regulators of adipocytes metabolism
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Kim SY, Barnes MA, Sureshchandra S, Menicucci AR, Patel JJ, Messaoudi I, Nair MG. CX3CR1-Expressing Myeloid Cells Regulate Host-Helminth Interaction and Lung Inflammation. Adv Biol (Weinh) 2022; 6:e2101078. [PMID: 35119218 PMCID: PMC8934291 DOI: 10.1002/adbi.202101078] [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: 07/12/2021] [Revised: 12/31/2021] [Indexed: 11/06/2022]
Abstract
Many helminth life cycles, including hookworm, involve a mandatory lung phase, where myeloid and granulocyte subsets interact with the helminth and respond to infection-induced lung injury. To evaluate these innate subsets in Nippostrongylus brasiliensis infection, reporter mice for myeloid cells (CX3CR1GFP ) and granulocytes (PGRPdsRED ) are employed. Nippostrongylus infection induces lung infiltration of reporter cells, including CX3CR1+ myeloid cells and PGRP+ eosinophils. Strikingly, CX3CR1GFP/GFP mice, which are deficient in CX3CR1, are protected from Nippostrongylus infection with reduced weight loss, lung leukocyte infiltration, and worm burden compared to CX3CR1+/+ mice. This protective effect is specific for CX3CR1 as CCR2-deficient mice do not exhibit reduced worm burdens. Nippostrongylus co-culture with lung Ly6C+ monocytes or CD11c+ cells demonstrates that CX3CR1GFP/GFP monocytes secrete more pro-inflammatory cytokines and actively bind the parasites causing reduced motility. RNA sequencing of Ly6C+ or CD11c+ cells shows Nippostrongylus-induced gene expression changes, particularly in monocytes, associated with inflammation, chemotaxis, and extracellular matrix remodeling pathways. Analysis reveals cytotoxic and adhesion molecules as potential effectors against the parasite, such as Gzma and Gzmb, which are elevated in CX3CR1GFP/GFP monocytes. These studies validate a dual innate cell reporter for lung helminth infection and demonstrate that CX3CR1 impairs monocyte-helminth interaction.
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Affiliation(s)
| | | | | | - Andrea R. Menicucci
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, California 92697-3900, United States
| | - Jay J. Patel
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California 92521, United States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, California 92697-3900, United States
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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: 10] [Impact Index Per Article: 3.3] [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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Pinski AN, Steffen TL, Zulu MZ, George SL, Dickson A, Tifrea D, Maroney KJ, Tedeschi N, Zhang Y, Scheuermann RH, Pinto AK, Brien JD, Messaoudi I. Corticosteroid treatment in COVID-19 modulates host inflammatory responses and transcriptional signatures of immune dysregulation. J Leukoc Biol 2021; 110:1225-1239. [PMID: 34730254 PMCID: PMC8667650 DOI: 10.1002/jlb.4cova0121-084rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease-2019 (COVID-19), a respiratory disease that varies in severity from mild to severe/fatal. Several risk factors for severe disease have been identified, notably age, male sex, and pre-existing conditions such as diabetes, obesity, and hypertension. Several advancements in clinical care have been achieved over the past year, including the use of corticosteroids (e.g., corticosteroids) and other immune-modulatory treatments that have now become standard of care for patients with acute severe COVID-19. While the understanding of the mechanisms that underlie increased disease severity with age has improved over the past few months, it remains incomplete. Furthermore, the molecular impact of corticosteroid treatment on host response to acute SARS-CoV-2 infection has not been investigated. In this study, a cross-sectional and longitudinal analysis of Ab, soluble immune mediators, and transcriptional responses in young (65 ≤ years) and aged (≥ 65 years) diabetic males with obesity hospitalized with acute severe COVID-19 was conducted. Additionally, the transcriptional profiles in samples obtained before and after corticosteroids became standard of care were compared. The analysis indicates that severe COVID-19 is characterized by robust Ab responses, heightened systemic inflammation, increased expression of genes related to inflammatory and pro-apoptotic processes, and reduced expression of those important for adaptive immunity regardless of age. In contrast, COVID-19 patients receiving steroids did not show high levels of systemic immune mediators and lacked transcriptional indicators of heightened inflammatory and apoptotic responses. Overall, these data suggest that inflammation and cell death are key drivers of severe COVID-19 pathogenesis in the absence of corticosteroid therapy.
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Affiliation(s)
- Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, Irvine, California, USA
- Institute for Immunology, University of California, Irvine, California, USA
| | - Tara L Steffen
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, Missouri, USA
| | - Michael Z Zulu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, Irvine, California, USA
- Institute for Immunology, University of California, Irvine, California, USA
| | - Sarah L George
- Department of Medicine, Division of Infectious Diseases, Saint Louis University, St Louis, Missouri, USA
| | - Alexandria Dickson
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, Missouri, USA
| | - Delia Tifrea
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, USA
| | - Kevin J Maroney
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Neil Tedeschi
- J. Craig Venter Institute, La Jolla, California, USA
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Amelia K Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, Missouri, USA
| | - James D Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, Missouri, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, Irvine, California, USA
- Institute for Immunology, University of California, Irvine, California, USA
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Nadel BB, Oliva M, Shou BL, Mitchell K, Ma F, Montoya DJ, Mouton A, Kim-Hellmuth S, Stranger BE, Pellegrini M, Mangul S. Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Brief Bioinform 2021; 22:bbab265. [PMID: 34346485 PMCID: PMC8768458 DOI: 10.1093/bib/bbab265] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/07/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Estimating cell type composition of blood and tissue samples is a biological challenge relevant in both laboratory studies and clinical care. In recent years, a number of computational tools have been developed to estimate cell type abundance using gene expression data. Although these tools use a variety of approaches, they all leverage expression profiles from purified cell types to evaluate the cell type composition within samples. In this study, we compare 12 cell type quantification tools and evaluate their performance while using each of 10 separate reference profiles. Specifically, we have run each tool on over 4000 samples with known cell type proportions, spanning both immune and stromal cell types. A total of 12 of these represent in vitro synthetic mixtures and 300 represent in silico synthetic mixtures prepared using single-cell data. A final 3728 clinical samples have been collected from the Framingham cohort, for which cell populations have been quantified using electrical impedance cell counting. When tools are applied to the Framingham dataset, the tool Estimating the Proportions of Immune and Cancer cells (EPIC) produces the highest correlation, whereas Gene Expression Deconvolution Interactive Tool (GEDIT) produces the lowest error. The best tool for other datasets is varied, but CIBERSORT and GEDIT most consistently produce accurate results. We find that optimal reference depends on the tool used, and report suggested references to be used with each tool. Most tools return results within minutes, but on large datasets runtimes for CIBERSORT can exceed hours or even days. We conclude that deconvolution methods are capable of returning high-quality results, but that proper reference selection is critical.
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Affiliation(s)
- Brian B Nadel
- Corresponding authors: Brian B. Nadel, Tel: 310-963-7077; E-mail: ; Matteo Pellegrini, Tel: 310-825-0012, E-mail: ; Serghei Mangul, Tel: 323-442-0043, E-mail:
| | | | | | | | | | | | | | | | | | | | - Serghei Mangul
- Corresponding authors: Brian B. Nadel, Tel: 310-963-7077; E-mail: ; Matteo Pellegrini, Tel: 310-825-0012, E-mail: ; Serghei Mangul, Tel: 323-442-0043, E-mail:
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11
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Maroney KJ, Pinski AN, Marzi A, Messaoudi I. Transcriptional Analysis of Infection With Early or Late Isolates From the 2013-2016 West Africa Ebola Virus Epidemic Does Not Suggest Attenuated Pathogenicity as a Result of Genetic Variation. Front Microbiol 2021; 12:714817. [PMID: 34484156 PMCID: PMC8415004 DOI: 10.3389/fmicb.2021.714817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
The 2013-2016 West Africa Ebola virus (EBOV) epidemic caused by the EBOV-Makona isolate is the largest and longest recorded to date. It incurred over 28,000 infections and ∼11,000 deaths. Early in this epidemic, several mutations in viral glycoprotein (A82V), nucleoprotein (R111C), and polymerase L (D759G) emerged and stabilized. In vitro studies of these new EBOV-Makona isolates showed enhanced fitness and viral replication capacity. However, in vivo studies in mice and rhesus macaques did not provide any evidence of enhanced viral fitness or shedding. Infection with late isolates carrying or early isolates lacking (early) these mutations resulted in uniformly lethal disease in nonhuman primates (NHPs), albeit with slightly delayed kinetics with late isolates. The recent report of a possible reemergence of EBOV from a persistent infection in a survivor of the epidemic highlights the urgency for understanding the impact of genetic variation on EBOV pathogenesis. However, potential molecular differences in host responses remain unknown. To address this gap in knowledge, we conducted the first comparative analysis of the host responses to lethal infection with EBOV-Mayinga and EBOV-Makona isolates using bivariate, longitudinal, regression, and discrimination transcriptomic analyses. Our analysis shows a conserved core of differentially expressed genes (DEGs) involved in antiviral defense, immune cell activation, and inflammatory processes in response to EBOV-Makona and EBOV-Mayinga infections. Additionally, EBOV-Makona and EBOV-Mayinga infections could be discriminated based on the expression pattern of a small subset of genes. Transcriptional responses to EBOV-Makona isolates that emerged later during the epidemic, specifically those from Mali and Liberia, lacked signatures of profound lymphopenia and excessive inflammation seen following infection with EBOV-Mayinga and early EBOV-Makona isolate C07. Overall, these findings provide novel insight into the mechanisms underlying the lower case fatality rate (CFR) observed with EBOV-Makona compared to EBOV-Mayinga.
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Affiliation(s)
- Kevin J Maroney
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Rocky Mountain Laboratories, Hamilton, MT, United States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States.,Center for Virus Research, University of California, Irvine, Irvine, CA, United States.,Institute for Immunology, University of California, Irvine, Irvine, CA, United States
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12
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Rhoades NS, Hendrickson SM, Prongay K, Haertel A, Gill L, Edwards RA, Garzel L, Slifka MK, Messaoudi I. Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen. Mucosal Immunol 2021; 14:1113-1126. [PMID: 34158595 PMCID: PMC8379072 DOI: 10.1038/s41385-021-00418-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023]
Abstract
Despite the impact of childhood diarrhea on morbidity and mortality, our understanding of its sequelae has been significantly hampered by the lack of studies that examine samples across the entire intestinal tract. Infant rhesus macaques are naturally susceptible to human enteric pathogens and recapitulate the hallmarks of diarrheal disease such as intestinal inflammation and growth faltering. Here, we examined intestinal biopsies, lamina propria leukocytes, luminal contents, and fecal samples from healthy infants and those experiencing growth faltering with distant acute or chronic active diarrhea. We show that growth faltering in the presence or absence of active diarrhea is associated with a heightened systemic and mucosal pro-inflammatory state centered in the colon. Moreover, polyclonal stimulation of colonic lamina propria leukocytes resulted in a dampened cytokine response, indicative of immune exhaustion. We also detected a functional and taxonomic shift in the luminal microbiome across multiple gut sites including the migration of Streptococcus and Prevotella species between the small and large intestine, suggesting a decompartmentalization of gut microbial communities. Our studies provide valuable insight into the outcomes of diarrheal diseases and growth faltering not attainable in humans and lays the groundwork to test interventions in a controlled and reproducible setting.
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Affiliation(s)
- Nicholas S Rhoades
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Sara M Hendrickson
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Kamm Prongay
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Andrew Haertel
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Leanne Gill
- California National Primate Research Center, Davis, Davis, CA, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Laura Garzel
- California National Primate Research Center, Davis, Davis, CA, USA
| | - Mark K Slifka
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA.
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13
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Fantecelle CH, Covre LP, Garcia de Moura R, Guedes HLDM, Amorim CF, Scott P, Mosser D, Falqueto A, Akbar AN, Gomes DCO. Transcriptomic landscape of skin lesions in cutaneous leishmaniasis reveals a strong CD8 + T cell immunosenescence signature linked to immunopathology. Immunology 2021; 164:754-765. [PMID: 34432883 DOI: 10.1111/imm.13410] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022] Open
Abstract
The severity of lesions that develop in patients infected by Leishmania braziliensis is mainly associated with a highly cytotoxic and inflammatory cutaneous environment. Recently, we demonstrated that senescent T and NK cells play a role in the establishment and maintenance of this tissue inflammation. Here, we extended those findings using transcriptomic analyses that demonstrate a strong co-induction of senescence and pro-inflammatory gene signatures in cutaneous leishmaniasis (CL) lesions. The senescence-associated signature was characterized by marked expression of key genes such as ATM, Sestrin 2, p16, p21 and p38. The cell type identification from deconvolution of bulk sequencing data showed that the senescence signature was linked with CD8+ effector memory and TEMRA subsets and also senescent NK cells. A key observation was that the senescence markers in the skin lesions are age-independent of patients and were correlated with lesion size. Moreover, a striking expression of the senescence-associated secretory phenotype (SASP), pro-inflammatory cytokine and chemokines genes was found within lesions that were most strongly associated with the senescent CD8 TEMRA subset. Collectively, our results confirm that there is a senescence transcriptomic signature in CL lesions and supports the hypothesis that lesional senescent cells have a major role in mediating immunopathology of the disease.
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Affiliation(s)
| | - Luciana Polaco Covre
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitoria, Brazil.,Division of Medicine, University College London, London, UK
| | - Renan Garcia de Moura
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitoria, Brazil
| | - Herbert Leonel de Matos Guedes
- Instituto de Microbiologia Professor Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Camila Farias Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Mosser
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Aloisio Falqueto
- Departamento de Medicina Social, Universidade Federal do Espírito Santo, Vitoria, Brazil
| | - Arne N Akbar
- Division of Medicine, University College London, London, UK
| | - Daniel Claudio Oliveira Gomes
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitoria, Brazil.,Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitoria, Brazil
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14
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Bountress KE, Vladimirov V, McMichael G, Taylor ZN, Hardiman G, Chung D, Adams ZW, Danielson CK, Amstadter AB. Gene Expression Differences Between Young Adults Based on Trauma History and Post-traumatic Stress Disorder. Front Psychiatry 2021; 12:581093. [PMID: 33897478 PMCID: PMC8060466 DOI: 10.3389/fpsyt.2021.581093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/15/2021] [Indexed: 11/29/2022] Open
Abstract
Background: The purpose of this study was to identify gene expression differences associated with post-traumatic stress disorder (PTSD) and trauma exposure (TE) in a three-group study design comprised of those with and without trauma exposure and PTSD. Methods: We conducted gene expression and gene network analyses in a sample (n = 45) composed of female subjects of European Ancestry (EA) with PTSD, TE without PTSD, and controls. Results: We identified 283 genes differentially expressed between PTSD-TE groups. In an independent sample of Veterans (n = 78) a small minority of these genes were also differentially expressed. We identified 7 gene network modules significantly associated with PTSD and TE (Bonferroni corrected p ≤ 0.05), which at a false discovery rate (FDR) of q ≤ 0.2, were significantly enriched for biological pathways involved in focal adhesion, neuroactive ligand receptor interaction, and immune related processes among others. Conclusions: This study uses gene network analyses to identify significant gene modules associated with PTSD, TE, and controls. On an individual gene level, we identified a large number of differentially expressed genes between PTSD-TE groups, a minority of which were also differentially expressed in the independent sample. We also demonstrate a lack of network module preservation between PTSD and TE, suggesting that the molecular signature of PTSD and trauma are likely independent of each other. Our results provide a basis for the identification of likely disease pathways and biomarkers involved in the etiology of PTSD.
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Affiliation(s)
- Kaitlin E. Bountress
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Vladimir Vladimirov
- Department of Psychiatry and Behavioral Sciences, College of Medicine Texas A&M University, Richmond, VA, United States
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States
| | - Gowon McMichael
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Z. Nathan Taylor
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Gary Hardiman
- Institute for Global Food Security, Queens University Belfast, Belfast, United Kingdom
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Zachary W. Adams
- Department of Psychiatry, Indiana University of Medicine, Indianapolis, IN, United States
| | - Carla Kmett Danielson
- National Crime Victim Research and Treatment Center, Medical University of South Carolina, Charleston, SC, United States
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Ananda B. Amstadter
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
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15
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Nakamizo S, Honda T, Sato T, Al Mamun M, Chow Z, Duan K, Lum J, Tan KJ, Tomari K, Sato R, Kitoh A, Tay ASL, Common JEA, Guan NL, Setou M, Ginhoux F, Kabashima K. High-fat diet induces a predisposition to follicular hyperkeratosis and neutrophilic folliculitis in mice. J Allergy Clin Immunol 2021; 148:473-485.e10. [PMID: 33713763 DOI: 10.1016/j.jaci.2021.02.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Neutrophilic folliculitis is an inflammatory condition of hair follicles. In some neutrophilic folliculitis, such as in patients with acne and hidradenitis suppurativa, follicular hyperkeratosis is also observed. Neutrophilic folliculitis is often induced and/or exacerbated by a high-fat diet (HFD). However, the molecular mechanisms by which an HFD affects neutrophilic folliculitis are not fully understood. OBJECTIVE Our aim was to elucidate how an HFD promotes the development of neutrophilic folliculitis. METHODS Mice were fed an HFD, and their skin was subjected to histologic, RNA sequencing, and imaging mass spectrometry analyses. To examine the effect of an HFD on neutrophil accumulation around the hair follicles, phorbol 12-myristate 13-acetate (PMA) was used as an irritant to the skin. RESULTS Histologic analysis revealed follicular hyperkeratosis in the skin of HFD-fed mice. RNA sequencing analysis showed that genes related to keratinization, especially in upper hair follicular keratinocytes, were significantly upregulated in HFD-fed mice. Application of PMA to the skin induced neutrophilic folliculitis in HFD-fed mice but not in mice fed a normal diet. Accumulation of neutrophils in the skin and around hair follicles was dependent on CXCR2 signaling, and CXCL1 (a CXCR2 ligand) was produced mainly by hair follicular keratinocytes. Imaging mass spectrometry analysis revealed an increase in fatty acids in the skin of HFD-fed mice. Application of these fatty acids to the skin induced follicular hyperkeratosis and caused PMA-induced neutrophilic folliculitis even in mice fed a normal diet. CONCLUSION An HFD can facilitate the development of neutrophilic folliculitis with the induction of hyperkeratosis of hair follicles and increased neutrophil infiltration around the hair follicles via CXCR2 signaling.
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Affiliation(s)
- Satoshi Nakamizo
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore; Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore; Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tetsuya Honda
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Dermatology, School of Medicine, Hamamatsu University, Hamamatsu, Shizuoka, Japan.
| | - Tomohito Sato
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Al Mamun
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Zachary Chow
- Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Kaibo Duan
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Josephine Lum
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Kahbing Jasmine Tan
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore; Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Kaori Tomari
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Reiko Sato
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore; Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akihiko Kitoh
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Angeline S L Tay
- Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - John E A Common
- Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Ng Lai Guan
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore; Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore.
| | - Kenji Kabashima
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore; Skin Research Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore; Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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16
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Chen Z, Wu A. Progress and challenge for computational quantification of tissue immune cells. Brief Bioinform 2021; 22:6065002. [PMID: 33401306 DOI: 10.1093/bib/bbaa358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 12/28/2022] Open
Abstract
Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.
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Affiliation(s)
- Ziyi Chen
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
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17
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O’Connor D, Pinto MV, Sheerin D, Tomic A, Drury RE, Channon‐Wells S, Galal U, Dold C, Robinson H, Kerridge S, Plested E, Hughes H, Stockdale L, Sadarangani M, Snape MD, Rollier CS, Levin M, Pollard AJ. Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine. Mol Syst Biol 2020; 16:e9888. [PMID: 33210468 PMCID: PMC7674973 DOI: 10.15252/msb.20209888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Neisseria meningitidis is a major cause of meningitis and septicaemia. A MenB vaccine (4CMenB) was licensed by the European Medicines Agency in January 2013. Here we describe the blood transcriptome and proteome following infant immunisations with or without concomitant 4CMenB, to gain insight into the molecular mechanisms underlying post-vaccination reactogenicity and immunogenicity. Infants were randomised to receive control immunisations (PCV13 and DTaP-IPV-Hib) with or without 4CMenB at 2 and 4 months of age. Blood gene expression and plasma proteins were measured prior to, then 4 h, 24 h, 3 days or 7 days post-vaccination. 4CMenB vaccination was associated with increased expression of ENTPD7 and increased concentrations of 4 plasma proteins: CRP, G-CSF, IL-1RA and IL-6. Post-vaccination fever was associated with increased expression of SELL, involved in neutrophil recruitment. A murine model dissecting the vaccine components found the concomitant regimen to be associated with increased gene perturbation compared with 4CMenB vaccine alone with enhancement of pathways such as interleukin-3, -5 and GM-CSF signalling. Finally, we present transcriptomic profiles predictive of immunological and febrile responses following 4CMenB vaccine.
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Affiliation(s)
- Daniel O’Connor
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Marta Valente Pinto
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Dylan Sheerin
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Adriana Tomic
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
- Institute of Immunity, Transplantation and InfectionStanford University School of MedicineStanfordCAUSA
| | - Ruth E Drury
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Samuel Channon‐Wells
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Ushma Galal
- Nuffield Department of Primary Health CareClinical Trials UnitUniversity of OxfordOxfordUK
| | - Christina Dold
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Hannah Robinson
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Simon Kerridge
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Emma Plested
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Harri Hughes
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Lisa Stockdale
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | | | - Matthew D Snape
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Christine S Rollier
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Michael Levin
- Division of Infectious DiseasesDepartment of MedicineImperial College LondonLondonUK
| | - Andrew J Pollard
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
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18
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Ross C, Szczepanek K, Lee M, Yang H, Peer CJ, Kindrick J, Shankarappa P, Lin ZW, Sanford JD, Figg WD, Hunter KW. Metastasis-Specific Gene Expression in Autochthonous and Allograft Mouse Mammary Tumor Models: Stratification and Identification of Targetable Signatures. Mol Cancer Res 2020; 18:1278-1289. [PMID: 32513899 PMCID: PMC7483845 DOI: 10.1158/1541-7786.mcr-20-0046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/22/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
Breast cancer metastasis is a leading cause of cancer-related death of women in the United States. A hurdle in advancing metastasis-targeted intervention is the phenotypic heterogeneity between primary and secondary lesions. To identify metastasis-specific gene expression profiles we performed RNA-sequencing of breast cancer mouse models; analyzing metastases from models of various drivers and routes. We contrasted the models and identified common, targetable signatures. Allograft models exhibited more mesenchymal-like gene expression than genetically engineered mouse models (GEMM), and primary culturing of GEMM-derived metastatic tissue induced mesenchymal-like gene expression. In addition, metastasis-specific transcriptomes differed between tail vein and orthotopic injection of the same cell line. Gene expression common to models of spontaneous metastasis included sildenafil response and nicotine degradation pathways. Strikingly, in vivo sildenafil treatment significantly reduced metastasis by 54%, while nicotine significantly increased metastasis by 46%. These data suggest that (i) actionable metastasis-specific pathways can be readily identified, (ii) already available drugs may have great potential to alleviate metastatic incidence, and (iii) metastasis may be influenced greatly by lifestyle choices such as the choice to consume nicotine products. In summary, while mouse models of breast cancer metastasis vary in ways that must not be ignored, there are shared features that can be identified and potentially targeted therapeutically. IMPLICATIONS: The data we present here exposes critical variances between preclinical models of metastatic breast cancer and identifies targetable pathways integral to metastatic spread. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/18/9/1278/F1.large.jpg.
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Affiliation(s)
- Christina Ross
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Karol Szczepanek
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Maxwell Lee
- Laboratory of Cancer Biology and Genetics, High-Dimension Data Analysis Group, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Howard Yang
- Laboratory of Cancer Biology and Genetics, High-Dimension Data Analysis Group, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Cody J Peer
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, NIH, Bethesda, Maryland
| | - Jessica Kindrick
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, NIH, Bethesda, Maryland
| | - Priya Shankarappa
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, NIH, Bethesda, Maryland
| | - Zhi-Wei Lin
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, NIH, Bethesda, Maryland
| | - Jack D Sanford
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, NCI, Bethesda, Maryland
| | - William D Figg
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, NIH, Bethesda, Maryland
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, NCI, Bethesda, Maryland.
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19
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Vacca M, Leslie J, Virtue S, Lam BYH, Govaere O, Tiniakos D, Snow S, Davies S, Petkevicius K, Tong Z, Peirce V, Nielsen MJ, Ament Z, Li W, Kostrzewski T, Leeming DJ, Ratziu V, Allison MED, Anstee QM, Griffin JL, Oakley F, Vidal-Puig A. Bone morphogenetic protein 8B promotes the progression of non-alcoholic steatohepatitis. Nat Metab 2020; 2:514-531. [PMID: 32694734 PMCID: PMC7617436 DOI: 10.1038/s42255-020-0214-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
Non-alcoholic steatohepatitis (NASH) is characterized by lipotoxicity, inflammation and fibrosis, ultimately leading to end-stage liver disease. The molecular mechanisms promoting NASH are poorly understood, and treatment options are limited. Here, we demonstrate that hepatic expression of bone morphogenetic protein 8B (BMP8B), a member of the transforming growth factor beta (TGFβ)-BMP superfamily, increases proportionally to disease stage in people and animal models with NASH. BMP8B signals via both SMAD2/3 and SMAD1/5/9 branches of the TGFβ-BMP pathway in hepatic stellate cells (HSCs), promoting their proinflammatory phenotype. In vivo, the absence of BMP8B prevents HSC activation, reduces inflammation and affects the wound-healing responses, thereby limiting NASH progression. Evidence is featured in primary human 3D microtissues modelling NASH, when challenged with recombinant BMP8. Our data show that BMP8B is a major contributor to NASH progression. Owing to the near absence of BMP8B in healthy livers, inhibition of BMP8B may represent a promising new therapeutic avenue for NASH treatment.
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Affiliation(s)
- Michele Vacca
- TVP Lab, WT/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit - Metabolic Research Laboratories, University of Cambridge, Cambridge, UK.
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
| | - Jack Leslie
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Samuel Virtue
- TVP Lab, WT/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit - Metabolic Research Laboratories, University of Cambridge, Cambridge, UK
| | - Brian Y H Lam
- Yeo Group and Genomics and Transcriptomics Core, WT/MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Pathology, Aretaieion Hospital, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | | | - Susan Davies
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University Hospitals, Cambridge, UK
| | - Kasparas Petkevicius
- TVP Lab, WT/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit - Metabolic Research Laboratories, University of Cambridge, Cambridge, UK
| | - Zhen Tong
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Vivian Peirce
- TVP Lab, WT/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit - Metabolic Research Laboratories, University of Cambridge, Cambridge, UK
| | | | - Zsuzsanna Ament
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Wei Li
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Vlad Ratziu
- Sorbonne Université, Institute for Cardiometabolism and Nutrition (ICAN), Hôpital Pitié-Salpêtrière, Paris, France
| | - Michael E D Allison
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University Hospitals, Cambridge, UK
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Biomolecular Medicine, Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Antonio Vidal-Puig
- TVP Lab, WT/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit - Metabolic Research Laboratories, University of Cambridge, Cambridge, UK.
- Welcome Trust Sanger Institute, Hinxton, UK.
- Cambridge University Nanjing Centre of Technology and Innovation, Jiangbei Area, Nanjing, P R China.
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20
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Early Transcriptional Changes within Liver, Adrenal Gland, and Lymphoid Tissues Significantly Contribute to Ebola Virus Pathogenesis in Cynomolgus Macaques. J Virol 2020; 94:JVI.00250-20. [PMID: 32213610 DOI: 10.1128/jvi.00250-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/11/2020] [Indexed: 01/05/2023] Open
Abstract
Ebola virus (EBOV) continues to pose a significant threat to human health, as evidenced by the 2013-2016 epidemic in West Africa and the ongoing outbreak in the Democratic Republic of the Congo. EBOV causes hemorrhagic fever, organ damage, and shock culminating in death, with case fatality rates as high as 90%. This high lethality combined with the paucity of licensed medical countermeasures makes EBOV a critical human pathogen. Although EBOV infection results in significant damage to the liver and the adrenal glands, little is known about the molecular signatures of injury in these organs. Moreover, while changes in peripheral blood cells are becoming increasingly understood, the host responses within organs and lymphoid tissues remain poorly characterized. To address this knowledge gap, we tracked longitudinal transcriptional changes in tissues collected from EBOV-Makona-infected cynomolgus macaques. Following infection, both liver and adrenal glands exhibited significant and early downregulation of genes involved in metabolism, coagulation, hormone synthesis, and angiogenesis; upregulated genes were associated with inflammation. Analysis of lymphoid tissues showed early upregulation of genes that play a role in innate immunity and inflammation and downregulation of genes associated with cell cycle and adaptive immunity. Moreover, transient activation of innate immune responses and downregulation of humoral immune responses in lymphoid tissues were confirmed with flow cytometry. Together, these data suggest that the liver, adrenal gland, and lymphatic organs are important sites of EBOV infection and that dysregulating the function of these vital organs contributes to the development of Ebola virus disease.IMPORTANCE Ebola virus (EBOV) remains a high-priority pathogen since it continues to cause outbreaks with high case fatality rates. Although it is well established that EBOV results in severe organ damage, our understanding of tissue injury in the liver, adrenal glands, and lymphoid tissues remains limited. We begin to address this knowledge gap by conducting longitudinal gene expression studies in these tissues, which were collected from EBOV-infected cynomolgus macaques. We report robust and early gene expression changes within these tissues, indicating they are primary sites of EBOV infection. Furthermore, genes involved in metabolism, coagulation, and adaptive immunity were downregulated, while inflammation-related genes were upregulated. These results indicate significant tissue damage consistent with the development of hemorrhagic fever and lymphopenia. Our study provides novel insight into EBOV-host interactions and elucidates how host responses within the liver, adrenal glands, and lymphoid tissues contribute to EBOV pathogenesis.
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21
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Immune correlates of postexposure vaccine protection against Marburg virus. Sci Rep 2020; 10:3071. [PMID: 32080323 PMCID: PMC7033120 DOI: 10.1038/s41598-020-59976-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/28/2020] [Indexed: 12/19/2022] Open
Abstract
Postexposure immunization can prevent disease and reduce transmission following pathogen exposure. The rapid immunostimulatory properties of recombinant vesicular stomatitis virus (rVSV)-based vaccines make them suitable postexposure treatments against the filoviruses Ebola virus and Marburg virus (MARV); however, the mechanisms that drive this protection are undefined. Previously, we reported 60–75% survival of rhesus macaques treated with rVSV vectors expressing MARV glycoprotein (GP) 20–30 minutes after a low dose exposure to the most pathogenic variant of MARV, Angola. Survival in this model was linked to production of GP-specific antibodies and lower viral load. To confirm these results and potentially identify novel correlates of postexposure protection, we performed a similar experiment, but analyzed plasma cytokine levels, frequencies of immune cell subsets, and the transcriptional response to infection in peripheral blood. In surviving macaques (80–89%), we observed induction of genes mapping to antiviral and interferon-related pathways early after treatment and a higher percentage of T helper 1 (Th1) and NK cells. In contrast, the response of non-surviving macaques was characterized by hypercytokinemia; a T helper 2 signature; recruitment of low HLA-DR expressing monocytes and regulatory T-cells; and transcription of immune checkpoint (e.g., PD-1, LAG3) genes. These results suggest dysregulated immunoregulation is associated with poor prognosis, whereas early innate signaling and Th1-skewed immunity are important for survival.
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22
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Khaliullin TO, Yanamala N, Newman MS, Kisin ER, Fatkhutdinova LM, Shvedova AA. Comparative analysis of lung and blood transcriptomes in mice exposed to multi-walled carbon nanotubes. Toxicol Appl Pharmacol 2020; 390:114898. [PMID: 31978390 DOI: 10.1016/j.taap.2020.114898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022]
Abstract
Pulmonary exposure to multi-walled carbon nanotubes (MWCNT) causes inflammation, fibroproliferation, immunotoxicity, and systemic responses in rodents. However, the search for representative biomarkers of exposure is an ongoing endeavor. Whole blood gene expression profiling is a promising new approach for the identification of novel disease biomarkers. We asked if the whole blood transcriptome reflects pathology-specific changes in lung gene expression caused by MWCNT. To answer this question, we performed mRNA sequencing analysis of the whole blood and lung in mice administered MWCNT or vehicle solution via pharyngeal aspiration and sacrificed 56 days later. The pattern of lung mRNA expression as determined using Ingenuity Pathway Analysis (IPA) was indicative of continued inflammation, immune cell trafficking, phagocytosis, and adaptive immune responses. Simultaneously, innate immunity-related transcripts (Plunc, Bpifb1, Reg3g) and cancer-related pathways were downregulated. IPA analysis of the differentially expressed genes in the whole blood suggested increased hematopoiesis, predicted activation of cancer/tumor development pathways, and atopy. There were several common upregulated genes between whole blood and lungs, important for adaptive immune responses: Cxcr1, Cd72, Sharpin, and Slc11a1. Trim24, important for TH2 cell effector function, was downregulated in both datasets. Hla-dqa1 mRNA was upregulated in the lungs and downregulated in the blood, as was Lilrb4, which controls the reactivity of immune response. "Cancer" disease category had opposing activation status in the two datasets, while the only commonality was "Hypersensitivity". Transcriptome changes occurring in the lungs did not produce a completely replicable pattern in whole blood; however, specific systemic responses may be shared between transcriptomic profiles.
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Affiliation(s)
- Timur O Khaliullin
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA; Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
| | - Naveena Yanamala
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
| | - Mackenzie S Newman
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA.
| | - Elena R Kisin
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
| | - Liliya M Fatkhutdinova
- Department of Hygiene and Occupational Medicine, Kazan State Medical University, Kazan, Russia
| | - Anna A Shvedova
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA; Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
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23
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Mariotte A, De Cauwer A, Po C, Abou-Faycal C, Pichot A, Paul N, Aouadi I, Carapito R, Frisch B, Macquin C, Chatelus E, Sibilia J, Armspach JP, Bahram S, Georgel P. A mouse model of MSU-induced acute inflammation in vivo suggests imiquimod-dependent targeting of Il-1β as relevant therapy for gout patients. Am J Cancer Res 2020; 10:2158-2171. [PMID: 32104502 PMCID: PMC7019178 DOI: 10.7150/thno.40650] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/24/2019] [Indexed: 12/11/2022] Open
Abstract
Rationale: The role of Monosodium Urate (MSU) crystals in gout pathophysiology is well described, as is the major impact of IL-1β in the inflammatory reaction that constitutes the hallmark of the disease. However, despite the discovery of the NLRP3 inflammasome and its role as a Pattern Recognition Receptor linking the detection of a danger signal (MSU) to IL-1β secretion in vitro, the precise mechanisms leading to joint inflammation in gout patients are still poorly understood. Methods: Acute urate crystal inflammation was obtained by subcutaneous injections of MSU crystals in mice. Symptoms were followed by scoring, cytokine quantification by ELISA and western blot, gene expression by RT-qPCR and RNAseq; Magnetic Resonance Imaging was also used to assess inflammation. Results: We provide an extensive clinical, biological and molecular characterization of an acute uratic inflammation mouse model which accurately mimics human gout. We report the efficacy of topical imiquimod treatment and its impact on Interferon-dependent down modulation of Il-1β gene expression in this experimental model. Conclusion: Our work reveals several key features of MSU-dependent inflammation and identifies novel therapeutic opportunities for gout patients.
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24
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Chiodoni C, Cancila V, Renzi TA, Perrone M, Tomirotti AM, Sangaletti S, Botti L, Dugo M, Milani M, Bongiovanni L, Marrale M, Tripodo C, Colombo MP. Transcriptional Profiles and Stromal Changes Reveal Bone Marrow Adaptation to Early Breast Cancer in Association with Deregulated Circulating microRNAs. Cancer Res 2019; 80:484-498. [PMID: 31776132 DOI: 10.1158/0008-5472.can-19-1425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 10/17/2019] [Accepted: 11/21/2019] [Indexed: 11/16/2022]
Abstract
The presence of a growing tumor establishes a chronic state of inflammation that acts locally and systemically. Bone marrow responds to stress signals by expanding myeloid cells endowed with immunosuppressive functions, further fostering tumor growth and dissemination. How early in transformation the cross-talk with the bone marrow begins and becomes detectable in blood is unknown. Here, gene expression profiling of the bone marrow along disease progression in a spontaneous model of mammary carcinogenesis demonstrates that transcriptional modifications in the hematopoietic compartment occurred as early as preinvasive disease stages. The transcriptional profile showed downregulation of adaptive immunity and induction of programs related to innate immunity and response to danger signals triggered by activating transcription factor 3. Transcriptional reprogramming was paralleled by the expansion of myeloid populations at the expense of erythroid and B lymphoid fractions. Hematopoietic changes were associated with modifications of the bone marrow stromal architecture through relocalization and increased density in the interstitial area of Nestin+ mesenchymal cells expressing CXCL12 and myeloid cells expressing CXCL12 receptor CXCR4. These early events were concomitant with deregulation of circulating miRNAs, which were predicted regulators of transcripts downregulated in the bone marrow and involved in lymphoid differentiation and activation. These data provide a link between sensing of peripheral cancer initiation by the bone marrow and hematopoietic adaptation to distant noxia through transcriptional rewiring toward innate/inflammatory response programs. SIGNIFICANCE: The bone marrow senses distant tissue transformation at premalignant/preinvasive stages, suggesting that circulating messengers, intercepted in the blood, could serve as early diagnostic markers.
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Affiliation(s)
- Claudia Chiodoni
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy
| | - Tiziana A Renzi
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Milena Perrone
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea M Tomirotti
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sabina Sangaletti
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Laura Botti
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Platform of Integrated Biology - Bioinformatics, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori Milan, Italy
| | - Matteo Milani
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucia Bongiovanni
- Tumor Immunology Unit, Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy
| | - Maurizio Marrale
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy
| | - Mario P Colombo
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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25
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Amorim CF, Novais FO, Nguyen BT, Misic AM, Carvalho LP, Carvalho EM, Beiting DP, Scott P. Variable gene expression and parasite load predict treatment outcome in cutaneous leishmaniasis. Sci Transl Med 2019; 11:eaax4204. [PMID: 31748229 PMCID: PMC7068779 DOI: 10.1126/scitranslmed.aax4204] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
Abstract
Patients infected with Leishmania braziliensis develop chronic lesions that often fail to respond to treatment with antiparasite drugs. To determine whether genes whose expression is highly variable in lesions between patients might influence disease outcome, we obtained biopsies of lesions from patients before treatment with pentavalent antimony and performed transcriptomic profiling on these clinical samples. We identified genes that were highly variably expressed between patients, and the variable expression of these genes correlated with treatment outcome. Among the most variable genes in all the patients were components of the cytolytic pathway, and the expression of these genes correlated with parasite load in the skin. We demonstrated that treatment failure was linked to the cytolytic pathway activated during infection. Using a host-pathogen marker profile of as few as three genes, we showed that eventual treatment outcome could be predicted before the start of treatment in two separate cohorts of patients with cutaneous leishmaniasis (n = 21 and n = 25). These findings raise the possibility of point-of-care diagnostic screening to identify patients at high risk of treatment failure and provide a rationale for a precision medicine approach to drug selection in cutaneous leishmaniasis. This work more broadly demonstrates the value of identifying genes of high variability in other diseases to better understand and predict diverse clinical outcomes.
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Affiliation(s)
- Camila Farias Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Fernanda O Novais
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Ba T Nguyen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Ana M Misic
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Lucas P Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia 40110-060, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, 40296-710, Brazil
| | - Edgar M Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia 40110-060, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, 40296-710, Brazil
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA.
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA.
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26
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Barrenas F, Raehtz K, Xu C, Law L, Green RR, Silvestri G, Bosinger SE, Nishida A, Li Q, Lu W, Zhang J, Thomas MJ, Chang J, Smith E, Weiss JM, Dawoud RA, Richter GH, Trichel A, Ma D, Peng X, Komorowski J, Apetrei C, Pandrea I, Gale M. Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control. Nat Commun 2019; 10:5101. [PMID: 31704931 PMCID: PMC6841668 DOI: 10.1038/s41467-019-12987-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/08/2019] [Indexed: 01/13/2023] Open
Abstract
Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-β and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.
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Affiliation(s)
- Fredrik Barrenas
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Kevin Raehtz
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cuiling Xu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA, USA
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA
| | - Richard R Green
- Department of Immunology, University of Washington, Seattle, WA, USA
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA
| | - Guido Silvestri
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew Nishida
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wuxun Lu
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jianshui Zhang
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew J Thomas
- Department of Immunology, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jean Chang
- Department of Immunology, University of Washington, Seattle, WA, USA
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA
| | - Elise Smith
- Department of Immunology, University of Washington, Seattle, WA, USA
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Reem A Dawoud
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - George H Richter
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anita Trichel
- Divison of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dongzhu Ma
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Institute of Computer Science, PAN, Warsaw, Poland
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivona Pandrea
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA, USA.
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA.
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA.
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27
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Avila Cobos F, Vandesompele J, Mestdagh P, De Preter K. Computational deconvolution of transcriptomics data from mixed cell populations. Bioinformatics 2019; 34:1969-1979. [PMID: 29351586 DOI: 10.1093/bioinformatics/bty019] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/10/2018] [Indexed: 12/22/2022] Open
Abstract
Summary Gene expression analyses of bulk tissues often ignore cell type composition as an important confounding factor, resulting in a loss of signal from lowly abundant cell types. In this review, we highlight the importance and value of computational deconvolution methods to infer the abundance of different cell types and/or cell type-specific expression profiles in heterogeneous samples without performing physical cell sorting. We also explain the various deconvolution scenarios, the mathematical approaches used to solve them and the effect of data processing and different confounding factors on the accuracy of the deconvolution results. Contact katleen.depreter@ugent.be. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Francisco Avila Cobos
- Center for Medical Genetics Ghent (CMGG), Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), 9000 Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics Ghent (CMGG), Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), 9000 Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics Ghent (CMGG), Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), 9000 Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics Ghent (CMGG), Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), 9000 Ghent, Belgium
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28
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Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten LAB, Netea MG, Avraham R. Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells. Nat Commun 2019; 10:3266. [PMID: 31332193 PMCID: PMC6646406 DOI: 10.1038/s41467-019-11257-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 07/03/2019] [Indexed: 12/20/2022] Open
Abstract
Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Advances in single cell RNA-sequencing (scRNA-seq) allow probing of these immune interactions, such as cell-type compositions, which are then interpreted by deconvolution algorithms using bulk RNA-seq measurements. However, not all aspects of immune surveillance are represented by current algorithms. Here, using scRNA-seq of human peripheral blood cells infected with Salmonella, we develop a deconvolution algorithm for inferring cell-type specific infection responses from bulk measurements. We apply our dynamic deconvolution algorithm to a cohort of healthy individuals challenged ex vivo with Salmonella, and to three cohorts of tuberculosis patients during different stages of disease. We reveal cell-type specific immune responses associated not only with ex vivo infection phenotype but also with clinical disease stage. We propose that our approach provides a predictive power to identify risk for disease, and human infection outcomes. Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Here, Avraham and colleagues present a deconvolution algorithm that uses single-cell RNA and bulk RNA sequencing measurements of pathogen-infected cells to predict disease risk outcomes.
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Affiliation(s)
- Noa Bossel Ben-Moshe
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Shelly Hen-Avivi
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Natalia Levitin
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Dror Yehezkel
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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Abstract
Ebola virus (EBOV) is a single-stranded RNA virus that causes Ebola virus disease (EVD), characterized by excessive inflammation, lymphocyte apoptosis, hemorrhage, and coagulation defects leading to multiorgan failure and shock. Recombinant vesicular stomatitis virus expressing the EBOV glycoprotein (VSV-EBOV), which is highly efficacious against lethal challenge in nonhuman primates, is the only vaccine that successfully completed a phase III clinical trial. Additional studies showed VSV-EBOV provides complete and partial protection to macaques immunized 7 and 3 days before EBOV challenge, respectively. However, the mechanisms by which this live-attenuated vaccine elicits rapid protection are only partially understood. To address this, we carried out a longitudinal transcriptome analysis of host responses in whole-blood samples collected from cynomolgus macaques vaccinated with VSV-EBOV 28, 21, 14, 7, and 3 days before EBOV challenge. Our findings indicate the transcriptional response to the vaccine peaks 7 days following vaccination and contains signatures of both innate antiviral immunity as well as B-cell activation. EBOV challenge 1 week after vaccination resulted in large gene expression changes suggestive of a recall adaptive immune response 14 days postchallenge. Lastly, the timing and magnitude of innate immunity and interferon-stimulated gene expression correlated with viral burden and disease outcome in animals vaccinated 3 days before challenge.IMPORTANCE Ebola virus (EBOV) is the causative agent of Ebola virus disease (EVD), a deadly disease and major public health threat worldwide. A safe and highly efficacious vesicular stomatitis virus-based vaccine against EBOV is the only platform that has successfully completed phase III clinical trials and has been used in recent and ongoing outbreaks. Earlier studies showed that antibodies are the main mode of protection when this vaccine is administered 28 days before EBOV challenge. Recently, we showed this vaccine can provide protection when administered as early as 3 days before challenge and before antibodies are detected. This study seeks to identify the mechanisms of rapid protection, which in turn will pave the way for improved vaccines and therapeutics. Additionally, this study provides insight into host gene expression signatures that could provide early biomarkers to identify infected individuals who are at highest risk of poor outcomes.
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30
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Deasy SK, Uehara R, Vodnala SK, Yang HH, Dass RA, Hu Y, Lee MP, Crouch RJ, Hunter KW. Aicardi-Goutières syndrome gene Rnaseh2c is a metastasis susceptibility gene in breast cancer. PLoS Genet 2019; 15:e1008020. [PMID: 31125342 PMCID: PMC6553800 DOI: 10.1371/journal.pgen.1008020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/06/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the second leading cause of cancer-related deaths in the United States, with the majority of these deaths due to metastatic lesions rather than the primary tumor. Thus, a better understanding of the etiology of metastatic disease is crucial for improving survival. Using a haplotype mapping strategy in mouse and shRNA-mediated gene knockdown, we identified Rnaseh2c, a scaffolding protein of the heterotrimeric RNase H2 endoribonuclease complex, as a novel metastasis susceptibility factor. We found that the role of Rnaseh2c in metastatic disease is independent of RNase H2 enzymatic activity, and immunophenotyping and RNA-sequencing analysis revealed engagement of the T cell-mediated adaptive immune response. Furthermore, the cGAS-Sting pathway was not activated in the metastatic cancer cells used in this study, suggesting that the mechanism of immune response in breast cancer is different from the mechanism proposed for Aicardi-Goutières Syndrome, a rare interferonopathy caused by RNase H2 mutation. These results suggest an important novel, non-enzymatic role for RNASEH2C during breast cancer progression and add Rnaseh2c to a panel of genes we have identified that together could determine patients with high risk for metastasis. These results also highlight a potential new target for combination with immunotherapies and may contribute to a better understanding of the etiology of Aicardi-Goutières Syndrome autoimmunity.
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Affiliation(s)
- Sarah K. Deasy
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Institute for Biomedical Sciences, The George Washington University, Washington, District of Columbia, United States of America
| | - Ryo Uehara
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Suman K. Vodnala
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard H. Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Randall A. Dass
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maxwell P. Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert J. Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kent W. Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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31
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Barr T, Lewis SA, Sureshchandra S, Doratt B, Grant KA, Messaoudi I. Chronic ethanol consumption alters lamina propria leukocyte response to stimulation in a region-dependent manner. FASEB J 2019; 33:7767-7777. [PMID: 30897342 DOI: 10.1096/fj.201802780r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chronic heavy alcohol consumption, also referred to as chronic heavy drinking (CHD), results in intestinal injury characterized by increased permeability, dysbiosis, nutrient malabsorption, potentially higher susceptibility to infection, and increased risk of colorectal cancer. However, our understanding of the mechanisms by which CHD results in intestinal damage remains incomplete. Here, we investigated the impact of chronic drinking on transcriptional and functional responses of lamina propria leukocytes (LPLs) isolated from the 4 major gut sections. Although no significant differences were detected between LPLs isolated from the ethanol and control groups at resting state within each major gut section, our analysis uncovered key regional differences in composition and function of LPLs independent of alcohol consumption. However, in response to phorbol myristate acetate and ionomycin, duodenal LPLs from ethanol-drinking animals generated a dampened response, whereas jejunal and ileal LPLs from ethanol-drinking animals produced a heightened response. Transcriptional responses following stimulation were pronounced in ileal and duodenal LPLs from the ethanol-drinking group but less evident in jejunal and colonic LPLs compared with controls, suggesting a more significant impact of alcohol on these gut regions. The altered intestinal LPL function detected in our study reveals remarkable region specificity and novel insight into potential mechanisms of intestinal injury associated with CHD.-Barr, T., Lewis, S. A., Sureshchandra, S., Doratt, B., Grant, K. A., Messaoudi, I. Chronic ethanol consumption alters lamina propria leukocyte response to stimulation in a region-dependent manner.
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Affiliation(s)
- Tasha Barr
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, California, USA
| | - Sloan A Lewis
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, California, USA
| | - Suhas Sureshchandra
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, California, USA
| | - Brianna Doratt
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, California, USA
| | - Kathleen A Grant
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, California, USA.,Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, USA
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32
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Frishberg A, Peshes-Yaloz N, Cohn O, Rosentul D, Steuerman Y, Valadarsky L, Yankovitz G, Mandelboim M, Iraqi FA, Amit I, Mayo L, Bacharach E, Gat-Viks I. Cell composition analysis of bulk genomics using single-cell data. Nat Methods 2019; 16:327-332. [PMID: 30886410 PMCID: PMC6443043 DOI: 10.1038/s41592-019-0355-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022]
Abstract
Single-cell expression profiling (scRNA-seq) is a rich resource of cellular heterogeneity. While profiling every sample under study would be advantageous, it is time-consuming and costly. Here we introduce Cell Population Mapping (CPM), a deconvolution algorithm in which the composition of cell types and states is inferred from the bulk transcriptome using reference scRNA-seq profiles ('scBio' CRAN R-package). Analysis of individual variations in lungs of influenza virus-infected mice, using CPM, revealed that the relationship between cell abundance and clinical symptoms is a cell-state-specific property that varies gradually along the continuum of cell-activation states. The gradual change was confirmed in subsequent experiments and was further explained by a mathematical model in which clinical outcomes relate to cell-state dynamics along the activation process. Our results demonstrate the power of CPM in reconstructing the continuous spectrum of cell states within heterogeneous tissues.
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Affiliation(s)
- Amit Frishberg
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Naama Peshes-Yaloz
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ofir Cohn
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Diana Rosentul
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Steuerman
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Liran Valadarsky
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gal Yankovitz
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Mandelboim
- National Center for Influenza and Respiratory Viruses, Central Virology Laboratory, Sheba Medical Center at Tel HaShomer, Ramat-Gan, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Amit
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Lior Mayo
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Irit Gat-Viks
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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33
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Rhoades N, Mendoza N, Jankeel A, Sureshchandra S, Alvarez AD, Doratt B, Heidari O, Hagan R, Brown B, Scheibel S, Marbley T, Taylor J, Messaoudi I. Altered Immunity and Microbial Dysbiosis in Aged Individuals With Long-Term Controlled HIV Infection. Front Immunol 2019; 10:463. [PMID: 30915086 PMCID: PMC6423162 DOI: 10.3389/fimmu.2019.00463] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/20/2019] [Indexed: 01/22/2023] Open
Abstract
The introduction of highly active antiretroviral therapy (HAART) resulted in a significant increase in life expectancy for HIV patients. Indeed, in 2015, 45% of the HIV+ individuals in the United States were ≥55 years of age. Despite improvements in diagnosis and treatment of HIV infection, geriatric HIV+ patients suffer from higher incidence of comorbidities compared to age-matched HIV- individuals. Both chronic inflammation and dysbiosis of the gut microbiome are believed to be major contributors to this phenomenon, however carefully controlled studies investigating the impact of long-term (>10 years) controlled HIV (LTC-HIV) infection are lacking. To address this question, we profiled circulating immune cells, immune mediators, and the gut microbiome from elderly (≥55 years old) LTC-HIV+ and HIV- gay men living in the Palm Springs area. LTC-HIV+ individuals had lower frequency of circulating monocytes and CD4+ T-cells, and increased frequency CD8+ T-cells. Moreover, levels of systemic INFγ and several growth factors were increased while levels of IL-2 and several chemokines were reduced. Upon stimulation, immune cells from LTC-HIV+ individuals produced higher levels of pro-inflammatory cytokines. Last but not least, the gut microbiome of LTC-HIV+ individuals was enriched in bacterial taxa typically found in the oral cavity suggestive of loss of compartmentalization, while levels of beneficial butyrate producing taxa were reduced. Additionally, prevalence of Prevotella negatively correlated with CD4+ T-cells numbers in LTC-HIV+ individuals. These results indicate that despite long-term adherence and undetectable viral loads, LTC-HIV infection results in significant shifts in immune cell frequencies and gut microbial communities.
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Affiliation(s)
- Nicholas Rhoades
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
| | - Norma Mendoza
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
| | - Allen Jankeel
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
| | - Suhas Sureshchandra
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
| | - Alexander D Alvarez
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
| | - Brianna Doratt
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
| | - Omeid Heidari
- School of Nursing, John Hopkins University, Baltimore, MD, United States
| | - Rod Hagan
- Stonewall Medical Center, Borrego Health, Cathedral City, CA, United States
| | - Brandon Brown
- School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Steven Scheibel
- Stonewall Medical Center, Borrego Health, Cathedral City, CA, United States
| | - Theodore Marbley
- Stonewall Medical Center, Borrego Health, Cathedral City, CA, United States
| | - Jeff Taylor
- HIV+ Aging-Palm Springs, Palm Springs, CA, United States
| | - Ilhem Messaoudi
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, United States
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34
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Cross RW, Speranza E, Borisevich V, Widen SG, Wood TG, Shim RS, Adams RD, Gerhardt DM, Bennett RS, Honko AN, Johnson JC, Hensley LE, Geisbert TW, Connor JH. Comparative Transcriptomics in Ebola Makona-Infected Ferrets, Nonhuman Primates, and Humans. J Infect Dis 2018; 218:S486-S495. [PMID: 30476250 PMCID: PMC6249602 DOI: 10.1093/infdis/jiy455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The domestic ferret is a uniformly lethal model of infection for 3 species of Ebolavirus known to be pathogenic in humans. Reagents to systematically analyze the ferret host response to infection are lacking; however, the recent publication of a draft ferret genome has opened the potential for transcriptional analysis of ferret models of disease. In this work, we present comparative analysis of longitudinally sampled blood taken from ferrets and nonhuman primates infected with lethal doses of the Makona variant of Zaire ebolavirus. Strong induction of proinflammatory and prothrombotic signaling programs were present in both ferrets and nonhuman primates, and both transcriptomes were similar to previously published datasets of fatal cases of human Ebola virus infection.
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Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Steven G Widen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Thomas G Wood
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Rebecca S Shim
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Ricky D Adams
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Dawn M Gerhardt
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Richard S Bennett
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - John H Connor
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
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35
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Finotello F, Trajanoski Z. Quantifying tumor-infiltrating immune cells from transcriptomics data. Cancer Immunol Immunother 2018; 67:1031-1040. [PMID: 29541787 PMCID: PMC6006237 DOI: 10.1007/s00262-018-2150-z] [Citation(s) in RCA: 279] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/09/2018] [Indexed: 12/22/2022]
Abstract
By exerting pro- and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the quantification of tumor-infiltrating immune cells holds the promise to unveil the multi-faceted role of the immune system in human cancers and its involvement in tumor escape mechanisms and response to therapy. Tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches. In this review, we describe state-of-the-art computational methods for the quantification of immune cells from transcriptomics data and discuss the open challenges that must be addressed to accurately quantify immune infiltrates from RNA sequencing data of human bulk tumors.
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Affiliation(s)
- Francesca Finotello
- Biocenter, Division for Bioinformatics, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria.
| | - Zlatko Trajanoski
- Biocenter, Division for Bioinformatics, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria.
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36
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The immunosuppressive face of sepsis early on intensive care unit-A large-scale microarray meta-analysis. PLoS One 2018; 13:e0198555. [PMID: 29920518 PMCID: PMC6007920 DOI: 10.1371/journal.pone.0198555] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/21/2018] [Indexed: 12/15/2022] Open
Abstract
Background Sepsis is defined as a life-threatening condition, resulting from a dysregulated and harmful response of the hosts’ immune system to infection. Apart from this, the (over-)compensating mechanisms counterbalancing the inflammatory response have been proven to render the host susceptible to further infections and increase delayed mortality. Our study aimed to unravel the heterogeneity of immune response in early sepsis and to explain the biology behind it. Methods A systematic search of public repositories yielded 949 microarray samples from patients with sepsis of different infectious origin and early after clinical manifestation. These were merged into a meta-expression set, and after applying sequential conservative bioinformatics filtering, an in-deep analysis of transcriptional heterogeneity, as well as a comparison to samples of healthy controls was performed. Results We can identify two distinct clusters of patients (cluster 1: 655 subjects, cluster 2: 294 subjects) according to their global blood transcriptome. While both clusters exhibit only moderate differences in direct comparison, a comparison of both clusters individually to healthy controls yielded strong expression changes of genes involved in immune responses. Both comparisons found similar regulated genes, with a stronger dysregulation occurring in the larger patient cluster and implicating a loss of monocyte and T cell function, co-occurring with an activation of neutrophil granulocytes. Conclusion We propose a consistent—but in its extent varying—presence of immunosuppression, occurring as early in sepsis as its clinical manifestation and irrespective of the infectious origin. While certain cell types possess contradictory activation states, our finding underlines the urgent need for an early host-directed therapy of sepsis side-by-side with antibiotics.
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37
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Titus AJ, Gallimore RM, Salas LA, Christensen BC. Cell-type deconvolution from DNA methylation: a review of recent applications. Hum Mol Genet 2018; 26:R216-R224. [PMID: 28977446 PMCID: PMC5886462 DOI: 10.1093/hmg/ddx275] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023] Open
Abstract
Recent advances in cell-type deconvolution approaches are adding to our understanding of the biology underlying disease development and progression. DNA methylation (DNAm) can be used as a biomarker of cell types, and through deconvolution approaches, to infer underlying cell type proportions. Cell-type deconvolution algorithms have two main categories: reference-based and reference-free. Reference-based algorithms are supervised methods that determine the underlying composition of cell types within a sample by leveraging differentially methylated regions (DMRs) specific to cell type, identified from DNAm measures of purified cell populations. Reference-free algorithms are unsupervised methods for use when cell-type specific DMRs are not available, allowing scientists to estimate putative cellular proportions or control for potential confounding from cell type. Reference-based deconvolution is typically applied to blood samples and has potentiated our understanding of the relation between immune profiles and disease by allowing estimation of immune cell proportions from archival DNA. Bioinformatic analyses using DNAm to infer immune cell proportions, part of a new field known as Immunomethylomics, provides a new direction for consideration in epigenome wide association studies (EWAS).
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Affiliation(s)
- Alexander J Titus
- Program in Quantitative Biomedical Sciences.,Department of Epidemiology
| | | | | | - Brock C Christensen
- Department of Epidemiology.,Department of Molecular and Systems Biology.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
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38
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Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PLoS One 2018; 13:e0193067. [PMID: 29494600 PMCID: PMC5832224 DOI: 10.1371/journal.pone.0193067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/02/2018] [Indexed: 11/30/2022] Open
Abstract
Bulk tissue samples examined by gene expression studies are usually heterogeneous. The data gained from these samples display the confounding patterns of mixtures consisting of multiple cell types or similar cell types in various functional states, which hinders the elucidation of the molecular mechanisms underlying complex biological phenomena. A realistic approach to compensate for the limitations of experimentally separating homogenous cell populations from mixed tissues is to computationally identify cell-type specific patterns from bulk, heterogeneous measurements. We designed the CellDistinguisher algorithm to analyze the gene expression data of mixed samples, identifying genes that best distinguish biological processes and cell types. Coupled with a deconvolution algorithm that takes cell type specific gene lists as input, we show that CellDistinguisher performs as well as partial deconvolution algorithms in predicting cell type composition without the need for prior knowledge of cell type signatures. This approach is also better in predicting cell type signatures than the one-step traditional complete deconvolution methods. To illustrate its wide applicability, the algorithm was tested on multiple publicly available data sets. In each case, CellDistinguisher identified genes reflecting biological processes typical for the tissues and development stages of interest and estimated the sample compositions accurately.
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39
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Falik-Zaccai TC, Barsheshet Y, Mandel H, Segev M, Lorber A, Gelberg S, Kalfon L, Ben Haroush S, Shalata A, Gelernter-Yaniv L, Chaim S, Raviv Shay D, Khayat M, Werbner M, Levi I, Shoval Y, Tal G, Shalev S, Reuveni E, Avitan-Hersh E, Vlodavsky E, Appl-Sarid L, Goldsher D, Bergman R, Segal Z, Bitterman-Deutsch O, Avni O. Sequence variation in PPP1R13L results in a novel form of cardio-cutaneous syndrome. EMBO Mol Med 2017; 9:319-336. [PMID: 28069640 PMCID: PMC5331242 DOI: 10.15252/emmm.201606523] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is a life-threatening disorder whose genetic basis is heterogeneous and mostly unknown. Five Arab Christian infants, aged 4-30 months from four families, were diagnosed with DCM associated with mild skin, teeth, and hair abnormalities. All passed away before age 3. A homozygous sequence variation creating a premature stop codon at PPP1R13L encoding the iASPP protein was identified in three infants and in the mother of the other two. Patients' fibroblasts and PPP1R13L-knocked down human fibroblasts presented higher expression levels of pro-inflammatory cytokine genes in response to lipopolysaccharide, as well as Ppp1r13l-knocked down murine cardiomyocytes and hearts of Ppp1r13l-deficient mice. The hypersensitivity to lipopolysaccharide was NF-κB-dependent, and its inducible binding activity to promoters of pro-inflammatory cytokine genes was elevated in patients' fibroblasts. RNA sequencing of Ppp1r13l-knocked down murine cardiomyocytes and of hearts derived from different stages of DCM development in Ppp1r13l-deficient mice revealed the crucial role of iASPP in dampening cardiac inflammatory response. Our results determined PPP1R13L as the gene underlying a novel autosomal-recessive cardio-cutaneous syndrome in humans and strongly suggest that the fatal DCM during infancy is a consequence of failure to regulate transcriptional pathways necessary for tuning cardiac threshold response to common inflammatory stressors.
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Affiliation(s)
- Tzipora C Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel .,Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Yiftah Barsheshet
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Hanna Mandel
- Metabolic Disease Unit, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Meital Segev
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Avraham Lorber
- Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,Department of Pediatric Cardiology, Rambam Health Care Campus, Haifa, Israel
| | - Shachaf Gelberg
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Limor Kalfon
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Shani Ben Haroush
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Adel Shalata
- The Winter Genetic Institute, Bnei Zion Medical Center, Haifa, Israel
| | | | - Sarah Chaim
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Dorith Raviv Shay
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Morad Khayat
- The Genetic Institute, Ha'emek Medical Center, Afula, Israel
| | - Michal Werbner
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Inbar Levi
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Yishay Shoval
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Galit Tal
- Metabolic Disease Unit, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Stavit Shalev
- Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,The Genetic Institute, Ha'emek Medical Center, Afula, Israel
| | - Eli Reuveni
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | | | - Eugene Vlodavsky
- Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,Department of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Liat Appl-Sarid
- Department of Pathology, Galilee Medical Center, Nahariya, Israel
| | - Dorit Goldsher
- Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,Department of Diagnostic Imaging, Rambam Health Care Campus, Haifa, Israel
| | - Reuven Bergman
- Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,Department of Dermatology, Rambam Health Care Campus, Haifa, Israel
| | - Zvi Segal
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel.,Department of Ophthalmology, Galilee Medical Center, Nahariya, Israel
| | - Ora Bitterman-Deutsch
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel.,Dermatology Clinic, Galilee Medical Center, Nahariya, Israel
| | - Orly Avni
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
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