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Namulondo J, Nyangiri OA, Kimuda MP, Nambala P, Nassuuna J, Egesa M, Nerima B, Biryomumaisho S, Mugasa CM, Nabukenya I, Kato D, Elliott A, Noyes H, Tweyongyere R, Matovu E, Mulindwa J. Transcriptome analysis of peripheral blood of Schistosoma mansoni infected children from the Albert Nile region in Uganda reveals genes implicated in fibrosis pathology. PLoS Negl Trop Dis 2023; 17:e0011455. [PMID: 37967122 PMCID: PMC10686515 DOI: 10.1371/journal.pntd.0011455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/29/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023] Open
Abstract
Over 290 million people are infected by schistosomes worldwide. Schistosomiasis control efforts focus on mass drug treatment with praziquantel (PZQ), a drug that kills the adult worm of all Schistosoma species. Nonetheless, re-infections have continued to be detected in endemic areas with individuals living in the same area presenting with varying infection intensities. Our objective was to characterize the transcriptome profiles in peripheral blood of children between 10-15 years with varying intensities of Schistosoma mansoni infection living along the Albert Nile in Uganda. RNA extracted from peripheral blood collected from 44 S. mansoni infected (34 high and 10 low by circulating anodic antigen [CAA] level) and 20 uninfected children was sequenced using Illumina NovaSeq S4 and the reads aligned to the GRCh38 human genome. Differential gene expression analysis was done using DESeq2. Principal component analysis revealed clustering of gene expression by gender when S. mansoni infected children were compared with uninfected children. In addition, we identified 14 DEGs between S. mansoni infected and uninfected individuals, 56 DEGs between children with high infection intensity and uninfected individuals, 33 DEGs between those with high infection intensity and low infection intensity and no DEGs between those with low infection and uninfected individuals. We also observed upregulation and downregulation of some DEGs that are associated with fibrosis and its regulation. These data suggest expression of fibrosis associated genes as well as genes that regulate fibrosis in S. mansoni infection. The relatively few significant DEGS observed in children with schistosomiasis suggests that chronic S. mansoni infection is a stealth infection that does not stimulate a strong immune response.
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Affiliation(s)
- Joyce Namulondo
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Oscar Asanya Nyangiri
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Magambo Phillip Kimuda
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Peter Nambala
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Jacent Nassuuna
- Vaccine Research Theme, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Moses Egesa
- Vaccine Research Theme, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Barbara Nerima
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Savino Biryomumaisho
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Claire Mack Mugasa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Immaculate Nabukenya
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Drago Kato
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Alison Elliott
- Vaccine Research Theme, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, United Kingdom
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- College of Natural Sciences, Makerere University, Kampala, Uganda
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Abstract
Most patients with Lyme disease will fully recover with recommended antibiotic therapy. However, some patients report persisting nonspecific symptoms after treatment, referred to as posttreatment Lyme disease symptoms (PTLDs) or syndrome (PTLDS), depending on the degree to which the individual's symptoms impact their quality of life. PTLDs occur in a portion of patients diagnosed with chronic Lyme disease (CLD), a controversial term describing different patient populations, diagnosed based on unvalidated tests and criteria. Practitioners should review the evidence for the Lyme disease diagnosis and not overlook unrelated conditions. Current evidence shows that prolonged antibiotic therapy provides little benefit and carries significant risk. Further research to elucidate the mechanisms underlying persistent symptoms after Lyme disease and to understand CLD is needed.
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Affiliation(s)
- Adriana Marques
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, BG 10 RM 12C118 MSC 1888 10 Center, Bethesda, MD 20892-1888, USA.
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Siddiqi KZ, Wilhelm TR, Ulff-Møller CJ, Jacobsen S. Cluster of highly expressed interferon-stimulated genes associate more with African ancestry than disease activity in patients with systemic lupus erythematosus. A systematic review of cross-sectional studies. Transl Res 2021; 238:63-75. [PMID: 34343626 DOI: 10.1016/j.trsl.2021.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023]
Abstract
Type I interferons (IFN) are central players in the pathogenesis of systemic lupus erythematosus (SLE) and the up-regulation of interferon-stimulated genes (ISGs) in SLE patients is subjected to increasing scrutiny as for its use in diagnosis, stratification and monitoring of SLE patients. Determinants of this immunological phenomenon are yet to be fully charted. The purpose of this systematic review was to characterize expressions of ISGs in blood of SLE patients and to analyze if they associated with core demographic and clinical features of SLE. Twenty cross-sectional, case-control studies comprising 1033 SLE patients and 602 study controls could be included. ISG fold-change expression values (SLE vs controls), demographic and clinical data were extracted from the published material and analyzed by hierarchical cluster analysis and generalized linear modelling. ISG expression varied substantially within each study with IFI27, IFI44, IFI44L, IFIT4 and RSAD2, being the top-five upregulated ISGs. Analysis of inter-study variation showed that IFI27, IFI44, IFI44L, IFIT1, PRKR and RSAD2 expression clustered with the fraction of SLE cases having African ancestry or lupus nephritis. Generalized linear models adjusted for prevalence of lupus nephritis and usage of hydroxychloroquine confirmed the observed association between African ancestry and IFI27, IFI44L, IFIT1, PRKR and RSAD2, whereas disease activity was associated with expression of IFI27 and RNASE2. In conclusion, this systematic review revealed that expression of ISGs often used for deriving an IFN signature in SLE patients were influenced by African ancestry rather than disease activity. This underscores the necessity of taking ancestry into account when employing the IFN signature for clinical research in SLE.
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Affiliation(s)
- Kanwal Z Siddiqi
- Copenhagen Lupus and Vasculitis Clinic, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Theresa R Wilhelm
- Copenhagen Lupus and Vasculitis Clinic, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Constance J Ulff-Møller
- Copenhagen Lupus and Vasculitis Clinic, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Søren Jacobsen
- Copenhagen Lupus and Vasculitis Clinic, Rigshospitalet, Copenhagen University Hospital, Denmark.
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Zhang S, Li X, Lin Q, Wong KC. Nature-Inspired Compressed Sensing for Transcriptomic Profiling From Random Composite Measurements. IEEE TRANSACTIONS ON CYBERNETICS 2021; 51:4476-4487. [PMID: 31751263 DOI: 10.1109/tcyb.2019.2951402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcriptomic profiling is a high-throughput approach to measure gene expression levels under different experimental conditions at different timings. With the development of the related technologies such as single-cell RNA-Seq, the dimensions of gene expression data are increased to hundreds of thousands or more for high-resolution insights. There is a long-lasting challenge in exploiting the relations between transcriptomic profiles and random composite measurements. To address it, we proposed a mathematical framework based on differential evolution (global search) with the help of compressed sensing (local search) termed as DECS. Exploiting the inherent sparse nature of gene expression data, the proposed DECS method can learn the sparse module dictionaries and levels from the low-dimensional random composite measurements for reconstructing the high-dimensional gene expression data with significant orders of magnitude (e.g. 200 × ). Several experiments were conducted to compare DECS with three benchmark methods, demonstrating that the proposed DECS outperforms the benchmark methods and can recover most of the gene expression patterns. The underlying reasons are discussed and illustrated by revealing the related mechanistic insights through extensive benchmarks on nine GSE datasets and their sensitivity analysis.
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Malato J, Sotzny F, Bauer S, Freitag H, Fonseca A, Grabowska AD, Graça L, Cordeiro C, Nacul L, Lacerda EM, Castro-Marrero J, Scheibenbogen C, Westermeier F, Sepúlveda N. The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in myalgic encephalomyelitis/chronic fatigue syndrome: A meta-analysis of public DNA methylation and gene expression data. Heliyon 2021; 7:e07665. [PMID: 34341773 PMCID: PMC8320404 DOI: 10.1016/j.heliyon.2021.e07665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/23/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
People with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) often report a high frequency of viral infections and flu-like symptoms during their disease course. Given that this reporting agrees with different immunological abnormalities and altered gene expression profiles observed in the disease, we aimed at answering whether the expression of the human angiotensin-converting enzyme 2 (ACE2), the major cell entry receptor for SARS-CoV-2, is also altered in these patients. In particular, a low expression of ACE2 could be indicative of a high risk of developing COVID-19. We then performed a meta-analysis of public data on CpG DNA methylation and gene expression of this enzyme and its homologous ACE protein in peripheral blood mononuclear cells and related subsets. We found that patients with ME/CFS have decreased methylation levels of four CpG probes in the ACE locus (cg09920557, cg19802564, cg21094739, and cg10468385) and of another probe in the promoter region of the ACE2 gene (cg08559914). We also found a decreased expression of ACE2 but not of ACE in patients when compared to healthy controls. Accordingly, in newly collected data, there was evidence for a significant higher proportion of samples with an ACE2 expression below the limit of detection in patients than healthy controls. Altogether, patients with ME/CFS can be at a higher COVID-19 risk and, if so, they should be considered a priority group for vaccination by public health authorities. To further support this conclusion, similar research is recommended for other human cell entry receptors and cell types, namely, those cells targeted by the virus.
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Affiliation(s)
- João Malato
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- CEAUL – Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Franziska Sotzny
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Sandra Bauer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Helma Freitag
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - André Fonseca
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
| | - Anna D. Grabowska
- Department of Biophysics, Physiology, and Pathophysiology, Medical University of Warsaw, Warsaw, Poland
| | - Luís Graça
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Clara Cordeiro
- CEAUL – Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
| | - Luís Nacul
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Complex Chronic Diseases Program, British Columbia Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Eliana M. Lacerda
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jesus Castro-Marrero
- Vall d’Hebron Hospital Research Institute, Division of Rheumatology, ME/CFS Unit, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Scheibenbogen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Francisco Westermeier
- Institute of Biomedical Science, Department of Health Studies, FH Joanneum University of Applied Sciences, Graz, Austria
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O´Higgins, Santiago, Chile
| | - Nuno Sepúlveda
- CEAUL – Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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6
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O'Neal AJ, Hanson MR. The Enterovirus Theory of Disease Etiology in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Critical Review. Front Med (Lausanne) 2021; 8:688486. [PMID: 34222292 PMCID: PMC8253308 DOI: 10.3389/fmed.2021.688486] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system disease whose etiological basis has not been established. Enteroviruses (EVs) as a cause of ME/CFS have sometimes been proposed, as they are known agents of acute respiratory and gastrointestinal infections that may persist in secondary infection sites, including the central nervous system, muscle, and heart. To date, the body of research that has investigated enterovirus infections in relation to ME/CFS supports an increased prevalence of chronic or persistent enteroviral infections in ME/CFS patient cohorts than in healthy individuals. Nevertheless, inconsistent results have fueled a decline in related studies over the past two decades. This review covers the aspects of ME/CFS pathophysiology that are consistent with a chronic enterovirus infection and critically reviews methodologies and approaches used in past EV-related ME/CFS studies. We describe the prior sample types that were interrogated, the methods used and the limitations to the approaches that were chosen. We conclude that there is considerable evidence that prior outbreaks of ME/CFS were caused by one or more enterovirus groups. Furthermore, we find that the methods used in prior studies were inadequate to rule out the presence of chronic enteroviral infections in individuals with ME/CFS. Given the possibility that such infections could be contributing to morbidity and preventing recovery, further studies of appropriate biological samples with the latest molecular methods are urgently needed.
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Affiliation(s)
- Adam J O'Neal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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7
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Melnick M, Gonzales P, LaRocca TJ, Song Y, Wuu J, Benatar M, Oskarsson B, Petrucelli L, Dowell RD, Link CD, Prudencio M. Application of a bioinformatic pipeline to RNA-seq data identifies novel viruslike sequence in human blood. G3-GENES GENOMES GENETICS 2021; 11:6259144. [PMID: 33914880 PMCID: PMC8661426 DOI: 10.1093/g3journal/jkab141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022]
Abstract
Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data and in a reconstruction experiment using synthetic data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq datasets currently being generated.
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Affiliation(s)
- Marko Melnick
- Integrative Physiology, University of Colorado, Boulder, Colorado, 80303, USA
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, 80303, USA
| | - Thomas J LaRocca
- Department of Health and Exercise Science, Center for Healthy Aging, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Yuping Song
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida, 32224, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami, Miami, Florida, 33136, USA
| | - Michael Benatar
- Department of Neurology, University of Miami, Miami, Florida, 33136, USA
| | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville FL, 32224, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida, 32224, USA.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, 32224, USA
| | - Robin D Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, 80303, USA
| | - Christopher D Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, 80303, USA.,Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, 80303, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida, 32224, USA.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida, 32224, USA
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8
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Malato J, Sotzny F, Bauer S, Freitag H, Fonseca A, Grabowska AD, Graça L, Cordeiro C, Nacul L, Lacerda EM, Castro-Marrero J, Scheibenbogen C, Westermeier F, Sepúlveda N. The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: analysis of high-throughput epigenetic and gene expression studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.23.21254175. [PMID: 33791744 PMCID: PMC8010776 DOI: 10.1101/2021.03.23.21254175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Patients affected by Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) show specific epigenetic and gene expression signatures of the disease. However, it is unknown whether these signatures include abnormal levels of the human angiotensin-converting enzymes, ACE and ACE2, the latter being the main receptor described for the host-cell invasion by SARS-CoV-2. To investigate that, we first re-analyzed available case-control epigenome-wide association studies based on DNA methylation data, and case-control gene expression studies based on microarray data. From these published studies, we found an association between ME/CFS and 4 potentially hypomethylated probes located in the ACE locus. We also found another disease association with one hypomethylated probe located in the transcription start site of ACE2. The same disease associations were obtained for women but not for men after performing sex-specific analyses. In contrast, a meta-analysis of gene expression levels could not provide evidence for a differentially expression of ACE and ACE2 in affected patients when compared to healthy controls. In line with this negative finding, the analysis of a new data set on the gene expression of ACE and ACE2 in peripheral blood mononuclear cells did not find any differences between a female cohort of 37 patients and 34 age-matched healthy controls. Future studies should be conducted to extend this investigation to other potential receptors used by SARS-CoV-2. These studies will help researchers and clinicians to improve the understanding of the health risk imposed by this virus when infecting patients affected by this debilitating disease.
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Affiliation(s)
- João Malato
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- CEAUL – Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Franziska Sotzny
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Sandra Bauer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Helma Freitag
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - André Fonseca
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
| | - Anna D Grabowska
- Department of Biophysics and Human Physiology, Medical University of Warsaw, Warsaw, Poland
| | - Luís Graça
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Clara Cordeiro
- CEAUL – Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
| | - Luís Nacul
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Complex Chronic Diseases Program, British Columbia Women’s Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Eliana M Lacerda
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jesus Castro-Marrero
- Vall d’Hebron Hospital Research Institute, Division of Rheumatology, ME/CFS Unit, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Scheibenbogen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Francisco Westermeier
- Institute of Biomedical Science, FH Joanneum University of Applied Sciences, Graz, Austria
- Centro de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Nuno Sepúlveda
- CEAUL – Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Sweetman E, Kleffmann T, Edgar C, de Lange M, Vallings R, Tate W. A SWATH-MS analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome peripheral blood mononuclear cell proteomes reveals mitochondrial dysfunction. J Transl Med 2020; 18:365. [PMID: 32972442 PMCID: PMC7512220 DOI: 10.1186/s12967-020-02533-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
Background Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a serious and complex physical illness that affects all body systems with a multiplicity of symptoms, but key hallmarks of the disease are pervasive fatigue and ‘post-exertional malaise’, exacerbation after physical and/or mental activity of the intrinsic fatigue and other symptoms that can be highly debilitating and last from days to months. Although the disease can vary widely between individuals, common symptoms also include pain, cognitive deficits, sleep dysfunction, as well as immune, neurological and autonomic symptoms. Typically, it is a very isolating illness socially, carrying a stigma because of the lack of understanding of the cause and pathophysiology. Methods To gain insight into the pathophysiology of ME/CFS, we examined the proteomes of peripheral blood mononuclear cells (PBMCs) by SWATH-MS analysis in a small well-characterised group of patients and matched controls. A principal component analysis (PCA) was used to stratify groups based on protein abundance patterns, which clearly segregated the majority of the ME/CFS patients (9/11) from the controls. This majority subgroup of ME/CFS patients was then further compared to the control group. Results A total of 60 proteins in the ME/CFS patients were differentially expressed (P < 0.01, Log10 (Fold Change) > 0.2 and < −0.2). Comparison of the PCA selected subgroup of ME/CFS patients (9/11) with controls increased the number of proteins differentially expressed to 99. Of particular relevance to the core symptoms of fatigue and post-exertional malaise experienced in ME/CFS, a proportion of the identified proteins in the ME/CFS groups were involved in mitochondrial function, oxidative phosphorylation, electron transport chain complexes, and redox regulation. A significant number were also involved in previously implicated disturbances in ME/CFS, such as the immune inflammatory response, DNA methylation, apoptosis and proteasome activation. Conclusions The results from this study support a model of deficient ATP production in ME/CFS, compensated for by upregulation of immediate pathways upstream of Complex V that would suggest an elevation of oxidative stress. This study and others have found evidence of a distinct pathology in ME/CFS that holds promise for developing diagnostic biomarkers.
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Affiliation(s)
- Eiren Sweetman
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Christina Edgar
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Michel de Lange
- Centre for Biostatistics, University of Otago, Dunedin, 9016, New Zealand
| | | | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand.
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Fu K, Hui B, Wang Q, Lu C, Shi W, Zhang Z, Rong D, Zhang B, Tian Z, Tang W, Cao H, Wang X, Chen Z. Single-cell RNA sequencing of immune cells in gastric cancer patients. Aging (Albany NY) 2020; 12:2747-2763. [PMID: 32039830 PMCID: PMC7041746 DOI: 10.18632/aging.102774] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/12/2020] [Indexed: 12/16/2022]
Abstract
Cancer immunotherapy has achieved positive clinical responses in the treatment of various cancers, including gastric cancer (GC). In this study, we characterized the heterogeneity of T cells isolated from GC patients at the single-cell level using single-cell RNA sequencing. We identified different immune cell subtypes and their heterogeneous transcription factors and depicted their developmental trajectories. In particular, we focused on exhausted CD8+ cells and Tregs and discovered that, as compared to control, the IRF8 transcription factor was downregulated in CD8+ tumour-infiltrating lymphocytes (TILs) from GC tissues, and that GC patients with lower IRF8 levels in blood CD8+ T cells tended to be a at a more advanced disease stage. These findings provide a theoretical basis for targeted immune therapy in GC.
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Affiliation(s)
- Kai Fu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bingqing Hui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qian Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chen Lu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Weihong Shi
- Jiangsu Research Center for Primary Health Development and General Education, Jiangsu Vocational College of Medicine, Yancheng, China
| | - Zhigang Zhang
- Department of General Surgery, Zhongda Hospital, Medical School, Southeast University, Nanjing, China
| | - Dawei Rong
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Betty Zhang
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Zhaofeng Tian
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Ziyi Chen
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
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11
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Morris MC, Cooney KE, Sedghamiz H, Abreu M, Collado F, Balbin EG, Craddock TJA, Klimas NG, Broderick G, Fletcher MA. Leveraging Prior Knowledge of Endocrine Immune Regulation in the Therapeutically Relevant Phenotyping of Women With Chronic Fatigue Syndrome. Clin Ther 2019; 41:656-674.e4. [PMID: 30929860 DOI: 10.1016/j.clinthera.2019.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/28/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE The complex and varied presentation of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) has made it difficult to diagnose, study, and treat. Its symptoms and likely etiology involve multiple components of endocrine and immune regulation, including the hypothalamic-pituitary-adrenal axis, the hypothalamic-pituitary-gonadal axis, and their interactive oversight of immune function. We propose that the persistence of ME/CFS may involve changes in the regulatory interactions across these physiological axes. We also propose that the robustness of this new pathogenic equilibrium may at least in part explain the limited success of conventional single-target therapies. METHODS A comprehensive model was constructed of female endocrine-immune signaling consisting of 28 markers linked by 214 documented regulatory interactions. This detailed model was then constrained to adhere to experimental measurements in a subset of 17 candidate immune markers measured in peripheral blood of patients with ME/CFS and healthy control subjects before, during, and after a maximal exercise challenge. A set of 26 competing numerical models satisfied these data to within 5% error. FINDINGS Mechanistically informed predictions of endocrine and immune markers that were either unmeasured or exhibited high subject-to-subject variability pointed to possible context-specific overexpression in ME/CFS at rest of corticotropin-releasing hormone, chemokine (C-X-C motif) ligand 8, estrogen, follicle-stimulating hormone (FSH), gonadotropin-releasing hormone 1, interleukin (IL)-23, and luteinizing hormone, and underexpression of adrenocorticotropic hormone, cortisol, interferon-γ, IL-10, IL-17, and IL-1α. Simulations of rintatolimod and rituximab treatment predicted a shift in the repertoire of available endocrine-immune regulatory regimens. Rintatolimod was predicted to make available substantial remission in a significant subset of subjects, in particular those with low levels of IL-1α, IL-17, and cortisol; intermediate levels of progesterone and FSH; and high estrogen levels. Rituximab treatment was predicted to support partial remission in a smaller subset of patients with ME/CFS, specifically those with low norepinephrine, IL-1α, chemokine (C-X-C motif) ligand 8, and cortisol levels; intermediate FSH and gonadotropin-releasing hormone 1 levels; and elevated expression of tumor necrosis factor-α, luteinizing hormone, IL-12, and B-cell activation. IMPLICATIONS Applying a rigorous filter of known signaling mechanisms to experimentally measured immune marker expression in ME/CFS has highlighted potential new context-specific markers of illness. These novel endocrine and immune markers may offer useful candidates in delineating new subtypes of ME/CFS and may inform on refinements to the inclusion criteria and instrumentation of new and ongoing trials involving rintatolimod and rituximab treatment protocols.
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Affiliation(s)
- Matthew C Morris
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, USA
| | - Katherine E Cooney
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, USA
| | - Hooman Sedghamiz
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, USA
| | - Maria Abreu
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Miami Veterans Affairs Medical Center, Miami, FL, USA
| | - Fanny Collado
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Miami Veterans Affairs Medical Center, Miami, FL, USA
| | - Elizabeth G Balbin
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Miami Veterans Affairs Medical Center, Miami, FL, USA
| | - Travis J A Craddock
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Departments of Psychology and Neuroscience, Computer Science, and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Nancy G Klimas
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Miami Veterans Affairs Medical Center, Miami, FL, USA
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, USA; Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, USA.
| | - Mary Ann Fletcher
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA; Miami Veterans Affairs Medical Center, Miami, FL, USA
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12
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Bouquet J, Li T, Gardy JL, Kang X, Stevens S, Stevens J, VanNess M, Snell C, Potts J, Miller RR, Morshed M, McCabe M, Parker S, Uyaguari M, Tang P, Steiner T, Chan WS, De Souza AM, Mattman A, Patrick DM, Chiu CY. Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing. PLoS One 2019; 14:e0212193. [PMID: 30897114 PMCID: PMC6428308 DOI: 10.1371/journal.pone.0212193] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/24/2019] [Indexed: 11/19/2022] Open
Abstract
Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a syndrome of unknown etiology characterized by profound fatigue exacerbated by physical activity, also known as post-exertional malaise (PEM). Previously, we did not detect evidence of immune dysregulation or virus reactivation outside of PEM periods. Here we sought to determine whether cardiopulmonary exercise stress testing of ME/CFS patients could trigger such changes. ME/CFS patients (n = 14) and matched sedentary controls (n = 11) were subjected to cardiopulmonary exercise on 2 consecutive days and followed up to 7 days post-exercise, and longitudinal whole blood samples analyzed by RNA-seq. Although ME/CFS patients showed significant worsening of symptoms following exercise versus controls, with 8 of 14 ME/CFS patients showing reduced oxygen consumption ([Formula: see text]) on day 2, transcriptome analysis yielded only 6 differentially expressed gene (DEG) candidates when comparing ME/CFS patients to controls across all time points. None of the DEGs were related to immune signaling, and no DEGs were found in ME/CFS patients before and after exercise. Virome composition (P = 0.746 by chi-square test) and number of viral reads (P = 0.098 by paired t-test) were not significantly associated with PEM. These observations do not support transcriptionally-mediated immune cell dysregulation or viral reactivation in ME/CFS patients during symptomatic PEM episodes.
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Affiliation(s)
- Jerome Bouquet
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Tony Li
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jennifer L. Gardy
- Communicable Disease Prevention and Control Services, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Xiaoying Kang
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Staci Stevens
- Workwell Foundation, Ripon, California, United States of America
| | - Jared Stevens
- Workwell Foundation, Ripon, California, United States of America
| | - Mark VanNess
- Workwell Foundation, Ripon, California, United States of America
| | | | - James Potts
- Department of Pediatrics, Division of Cardiology, University of British Columbia, Vancouver, Canada
| | - Ruth R. Miller
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Muhammad Morshed
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mark McCabe
- Communicable Disease Prevention and Control Services, Vancouver, Canada
| | - Shoshana Parker
- Centre for Health Evaluation Outcome Sciences, Vancouver, Canada
| | - Miguel Uyaguari
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Theodore Steiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, Canada
| | - Wee-Shian Chan
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, Canada
| | | | - Andre Mattman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Adult Metabolic Disease Clinic, Vancouver General Hospital, Vancouver, Canada
| | - David M. Patrick
- Communicable Disease Prevention and Control Services, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
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13
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Bai Y, Wang D, Li W, Huang Y, Ye X, Waite J, Barry T, Edelmann KH, Levenkova N, Guo C, Skokos D, Wei Y, Macdonald LE, Fury W. Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data. PLoS One 2018; 13:e0207020. [PMID: 30439982 PMCID: PMC6237323 DOI: 10.1371/journal.pone.0207020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/22/2018] [Indexed: 11/18/2022] Open
Abstract
Profiling T cell receptor (TCR) repertoire via short read transcriptome sequencing (RNA-Seq) has a unique advantage of probing simultaneously TCRs and the genome-wide RNA expression of other genes. However, compared to targeted amplicon approaches, the shorter read length is more prone to mapping error. In addition, only a small percentage of the genome-wide reads may cover the TCR loci and thus the repertoire could be significantly under-sampled. Although this approach has been applied in a few studies, the utility of transcriptome sequencing in probing TCR repertoires has not been evaluated extensively. Here we present a systematic assessment of RNA-Seq in TCR profiling. We evaluate the power of both Fluidigm C1 full-length single cell RNA-Seq and bulk RNA-Seq in characterizing the repertoires of different diversities under either naïve conditions or after immunogenic challenges. Standard read length and sequencing coverage were employed so that the evaluation was conducted in accord with the current RNA-Seq practices. Despite high sequencing depth in bulk RNA-Seq, we encountered difficulty quantifying TCRs with low transcript abundance (<1%). Nevertheless, top enriched TCRs with an abundance of 1–3% or higher can be faithfully detected and quantified. When top TCR sequences are of interest and transcriptome sequencing is available, it is worthwhile to conduct a TCR profiling using the RNA-Seq data.
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Affiliation(s)
- Yu Bai
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
- * E-mail: (YB); (WF)
| | - David Wang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Wentian Li
- Robert S. Boas Center for Genomics & Human Genetics, Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, United States of America
| | - Ying Huang
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Xuan Ye
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Janelle Waite
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Thomas Barry
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Kurt H. Edelmann
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Natasha Levenkova
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Chunguang Guo
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Dimitris Skokos
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Yi Wei
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Lynn E. Macdonald
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Wen Fury
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
- * E-mail: (YB); (WF)
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14
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Günther OP, Gardy JL, Stafford P, Fluge Ø, Mella O, Tang P, Miller RR, Parker SM, Johnston SA, Patrick DM. Immunosignature Analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Mol Neurobiol 2018; 56:4249-4257. [PMID: 30298340 PMCID: PMC6505503 DOI: 10.1007/s12035-018-1354-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
A random-sequence peptide microarray can interrogate serum antibodies in a broad, unbiased fashion to generate disease-specific immunosignatures. This approach has been applied to cancer detection, diagnosis of infections, and interrogation of vaccine response. We hypothesized that there is an immunosignature specific to ME/CFS and that this could aid in the diagnosis. We studied two subject groups meeting the Canadian Consensus Definition of ME/CFS. ME/CFS (n = 25) and matched control (n = 25) sera were obtained from a Canadian study. ME/CFS (n = 25) sera were obtained from phase 1/2 Norwegian trials (NCT01156909). Sera from six healthy controls from the USA were included in the analysis. Canadian cases and controls were tested for a disease immunosignature. By combining results from unsupervised and supervised analyses, a candidate immunosignature with 654 peptides was able to differentiate ME/CFS from controls. The immunosignature was tested and further refined using the Norwegian and USA samples. This resulted in a 256-peptide immunosignature with the ability to separate ME/CFS cases from controls in the international data sets. We were able to identify a 256-peptide signature that separates ME/CFS samples from healthy controls, suggesting that the hit-and-run hypothesis of immune dysfunction merits further investigation. By extending testing of both our signature and one previously reported in the literature to larger cohorts, and further interrogating the specific peptides we and others have identified, we may deepen our understanding of the origins of ME/CFS and work towards a clinically meaningful diagnostic biomarker.
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Affiliation(s)
| | - Jennifer L Gardy
- British Columbia Centre for Disease Control, Vancouver, BC, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | | | - Øystein Fluge
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | - Olav Mella
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | | | - Ruth R Miller
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Shoshana M Parker
- Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, BC, Canada
| | | | - David M Patrick
- British Columbia Centre for Disease Control, Vancouver, BC, Canada. .,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
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15
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Breden F, Watson CT. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1053:245-263. [PMID: 29549643 DOI: 10.1007/978-3-319-72077-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High throughput sequencing (HTS) approaches have only recently been applied to describing the antibody/B-cell repertoire in fine detail, but these data sets have already become critical to the design of vaccines and therapeutics, and monitoring of cancer immunotherapy. As a case study, we describe the potential and present limitations of HTS studies of the Ab repertoire during infection with HIV-1. Most of the present studies restrict their analyses to lineages of specific bnAbs. We discuss future initiatives to expand this type of analysis to more complete repertoires and to improve comparing and sharing of these Ab repertoire data across studies and institutions.
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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16
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Blomberg J, Gottfries CG, Elfaitouri A, Rizwan M, Rosén A. Infection Elicited Autoimmunity and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: An Explanatory Model. Front Immunol 2018; 9:229. [PMID: 29497420 PMCID: PMC5818468 DOI: 10.3389/fimmu.2018.00229] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022] Open
Abstract
Myalgic encephalomyelitis (ME) often also called chronic fatigue syndrome (ME/CFS) is a common, debilitating, disease of unknown origin. Although a subject of controversy and a considerable scientific literature, we think that a solid understanding of ME/CFS pathogenesis is emerging. In this study, we compiled recent findings and placed them in the context of the clinical picture and natural history of the disease. A pattern emerged, giving rise to an explanatory model. ME/CFS often starts after or during an infection. A logical explanation is that the infection initiates an autoreactive process, which affects several functions, including brain and energy metabolism. According to our model for ME/CFS pathogenesis, patients with a genetic predisposition and dysbiosis experience a gradual development of B cell clones prone to autoreactivity. Under normal circumstances these B cell offsprings would have led to tolerance. Subsequent exogenous microbial exposition (triggering) can lead to comorbidities such as fibromyalgia, thyroid disorder, and orthostatic hypotension. A decisive infectious trigger may then lead to immunization against autoantigens involved in aerobic energy production and/or hormone receptors and ion channel proteins, producing postexertional malaise and ME/CFS, affecting both muscle and brain. In principle, cloning and sequencing of immunoglobulin variable domains could reveal the evolution of pathogenic clones. Although evidence consistent with the model accumulated in recent years, there are several missing links in it. Hopefully, the hypothesis generates testable propositions that can augment the understanding of the pathogenesis of ME/CFS.
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Affiliation(s)
- Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Clinical Microbiology, Academic Hospital, Uppsala, Sweden
| | | | - Amal Elfaitouri
- Department of Infectious Disease and Tropical Medicine, Faculty of Public Health, Benghazi University, Benghazi, Libya
| | - Muhammad Rizwan
- Department of Medical Sciences, Uppsala University, Clinical Microbiology, Academic Hospital, Uppsala, Sweden
| | - Anders Rosén
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Linköping University, Linköping, Sweden
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