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Boruch A, Branchaw G, O'Connor PJ, Cook DB. Physical Activity and Fatigue Symptoms: Neurotypical Adults and People with Chronic Multisymptom Illnesses. Curr Top Behav Neurosci 2024. [PMID: 39037494 DOI: 10.1007/7854_2024_502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
For neurotypical adults, a single bout of low-to-moderate intensity physical activity usually transiently improves feelings of energy. Similar bouts of exercise have the opposite effect of increased feelings of fatigue when performed by samples with chronic multisymptom illnesses (CMIs) such as Long-COVID, Gulf War Illness (GWI), or Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). The short-term adoption of regular moderate intensity physical activity (typical experiments are 1 to 6 months) among neurotypical adults results in small-to-moderate improvements in self-reported feelings of fatigue, energy, and vitality. Small improvements in these feelings, or no change at all, occur for CMIs, but limited data precludes strong conclusions. The mechanisms of exercise effects on fatigue, whether acute or chronic, are poorly understood but likely involve multiple neural circuits and associated transmitters. For CMIs, the mechanisms of acute worsening of fatigue with exercise may be driven by the yet unknown pathophysiological mechanisms of the disease (perhaps involving brain, immune and autonomic system dysfunction, and their interactions). Likewise, fatigue improvements may depend on whether chronic physical activity is a disease-modifying treatment.
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Affiliation(s)
- Alex Boruch
- Research Service, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, USA
| | - Grace Branchaw
- Research Service, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Dane B Cook
- Research Service, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, USA.
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Pérez-Prieto I, Plaza-Florido A, Ubago-Guisado E, Ortega FB, Altmäe S. Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis. J Sci Med Sport 2024:S1440-2440(24)00227-5. [PMID: 39048485 DOI: 10.1016/j.jsams.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/18/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the composition and function of microbial communities, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations. METHODS A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive/athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed. RESULTS Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. Most of studies reported an increase in short-chain fatty acid-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella or Roseburia in active individuals and after physical activity interventions. CONCLUSIONS Physical activity levels were positively associated with the relative abundance of short-chain fatty acid-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids obtaining conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome.
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Affiliation(s)
- Inmaculada Pérez-Prieto
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Spain.
| | - Abel Plaza-Florido
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Spain; Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, United States.
| | - Esther Ubago-Guisado
- Instituto de Investigación Biosanitaria ibs.GRANADA, Spain; Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Spain
| | - Francisco B Ortega
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Spain; CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Granada, Spain; Faculty of Sport and Health Sciences, University of Jyväskylä, Finland.
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Spain; Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden.
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Xiong R, Fleming E, Caldwell R, Vernon SD, Kozhaya L, Gunter C, Bateman L, Unutmaz D, Oh J. BioMapAI: Artificial Intelligence Multi-Omics Modeling of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600378. [PMID: 38979186 PMCID: PMC11230215 DOI: 10.1101/2024.06.24.600378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Chronic diseases like ME/CFS and long COVID exhibit high heterogeneity with multifactorial etiology and progression, complicating diagnosis and treatment. To address this, we developed BioMapAI, an explainable Deep Learning framework using the richest longitudinal multi-'omics dataset for ME/CFS to date. This dataset includes gut metagenomics, plasma metabolome, immune profiling, blood labs, and clinical symptoms. By connecting multi-'omics to asymptom matrix, BioMapAI identified both disease- and symptom-specific biomarkers, reconstructed symptoms, and achieved state-of-the-art precision in disease classification. We also created the first connectivity map of these 'omics in both healthy and disease states and revealed how microbiome-immune-metabolome crosstalk shifted from healthy to ME/CFS. Thus, we proposed several innovative mechanistic hypotheses for ME/CFS: Disrupted microbial functions - SCFA (butyrate), BCAA (amino acid), tryptophan, benzoate - lost connection with plasma lipids and bile acids, and activated inflammatory and mucosal immune cells (MAIT, γδT cells) with INFγ and GzA secretion. These abnormal dynamics are linked to key disease symptoms, including gastrointestinal issues, fatigue, and sleep problems.
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Affiliation(s)
- Ruoyun Xiong
- The Jackson Laboratory, Farmington, Connecticut, USA. 06032
- The University of Connecticut Health Center, Farmington, Connecticut, USA. 06030
| | | | - Ryan Caldwell
- The Jackson Laboratory, Farmington, Connecticut, USA. 06032
| | | | - Lina Kozhaya
- The Jackson Laboratory, Farmington, Connecticut, USA. 06032
| | - Courtney Gunter
- The Jackson Laboratory, Farmington, Connecticut, USA. 06032
- The University of Connecticut Health Center, Farmington, Connecticut, USA. 06030
| | | | - Derya Unutmaz
- The Jackson Laboratory, Farmington, Connecticut, USA. 06032
| | - Julia Oh
- The Jackson Laboratory, Farmington, Connecticut, USA. 06032
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Shankar V, Wilhelmy J, Curtis EJ, Michael B, Cervantes L, Mallajosyula VA, Davis RW, Snyder M, Younis S, Robinson WH, Shankar S, Mischel PS, Bonilla H, Davis MM. Oxidative Stress is a shared characteristic of ME/CFS and Long COVID. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592477. [PMID: 38746454 PMCID: PMC11092775 DOI: 10.1101/2024.05.04.592477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
More than 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition, wherein patients of all ages report fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). With no current treatments or reliable diagnostic markers, there is an urgent need to define the molecular underpinnings of these conditions. By studying bioenergetic characteristics of peripheral blood lymphocytes in over 16 healthy controls, 15 ME/CFS, and 15 LC, we find both ME/CFS and LC donors exhibit signs of elevated oxidative stress, relative to healthy controls, especially in the memory subset. Using a combination of flow cytometry, bulk RNA-seq analysis, mass spectrometry, and systems chemistry analysis, we also observed aberrations in ROS clearance pathways including elevated glutathione levels, decreases in mitochondrial superoxide dismutase levels, and glutathione peroxidase 4 mediated lipid oxidative damage. Critically, these changes in redox pathways show striking sex-specific trends. While females diagnosed with ME/CFS exhibit higher total ROS and mitochondrial calcium levels, males with an ME/CFS diagnosis have normal ROS levels, but larger changes in lipid oxidative damage. Further analyses show that higher ROS levels correlates with hyperproliferation of T cells in females, consistent with the known role of elevated ROS levels in the initiation of proliferation. This hyperproliferation of T cells can be attenuated by metformin, suggesting this FDA-approved drug as a possible treatment, as also suggested by a recent clinical study of LC patients. Thus, we report that both ME/CFS and LC are mechanistically related and could be diagnosed with quantitative blood cell measurements. We also suggest that effective, patient tailored drugs might be discovered using standard lymphocyte stimulation assays.
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Pietrangelo T, Cagnin S, Bondi D, Santangelo C, Marramiero L, Purcaro C, Bonadio RS, Di Filippo ES, Mancinelli R, Fulle S, Verratti V, Cheng X. Myalgic encephalomyelitis/chronic fatigue syndrome from current evidence to new diagnostic perspectives through skeletal muscle and metabolic disturbances. Acta Physiol (Oxf) 2024; 240:e14122. [PMID: 38483046 DOI: 10.1111/apha.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 04/17/2024]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a demanding medical condition for patients and society. It has raised much more public awareness after the COVID-19 pandemic since ME/CFS and long-COVID patients share many clinical symptoms such as debilitating chronic fatigue. However, unlike long COVID, the etiopathology of ME/CFS remains a mystery despite several decades' research. This review moves from pathophysiology of ME/CFS through the compelling evidence and most interesting hypotheses. It focuses on the pathophysiology of skeletal muscle by proposing the hypothesis that skeletal muscle tissue offers novel opportunities for diagnosis and treatment of this syndrome and that new evidence can help resolve the long-standing debate on terminology.
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Affiliation(s)
- Tiziana Pietrangelo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padua, Padova, Italy
- CIR-Myo Myology Center, University of Padua, Padova, Italy
| | - Danilo Bondi
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Carmen Santangelo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Lorenzo Marramiero
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Cristina Purcaro
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | | | - Ester Sara Di Filippo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Rosa Mancinelli
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Stefania Fulle
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Vittore Verratti
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Xuanhong Cheng
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Materials Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
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Cheng Y, Xu SM, Takenaka K, Lindner G, Curry-Hyde A, Janitz M. A Unique Circular RNA Expression Pattern in the Peripheral Blood of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients. Gene 2023:147568. [PMID: 37328077 DOI: 10.1016/j.gene.2023.147568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with obscure aetiology. The underdiagnosis rate of ME/CFS is high due to the lack of diagnostic criteria based on objective markers. In recent years, circRNAs have emerged as potential genetic biomarkers for neurological diseases, including Parkinson's disease and Alzheimer's disease, making them likely to have the same prospect of being biomarkers in ME/CFS. However, despite the extensive amount of research that has been performed on the transcriptomes of ME/CFS patients, all of them are solely focused on linear RNAs, and the profiling of circRNAs in ME/CFS has been completely omitted. In this study, we investigated the expression profiles of circRNAs, comparing ME/CFS patients and controls before and after two sessions of cardiopulmonary exercise longitudinally. In patients with ME/CFS, the number of detected circRNAs was higher compared to healthy controls, indicating potential differences in circRNA expression associated with the disease. Additionally, healthy controls showed an increase in the number of circRNAs following exercise testing, while no similar pattern was evident in ME/CFS patients, further highlighting physiological differences between the two groups. A lack of correlation was observed between differentially expressed circRNAs and their corresponding coding genes in terms of expression and function, suggesting the potential of circRNAs as independent biomarkers in ME/CFS. Specifically, 14 circRNAs were highly expressed in ME/CFS patients but absent in controls throughout the exercise study, indicating a unique molecular signature specific to ME/CFS patients and providing potential diagnostic biomarkers for the disease. Significant enrichment of protein and gene regulative pathways were detected in relation to five of these 14 circRNAs based on their predicted miRNA target genes. Overall, this is the first study to describe the circRNA expression profile in peripheral blood of ME/CFS patients, providing valuable insights into the molecular mechanisms underlying the disease.
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Affiliation(s)
- Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Grace Lindner
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ashton Curry-Hyde
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Van Booven DJ, Gamer J, Joseph A, Perez M, Zarnowski O, Pandya M, Collado F, Klimas N, Oltra E, Nathanson L. Stress-Induced Transcriptomic Changes in Females with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Reveal Disrupted Immune Signatures. Int J Mol Sci 2023; 24:2698. [PMID: 36769022 PMCID: PMC9916639 DOI: 10.3390/ijms24032698] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic, complex multi-organ illness characterized by unexplained debilitating fatigue and post-exertional malaise (PEM), which is defined as a worsening of symptoms following even minor physical or mental exertion. Our study aimed to evaluate transcriptomic changes in ME/CFS female patients undergoing an exercise challenge intended to precipitate PEM. Our time points (baseline before exercise challenge, the point of maximal exertion, and after an exercise challenge) allowed for the exploration of the transcriptomic response to exercise and recovery in female patients with ME/CFS, as compared to healthy controls (HCs). Under maximal exertion, ME/CFS patients did not show significant changes in gene expression, while HCs demonstrated altered functional gene networks related to signaling and integral functions of their immune cells. During the recovery period (commonly during onset of PEM), female ME/CFS patients showed dysregulated immune signaling pathways and dysfunctional cellular responses to stress. The unique functional pathways identified provide a foundation for future research efforts into the disease, as well as for potential targeted treatment options.
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Affiliation(s)
- Derek J. Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jackson Gamer
- Institute for Neuro-Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Andrew Joseph
- Institute for Neuro-Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Melanie Perez
- Institute for Neuro-Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Oskar Zarnowski
- Institute for Neuro-Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Meha Pandya
- Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Farquhar Honors College, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Fanny Collado
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, FL 33125, USA
- South Florida Veterans Affairs Foundation for Research and Education Inc., Fort Lauderdale, FL 33125, USA
| | - Nancy Klimas
- Institute for Neuro-Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, FL 33125, USA
| | - Elisa Oltra
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - Lubov Nathanson
- Institute for Neuro-Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
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Chrisman BS, He C, Jung JY, Stockham N, Paskov K, Wall DP. Transmission dynamics of human herpesvirus 6A, 6B and 7 from whole genome sequences of families. Virol J 2022; 19:225. [PMID: 36566197 PMCID: PMC9789512 DOI: 10.1186/s12985-022-01941-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/30/2022] [Indexed: 12/25/2022] Open
Abstract
While hundreds of thousands of human whole genome sequences (WGS) have been collected in the effort to better understand genetic determinants of disease, these whole genome sequences have less frequently been used to study another major determinant of human health: the human virome. Using the unmapped reads from WGS of over 1000 families, we present insights into the human blood DNA virome, focusing particularly on human herpesvirus (HHV) 6A, 6B, and 7. In addition to extensively cataloguing the viruses detected in WGS of human whole blood and lymphoblastoid cell lines, we use the family structure of our dataset to show that household drives transmission of several viruses, and identify the Mendelian inheritance patterns characteristic of inherited chromsomally integrated human herpesvirus 6 (iciHHV-6). Consistent with prior studies, we find that 0.6% of our dataset's population has iciHHV, and we locate candidate integration sequences for these cases. We document genetic diversity within exogenous and integrated HHV species and within integration sites of HHV-6. Finally, in the first observation of its kind, we present evidence that suggests widespread de novo HHV-6B integration and HHV-7 integration and reactivation in lymphoblastoid cell lines. These findings show that the unmapped read space of WGS is a promising source of data for virology research.
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Affiliation(s)
- Brianna S. Chrisman
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Serra Mall, Stanford, USA ,grid.266818.30000 0004 1936 914XNevada Bioinformatics Center, University of Nevada, Reno, USA
| | - Chloe He
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Serra Mall, Stanford, USA
| | - Jae-Yoon Jung
- grid.168010.e0000000419368956Department of Pediatrics (Systems Medicine), Stanford University, Serra Mall, Stanford, USA
| | - Nate Stockham
- grid.168010.e0000000419368956Department of Neuroscience, Stanford University, Serra Mall, Stanford, USA
| | - Kelley Paskov
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Serra Mall, Stanford, USA
| | - Dennis P. Wall
- grid.168010.e0000000419368956Department of Pediatrics (Systems Medicine), Stanford University, Serra Mall, Stanford, USA
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Lv Y, Zhang T, Cai J, Huang C, Zhan S, Liu J. Bioinformatics and systems biology approach to identify the pathogenetic link of Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Front Immunol 2022; 13:952987. [PMID: 36189286 PMCID: PMC9524193 DOI: 10.3389/fimmu.2022.952987] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global crisis. Although many people recover from COVID-19 infection, they are likely to develop persistent symptoms similar to those of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) after discharge. Those constellations of symptoms persist for months after infection, called Long COVID, which may lead to considerable financial burden and healthcare challenges. However, the mechanisms underlying Long COVID and ME/CFS remain unclear. Methods We collected the genes associated with Long COVID and ME/CFS in databases by restricted screening conditions and clinical sample datasets with limited filters. The common genes for Long COVID and ME/CFS were finally obtained by taking the intersection. We performed several advanced bioinformatics analyses based on common genes, including gene ontology and pathway enrichment analyses, protein–protein interaction (PPI) analysis, transcription factor (TF)–gene interaction network analysis, transcription factor–miRNA co-regulatory network analysis, and candidate drug analysis prediction. Results We found nine common genes between Long COVID and ME/CFS and gained a piece of detailed information on their biological functions and signaling pathways through enrichment analysis. Five hub proteins (IL-6, IL-1B, CD8A, TP53, and CXCL8) were collected by the PPI network. The TF–gene and TF–miRNA coregulatory networks were demonstrated by NetworkAnalyst. In the end, 10 potential chemical compounds were predicted. Conclusion This study revealed common gene interaction networks of Long COVID and ME/CFS and predicted potential therapeutic drugs for clinical practice. Our findings help to identify the potential biological mechanism between Long COVID and ME/CFS. However, more laboratory and multicenter evidence is required to explore greater mechanistic insight before clinical application in the future.
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Affiliation(s)
- Yongbiao Lv
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tian Zhang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junxiang Cai
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Chushuan Huang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianbo Liu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Jianbo Liu,
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Renz-Polster H, Tremblay ME, Bienzle D, Fischer JE. The Pathobiology of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: The Case for Neuroglial Failure. Front Cell Neurosci 2022; 16:888232. [PMID: 35614970 PMCID: PMC9124899 DOI: 10.3389/fncel.2022.888232] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/13/2022] [Indexed: 12/20/2022] Open
Abstract
Although myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) has a specific and distinctive profile of clinical features, the disease remains an enigma because causal explanation of the pathobiological matrix is lacking. Several potential disease mechanisms have been identified, including immune abnormalities, inflammatory activation, mitochondrial alterations, endothelial and muscular disturbances, cardiovascular anomalies, and dysfunction of the peripheral and central nervous systems. Yet, it remains unclear whether and how these pathways may be related and orchestrated. Here we explore the hypothesis that a common denominator of the pathobiological processes in ME/CFS may be central nervous system dysfunction due to impaired or pathologically reactive neuroglia (astrocytes, microglia and oligodendrocytes). We will test this hypothesis by reviewing, in reference to the current literature, the two most salient and widely accepted features of ME/CFS, and by investigating how these might be linked to dysfunctional neuroglia. From this review we conclude that the multifaceted pathobiology of ME/CFS may be attributable in a unifying manner to neuroglial dysfunction. Because the two key features - post exertional malaise and decreased cerebral blood flow - are also recognized in a subset of patients with post-acute sequelae COVID, we suggest that our findings may also be pertinent to this entity.
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Affiliation(s)
- Herbert Renz-Polster
- Division of General Medicine, Center for Preventive Medicine and Digital Health Baden-Württemberg (CPD-BW), University Medicine Mannheim, Heidelberg University, Mannheim, Germany
| | - Marie-Eve Tremblay
- Axe Neurosciences, Centre de recherche du CHU de Québec, Université Laval, Quebec, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Quebec, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Center for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Dorothee Bienzle
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Joachim E. Fischer
- Division of General Medicine, Center for Preventive Medicine and Digital Health Baden-Württemberg (CPD-BW), University Medicine Mannheim, Heidelberg University, Mannheim, Germany
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11
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Cook DB, VanRiper S, Dougherty RJ, Lindheimer JB, Falvo MJ, Chen Y, Lin JMS, Unger ER. Cardiopulmonary, metabolic, and perceptual responses during exercise in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): A Multi-site Clinical Assessment of ME/CFS (MCAM) sub-study. PLoS One 2022; 17:e0265315. [PMID: 35290404 PMCID: PMC8923458 DOI: 10.1371/journal.pone.0265315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cardiopulmonary exercise testing has demonstrated clinical utility in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). However, to what extent exercise responses are independent of, or confounded by, aerobic fitness remains unclear. Purpose To characterize and compare exercise responses in ME/CFS and controls with and without matching for aerobic fitness. Methods As part of the Multi-site Clinical Assessment of ME/CFS (MCAM) study, 403 participants (n = 214 ME/CFS; n = 189 controls), across six ME/CFS clinics, completed ramped cycle ergometry to volitional exhaustion. Metabolic, heart rate (HR), and ratings of perceived exertion (RPE) were measured. Ventilatory equivalent ( V˙E/V˙O2, V˙E/V˙CO2), metrics of ventilatory efficiency, and chronotropic incompetence (CI) were calculated. Exercise variables were compared using Hedges’ g effect size with 95% confidence intervals. Differences in cardiopulmonary and perceptual features during exercise were analyzed using linear mixed effects models with repeated measures for relative exercise intensity (20–100% peak V˙O2). Subgroup analyses were conducted for 198 participants (99 ME/CFS; 99 controls) matched for age (±5 years) and peak V˙O2 (~1 ml/kg/min-1). Results Ninety percent of tests (n = 194 ME/CFS, n = 169 controls) met standard criteria for peak effort. ME/CFS responses during exercise (20–100% peak V˙O2) were significantly lower for ventilation, breathing frequency, HR, measures of efficiency, and CI and significantly higher for V˙E/V˙O2, V˙E/V˙CO2 and RPE (p<0.05adjusted). For the fitness-matched subgroup, differences remained for breathing frequency, V˙E/V˙O2, V˙E/V˙CO2, and RPE (p<0.05adjusted), and higher tidal volumes were identified for ME/CFS (p<0.05adjusted). Exercise responses at the gas exchange threshold, peak, and for measures of ventilatory efficiency (e.g., V˙E/V˙CO2nadir) were generally reflective of those seen throughout exercise (i.e., 20–100%). Conclusion Compared to fitness-matched controls, cardiopulmonary responses to exercise in ME/CFS are characterized by inefficient exercise ventilation and augmented perception of effort. These data highlight the importance of distinguishing confounding fitness effects to identify responses that may be more specifically associated with ME/CFS.
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Affiliation(s)
- Dane B. Cook
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, United States of America
- * E-mail:
| | - Stephanie VanRiper
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Ryan J. Dougherty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jacob B. Lindheimer
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michael J. Falvo
- War Related Illness and Injury Study Center, Department of Veterans Affairs New Jersey Health Care System, East Orange, NJ, United States of America
- New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ, United States of America
| | - Yang Chen
- Centers for Disease Control and Prevention/ Division of High-Consequence Pathogens and Pathology/Chronic Viral Diseases Branch, Atlanta, Georgia, United States of America
| | - Jin-Mann S. Lin
- Centers for Disease Control and Prevention/ Division of High-Consequence Pathogens and Pathology/Chronic Viral Diseases Branch, Atlanta, Georgia, United States of America
| | - Elizabeth R. Unger
- Centers for Disease Control and Prevention/ Division of High-Consequence Pathogens and Pathology/Chronic Viral Diseases Branch, Atlanta, Georgia, United States of America
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12
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Mathur R, Carnes MU, Harding A, Moore A, Thomas I, Giarrocco A, Long M, Underwood M, Townsend C, Ruiz-Esparza R, Barnette Q, Brown LM, Schu M. mapMECFS: a portal to enhance data discovery across biological disciplines and collaborative sites. J Transl Med 2021; 19:461. [PMID: 34749736 PMCID: PMC8576927 DOI: 10.1186/s12967-021-03127-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 12/02/2022] Open
Abstract
Background Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease which involves multiple body systems (e.g., immune, nervous, digestive, circulatory) and research domains (e.g., immunology, metabolomics, the gut microbiome, genomics, neurology). Despite several decades of research, there are no established ME/CFS biomarkers available to diagnose and treat ME/CFS. Sharing data and integrating findings across these domains is essential to advance understanding of this complex disease by revealing diagnostic biomarkers and facilitating discovery of novel effective therapies. Methods The National Institutes of Health funded the development of a data sharing portal to support collaborative efforts among an initial group of three funded research centers. This was subsequently expanded to include the global ME/CFS research community. Using the open-source comprehensive knowledge archive network (CKAN) framework as the base, the ME/CFS Data Management and Coordinating Center developed an online portal with metadata collection, smart search capabilities, and domain-agnostic data integration to support data findability and reusability while reducing the barriers to sustainable data sharing. Results We designed the mapMECFS data portal to facilitate data sharing and integration by allowing ME/CFS researchers to browse, share, compare, and download molecular datasets from within one data repository. At the time of publication, mapMECFS contains data curated from public data repositories, peer-reviewed publications, and current ME/CFS Research Network members. Conclusions mapMECFS is a disease-specific data portal to improve data sharing and collaboration among ME/CFS researchers around the world. mapMECFS is accessible to the broader research community with registration. Further development is ongoing to include novel systems biology and data integration methods. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03127-3.
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Affiliation(s)
- Ravi Mathur
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Megan U Carnes
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Alexander Harding
- Center for Data Science, RTI International, Research Triangle Park, NC, USA
| | - Amy Moore
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Ian Thomas
- Center for Data Science, RTI International, Research Triangle Park, NC, USA
| | - Alex Giarrocco
- Center for Data Science, RTI International, Research Triangle Park, NC, USA
| | - Michael Long
- Center for Data Science, RTI International, Research Triangle Park, NC, USA
| | - Marcia Underwood
- Center for Data Science, RTI International, Research Triangle Park, NC, USA
| | | | - Roman Ruiz-Esparza
- Center for Data Science, RTI International, Research Triangle Park, NC, USA
| | - Quinn Barnette
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Linda Morris Brown
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Matthew Schu
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.
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13
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Chronic Fatigue Syndrome and Cardiovascular Disease: JACC State-of-the-Art Review. J Am Coll Cardiol 2021; 78:1056-1067. [PMID: 34474739 DOI: 10.1016/j.jacc.2021.06.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a medically unexplained illness characterized by severe fatigue limiting normal daily activities for at least 6 months accompanied by problems with unrefreshing sleep, exacerbation of symptoms following physical or mental efforts (postexertional malaise [PEM]), and either cognitive reports or physiological evidence of orthostatic intolerance in the form of either orthostatic tachycardia and/or hypocapnia. Although rarely considered to have cardiac dysfunction, ME/CFS patients frequently have reduced stroke volume with a significant inverse relation between cardiac output and PEM severity. Magnetic resonance imaging of ME/CFS patients compared with normal control subjects found significantly reduced stroke, end-systolic, and end-diastolic volumes together with reduced end-diastolic wall mass. Another cardiovascular abnormality is reduced nocturnal blood pressure assessed by 24-hour monitoring. Autonomic dysfunction is also frequently observed with postural orthostatic tachycardia and/or hypocapnia. Two consecutive cardiopulmonary stress tests may provide metabolic data substantiating PEM.
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14
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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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15
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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: 19] [Impact Index Per Article: 6.3] [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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16
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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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17
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Establishment of a murine, lipopolysaccharide-induced sepsis model for testing anaerobic exercise thresholds and early mobilization. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2020.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Comella PH, Gonzalez-Kozlova E, Kosoy R, Charney AW, Peradejordi IF, Chandrasekar S, Tyler SR, Wang W, Losic B, Zhu J, Hoffman GE, Kim-Schulze S, Qi J, Patel M, Kasarskis A, Suarez-Farinas M, Gümüş ZH, Argmann C, Merad M, Becker C, Beckmann ND, Schadt EE. A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.29.21250755. [PMID: 33564792 PMCID: PMC7872387 DOI: 10.1101/2021.01.29.21250755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
IntroThe molecular mechanisms of chronic fatigue syndrome (CFS, or Myalgic encephalomyelitis), a disease defined by extreme, long-term fatigue, remain largely uncharacterized, and presently no molecular diagnostic test and no specific treatments exist to diagnose and treat CFS patients. While CFS has historically had an estimated prevalence of 0.1-0.5% [1], concerns of a “long hauler” version of Coronavirus disease 2019 (COVID-19) that symptomatically overlaps CFS to a significant degree(Supplemental Table-1)and appears to occur in 10% of COVID-19 patients[2], has raised concerns of a larger spike in CFS [3]. Here, we established molecular signatures of CFS and a corresponding network-based disease context from RNA-sequencing data generated on whole blood and FACs sorted specific peripheral blood mononuclear cells (PBMCs) isolated from CFS cases and non-CFS controls. The immune cell type specific molecular signatures of CFS we identified, overlapped molecular signatures from other fatiguing illnesses, demonstrating a common molecular etiology. Further, after constructing a probabilistic causal model of the CFS gene expression data, we identified master regulator genes modulating network states associated with CFS, suggesting potential therapeutic targets for CFS.
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Affiliation(s)
- Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Irene Font Peradejordi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Shreya Chandrasekar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Scott R. Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jingjing Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Population Health Science and Policy at the Icahn School of Medicine at Mount Sinai
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
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19
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Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med 2021; 13:7. [PMID: 33441124 DOI: 10.1101/2020.07.07.20148395] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/18/2020] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. METHODS In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. RESULTS Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. CONCLUSIONS Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Mouktaroudi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Benjamin Krämer
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikolaos Antonakos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Konstantina Gkizeli
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarandia Doulou
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Miriam Herbert
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ioanna D Gemünd
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikoletta Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Shobhit Agrawal
- West German Genome Center (WGGC), University of Bonn, Bonn, Germany
| | - Kilian Dahm
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Anna Drews
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Lenkeit
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Gierlich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Simachew Mengiste
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Seep
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan Raabe
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | | | - Michael ToVinh
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Rieke
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, Section of Pneumology, University Hospital of Bonn (UKB), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
- German Center for Infection Research (DZIF), Bonn, Germany
| | - Antonia Koutsoukou
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.
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20
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Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med 2021; 13:7. [PMID: 33441124 PMCID: PMC7805430 DOI: 10.1186/s13073-020-00823-5] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. METHODS In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. RESULTS Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. CONCLUSIONS Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Mouktaroudi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Benjamin Krämer
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikolaos Antonakos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Konstantina Gkizeli
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarandia Doulou
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Miriam Herbert
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ioanna D Gemünd
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikoletta Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Shobhit Agrawal
- West German Genome Center (WGGC), University of Bonn, Bonn, Germany
| | - Kilian Dahm
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Anna Drews
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Lenkeit
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Gierlich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Simachew Mengiste
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Seep
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan Raabe
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | | | - Michael ToVinh
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Rieke
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, Section of Pneumology, University Hospital of Bonn (UKB), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
- German Center for Infection Research (DZIF), Bonn, Germany
| | - Antonia Koutsoukou
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.
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21
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Lindheimer JB, Alexander T, Qian W, Klein‐Adams JC, Lange G, H. Natelson B, Cook DB, Hill HZ, Falvo MJ. An analysis of 2-day cardiopulmonary exercise testing to assess unexplained fatigue. Physiol Rep 2020; 8:e14564. [PMID: 32889791 PMCID: PMC7507580 DOI: 10.14814/phy2.14564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/29/2022] Open
Abstract
Two consecutive maximal cardiopulmonary exercise tests (CPETs) performed 24 hr apart (2-day CPET protocol) are increasingly used to evaluate post-exertional malaise (PEM) and related disability among individuals with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). This protocol may extend to other fatiguing illnesses with similar characteristics to ME/CFS; however, 2-day CPET protocol reliability and minimum change required to be considered clinically meaningful (i.e., exceeding the standard error of the measure) are not well characterized. To address this gap, we evaluated the 2-day CPET protocol in Gulf War Illness (GWI) by quantifying repeatability of seven CPET parameters, establishing their thresholds of clinically significant change, and determining whether changes differed between veterans with GWI and controls. Excluding those not attaining peak effort criteria (n = 15), we calculated intraclass correlation coefficients (ICCs), the smallest real difference (SRD%), and repeated measures analysis of variance (RM-ANOVA) at the ventilatory anaerobic threshold (VAT) and peak exercise in 15 veterans with GWI and eight controls. ICC values at peak ranged from moderate to excellent for veterans with GWI (mean [range]; 0.84 [0.65 - 0.92]) and were reduced at the VAT (0.68 [0.37 - 0.78]). Across CPET variables, the SRD% at peak exercise for veterans with GWI (18.8 [8.8 - 28.8]) was generally lower than at the VAT (28.1 [9.5 - 34.8]). RM-ANOVAs did not detect any significant group-by-time interactions (all p > .05). The methods and findings reported here provide a framework for evaluating 2-day CPET reliability, and reinforce the importance of carefully considering measurement error in the population of interest when interpreting findings.
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Affiliation(s)
- Jacob B. Lindheimer
- William S. Middleton Memorial Veterans HospitalMadisonWIUSA
- Department of KinesiologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Thomas Alexander
- VA Airborne Hazards and Burn Pits Center of ExcellenceWar Related Illness and Injury Study CenterVA New Jersey Health Care SystemEast OrangeNJUSA
| | - Wei Qian
- VA Airborne Hazards and Burn Pits Center of ExcellenceWar Related Illness and Injury Study CenterVA New Jersey Health Care SystemEast OrangeNJUSA
- New Jersey Medical SchoolRutgers Biomedical and Health SciencesNewarkNJUSA
| | - Jacquelyn C. Klein‐Adams
- VA Airborne Hazards and Burn Pits Center of ExcellenceWar Related Illness and Injury Study CenterVA New Jersey Health Care SystemEast OrangeNJUSA
| | - Gudrun Lange
- Department of NeurologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | | | - Dane B. Cook
- William S. Middleton Memorial Veterans HospitalMadisonWIUSA
- Department of KinesiologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Helene Z. Hill
- New Jersey Medical SchoolRutgers Biomedical and Health SciencesNewarkNJUSA
| | - Michael J. Falvo
- VA Airborne Hazards and Burn Pits Center of ExcellenceWar Related Illness and Injury Study CenterVA New Jersey Health Care SystemEast OrangeNJUSA
- New Jersey Medical SchoolRutgers Biomedical and Health SciencesNewarkNJUSA
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22
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Abstract
Muscle failure has been demonstrated in patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Neurophysiological tools demonstrate the existence of both central and peripheral fatigue in these patients. Central fatigue is deduced from the reduced amplitude of myopotentials evoked by transcranial magnetic stimulation of the motor cortex as well as by the muscle response to interpolated twitches during sustained fatiguing efforts. An impaired muscle membrane conduction velocity assessed by the reduced amplitude and lengthened duration of myopotentials evoked by direct muscle stimulation is the defining feature of peripheral fatigue. Some patients with ME/CFS show an increased oxidative stress response to exercise. The formation of lipid hydroperoxides in the sarcolemma, which alters ionic fluxes, could explain the reduction of muscle membrane excitability and potassium outflow often measured in these patients. In patients with ME/CFS, the formation of heat shock proteins (HSPs) is also reduced. Because HSPs protect muscle cells against the deleterious effects of reactive oxygen species, the lack of their production could explain the augmented oxidative stress and the consecutive alterations of myopotentials which could open a way for future treatment of ME/CFS.
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Affiliation(s)
- Yves Jammes
- C2VN Inserm Inra, Faculty of Medicine, Aix Marseille University, Marseille, France, France
| | - Frédérique Retornaz
- Department of Internal Medicine, European Hospital, Marseille, France, France
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