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Przybylowicz PK, Sokolowska KE, Rola H, Wojdacz TK. DNA Methylation Changes in Blood Cells of Fibromyalgia and Chronic Fatigue Syndrome Patients. J Pain Res 2023; 16:4025-4036. [PMID: 38054109 PMCID: PMC10695140 DOI: 10.2147/jpr.s439412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
Purpose Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) affect 0.4% and 1% of society, respectively, and the prevalence of these pain syndromes is increasing. To date, no strong association between these syndromes and the genetic background of affected individuals has been shown. Therefore, it is plausible that epigenetic changes might play a role in the development of these syndromes. Patients and Methods Three previous studies have attempted to elaborate the involvement of genome-wide methylation changes in blood cells in the development of fibromyalgia and chronic fatigue syndrome. These studies included 22 patients with fibromyalgia and 127 patients with CFS, and the results of the studies were largely discrepant. Contradicting results of those studies may be attributed to differences in the omics data analysis approaches used in each study. We reanalyzed the data collected in these studies using an updated and coherent data-analysis framework. Results Overall, the methylation changes that we observed overlapped with previous results only to some extent. However, the gene set enrichment analyses based on genes annotated to methylation changes identified in each of the analyzed datasets were surprisingly coherent and uniformly associated with the physiological processes that, when affected, may result in symptoms characteristic of fibromyalgia and chronic fatigue syndrome. Conclusion Methylomes of the blood cells of patients with FM and CFS in three independent studies have shown methylation changes that appear to be implicated in the pathogenesis of these syndromes.
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Affiliation(s)
| | | | - Hubert Rola
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Szczecin, Poland
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2
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Bernhoff G, Rasmussen-Barr E, Bunketorp Käll L. A comparison of health-related factors between patients diagnosed with ME/CFS and patients with a related symptom picture but no ME/CFS diagnosis: a cross-sectional exploratory study. J Transl Med 2022; 20:577. [PMID: 36494693 PMCID: PMC9733040 DOI: 10.1186/s12967-022-03769-x] [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: 09/15/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In chronic fatigue syndrome/myalgic encephalomyelitis (ME/CFS), the capacity for activity and participation is strongly limited. The disease definition is very broad, and considering the lack of evidence for best treatment, it is important to understand what is ME/CFS-specific in the biopsychosocial perspective in comparison with similar syndromes. The objective was to study the difference between those diagnosed with ME/CFS and those with similar symptoms but no ME/CFS diagnosis for self-perceived level of physical activity, work ability, anxiety/depression, and health-related quality of life. METHODS This was a clinical cross-sectional study with data collected from mailed questionnaires. The following variables were compared between patients diagnosed with ME/CFS (n = 205) and those with similar symptoms but no diagnosis (n = 57); level of physical activity, Work ability index (WAI), Hospital anxiety and depression scale (HAD-A/HAD-D), and RAND-36 Physical functioning, Role limitations due to physical health problems, Role limitations due to personal or emotional problems, Social functioning, Energy/fatigue, Bodily pain, Emotional well-being, and General health perceptions. The Chi-squared test (nominal data), the Mann-Whitney U test, the Student's t test and regression analysis were used to analyze the data. RESULTS The group diagnosed with ME/CFS had a more impaired physical and mental exertion ability as compared to the group that had similar symptoms but was not diagnosed with ME/CFS, shown by a RAND-36 lower index of physical role functioning, social functioning, energy, worse pain and poorer overall health (p ≤ 0.05). In contrast, no significant group differences emerged for weekly level of physical activity, work ability, anxiety/depression, and RAND-36 Emotional role limitation and well-being. CONCLUSION Our results indicate that those with a diagnosis of ME/CFS are characterized by an impaired ability for physical or mental exertion, worse pain, and poorer overall health as compared to individuals with similar symptoms but for whom ME/CFS-diagnosis was not established. The results may be cautiously interpreted as support when focusing on patients' self-care in terms of management of energy levels. The results must however be verified in future studies.
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Affiliation(s)
- Gabriella Bernhoff
- grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Division of Family Medicine and Primary Care, Karolinska Institute, Alfred Nobels allé 23 D2, Huddinge, 141 83, Stockholm, Sweden ,ME Centre, Bragée Clinics, Stockholm, Sweden
| | - Eva Rasmussen-Barr
- grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Division of Physiotherapy, Karolinska Institute, Stockholm, Sweden
| | - Lina Bunketorp Käll
- grid.8761.80000 0000 9919 9582Department of Health and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden ,grid.1649.a000000009445082XCentre for Advanced Reconstruction of Extremities, Sahlgrenska University Hospital/Mölndal, Mölndal, Sweden
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3
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Sasaki A, Murphy KE, Briollais L, McGowan PO, Matthews SG. DNA methylation profiles in the blood of newborn term infants born to mothers with obesity. PLoS One 2022; 17:e0267946. [PMID: 35500004 PMCID: PMC9060365 DOI: 10.1371/journal.pone.0267946] [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: 01/11/2022] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
Maternal obesity is an important risk factor for childhood obesity and influences the prevalence of metabolic diseases in offspring. As childhood obesity is influenced by postnatal factors, it is critical to determine whether children born to women with obesity during pregnancy show alterations that are detectable at birth. Epigenetic mechanisms such as DNA methylation modifications have been proposed to mediate prenatal programming. We investigated DNA methylation signatures in male and female infants from mothers with a normal Body Mass Index (BMI 18.5-24.9 kg/m2) compared to mothers with obesity (BMI≥30 kg/m2). BMI was measured during the first prenatal visit from women recruited into the Ontario Birth Study (OBS) at Mount Sinai Hospital in Toronto, ON, Canada. DNA was extracted from neonatal dried blood spots collected from heel pricks obtained 24 hours after birth at term (total n = 40) from women with a normal BMI and women with obesity matched for parity, age, and neonatal sex. Reduced representation bisulfite sequencing was used to identify genomic loci associated with differentially methylated regions (DMRs) in CpG-dense regions most likely to influence gene regulation. DMRs were predominantly localized to intergenic regions and gene bodies, with only 9% of DMRs localized to promoter regions. Genes associated with DMRs were compared to those from a large publicly available cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC; total n = 859). Hypergeometric tests revealed a significant overlap in genes associated with DMRs in the OBS and ALSPAC cohorts. PTPRN2, a gene involved in insulin secretion, and MAD1L1, which plays a role in the cell cycle and tumor suppression, contained DMRs in males and females in both cohorts. In males, KEGG pathway analysis revealed significant overrepresentation of genes involved in endocytosis and pathways in cancer, including IGF1R, which was previously shown to respond to diet-induced metabolic stress in animal models and in lymphocytes in the context of childhood obesity. These preliminary findings are consistent with Developmental Origins of Health and Disease paradigm, which posits that adverse prenatal exposures set developmental health trajectories.
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Affiliation(s)
- Aya Sasaki
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kellie E. Murphy
- Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Laurent Briollais
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Patrick O. McGowan
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
- Departments of Biological Sciences and Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen G. Matthews
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
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4
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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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5
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Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome. Sci Rep 2021; 11:4541. [PMID: 33633136 PMCID: PMC7907358 DOI: 10.1038/s41598-021-83660-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic disorder characterized by disabling fatigue. Several studies have sought to identify diagnostic biomarkers, with varying results. Here, we innovate this process by combining both mRNA expression and DNA methylation data. We performed recursive ensemble feature selection (REFS) on publicly available mRNA expression data in peripheral blood mononuclear cells (PBMCs) of 93 ME/CFS patients and 25 healthy controls, and found a signature of 23 genes capable of distinguishing cases and controls. REFS highly outperformed other methods, with an AUC of 0.92. We validated the results on a different platform (AUC of 0.95) and in DNA methylation data obtained from four public studies on ME/CFS (99 patients and 50 controls), identifying 48 gene-associated CpGs that predicted disease status as well (AUC of 0.97). Finally, ten of the 23 genes could be interpreted in the context of the derailed immune system of ME/CFS.
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6
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Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts. Int J Mol Sci 2021; 22:ijms22042046. [PMID: 33669532 PMCID: PMC7921983 DOI: 10.3390/ijms22042046] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
Although understanding of the biomedical basis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is growing, the underlying pathological mechanisms remain uncertain. We recently reported a reduction in the proportion of basal oxygen consumption due to ATP synthesis by Complex V in ME/CFS patient-derived lymphoblast cell lines, suggesting mitochondrial respiratory inefficiency. This was accompanied by elevated respiratory capacity, elevated mammalian target of rapamycin complex 1 (mTORC1) signaling activity and elevated expression of enzymes involved in the TCA cycle, fatty acid β-oxidation and mitochondrial transport. These and other observations led us to hypothesise the dysregulation of pathways providing the mitochondria with oxidisable substrates. In our current study, we aimed to revisit this hypothesis by applying a combination of whole-cell transcriptomics, proteomics and energy stress signaling activity measures using subsets of up to 34 ME/CFS and 31 healthy control lymphoblast cell lines from our growing library. While levels of glycolytic enzymes were unchanged in accordance with our previous observations of unaltered glycolytic rates, the whole-cell proteomes of ME/CFS lymphoblasts contained elevated levels of enzymes involved in the TCA cycle (p = 1.03 × 10−4), the pentose phosphate pathway (p = 0.034, G6PD p = 5.5 × 10−4), mitochondrial fatty acid β-oxidation (p = 9.2 × 10−3), and degradation of amino acids including glutamine/glutamate (GLS p = 0.034, GLUD1 p = 0.048, GOT2 p = 0.026), branched-chain amino acids (BCKDHA p = 0.028, BCKDHB p = 0.031) and essential amino acids (FAH p = 0.036, GCDH p = 0.006). The activity of the major cellular energy stress sensor, AMPK, was elevated but the increase did not reach statistical significance. The results suggest that ME/CFS metabolism is dysregulated such that alternatives to glycolysis are more heavily utilised than in controls to provide the mitochondria with oxidisable substrates.
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7
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Anderson G, Maes M. Mitochondria and immunity in chronic fatigue syndrome. Prog Neuropsychopharmacol Biol Psychiatry 2020; 103:109976. [PMID: 32470498 DOI: 10.1016/j.pnpbp.2020.109976] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
It is widely accepted that the pathophysiology and treatment of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) could be considerably improved. The heterogeneity of ME/CFS and the confusion over its classification have undoubtedly contributed to this, although this would seem a consequence of the complexity of the array of ME/CFS presentations and high levels of diverse comorbidities. This article reviews the biological underpinnings of ME/CFS presentations, including the interacting roles of the gut microbiome/permeability, endogenous opioidergic system, immune cell mitochondria, autonomic nervous system, microRNA-155, viral infection/re-awakening and leptin as well as melatonin and the circadian rhythm. This details not only relevant pathophysiological processes and treatment options, but also highlights future research directions. Due to the complexity of interacting systems in ME/CFS pathophysiology, clarification as to its biological underpinnings is likely to considerably contribute to the understanding and treatment of other complex and poorly managed conditions, including fibromyalgia, depression, migraine, and dementia. The gut and immune cell mitochondria are proposed to be two important hubs that interact with the circadian rhythm in driving ME/CFS pathophysiology.
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Affiliation(s)
- G Anderson
- CRC Scotland & London, Eccleston Square, London, UK.
| | - M Maes
- Dept Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Dept Psychiatry, Medical University Plovdiv, Plovdiv, Bulgaria.; IMPACT Research Center, Deakin University, Geelong, Australia
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8
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Sweetman E, Kleffmann T, Edgar C, de Lange M, Vallings R, Tate W. A SWATH-MS analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome peripheral blood mononuclear cell proteomes reveals mitochondrial dysfunction. J Transl Med 2020; 18:365. [PMID: 32972442 PMCID: PMC7512220 DOI: 10.1186/s12967-020-02533-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
Background Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a serious and complex physical illness that affects all body systems with a multiplicity of symptoms, but key hallmarks of the disease are pervasive fatigue and ‘post-exertional malaise’, exacerbation after physical and/or mental activity of the intrinsic fatigue and other symptoms that can be highly debilitating and last from days to months. Although the disease can vary widely between individuals, common symptoms also include pain, cognitive deficits, sleep dysfunction, as well as immune, neurological and autonomic symptoms. Typically, it is a very isolating illness socially, carrying a stigma because of the lack of understanding of the cause and pathophysiology. Methods To gain insight into the pathophysiology of ME/CFS, we examined the proteomes of peripheral blood mononuclear cells (PBMCs) by SWATH-MS analysis in a small well-characterised group of patients and matched controls. A principal component analysis (PCA) was used to stratify groups based on protein abundance patterns, which clearly segregated the majority of the ME/CFS patients (9/11) from the controls. This majority subgroup of ME/CFS patients was then further compared to the control group. Results A total of 60 proteins in the ME/CFS patients were differentially expressed (P < 0.01, Log10 (Fold Change) > 0.2 and < −0.2). Comparison of the PCA selected subgroup of ME/CFS patients (9/11) with controls increased the number of proteins differentially expressed to 99. Of particular relevance to the core symptoms of fatigue and post-exertional malaise experienced in ME/CFS, a proportion of the identified proteins in the ME/CFS groups were involved in mitochondrial function, oxidative phosphorylation, electron transport chain complexes, and redox regulation. A significant number were also involved in previously implicated disturbances in ME/CFS, such as the immune inflammatory response, DNA methylation, apoptosis and proteasome activation. Conclusions The results from this study support a model of deficient ATP production in ME/CFS, compensated for by upregulation of immediate pathways upstream of Complex V that would suggest an elevation of oxidative stress. This study and others have found evidence of a distinct pathology in ME/CFS that holds promise for developing diagnostic biomarkers.
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Affiliation(s)
- Eiren Sweetman
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Christina Edgar
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Michel de Lange
- Centre for Biostatistics, University of Otago, Dunedin, 9016, New Zealand
| | | | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand.
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Lande A, Fluge Ø, Strand EB, Flåm ST, Sosa DD, Mella O, Egeland T, Saugstad OD, Lie BA, Viken MK. Human Leukocyte Antigen alleles associated with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Sci Rep 2020; 10:5267. [PMID: 32210306 PMCID: PMC7093502 DOI: 10.1038/s41598-020-62157-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 03/03/2020] [Indexed: 01/06/2023] Open
Abstract
The etiology and pathogenesis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) are unknown, and autoimmunity is one of many proposed underlying mechanisms. Human Leukocyte Antigen (HLA) associations are hallmarks of autoimmune disease, and have not been thoroughly investigated in a large ME/CFS patient cohort. We performed high resolution HLA -A, -B, -C, -DRB1, -DQB1 and -DPB1 genotyping by next generation sequencing in 426 adult, Norwegian ME/CFS patients, diagnosed according to the Canadian Consensus Criteria. HLA associations were assessed by comparing to 4511 healthy and ethnically matched controls. Clinical information was collected through questionnaires completed by patients or relatives. We discovered two independent HLA associations, tagged by the alleles HLA-C*07:04 (OR 2.1 [95% CI 1.4–3.1]) and HLA-DQB1*03:03 (OR 1.5 [95% CI 1.1–2.0]). These alleles were carried by 7.7% and 12.7% of ME/CFS patients, respectively. The proportion of individuals carrying one or both of these alleles was 19.2% in the patient group and 12.2% in the control group (OR 1.7 [95% CI 1.3–2.2], pnc = 0.00003). ME/CFS is a complex disease, potentially with a substantial heterogeneity. We report novel HLA associations pointing toward the involvement of the immune system in ME/CFS pathogenesis.
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Affiliation(s)
- Asgeir Lande
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Øystein Fluge
- Department of Oncology and Medical Physics, Haukeland University Hospital and Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Elin B Strand
- National Advisory Unit on CFS/ME, Oslo University Hospital, Oslo, Norway.,Faculty of Health Science, VID Specialized University, Stavanger, Norway
| | - Siri T Flåm
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Daysi D Sosa
- CFS/ME Center, Oslo University Hospital, Oslo, Norway
| | - Olav Mella
- Department of Oncology and Medical Physics, Haukeland University Hospital and Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torstein Egeland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Ola D Saugstad
- Department of Pediatric Research, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Marte K Viken
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
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Ovejero T, Sadones O, Sánchez-Fito T, Almenar-Pérez E, Espejo JA, Martín-Martínez E, Nathanson L, Oltra E. Activation of Transposable Elements in Immune Cells of Fibromyalgia Patients. Int J Mol Sci 2020; 21:E1366. [PMID: 32085571 PMCID: PMC7072917 DOI: 10.3390/ijms21041366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/06/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
Advancements in nucleic acid sequencing technology combined with an unprecedented availability of metadata have revealed that 45% of the human genome constituted by transposable elements (TEs) is not only transcriptionally active but also physiologically necessary. Dysregulation of TEs, including human retroviral endogenous sequences (HERVs) has been shown to associate with several neurologic and autoimmune diseases, including Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). However, no study has yet addressed whether abnormal expression of these sequences correlates with fibromyalgia (FM), a disease frequently comorbid with ME/CFS. The work presented here shows, for the first time, that, in fact, HERVs of the H, K and W types are overexpressed in immune cells of FM patients with or without comorbid ME/CFS. Patients with increased HERV expression (N = 14) presented increased levels of interferon (INF-β and INF-γ) but unchanged levels of TNF-α. The findings reported in this study could explain the flu-like symptoms FM patients present with in clinical practice, in the absence of concomitant infections. Future work aimed at identifying specific genomic loci differentially affected in FM and/or ME/CFS is warranted.
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Affiliation(s)
- Tamara Ovejero
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | | | - Teresa Sánchez-Fito
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46008 Valencia, Spain; (T.S.-F.); (E.A.-P.)
| | - Eloy Almenar-Pérez
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46008 Valencia, Spain; (T.S.-F.); (E.A.-P.)
| | - José Andrés Espejo
- School of Biotechnology, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | | | - Lubov Nathanson
- Institute for Neuro Immune Medicine, Nova Southeastern University, Ft Lauderdale, FL 33314, USA;
| | - Elisa Oltra
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
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11
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Tost J. 10 years of Epigenomics: a journey with the epigenetic community through exciting times. Epigenomics 2020; 12:81-85. [DOI: 10.2217/epi-2019-0375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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12
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Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. AN INTERNATIONAL JOURNAL ON INFORMATION FUSION 2019; 50:71-91. [PMID: 30467459 PMCID: PMC6242341 DOI: 10.1016/j.inffus.2018.09.012] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include myriad properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of all the factors relevant to understanding a phenomenon such as a disease. Integrative methods that combine data from multiple technologies have thus emerged as critical statistical and computational approaches. The key challenge in developing such approaches is the identification of effective models to provide a comprehensive and relevant systems view. An ideal method can answer a biological or medical question, identifying important features and predicting outcomes, by harnessing heterogeneous data across several dimensions of biological variation. In this Review, we describe the principles of data integration and discuss current methods and available implementations. We provide examples of successful data integration in biology and medicine. Finally, we discuss current challenges in biomedical integrative methods and our perspective on the future development of the field.
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Affiliation(s)
- Marinka Zitnik
- Department of Computer Science, Stanford University,
Stanford, CA, USA
| | - Francis Nguyen
- Department of Medical Biophysics, University of Toronto,
Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Bo Wang
- Hikvision Research Institute, Santa Clara, CA, USA
| | - Jure Leskovec
- Department of Computer Science, Stanford University,
Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Anna Goldenberg
- Genetics & Genome Biology, SickKids Research Institute,
Toronto, ON, Canada
- Department of Computer Science, University of Toronto,
Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Michael M. Hoffman
- Department of Medical Biophysics, University of Toronto,
Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Computer Science, University of Toronto,
Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
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13
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Missailidis D, Annesley SJ, Fisher PR. Pathological Mechanisms Underlying Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Diagnostics (Basel) 2019; 9:E80. [PMID: 31330791 PMCID: PMC6787592 DOI: 10.3390/diagnostics9030080] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
The underlying molecular basis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is not well understood. Characterized by chronic, unexplained fatigue, a disabling payback following exertion ("post-exertional malaise"), and variably presenting multi-system symptoms, ME/CFS is a complex disease, which demands a concerted biomedical investigation from disparate fields of expertise. ME/CFS research and patient treatment have been challenged by the lack of diagnostic biomarkers and finding these is a prominent direction of current work. Despite these challenges, modern research demonstrates a tangible biomedical basis for the disorder across many body systems. This evidence is mostly comprised of disturbances to immunological and inflammatory pathways, autonomic and neurological dysfunction, abnormalities in muscle and mitochondrial function, shifts in metabolism, and gut physiology or gut microbiota disturbances. It is possible that these threads are together entangled as parts of an underlying molecular pathology reflecting a far-reaching homeostatic shift. Due to the variability of non-overlapping symptom presentation or precipitating events, such as infection or other bodily stresses, the initiation of body-wide pathological cascades with similar outcomes stemming from different causes may be implicated in the condition. Patient stratification to account for this heterogeneity is therefore one important consideration during exploration of potential diagnostic developments.
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Affiliation(s)
- Daniel Missailidis
- Department of Physiology Anatomy and Microbiology, La Trobe University, VIC 3086, Australia
| | - Sarah J Annesley
- Department of Physiology Anatomy and Microbiology, La Trobe University, VIC 3086, Australia
| | - Paul R Fisher
- Department of Physiology Anatomy and Microbiology, La Trobe University, VIC 3086, Australia.
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14
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Sweetman E, Noble A, Edgar C, Mackay A, Helliwell A, Vallings R, Ryan M, Tate W. Current Research Provides Insight into the Biological Basis and Diagnostic Potential for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Diagnostics (Basel) 2019; 9:diagnostics9030073. [PMID: 31295930 PMCID: PMC6787691 DOI: 10.3390/diagnostics9030073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/22/2019] [Accepted: 07/03/2019] [Indexed: 02/08/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a severe fatigue illness that occurs most commonly following a viral infection, but other physiological triggers are also implicated. It has a profound long-term impact on the life of the affected person. ME/CFS is diagnosed primarily by the exclusion of other fatigue illnesses, but the availability of multiple case definitions for ME/CFS has complicated diagnosis for clinicians. There has been ongoing controversy over the nature of ME/CFS, but a recent detailed report from the Institute of Medicine (Academy of Sciences, USA) concluded that ME/CFS is a medical, not psychiatric illness. Importantly, aspects of the biological basis of the ongoing disease have been revealed over the last 2-3 years that promise new leads towards an effective clinical diagnostic test that may have a general application. Our detailed molecular studies with a preclinical study of ME/CFS patients, along with the complementary research of others, have reported an elevation of inflammatory and immune processes, ongoing neuro-inflammation, and decreases in general metabolism and mitochondrial function for energy production in ME/CFS, which contribute to the ongoing remitting/relapsing etiology of the illness. These biological changes have generated potential molecular biomarkers for use in diagnostic ME/CFS testing.
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Affiliation(s)
- Eiren Sweetman
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Alex Noble
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Christina Edgar
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Angus Mackay
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Amber Helliwell
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | | | - Margaret Ryan
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand.
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15
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Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation. Clin Ther 2019; 41:675-698. [PMID: 30910331 DOI: 10.1016/j.clinthera.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease. METHODS A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool. FINDINGS Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection. IMPLICATIONS Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences ("junk repetitive DNA"), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.
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16
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Chard L. Welcome to the 11th volume of Epigenomics. Epigenomics 2019; 11:1-4. [DOI: 10.2217/epi-2018-0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Foreword by Lucy Chard Welcome to the 11th volume of Epigenomics. I would like to take this opportunity to wish all of our readers a Happy New Year. In this Foreword, I shall be taking a look back at some of the journal highlights of 2018. Over the past year, we have seen some great strides in the development of epigenetics for medical applications. However, this advancing field, while niche, still needs to overcome a number of obstacles before we see a more widespread application of this technology. It has been a privilege for Epigenomics to publish work in this fascinating field, which continues to be of the highest quality.
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Affiliation(s)
- Lucy Chard
- Future Medicine, Future Science Group Ltd, London, UK
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17
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Herrera S, de Vega WC, Ashbrook D, Vernon SD, McGowan PO. Genome-epigenome interactions associated with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Epigenetics 2018; 13:1174-1190. [PMID: 30516085 DOI: 10.1080/15592294.2018.1549769] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, potential interactions between DNA methylation and genetic background in relation to ME/CFS have not been examined. In this study we explored this association by characterizing the epigenetic (~480 thousand CpG loci) and genetic (~4.3 million SNPs) variation between cohorts of ME/CFS patients and healthy controls. We found significant associations of DNA methylation states in T-lymphocytes at several CpG loci and regions with ME/CFS phenotype. These methylation anomalies are in close proximity to genes involved with immune function and cellular metabolism. Finally, we found significant correlations of genotypes with methylation modifications associated with ME/CFS. The findings from this study highlight the role of epigenetic and genetic interactions in complex diseases, and suggest several genetic and epigenetic elements potentially involved in the mechanisms of disease in ME/CFS.
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Affiliation(s)
- Santiago Herrera
- a Centre for Environmental Epigenetics and Development , University of Toronto , Scarborough , Canada.,b Department of Biological Sciences , University of Toronto , Scarborough , Canada
| | - Wilfred C de Vega
- a Centre for Environmental Epigenetics and Development , University of Toronto , Scarborough , Canada.,b Department of Biological Sciences , University of Toronto , Scarborough , Canada.,c Department of Cell and Systems Biology , University of Toronto , Toronto , Canada
| | - David Ashbrook
- a Centre for Environmental Epigenetics and Development , University of Toronto , Scarborough , Canada.,b Department of Biological Sciences , University of Toronto , Scarborough , Canada
| | | | - Patrick O McGowan
- a Centre for Environmental Epigenetics and Development , University of Toronto , Scarborough , Canada.,b Department of Biological Sciences , University of Toronto , Scarborough , Canada.,c Department of Cell and Systems Biology , University of Toronto , Toronto , Canada.,e Department of Psychology , University of Toronto , Toronto , Canada.,f Department of Physiology, Faculty of Medicine , University of Toronto , Toronto , Canada
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