Tag: genome

Uncovering the genetic architecture of ME/CFS: a precision approach reveals impact of rare monogenic variation

Abstract:

Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling and heterogeneous disorder lacking validated biomarkers or targeted therapies. Clinical variability and elusive pathophysiology hinder progress toward effective diagnostics and treatment. Core symptoms include persistent fatigue, post-exertional malaise, unrefreshing sleep, cognitive dysfunction, and pain. We tested whether an individualized, “n-of-1” genomic and transcriptomic framework combined with comprehensive, participant-informed phenotyping could reveal molecular signatures unique to each patient.

Methods: Clinical-grade whole-genome sequencing was conducted in 31 affected individuals from 25 families, with RNA-seq performed on a subset (16 affected, 7 unaffected) using blood samples. Machine-learning assisted variant triage, transcript-aware damage prediction, and expert review identified pathogenic or likely pathogenic variants in 8 of 25 probands (32%) and 12 of 31 affected individuals (39%).

Results: Findings revealed marked genetic heterogeneity, including large-effect rare and more common variants. Implicated pathways included ATP generation, oxidative phosphorylation, fatty acid oxidation; regulation of glycolysis, amino acid and lipid turnover; ion and solute homeostasis; synaptic signaling, excitability, oxygen transport, and muscle integrity, resilience, and post-exertional recovery; previously implicated processes. Plausible modifiers influencing disease onset, severity, and relapsing–remitting patterns and possibly explaining intrafamilial variability and inconsistent findings across studies, were also identified. Despite gene-level diversity, downstream effects converged on impaired energy production, reduced stress resilience, and vulnerability to post-exertional metabolic failure; disruptions consistent with core ME/CFS symptoms of exertional intolerance, cognitive fog, and fatigue.

Conclusions: Our findings support the hypothesis that at least a subset of ME/CFS cases represent distinct molecular disorders that converge on shared physiological pathways. Validation in larger, more diverse cohorts will be essential to test this hypothesis and establish generalizability, but increase size alone is unlikely to resolve causation in a disorder defined by rarity, heterogeneity, and molecular complexity. We suggest that progress will require experimental designs that integrate individual-level genomic data with deep, participant-informed deep phenotyping, capturing the combined effects of rare and common variants and environmental modifiers on disease expression and progression. We believe that an individualized precision medicine framework will uncover molecular drivers and modifiers of ME/CFS previously obscured by heterogeneity, enabling biologically informed stratification, improved trial design, biomarker discovery, and targeted interventions in this historically neglected condition.

Source: Birch CL, Wilk BM, Gajapathy M, Hutchins SD, Kaur G, Brown DM, Mamidi TKK, Hodgin KS, Turgut A, Younger JW, Worthey EA. Uncovering the genetic architecture of ME/CFS: a precision approach reveals impact of rare monogenic variation. J Transl Med. 2025 Dec 24. doi: 10.1186/s12967-025-07586-w. Epub ahead of print. PMID: 41444612. https://link.springer.com/article/10.1186/s12967-025-07586-w (Full text available as PDF file)

The genetic architecture of fibromyalgia across 2.5 million individuals

Abstract:

Fibromyalgia is a common and debilitating chronic pain syndrome of poorly understood etiology. Here, we conduct a multi-ancestry genome-wide association study meta-analysis across 2,563,755 individuals (54,629 cases and 2,509,126 controls) from 11 cohorts, identifying the first 26 risk loci for fibromyalgia.

The strongest association was with a coding variant in HTT , the causal gene for Huntington’s disease. Gene prioritization implicated the HTT regulator GPR52 , as well as diverse genes with neural roles, including CAMKV ,  DCC ,  DRD2 / NCAM1 ,   MDGA2 , and CELF4 . Fibromyalgia heritability was exclusively enriched within brain tissues and neural cell types.

Fibromyalgia showed strong, positive genetic correlation with a wide range of chronic pain, psychiatric, and somatic disorders, including genetic correlations above 0.7 with low back pain, post-traumatic stress disorder and irritable bowel syndrome. Despite large sex differences in fibromyalgia prevalence, the genetic architecture of fibromyalgia was nearly identical between males and females.

This work provides the first robust genetic evidence defining fibromyalgia as a central nervous system disorder, thereby establishing a biological framework for its complex pathophysiology and extensive clinical comorbidities.

Source: Kerrebijn I, Bjornsdottir G, Arbabi K, Urpa L, Haapaniemi H, Thorleifsson G, Stefansdottir L, Frangakis S, Valliere J, Kunorozva L, Abner E, Ji C, Aagaard B, Bliddal H, Brunak S, Bruun MT, Didriksen M, Erikstrup C, Geirsson AJ, Gudbjartsson DF, Hansen TF, Jonsdottir I, Knight S, Knowlton KU, Mikkelsen C, Nadauld LD, Olafsdottir TA, Ostrowski SR, Pedersen OB, Saevarsdottir S, Skuladottir AT, Sørensen E, Stefansson H, Sulem P, Sveinsson OA, Thorlacius GE, Thorsteinsdottir U, Ullum H, Vikingsson A, Werge TM; Chronic Pain Genomics Consortium; FinnGen; DBDS Genomic Consortium; Estonian Biobank Research Team; Genes & Health Research Team; Saxena R, Stefansson K, Brummett CM, Glintborg B, Clauw DJ, Thorgeirsson TE, Williams FM, Sinnott-Armstrong N, Ollila HM, Wainberg M. The genetic architecture of fibromyalgia across 2.5 million individuals. medRxiv [Preprint]. 2025 Sep 19:2025.09.18.25335914. doi: 10.1101/2025.09.18.25335914. PMID: 41001472; PMCID: PMC12458511. https://pmc.ncbi.nlm.nih.gov/articles/PMC12458511/ (Full text available as PDF file)

Initial findings from the DecodeME genome-wide association study of myalgic encephalomyelitis/chronic fatigue syndrome

Abstract:

Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a common, poorly understood disease that has no effective treatments, and has long been underserved by scientific research and national health systems. It is a sex-biased disease towards females that is often triggered by an infection, and its hallmark symptom is post-exertional malaise. People with ME/CFS often report their symptoms being disbelieved. The biological mechanisms causing ME/CFS remain unclear.
We recruited 21,620 ME/CFS cases and performed genome-wide association studies (GWAS) for up to 15,579 cases and 259,909 population controls with European genetic ancestry. In these GWAS, we discovered eight loci that are significantly associated with ME/CFS, including three near BTN2A2, OLFM4, and RABGAP1L genes that act in the response to viral or bacterial infection. Four of the eight loci (RABGAP1L, FBXL4, OLFM4, CA10) were associated at p < 0.05 with cases ascertained using post-exertional malaise and fatigue in the UK Biobank and the Netherlands biobank Lifelines. We found no evidence of sex-bias among discovered associations, and replicated in males two genetic signals (ARFGEF2, CA10) discovered in females. The ME/CFS association near CA10 colocalises with a known association to multisite chronic pain. We found no evidence that the eight ME/CFS genetic signals share common causal genetic variants with depression or anxiety.
Our findings suggest that both immunological and neurological processes are involved in the genetic risk of ME/CFS.
Source: DecodeME collaboration. Initial findings from the DecodeME genome-wide association study of myalgic encephalomyelitis/chronic fatigue syndrome. https://www.research.ed.ac.uk/en/publications/initial-findings-from-the-decodeme-genome-wide-association-study- (Full text available as PDF file)

Causes of symptoms and symptom persistence in long COVID and myalgic encephalomyelitis/chronic fatigue syndrome

Abstract:

Debilitating symptoms for many years can follow acute COVID-19 (“long COVID”), myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and various post-acute infection syndromes (PAISs). Together, long COVID and ME/CFS affect 60-400 million individuals, globally. Many similar underlying biological abnormalities have been identified in both conditions including autoantibodies against neural targets, endothelial dysfunction, acquired mitochondrial dysfunction, and a pro-inflammatory gut microbiome. Each of these abnormalities may directly cause some of the symptoms.

In addition, the symptoms also may be caused by ancient, evolutionarily conserved symptomatic and metabolic responses to vital threats-sickness behavior and torpor-responses mediated by specific, recently discovered neural circuits. These neural circuits constitute a symptom-generating pathway, activated by neuroinflammation, which may be targeted by therapeutics to quell neuroinflammation.

Many factors cause the symptoms to become chronic, including persistent infectious agents (and/or their nucleic acids and antigens) and the fact that many of the underlying biological abnormalities reinforce each other, creating ongoing physiological vicious cycles.

Source:Komaroff AL, Dantzer R. Causes of symptoms and symptom persistence in long COVID and myalgic encephalomyelitis/chronic fatigue syndrome. Cell Rep Med. 2025 Jul 25:102259. doi: 10.1016/j.xcrm.2025.102259. Epub ahead of print. PMID: 40744021. https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(25)00332-5 (Full text)

Neurodevelopment Genes Encoding Olduvai Domains Link Myalgic Encephalomyelitis to Neuropsychiatric Disorders

Abstract:

Background/Objectives: The aetiology of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), a chronic and severe debilitating disease with a complex phenotype, remains elusive. Associations with infectious diseases and autoimmune and neuropsychiatric disorders have been observed, without the identification of mechanisms. Previous studies suggest that genetic predisposition plays a role, but results are difficult to replicate, with Genome-Wide Association Studies of ME/CFS being challenging due to the relative rareness and heterogeneity of the disorder.
Methods: We studied a well-defined Australian patient cohort diagnosed via the International Consensus Criteria, recruited by a specialist ME/CFS clinic. The whole-exome sequences of 77 patients were contrasted against genome variation in the 1000 Genome Project’s genome-matched population.
Results: Significant associations with ME/CFS were harboured in genes that belong to the Neuroblastoma Breakpoint Family encoding Olduvai (DUF1220) domains, namely NBPF1 (rs3897177, p-value = 3.15 × 10−8), NBPF10 (rs1553120233, p-value = 9.262 × 10−13), and NBPF16 (rs200632836, p-value = 1.04 × 10−6). Other significantly associated variants were detected in the ATR, RSPH10B, ADGRE5-CD97, and NTRK2 genes, among others. Replication of these results was attempted via a GWAS on raw data from a US cohort, which confirmed shared significant associations with variation identified in the PTPRD, CSMD3, RAPGEF5, DCC, ALDH18A1, GALNT16, UNC79, and NCOA3 genes.
Conclusions: These genes are involved in cortical neurogenesis, brain evolution, and neuroblastoma, and have been implicated by several studies in schizophrenia and autism. The sharing of these associations by the two cohorts supports their validity and grants the necessity of future studies to evaluate the implications for ME/CFS aetiology.
Source: Arcos-Burgos, M., Arcos-Holzinger, M., Mastronardi, C., Isaza-Ruget, M. A., Vélez, J. I., Lewis, D. P., Patel, H., & Lidbury, B. A. (2025). Neurodevelopment Genes Encoding Olduvai Domains Link Myalgic Encephalomyelitis to Neuropsychiatric Disorders. Diagnostics, 15(12), 1542. https://doi.org/10.3390/diagnostics15121542 https://www.mdpi.com/2075-4418/15/12/1542 (Full text)

Dissecting the genetic complexity of myalgic encephalomyelitis/chronic fatigue syndrome via deep learning-powered genome analysis

Abstract:

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex, heterogeneous, and systemic disease defined by a suite of symptoms, including unexplained persistent fatigue, post-exertional malaise (PEM), cognitive impairment, myalgia, orthostatic intolerance, and unrefreshing sleep. The disease mechanism of ME/CFS is unknown, with no effective curative treatments.

In this study, we present a multi-site ME/CFS whole-genome analysis, which is powered by a novel deep learning framework, HEAL2. We show that HEAL2 not only has predictive value for ME/CFS based on personal rare variants, but also links genetic risk to various ME/CFS-associated symptoms. Model interpretation of HEAL2 identifies 115 ME/CFS-risk genes that exhibit significant intolerance to loss-of-function (LoF) mutations. Transcriptome and network analyses highlight the functional importance of these genes across a wide range of tissues and cell types, including the central nervous system (CNS) and immune cells.

Patient-derived multi-omics data implicate reduced expression of ME/CFS risk genes within ME/CFS patients, including in the plasma proteome, and the transcriptomes of B and T cells, especially cytotoxic CD4 T cells, supporting their disease relevance. Pan-phenotype analysis of ME/CFS genes further reveals the genetic correlation between ME/CFS and other complex diseases and traits, including depression and long COVID-19.

Overall, HEAL2 provides a candidate genetic-based diagnostic tool for ME/CFS, and our findings contribute to a comprehensive understanding of the genetic, molecular, and cellular basis of ME/CFS, yielding novel insights into therapeutic targets. Our deep learning model also offers a potent, broadly applicable framework for parallel rare variant analysis and genetic prediction for other complex diseases and traits.

Source: Zhang S, Jahanbani F, Chander V, Kjellberg M, Liu M, Glass KA, Iu DS, Ahmed F, Li H, Maynard RD, Chou T, Cooper-Knock J, Zhang MJ, Thota D, Zeineh M, Grenier JK, Grimson A, Hanson MR, Snyder MP. Dissecting the genetic complexity of myalgic encephalomyelitis/chronic fatigue syndrome via deep learning-powered genome analysis. medRxiv [Preprint]. 2025 Apr 16:2025.04.15.25325899. doi: 10.1101/2025.04.15.25325899. PMID: 40321247; PMCID: PMC12047926. https://pmc.ncbi.nlm.nih.gov/articles/PMC12047926/ (Full text available as PDF file)

A comparison of genome-wide association analyses of persistent symptoms after Lyme disease, fibromyalgia, and myalgic encephalomyelitis – chronic fatigue syndrome

Abstract:

Background: Up to 20% of Lyme disease cases experience post-treatment Lyme disease syndrome (PTLDS). The biological basis for PTLDS is poorly understood and no evidence-based treatment has been identified. Genetic studies have the potential to elucidate PTLDS pathophysiology and identify treatment targets.

Methods: We used electronic health record data (EHR) and genetic data from a linked biorepository to conduct a genome-wide association study (GWAS) for PTLDS among patients from a Pennsylvania health system. We evaluated the validity of the GWAS results in two separate conditions that have hypothesized overlapping pathophysiology, fibromyalgia and myalgic encephalomyelitis – chronic fatigue syndrome (ME/CFS). GWAS analyses were performed using logistic regression in SUGEN, assuming an additive genetic model, and adjusting for age, sex, array, and the first 10 principal components calculated from whole genome genotyping to adjust for ancestry, and accounting for relatedness including all 1st degree relationships. The functional mapping and annotation analysis (FUMA) tool was used to explore top findings from our GWAS.

Results: Among the 161,875 eligible MyCode participants with genotyping, there were 3,585 who met the criteria for treated Lyme disease. A subset of 695 (19.4%) of these patients met the criteria for PTLDS and the remaining 2890 were classified as controls. We identified two PTLDS loci that reached the suggestive significance threshold (P < 5 × 10– 7), with lead variants rs77857587, near IRX1, and rs10833979, near GAS2. Our top index single nucleotide polymorphism (SNP), rs77857587, is in high linkage disequilibrium with a long-range protein quantitative locus SNP, rs111774530, for the MARC2 (Mitochondrial Amidoxime Reducing Component 2) protein. We identified 5,041 cases of fibromyalgia (150,599 controls) and 2,268 cases of ME/CFS (151,594 controls) among the MyCode participants. Neither of the two suggestively significant loci were associated with fibromyalgia or ME/CFS.

Conclusion: We identified two PTLDS loci that reached a suggestive significance threshold. Our top index SNP is associated with the MARC2 protein, a protein that has been linked to multiple immune checkpoints. Further study is needed in a larger population to evaluate whether there is genetic evidence of the role of immune response in the occurrence of PTLDS.

Source: Hirsch AG, Justice AE, Poissant A, Nordberg CM, Josyula NS, Aucott J, Rebman AW, Schwartz BS. A comparison of genome-wide association analyses of persistent symptoms after Lyme disease, fibromyalgia, and myalgic encephalomyelitis – chronic fatigue syndrome. BMC Infect Dis. 2025 Feb 24;25(1):265. doi: 10.1186/s12879-024-10238-x. PMID: 39994562; PMCID: PMC11853495. https://pmc.ncbi.nlm.nih.gov/articles/PMC11853495/ (Full text)

A Network Medicine Approach to Investigating ME/CFS Pathogenesis in Severely Ill Patients: A Pilot Study

Abstract:

This pilot study harnessed the power of network medicine to unravel the complex pathogenesis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). By utilizing a network analysis on whole genome sequencing (WGS) data from the Severely Ill Patient Study (SIPS), we identified ME/CFS-associated proteins and delineated the corresponding network-level module, termed the SIPS disease module, together with its relevant pathways. This module demonstrated significant overlap with genes implicated in fatigue, cognitive disorders, and neurodegenerative diseases.

Our pathway analysis revealed potential associations between ME/CFS and conditions such as COVID-19, Epstein-Barr virus (EBV) infection, neurodegenerative diseases, and pathways involved in cortisol synthesis and secretion, supporting the hypothesis that ME/CFS is a neuroimmune disorder. Additionally, our findings underscore a potential link between ME/CFS and estrogen signaling pathways, which may elucidate the higher prevalence of ME/CFS in females.

These findings provide insights into the pathogenesis of ME/CFS from a network medicine perspective and highlight potential therapeutic targets. Further research is needed to validate these findings and explore their implications for improving diagnosis and treatment.

Source: Li-Yuan Hung, Chan-Shuo Wu, Chia-Jung Chang, Peng Li, Kimberly Hicks, Becky Taurog, Joshua J Dibble, Braxton Morrison, Chimere L Smith, Ronald W Davis, Wenzhong Xiao. A Network Medicine Approach to Investigating ME/CFS Pathogenesis in Severely Ill Patients: A Pilot Study.
medRxiv 2024.09.26.24314417; doi: https://doi.org/10.1101/2024.09.26.24314417 https://www.medrxiv.org/content/10.1101/2024.09.26.24314417v1 (Full text available as PDF file)

Genome-wide Association Study of Long COVID

Abstract:

Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections(1,2). Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction(3-5). The biological mechanisms that contribute to the development of Long COVID remain to be clarified.

We leveraged the COVID-19 Host Genetics Initiative(6,7) to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity(6), lung function(8), and cancers(9), suggesting a broader role for lung function in the pathophysiology of Long COVID.

While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.

Source: Vilma Lammi, Tomoko Nakanishi, Samuel E. Jones, Shea J. Andrews, Juha Karjalainen, Beatriz Cortés, Heath E. O’Brien, Brian E. Fulton-Howard, Hele H. Haapaniemi, Axel Schmidt, Ruth E. Mitchell, Abdou Mousas, Massimo Mangino, Alicia Huerta-Chagoya, Nasa Sinnott-Armstrong, Elizabeth T. Cirulli, Marc Vaudel, Alex S.F. Kwong, Amit K. Maiti, Minttu Marttila, Chiara Batini, Francesca Minnai, Anna R. Dearman, C.A. Robert Warmerdam, Celia B. Sequeros, Thomas W. Winkler, Daniel M. Jordan, Lindsay Guare, Ekaterina Vergasova, Eirini Marouli, Pasquale Striano, Ummu Afeera Zainulabid, Ashutosh Kumar, Hajar Fauzan Ahmad, Ryuya Edahiro, Shuhei Azekawa, Long COVID Host Genetics Initiative, FinnGen, DBDS Genomic Consortium, GEN-COVID Multicenter Study, Joseph J. Grzymski, Makoto Ishii, Yukinori Okada, Noam D. Beckmann, Meena Kumari, Ralf Wagner, Iris M. Heid, Catherine John, Patrick J. Short, Per Magnus, Karina Banasik, Frank Geller, Lude H. Franke, Alexander Rakitko, Emma L. Duncan, Alessandra Renieri, Konstantinos K. Tsilidis, Rafael de Cid, Ahmadreza Niavarani, Teresa Tusié-Luna, Shefali S. Verma, George Davey Smith, Nicholas J. Timpson, Mark J. Daly, Andrea Ganna, Eva C. Schulte, J. Brent Richards, Kerstin U. Ludwig, Michael Hultström, Hugo Zeberg, Hanna M. Ollila. Genome-wide Association Study of Long COVID. medRxiv 2023.06.29.23292056; doi: https://doi.org/10.1101/2023.06.29.23292056  https://www.medrxiv.org/content/10.1101/2023.06.29.23292056v1.full-text (Full text)

SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence

Abstract:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 was reported to alter several cellular pathways, its impact on DNA integrity and the mechanisms involved remain unknown. Here we show that SARS-CoV-2 causes DNA damage and elicits an altered DNA damage response.

Mechanistically, SARS-CoV-2 proteins ORF6 and NSP13 cause degradation of the DNA damage response kinase CHK1 through proteasome and autophagy, respectively. CHK1 loss leads to deoxynucleoside triphosphate (dNTP) shortage, causing impaired S-phase progression, DNA damage, pro-inflammatory pathways activation and cellular senescence. Supplementation of deoxynucleosides reduces that. Furthermore, SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thus reducing DNA repair.

Key observations are recapitulated in SARS-CoV-2-infected mice and patients with COVID-19. We propose that SARS-CoV-2, by boosting ribonucleoside triphosphate levels to promote its replication at the expense of dNTPs and by hijacking damage-induced long non-coding RNAs’ biology, threatens genome integrity and causes altered DNA damage response activation, induction of inflammation and cellular senescence.

Source: Gioia U, Tavella S, Martínez-Orellana P, Cicio G, Colliva A, Ceccon M, Cabrini M, Henriques AC, Fumagalli V, Paldino A, Presot E, Rajasekharan S, Iacomino N, Pisati F, Matti V, Sepe S, Conte MI, Barozzi S, Lavagnino Z, Carletti T, Volpe MC, Cavalcante P, Iannacone M, Rampazzo C, Bussani R, Tripodo C, Zacchigna S, Marcello A, d’Adda di Fagagna F. SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence. Nat Cell Biol. 2023 Mar 9. doi: 10.1038/s41556-023-01096-x. Epub ahead of print. PMID: 36894671. https://www.nature.com/articles/s41556-023-01096-x (Full text)