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Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME / CFS) Post Treatment Lyme Disease Syndrome (PTLDS), Fibromyalgia Leading Research. Delivering Hope.Open Medicine Foundation® Canada
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Network Medicine to Identify Disease Mechanisms & Treatments

TECHNOLOGY VALUE

The goal of this project is to use data integration and network analyses to discover disease mechanisms and potential treatments.

LEAD INVESTIGATORS
  • Wenzhong Xiao, PhD
  • Jingcheng Yang, PhD
  • Li-Yuan Hung / Chanshuo Wu, PhD
  • Martha Eckey, Pharm D
  • Peng Li, PhD
  • Gonghua Li, PhD
  • Feifei Han, PhD
Study Hypothesis and Description

Disease knowledge-based networks reflect the current understanding of diseases between clinical phenotypes/symptoms, drugs, genotypes and other molecular interactions.

By applying network of biomedical knowledge to integrate clinical phenotypes and molecular signatures of ME/CFS, we hope to uncover disease gene modules and to prioritize drug candidates for repurposing to help disease symptoms and progression.

OBJECTIVES

Two researchers in a lab near equipment. Each looks at data on a screen.

  1. Develop a knowledge base of curated studies and the gene-disease-symptom map of ME/CFS available to the research community through the established ME/CFS Data Center.
  2. Conduct a deep-learning heterogeneous networks method for network medicine (MINDR) to discover disease modules and identify drug targets.
  3. Through the computational analysis, identify molecular modules underlying ME/CFS and prioritize in silico drug molecules for repurposing in ME/CFS
  4. Validate the top candidates by evaluation of their reported effects in real world patient data and recommend at least two drugs as candidates for pilot clinical trials.
  5.  
Updates and Potential
  • We identified diseases similar to ME/CFS and key genes involved.
  • We identified target genes for modulation and are investigating evidence in preclinical animal models and real-world evidence from electronic health records and patient self-reported outcomes.
  • We completed a patient treatment survey of ~4,000 ME/CFS and Long COVID patients on their self-reported outcomes of 150+ treatments. A manuscript has been published: Eckey, M., et al. (2025). Patient-reported treatment outcomes in ME/CFS and long COVID. PNAS. 122(28): e2426874122. doi:10.1073/pnas.2426874122
  • We identified candidate treatments and are discussing with potential partners and collaborators on follow-up human trials and preclinical studies.
  • We continue to retrain the model as new data emerges and identify changes to the results of the model based on the new information.

Consent management

Consent Preferences

Data Subject Access Request (DSAR) Form 

Microvesicles and viral sequencing
Microvesicles are a type of extracellular vesicle that is released from the cell membrane. Vesicles are small, fluid-filled sacs or vacuoles within the body. Sequencing is a technique used to determine the exact sequence of bases (A, C, G, and T) in a DNA (or viral) molecule.
NMR Metabolomics
NMR (Nuclear Magnetic Resonance) is an instrument/tool used to perform metabolic studies, metabolic profiling, and metabolomics in biofluids and tissues for more than 40 years using magnetic fields. There is a very close connection between metabolic measurements and NMR. This connection has flourished because of NMR’s many unique strengths for characterizing complex mixtures’ chemical composition.
Proteomics
The large-scale study of proteins, which are large, complex molecules that are required for structure, function, and regulation of the human body's tissues and organs.
Autoantibodies
Antibodies that react with self-molecules and that occur in healthy individuals and are referred to as natural antibodies or autoantibodies.
Extracellular DNA for viral reactivation and Mitochondrial DNA
exDNA (extracellular DNA), exDNA is often secreted actively and is used to perform several tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental, and general microbiological applications. Viruses are intracellular parasites that rely to a significant extent on the host cell for replication. Viral reactivation occurs when an active replication of the viral genome results in a lytic (degradation of the cell) infection characterized by the release of new progeny (descendant) virus particles.
Immune cell profiling
The immune system has many important regulatory roles in disease development and progression. Given the emergence of effective immune therapies, reliable predictors of response are needed. Immune cell profiling determines response by evaluating immune cell populations from treated and untreated samples. For our purposes, we will evaluate the white blood cell response to the viral infection using a process called “Cytof.”
Leukocyte Genomics
A leukocyte is a colorless cell circulating in the blood and body fluids and is involved in counteracting foreign substances and disease. A genome is all genetic material of an organism. Genomics is a biology field focusing on the structure, function, evolution, mapping, and editing of genomes. Therefore, leukocyte genomics is the study of all genetic material of leukocytes.
Metabolomics
Metabolomics is a way to study metabolism – that is, through measuring amounts of the metabolites (small molecules) produced by our bodies as we convert food into energy and other molecules that our cells need to survive. Metabolomics technology is ‘large-scale,’ meaning that several thousand metabolites can be measured from a single sample of e.g., blood or urine.
Micro RNA
Cells use Micro RNA to control whether a particular gene is making too much, too little or the normal amount of its protein at a particular time.