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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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BOSS-ME: Biological Outlier and Subtyping Software for ME/CFS

Study AIM

This project will develop a software tool to rapidly look for metabolism anomalies in an individual which might be explained by their genes. It will also look for potentially damaging genes in individuals and it will attempt to group ME/CFS patients based on their genetic and metabolic profiles.

LEAD INVESTIGATORS
  • Katherine Huang
  • Natalie Thomas, PhD
  • Robert Phair, PhD
  • David Ascher, PhD
  • Paul Gooley, PhD
  • Christopher Armstrong, PhD
Updates and Potential
  • Differential diagnosis paper accepted by Nature Communications Medicine.
  • Paper on metabolite and gene interactions in ME/CFS is in the submission process.
  • Review paper on applying machine learning to ME/CFS has been accepted with revisions by the Journal of Translational Medicine.
  • PhD Student Kathy Huang has submitted her thesis.
STUDY HYPOTHESIS AND DESCRIPTION

This project aims to create a tool that can quickly identify unusual metabolic patterns in individuals that might be linked to their genetic makeup. It will also search for genes that could potentially cause harm. Specifically, the tool will be used to classify patients with ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome) based on their genetic and metabolic information.

The tool will be designed using data from over 1,000 people who reported having ME/CFS in the UK Biobank, which holds clinical data and blood samples from more than 300,000 individuals. By comparing these ME/CFS patients with others who have similar illnesses, we have been able to spot unique metabolic patterns that help identify ME/CFS in a person.

This new tool will be especially useful for doctors as it will make diagnosing ME/CFS faster and more accurate by spotting genetic and metabolic issues that might otherwise go unnoticed.

 

OBJECTIVES

Chart paper with several colorful, parallel graph lines

  1. Observe the relationship between genes and metabolism to identify outlier genetic anomalies and pathways in ME/CFS.
  2. Determine the relationship between metabolism and genes in ME/CFS as compared to other similar diseases.
  3. Develop an algorithm to rapidly extract outlier and pattern pathways of disease.
  4. Test and validate algorithm produced on a well-curated set of ME/CFS patients with metabolism and gene data.
  5. Eventually produce software to simplify this process.

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.