Driving research of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME / CFS),
Post Treatment Lyme Disease Syndrome (PTLDS), Fibromyalgia and Post COVID .

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Severely iIl Patient

Severely ill Patient Study

STUDY AIM

The aim of the Severely Ill Patient Study (SIPS), which started in 2015, was to conduct a comprehensive “Big Data” analysis on severely ill ME/CFS patients in order to begin an exploration to find the molecular basis of ME/CFS.

LEAD INVESTIGATORS
  • Ronald W. Davis, PhD
  • Wenzhong Xiao, PhD
UPDATES AND POTENTIAL
Over 1,000 tests have been conducted per patient, which is the largest (to our knowledge) dataset ever generated in any patient. This large dataset has been made available online to all interested researchers in the ME/CFS Data Center at Stanford, with the purpose of inspiring research globally, eliminating duplication of effort, and building a collaborative network of scientists.

STUDY HYPOTHESIS AND DESCRIPTION

The hypothesis of the study was that molecular differences would show the strongest signal in severe cases of the illness when compared to healthy controls.

 OBJECTIVES

Big Data Technology

Using samples of saliva, blood, urine and feces, this big data study examines the following:

  • Genome
  • Gene expression on individual immune cell types
  • Metabolomics
  • Microbiome
  • Cell-free DNA sequencing and quantitation
  • Cytokines
  • Clinical tests

The value of a study of this magnitude is that it provides a foundation of invaluable information to generate hypotheses and to develop diagnostics and treatments. Further, all samples from one patient are taken at one point in time, enabling all measurements to reflect exactly what was happening in the body at that one time point. This allows the possibility for the discovery of biomarkers involving the relationships between different body systems that would not ordinarily be found.

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.
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.
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.
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.