Project Team

Christopher Dupont, PhD, Associate Professor in Genomic Medicine, Environment & Sustainability, and Synthetic Biology, the J. Craig Venter Institute

Marcelo Freire, PhD, DDS, Associate professor in the Genomic Medicine and Infectious Disease The J. Craig Venter Institute 

Nikos Kyrpides PhD, Senior Scientist, Genome Biology Program Lead, Metagenomics Program Head, Joint Genome Institute, Lawrence Berkeley National Laboratory.

Stephen Nayfach PhD, Microbiome Data Science Group, Joint Genome Institute, Lawrence Berkeley National Laboratory. 

Dr. Amy Proal PhD, President, Research Lead,  PolyBio Research Foundation.

Peter Novak MD, PhD, Inaugural Chief of the Autonomic Neurology Division, Brigham and Women’s Hospital.

Michael VanElzakker PhD, Instructor, Division of Neurotherapeutics, Harvard Medical School

Ilene Ruhoy MD, Chiari/EDS Center, Mt. Sinai South Nassau.

Paolo Bolognese MD, Chiari/EDS Center, Mt, Sinai South Nassau.

Marna Ericson PhD, The Hormel Institute, University of Minnesota



Project co-lead Dr. Nikos Kyrpides

Project Summary:

A multi-method collaborative research study supported by the Steve & Alexandra Cohen Foundation and conceptualized in concert with PolyBio scientists. The project team is deeply characterizing the microbial, viral, immune and genetic landscape of tissue samples collected from patients with infection-associated chronic disease (ME/CFS, LongCovid, LongLyme disease, and Ehlers-Danlos syndrome). Sample collection is facilitated by clinicians and researchers with extensive experience in treating and studying patients with these debilitating chronic conditions. Two central tissue types are being collected for analysis from study participants: 1) peripheral nerve tissue samples collected via skin punch biopsy 2) ligament and nerve root samples collected during surgery.

To analyze collected tissue samples, the project team has developed a pipeline that combines some of the most advanced molecular and sequencing technologies available in 2023 (including bulk metagenomic/ metatranscriptomic sequencing and spatial transcriptomics) in a manner that can identify 1) the entire organism (host, bacterial, fungal, archaeal, viral) content of each sample 2) the gene expression patterns for the entire organism content and host responses 3) both known and novel bacteriophage that may be modulating the survival of identified bacteria 4) the presence and expression of DNA or RNA viruses, both known and novel 5) the spatial location of identified pathogens in specific areas of a tissue sample (for example on a nerve) 6) the activity (transcriptome) of immune and host cells spatially identified near pathogens of interest.  

Project background: 

Across the globe, millions of patients are suffering from chronic conditions that share the same central trend: Patients sustain an acute bacterial or viral infection, but fail to fully recover. Instead, they go on to develop a range of debilitating chronic symptoms that can last a lifetime. These infection-associated chronic conditions include Myalgic encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), LongCovid, and LongLyme Disease. In addition, Ehlers-Danlos Syndrome (EDS) is an understudied condition in which patients develop severe connective tissue and vasculature problems resulting in symptoms such as myalgia, neuralgia, and loose/unstable joints. EDS patients often report symptom exacerbation after an infection.

The pathogens implicated in these conditions (herpesviruses, enteroviruses, SARS-CoV-2, Borrelia etc) often employ redundant molecular mechanisms to infect patient tissue or nerves. In addition, the four chronic conditions are frequently comorbid in the same patients. It follows that research efforts that analyze samples from patients with ME/CFS, LongCovid, LongLyme disease and EDS in concert could lead to a better understanding of all four disease processes. The project team has consequently created a “Tissue Analysis Pipeline” to characterize infectious, immune and genetic abnormalities in tissue samples collected from patients with all four diagnoses. 

Successful identification and characterization of organisms and/or dysregulated immune and genetic signals in study tissue samples could lead to improved tissue-based biomarkers for patients with infection-associated chronic disease. This is especially true of the peripheral tissue/nerve samples that can be collected at routine clinical visits via punch biopsy. The team’s long-term vision is to iterate the “Tissue Analysis Pipeline” so that in the future the same methods can be used to deeply study tissue samples collected from patients with other chronic diseases tied to infectious processes. These include understudied conditions that primarily impact women such as interstitial cystitis.