(Medford MA, March 25 2023) – PolyBio Research is excited to announce that the Steven & Alexandra Cohen Foundation (the Foundation) has formally awarded a $1M collaborative research grant to the University of California San Diego. The grant was facilitated by PolyBio’s core team and will support a multi-method research study to deeply characterize the microbial, viral, immune, and genetic landscape of tissue samples collected from patients with LongLyme disease, ME/CFS, LongCovid and Ehlers-Danlos syndrome (EDS). The “Tissue Analysis Pipeline” project’s findings could lead to improved tissue-based diagnostics for patients with these debilitating infection-associated chronic conditions.

Tissue samples will be analyzed for different organisms

The Steven & Alexandra Cohen Foundation is the largest private funder and has given over $85 million to Lyme and tickborne disease research.  The Foundation is broadening efforts to research other infection-associated chronic conditions to better understand how to diagnose and treat them.

“Infection-associated chronic conditions, including long or chronic Lyme disease, are a growing health crisis,” said Alexandra Cohen, President of the Steven & Alexandra Cohen Foundation. “We are proud to support UCSD with this collaborative research grant. By working together, we can increase our impact and help patients living with these devastating diseases.”

The Steven & Alexandra Cohen Foundation grant was facilitated by donations to PolyBio Research Foundation. The donations supported PolyBio microbiologist Dr. Amy Proal’s ability to bring together the study team and perform small analyses on patient tissue that demonstrated feasibility for the larger project. They also allowed PolyBio neuroscientist Michael VanElzakker to jump-start the process of obtaining ethical approval for the collection of study tissue samples.

SARS-CoV-2 in tissue as imaged via spatial transcriptomics – a method that will be used in the collaborative study

The Tissue Analysis Pipeline project will be formally led by Drs. Christopher Dupont and Marcelo Freire of University of California San Diego/the J. Craig Venter Institute. Dr. Dupont is an Associate Professor of Genomic Medicine and Synthetic Biology with extensive experience in using advanced computer-based technologies to identify bacteria, viruses, fungi, and other organisms in biological samples. Dr. Freire is an Associate Professor in Genomic Medicine & Infectious Disease and an expert in the biology of inflammation. Members of the study team also include Dr. Nikos Kyrpides and Dr. Stephen Nayfach from the Lawrence Berkeley National Laboratory Joint Genome Institute. Dr. Kyrpides is a senior scientist and a world expert on the use of innovative technologies to identify bacteriophage (small viruses that infect bacteria) in samples. PolyBio Research Foundation’s Dr. Amy Proal will coordinate the project team and assure completion of important milestones. Dr. Marna Ericson from The Hormel Institute at the University of Minnesota will draw from decades of experience on the identification of tickborne pathogens in tissue samples to serve as an advisor to the project.

Collection of tissue samples for the study will be facilitated by clinicians and researchers with extensive experience in treating and studying patients with infection-associated chronic disease: Dr. Peter Novak and Dr. Michael VanElzakker of Harvard Medical School and Drs. Ilene Ruhoy and Paolo Bolognese of the Chiari/EDS Center at Mt. Sinai South Nassau. Dr. Susan Wu M.D, Chairman of the Department of Pathology at Mount Sinai South Nassau will also play a key role in tissue collection and preservation.

Two central tissue types will be collected from LongLyme, ME/CFS, LongCovid, and EDS patients for analysis 1) peripheral tissue/nerve samples collected via skin punch biopsy 2) ligament and nerve root samples collected during surgery. “I’m excited that our project combines the expertise of both clinicians and researchers in the infection-associated chronic disease space” says project co-principal investigator Christopher Dupont. “It is this incredible project team and their unique knowledge of specific technologies and methods that should allow our project to succeed.”

An overview of the tissue analysis project pipeline

The pipeline the team has developed to analyze tissue samples 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.

“Successful identification and characterization of organisms and the immune and genetic signals in study tissue samples could lead to improved tissue-based biomarkers for patients with infection-associated chronic disease.” says project investigator Dr. Amy Proal. In addition, if certain methods used in the study successfully identify pathogens such as Borrelia burgdorferi, SARS-CoV-2, or the herpesviruses in samples, the findings could set the groundwork for improved tissue-based molecular diagnostics for such pathogens that could be used by clinicians at routine appointments. 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 project’s “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 persistent pathogen activity or infectious processes. These include understudied conditions that primarily impact women such as endometriosis and interstitial cystitis.

The Steven & Alexandra Cohen Foundation is also co-sponsoring the upcoming June 2023 event “Toward a Common Research Agenda in Infection-Associated Chronic Illnesses: A Workshop to Examine Common, Overlapping Clinical and Biological Factors.”

About Steven & Alexandra Cohen Foundation

The Steven & Alexandra Cohen Foundation is committed to inspiring philanthropy and community service by creating awareness, offering guidance, and leading by example to show the world what giving can do. The Foundation’s grants support nonprofit organizations based in the United States that either help people in need or solve complex problems. The Foundation also spearheads grassroots campaigns to encourage others to give. For more information, visit steveandalex.org .