Validating cfDNA biomarker

Investigators: Stephanie Eramo BS, Srinivas Ramachandran PhD, Sujatha Jagannathan PhD

Category: Research - Basic

FSHD is characterized by death of muscle cells due to aberrant expression of DUX4. Current means to monitor progression of FSHD and response to treatments at a molecular level require invasive muscle biopsies. Availability of FSHD biomarkers in blood can significantly reduce patient hardship and allow for more frequent tracking of disease status. Here, we propose to develop FSHD biomarkers from cell free DNA (cfDNA). Free-floating DNA in our blood, or cell-free DNA (cfDNA), promises a non-invasive means to monitor an individual’s health status before traditional diagnostic techniques become feasible. cfDNA arises from genomic DNA shed by cells during turnover, which then ends up in blood, saliva, and urine. Hence, harnessing information from cfDNA to identify which cells are shedding their DNA could be used to detect the physiological state of an individual. Our genome is packaged with proteins called histones, which form discrete units called nucleosomes. cfDNA arises because nucleases chew the genome when the cell dies, but nucleosomes block the action of nucleases. Thus, cfDNA is a snapshot of where the nucleosomes were arranged on the dying cell’s genome. Protected fragments shorter than 147 bp, “subnucleosomes”, represent DNA unwrapping from the histone complex during nucleosome disassembly or re-assembly that accompany active transcription. Enrichment of these short fragments next to the beginning of the gene correlates with the gene being expressed. Here, we will use the length of the cfDNA fragments near the start of genes to infer whether the gene was expressed in the cell that shed the cfDNA in the first place. During FSHD progression, we predict that we will observe subnucleosome profiles indicative of DUX4 gene expression program, due to release of cfDNA from muscle tissue. Development of cfDNA biomarkers will eventually lead to a sensitive and cheap method to track FSHD progression from a blood test at scale.