Alexey Fedulov, MD, PhD
Awards
Advance RI-CTR Pilot Projects Program (Cycle 9)
"Targeting human genes for epigenetic editing in lung fibrosis"
Multi-PI: Yang Zhou, PhD
Epigenetic editing entails targeted re-writing of the biochemical markup that dictates how the genetic code functions. This is accomplished by artificial fusion proteins in which a sequence-specific DNA-binding domain (DBD) tethers a DNA demethylase to specific promoter. Removal of DNA methylation residues leads to increased openness of the gene to transcriptional stimuli, which occurs in adaptive, contextappropriate manner, and can be therapeutic. This can be used not only as a research tool to test causality of epigenetic changes seen in disease, but as a therapeutic approach to gene-specifically upregulate the intrinsic expression of a gene of interest and to specifically reverse the altered DNA methylation patterns. However, the need for viral vectors currently employed to transduce the epigenetically –acting chimeras into recipient cells suiting the current in vitro exploration has hindered the translation to humans, and the side-effects or transduction or transfection are impairing immunological investigations. This proposal addresses these challenges and transforms the experimental technology by using affinity- purified epigenetically acting proteins as novel biologics rather than cumbersome transgenes, and will test them in human rather than murine genes and in human cells.
The specific example is lung fibrosis – an incurable and poorly treatable condition that is an outcome of lung injury and inflammation including COVID-19, hence this chronic illness is part of the RI health priorities, as defined by the RI Department of Health. A gene Cxcl11 encoding a protein with protective or therapeutic effect against lung fibrosis is silenced by DNA methylation and is our prototype target to employ epigenetic editors.
Based on the success of the murine-targeting demethylase constructs here we have set the following Specific Aims: 1) Design and test fusion protein demethylase constructs for gene-specific epigenetic editing of Cxcl11 gene in human cells. 2) Perform epigenomic profiling of cells from pulmonary fibrosis (IPF) patients to identify other epigenetically silenced gene candidates for therapeutic epigenetic editing. We use samples from Rhode Island population of patients consistent with the RFA requirements.
The epigenetically-acting proteins we develop will form the basis for a new class of epigenetic therapeutics. This study develops an innovative vector-free epigenetic editing technique as a novel type of treatment for lung fibrosis. Epigenomic profiling of primary cells from fibrosis patients, focused on promoter methylation status and targetability by epigenetic editing, will delineate the candidates for epigenetic therapy in pulmonary fibrosis. Overall, the study uses a transformative approach for translation of epigenetic editing to human treatments.