Objective
The objective of this project is to develop a new type of blood test for monitoring pancreatic beta cell death in type 1 diabetes. The test will be an epigenetic liquid biopsy, that uses beta cell-specific methylation markers to identify beta cell DNA in plasma.
Background Rationale
At present, there is no blood test that can detect early stages of type 1 diabetes. While autoantibodies can identify individuals at risk, actual autoimmune killing of beta cells cannot be monitored. This is a major barrier for efforts to understand the biology of the disease, e.g. acute environmental triggers of beta cell destruction. It also limits the ability to select patients during early stages of disease for immunotherapy, and to monitor disease progression and response to treatment. The field of cancer diagnosis has been revolutionized in recent years through the use of liquid biopsies – the analysis of short fragments of DNA that are released to blood from dying cells. This appraoch has failed in the context of type 1 diabetes, due to the limited number of beta cell markers that resulted in insufficient assay sensitivity. We have now identified a previously unrecognized feature of the beta cell epigenome, which allows to identify thousands of novel, unique markers of beta cell DNA. This discovery raises the hypothesis that use of these new markers would allow to establish effective detection of beta cell DNA in blood. The goal of this 1-year project is to test this hypothesis via optimization of the assay and assessment of plasma samples from patients.
Description of Project
A blood test that can monitor pancreatic beta cell death is a longstanding, unmet need that can revolutionize research and treatment in type 1 diabetes. Diagnostic medicine is currently being transformed by liquid biopsies, i.e. the analysis of cell-free DNA (cfDNA) fragments that are released from dying cells to blood. Sensitive methods for detecting the tissue origins of cfDNA, based on patterns of DNA methylation that characterize specific cell types, allow for early detection of cancer and other pathologies. These approaches have failed so far in the context of type 1 diabetes, mostly because of insufficient sensitivity for detection of cfDNA originating in beta cells, which is present in trace ammounts in the plasma of patients in early stages of the disease. Recent progress in cancer liquid biopsies revlealed that the key for success is the use of a large number of specific markers (hundreds or more) in parallel, thus maximizing the chances of identifying a signal from a rare contributing cell type. Unfortunately, so far only a few dozen specific markers have been identified for beta cell DNA, explaining failures. Using a comprehensive methylation atlas that we have recently developed (Loyfer Nature 2023), we now identified a novel, previously unrecognized landscape of the beta cell methylome, which provides thousands of specific beta cell markers. Theoretically, this exciting discovery opens the way for ultra-sensitive liquid biopsies that would be able to detect beta cell cfDNA during pre-clinical stages of type 1 diabetes as well as during disease progression and response to therapy, and in additional applications such as monitoring graft dynamics in islet transplantation and in stem cell-derived beta cell transplants. The goal of the propose research is to perform a 1-year examination of this exciting concept. We will optimize the computaional tools for identifying with confidence ultra-rare beta cell cfDNA fragments based on the novel methylation markers identified, and will test this new biomarker on a medium-size collection of plasma samples from healthy controls, islet transplant recipients, recent-onset type 1 diabetes patients and autoantibody positive individuals. If successful, this study will open the way for a breakthrough biomarker for beta cell dynamics, with important implications for the understanding the biology type 1 diabetes and for developing treatments.
Anticipated Outcome
The expected outcome of the project is an appreciation of the potential of ultra-sensitive epigentic liquid biopsies to serve as a blood test for the detection of beta cell death in type 1 diabetes. If successful, this will lead to a larger scale, multi-center study after which clinical translation for use, at least in drug development, will be straight forward.
Relevance to T1D
A blood test that can identify beta cell death is a long-standing unmet need that poses a barrier for progression of basic and translational research in type 1 diabetes, as well as for stratification of patients for receiving immunotherapies and for monitoring progression and response to therapy.