Periodic Reporting for period 2 - cfChIP (Plasma epigenomics: A new liquid biopsy paradigm)
Reporting period: 2023-02-01 to 2024-07-31
A key challenge in medical practice and research is identifying and interpreting events within the patient’s body during disease onset and recovery. Often this requires detailed molecular mapping of the cells in the disease site (organ or tumor) requiring invasive biopsy, a non-trivial, potentially risky, procedure. The goal of my lab is to develop tools for observing cellular processes in the body from samples of blood and other body fluids, which would overcome this major hurdle in medical research and practice.
Medicine has a long and rich history of biomarker development — molecules in the blood that report on processes in the body, e.g. ALT and AST (markers of liver damage), Troponin (marker of myocardial damage), and CRP (marker of inflammation). While crucial for modern medicine, such biomarkers provide indirect indications about underlying processes at best. The advent of genomic sequencing enabled the use of nucleic acids (DNA and RNA) as biomarkers. These can be read by generic procedures, with sensitive detection rates, and provide rich information about molecular states of cells. In the last decade liquid biopsy – specifically, the interrogation of circulating cell-free DNA fragments that are released into the bloodstream from dying cells – has become standard practice in prenatal testing and monitoring organ rejections and cancer recurrence.
My lab developed a revolutionary technology for capturing circulating cell-free DNA fragments together with their original protein packaging. These proteins, called histones, are marked in a stable way that records the identity and the state of the cells they originated from. These epigenetic chromatin modifications have been extensively studied in the last two decades and are directly connected to the regulation of gene activity within cells. In a highly cited paper in Nature Biotechnology we showed that this assay provides exquisitely detailed information about gene activity in dying cells in the body.
In this project we aim is to advance our understanding of this technology to make it a useful tool for non-invasive observations about human physiology in health and disease. This involves extending the method to multiple types of epigenetic information, improving its technical performance (robustness, sensitivity, and specificity) and defining the baseline of healthy population. Most importantly, however, is understanding how does do processes in the disease site manifest in the profiles we observe, and using this understanding to decipher assay results.
Achieving these goals will be great progress of progressing from a technical innovation to a tool that can be useful in medical practice and biomedical research. Such a tool can offer a promising avenue for observing and quantifying internal processes that were traditionally accessible only through invasive procedures and enable longitudinal observation of patients before, during, and after treatment.
Medicine has a long and rich history of biomarker development — molecules in the blood that report on processes in the body, e.g. ALT and AST (markers of liver damage), Troponin (marker of myocardial damage), and CRP (marker of inflammation). While crucial for modern medicine, such biomarkers provide indirect indications about underlying processes at best. The advent of genomic sequencing enabled the use of nucleic acids (DNA and RNA) as biomarkers. These can be read by generic procedures, with sensitive detection rates, and provide rich information about molecular states of cells. In the last decade liquid biopsy – specifically, the interrogation of circulating cell-free DNA fragments that are released into the bloodstream from dying cells – has become standard practice in prenatal testing and monitoring organ rejections and cancer recurrence.
My lab developed a revolutionary technology for capturing circulating cell-free DNA fragments together with their original protein packaging. These proteins, called histones, are marked in a stable way that records the identity and the state of the cells they originated from. These epigenetic chromatin modifications have been extensively studied in the last two decades and are directly connected to the regulation of gene activity within cells. In a highly cited paper in Nature Biotechnology we showed that this assay provides exquisitely detailed information about gene activity in dying cells in the body.
In this project we aim is to advance our understanding of this technology to make it a useful tool for non-invasive observations about human physiology in health and disease. This involves extending the method to multiple types of epigenetic information, improving its technical performance (robustness, sensitivity, and specificity) and defining the baseline of healthy population. Most importantly, however, is understanding how does do processes in the disease site manifest in the profiles we observe, and using this understanding to decipher assay results.
Achieving these goals will be great progress of progressing from a technical innovation to a tool that can be useful in medical practice and biomedical research. Such a tool can offer a promising avenue for observing and quantifying internal processes that were traditionally accessible only through invasive procedures and enable longitudinal observation of patients before, during, and after treatment.
The main activities since the beginning of the projects:
* Improving the assay, setting up experimental and IT infrastructure, and building the capacity to handle large number of samples in a consistent, reproducible manner.
* Detailed study of our method on hundreds of samples from Small-cell lung cancer patients. Importantly, many of these were matched with tissue biopsy and thus allowed us to prove the direct correspondence between molecular events in the tumor and observations we make from plasma samples. We show that the assay can non-invasively distinguish subtypes of the disease that previously required tissue biopsy followed by non-trivial assays.
* Study of auto-immune liver disease. Unlike most existing liquid biopsy approaches, ours is not limited to cancer. We applied our method to study liver diseases with the aim of providing information that usually would require liver tissue biopsy. Studying a cohort of matched blood samples and tissue biopsies we showed direct relationship between events in the liver and observations in our assay. In particular, we show we can distinguish auto-immune liver diseases from other sources of disease. Today, these diseases are diagnosed after a tissue biopsy and positive response to immune-suppressive treatment. Definite diagnosis before treatment could save unnecessary treatment, side-effects, and delays for patients suffering from similar diseases from other sources.
* Improving the assay, setting up experimental and IT infrastructure, and building the capacity to handle large number of samples in a consistent, reproducible manner.
* Detailed study of our method on hundreds of samples from Small-cell lung cancer patients. Importantly, many of these were matched with tissue biopsy and thus allowed us to prove the direct correspondence between molecular events in the tumor and observations we make from plasma samples. We show that the assay can non-invasively distinguish subtypes of the disease that previously required tissue biopsy followed by non-trivial assays.
* Study of auto-immune liver disease. Unlike most existing liquid biopsy approaches, ours is not limited to cancer. We applied our method to study liver diseases with the aim of providing information that usually would require liver tissue biopsy. Studying a cohort of matched blood samples and tissue biopsies we showed direct relationship between events in the liver and observations in our assay. In particular, we show we can distinguish auto-immune liver diseases from other sources of disease. Today, these diseases are diagnosed after a tissue biopsy and positive response to immune-suppressive treatment. Definite diagnosis before treatment could save unnecessary treatment, side-effects, and delays for patients suffering from similar diseases from other sources.
We plan to continue our studies to understand the abilities and the limitations of the assay, and where it can be of use in research and medicine. Our results change the landscape of liquid biopsies and enable a new generation of tools for non-invasive diagnosis, monitoring, and study of humans in health and disease.