Cell Free Chromatin in Ovarian Cancer

Cell-free DNA (cfDNA) are DNA fragments in human plasma which originate from dying cells.
These fragments are mostly in the form of chromatin (a complex made of DNA and histone
proteins) and maintain several of their histone modifications. The histone modification is
indicative of the fragment’s transcriptional status in the cell of origin and the DNA sequence
indicates which genomic region it came from. Our lab has developed a Chromatin
Immunoprecipitation technology (cfChIP-seq) to capture and sequence cfDNA fragments who
originate from active promoters in the cell of origin. Analysis of the resulting map of active
promoters allows us to learn about the general health of an individual as well as the state and
development of various diseases.
Here, we apply cfChIP-seq in a cohort of Ovarian Cancer patients before and during the first line
neoadjuvant treatment. As of today, we have approximately 120 plasma samples from 51
patients taken before treatment started, at four different time points throughout treatment, during
and after surgery.
Interim results show that the cfDNA profile of these patients differs from healthy plasma
samples and varies throughout treatment. In addition, we were able to identify a group of genes
unique to Ovarian Cancer patients which we refer to as a signature of Ovarian Cancer. We
show the changes in the signature throughout the patient’s treatment potentially implying the
success or failure of the treatment. This technology can allow medical temas to monitor and
predict a patient’s response to treatment.