Investigating treatment response and resistance in non-small cell lung cancer patients through epigenetic profiling of plasma nucleosomes

The detection of circulating tumor DNA (ctDNA) through the identification of somatic mutations has shown promising results for monitoring treatment response in cancer patients. However, mutation-based approaches are limited by factors such as clonal hematopoiesis, low sensitivity, and the inability to detect epigenetic tumor signals. Complementary approaches based on epigenetic profiling of cell-free DNA (cfDNA) in liquid biopsies have been developed to infer the gene expression profile in the cells of cfDNA origin. We investigated the application of cell-free chromatin immunoprecipitation (cfChIP) targeting H3K4me3 and H3K36me3 histone modifications of circulating nucleosomes in non-small cell lung cancer (NSCLC) patients treated with immunotherapy or targeted therapies. ctDNA dynamics were quantified using targeted sequencing of cfDNA to identify molecular responders to treatment based on ctDNA clearance. We performed cfChIP on healthy individuals and cancer patients followed by ddPCR or whole-genome sequencing at baseline, a few weeks after treatment initiation and at progression. High FGD2 expression and low CDH3 expression at baseline were associated with a durable response to immunotherapy. Genes, in which the cfChIP enrichment correlated with ctDNA burden included genes, such as PLCE1 and VASH2 , involved in developmental processes. Longitudinal monitoring of MET gene activity with H3K36me3 cfChIP ddPCR distinguished patients with crizotinib response from non-responders. cfChIP at progression indicated novel resistance mechanisms to targeted therapy through upregulation of genes such as FOXG1 and MT3 , involved in neural development. In conclusion, cfChIP-seq of cfDNA present in cancer patients' plasma has potential to provide valuable information on tumor specific transcriptional dynamics during treatment in NSCLC. Harnessing this information could enable earlier detection of resistance and guide treatment switching.