Cell‐free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients

Cell‐free DNA (cfDNA) in blood plasma can be bound to nucleosomes that contain post‐translational modifications representing the epigenetic profile of the cell of origin. This includes histone H3 lysine 36 trimethylation (H3K36me3), a marker of active transcription. We hypothesised that cell‐free chromatin immunoprecipitation (cfChIP) of H3K36me3‐modified nucleosomes present in blood plasma can delineate tumour gene expression levels. H3K36me3 cfChIP followed by targeted NGS (cfChIP‐seq) was performed on blood plasma samples from non‐small‐cell lung cancer (NSCLC) patients (NSCLC, n = 8), small‐cell lung cancer (SCLC) patients (SCLC, n = 4) and healthy controls (n = 4). H3K36me3 cfChIP‐seq demonstrated increased enrichment of mutated alleles compared with normal alleles in plasma from patients with known somatic cancer mutations. Additionally, genes identified to be differentially expressed in SCLC and NSCLC tumours had concordant H3K36me3 cfChIP enrichment profiles in NSCLC (sensitivity = 0.80) and SCLC blood plasma (sensitivity = 0.86). Findings here expand the utility of cfDNA in liquid biopsies to characterise treatment resistance, cancer subtyping and disease progression. Blood plasma contains H3K36me3‐modified nucleosomes representing active genes in the cell of origin. Our findings show that cell‐free chromatin immunoprecipitation (cfChIP) of H3K36me3‐nucleosomes in plasma from lung cancer patients can reveal tumour gene expression. cfChIP followed by next‐generation sequencing identifies genes that are differentially expressed in the tumour of non‐small‐cell and small‐cell lung cancer patients. Created with BioRender.com.