Projects
Tianqi (Kiki) Chen
Epigenetic modifications like cfDNA fragmentation and methylation are promising cancer biomarkers. DNA methylation refers to a chemical modification of a specific carbon with an added methyl group in the cytosine as 5-methylcytosine (5mC). The sequences that are most affected by methylation occur in the CpG rich region, leading to the silencing of tumor suppressor genes. 5-hydroxymethylcytosine (5hmC), an oxidization product of 5mC, acts an intermediate of DNA demethylation and gene activation. 5hmC is a stable epigenetic marker with reduced level in many cancers. 5mC and 5hmC patterns are specific to tissue and cancer types. 
We leveraged a nanopore-based single-molecule sequencing method analyze the fragmentation, 5mC methylation and 5hmC hydroxymethylation profiles in CSF derived-cfDNA from non-small cell lung cancer (NSCLC) patients with brain metastasis (BM). Our cohort consists of eleven patients with non-small cell lung cancer leptomeningeal metastasis (sample N = 15) and eleven non-cancer controls (N = 11). We observed three nucleosome peaks at 167 bp, 330 bp, and 500 bp in the cfDNA fragment size distribution. We obtained 5mC and 5hmC signals simultaneously from each sample. Distinct fragmentation, methylation, and hydroxymethylation patterns were found in cancer patients. We believe that integrating cfDNA methylation and fragmentation will provide important details about NSCLC-BM and may lead to new biomarkers.