Prevalence of autoimmune disease and associated 5-hydroxymethylcytosine cell-free DNA patterns in appendiceal neoplasms

Autoimmune diseases (AID) are associated with increased risk of developing gastrointestinal cancers, but their relationship with appendiceal neoplasms (AENs) remains unexplored. We performed a multi-institutional retrospective review of 179 AEN patients, identifying 44 (24.6%) with a history of AID, most commonly suspected Hashimoto’s thyroiditis (14.0%). 5-hydroxymethylcytosine (5hmC), an epigenetic marker involved in gene regulation and immune function, offers a promising tool for studying tumor biology. Plasma samples from 68 patients were analyzed using Nano-hmC-Seal (5hmC-Seal) technology to generate genome-wide 5hmC profiles from cfDNA. 5hmC profiling identified 58 candidate differentially hydroxymethylated regions (DhMRs) and 80 candidate differentially hydroxymethylated genes (DhMGs) between AID and non-AID patients based on nominal p-value and effect-size thresholds. These included. several oncogenes, proto-oncogenes, and tumor suppressor genes such as MNT, FYN, ERG, and KAT6B. Functional pathway analysis involving differentially hydroxymethylated regions or genes revealed significant hydroxymethylation of immune-related and oncogenic pathways in patients with autoimmune disease, including intestinal immune network for IgA production, along with the IgE high-affinity receptor, FcεRI, and MAPK and ErbB signaling pathways. These findings suggest that autoimmune conditions might contribute to a distinct epigenetic landscape in appendiceal cancers, supporting further investigation into immune-mediated mechanisms of tumorigenesis.