Abstract 2757: Hypermethylation of FAT4 linked to tumor progression in colorectal adenocarcinoma

Abstract Introduction: The gene FAT4 encodes a cell adhesion molecule of the protocadherin family. FAT4 can be linked to cancer progression at multiple levels, including metastasis, autophagy, epithelial-to-mesenchymal-transition, and as a tumor suppressor. Aberrant methylation, a common hallmark of colorectal adenocarcinoma, disrupts normal gene regulation. Purpose: We explored the methylation changes of FAT4 during colorectal cancer progression, using a large patient cohort with methylation microarray data. Methods: Raw data files of a collection of 2,356 colorectal tumor, adenoma, and normal samples from two microarray platforms (Illumina HM450K and EPIC) were processed in R using the minfi and the watermelon libraries. Based on a matrix of β-values, methylated regions and CpG loci were identified using Kruskal-Wallis-test complemented with ROC analysis. For data visualization we employed www.epigenplot.com, a web platform established based on our database. False discovery rate was set at 10%. Results: Based on UCSC RefGene data, 18 of the HM450K and 27 of the EPIC array probes were assigned to the FAT4 gene. All the probes hypermethylated in adenocarcinoma tissues compared to normal ones belonged to the CpG island chr4:126235895-126238930 of the proximal promoter region. When comparing to normal tissues, the TSS200 region had the most prominent hypermethylation (HM450K Δβ =0.28, AUC 0.9; EPIC Δβ = 0.22, AUC 0.85, p <0.0001), while the probes of the open sea CpGs in the protein coding region have shown a slight hypomethylation (HM450K Δβ = 0.1; EPIC Δβ = 0.14, p <0.0001). These changes were also present in adenoma tissues compared to normal ones. Based on KEGG classification, three other genes associated to the mTOR signaling pathway were similarly hypermethylated in the TSS200 region (Δβ >= 0.2), including WNT2, FZD10, and WNT7A. Conclusions: FAT4, a tumor suppressor gene with previously reported downregulation in CRC, shows significant hypermethylation in colon cancer, including the precursor lesions. Our results suggest that detection of these methylation changes in the promoter region of FAT4 might be utilized as a prognostic biomarker and in the early detection of CRC. Citation Format: Dalma Muller, Balazs Gyorffy. Hypermethylation of FAT4 linked to tumor progression in colorectal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2757.