Abstract 7067: Integrating blood-based biomarkers and RNA-Seq Data for enhanced colorectal cancer screening
Authors: Elba V. Caraballo-Rivera, Hilmaris Centeno-Girona, Camille Zenón-Meléndez, Sheila López -Acevedo, Brenda Torres-Velásquez, Josue Pérez-Santiago, Madeline M. Martir-Ocasio, Maria González-Pons, Marcia R. Cruz-Correa
Journal: Cancer Research (2025)

Abstract Colorectal cancer (CRC) is the second cause of cancer-related deaths in the United States and the first leading cause for Puerto Rican Hispanics (PRH). Despite its preventability through screening, compliance still needs to improve due to the invasiveness of current tools. There is a growing demand for validated molecular biomarker panels for minimally invasive blood-based CRC screening. This study evaluated the diagnostic accuracy of four promising blood-based biomarkers and incorporated RNA-seq data from an independent cohort to provide biological insights into biomarker performance. A retrospective case-control study was conducted in plasma samples from 124 CRC cases and 124 age- and sex-matched controls recruited through the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR). Biomarkers tested included methylated DNA encoding the Septin-9 gene (mSEPT9) using Epi proColon® 2.0 CE, insulin-like growth factor binding protein 2 (IGFBP2), dickkopf-3 (DKK3), and pyruvate kinase M2 (PKM2) by ELISA. Diagnostic accuracy was measured using the receiver operating characteristic (ROC) area under the curve (AUC) and sensitivity and specificity. For the RNA-seq (Illumina) assay, a case-case study was performed on 15 tumor and 15 adjacent mucosa samples from 7 early and 8 advanced-stage CRC cases. Differentially expressed genes (DEGs) with an adjusted p-value &amp;lt; 0.05 were identified between tumor and adjacent mucosa across stages. Pathway enrichment was performed using Gene Set Enrichment Analysis (GSEA) and KEGG databases. Biomarkers and gene expression patterns were cross-validated to identify shared pathways. Diagnostic accuracy for individual biomarkers mSEPT9, IGFBP2, DKK3, and PKM2 was 62.9%, 69.7%, 61.6%, and 50.8%, respectively. Combined biomarkers AUC was of 74.4%, outperforming all individual markers except IGFBP2 in advanced-stage CRC. RNA-seq identified 481 DEGs unique to early-stage and 849 to advanced-stage CRC. Genes DKK3 and PKM2, were differentially expressed in both stages. Additionally, DKK1 and DKK2, were uniquely upregulated in early-stage tumors. Dysregulation of Wnt signaling, PI3K-Akt signaling, and cytokine-cytokine receptor interaction pathways were observed across stages. Our results show that integrating plasma biomarker analysis with RNA-seq data enables the identification of critical shared pathways, supporting the utility of a multi-omics approach for CRC screening. Plasma biomarkers demonstrated promising diagnostic accuracy, with IGFBP2 as the most accurate individual marker across CRC stages. The differential expression of DKK1 and DKK2 in early-stage tumors highlights their potential as early CRC biomarkers, warranting validation in plasma samples. These findings support the development of minimally invasive blood-based screening tools for CRC, offering a promising strategy for early detection and improved patient outcomes for PRH. Citation Format: Elba V. Caraballo-Rivera, Hilmaris Centeno-Girona, Camille Zenón-Meléndez, Sheila López -Acevedo, Brenda Torres-Velásquez, Josue Pérez-Santiago, Madeline M. Martir-Ocasio, Maria González-Pons, Marcia R. Cruz-Correa. Integrating blood-based biomarkers and RNA-Seq Data for enhanced colorectal cancer screening [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 7067.