Two Transcriptomic Analyses Converge on a Five-Gene Core for Colorectal Cancer Discrimination: External Validation in Independent Tissue Cohorts

Abstract

Background/Objectives: Colorectal cancer (CRC) is a leading cause of neoplasia-related morbidity and mortality worldwide and the first cause of cancer death in Mexico, where early detection remains a challenge, and reliable molecular biomarkers could support earlier diagnosis. Transcriptomic signatures for CRC have been published, but different studies arrive at gene lists that barely overlap, and since each study differs in both cohort and analysis, the source of that disagreement cannot be identified. This study aimed to identify a gene set for CRC discrimination whose selection depends neither on how the batch effect is handled nor on the criterion by which candidates are chosen and to validate that set in repositories that took no part in its selection. Methods: The signature was identified in 104 public RNA-seq samples (79 tumor, 25 reference) obtained from six BioProjects of the NCBI Sequence Read Archive and analyzed twice. A functionally anchored route took one representative gene per enriched biological program, ranked by π-value, from a differential expression model including BioProject as a covariate; a regularization route selected genes by their stability under Elastic Net in nested cross-validation over a ComBat-Seq-adjusted matrix. The genes reached by both routes were corroborated in TCGA-COAD, TCGA-READ, and GTEx colon processed by recount3 (n = 1542), with every parameter held fixed, and in the GEO microarray series GSE37364 (the 65 carcinoma and normal-mucosa samples of a 94-sample series), where only the coefficient vector was transferred because the platform differs; they were further examined descriptively in a second adenoma series (GSE89076), published stool RNA-seq, and plasma cell-free RNA. Results: The two routes yielded a seven-gene and a five-gene signature sharing a single gene, RPGRIP1L. Five genes met both criteria: TRIP13, CEMIP, PUS7, RPGRIP1L, and SLC22A3. With every parameter held fixed, the five-gene core reached an AUC of 0.9993 in TCGA/GTEx (sensitivity 0.966, specificity 0.998); with its coefficients transferred and the intercept recalibrated, it reached 0.9737 in GSE37364 (sensitivity 0.926, specificity 0.974). All five were elevated in adenoma relative to normal mucosa in GSE37364, and three of the five reached significance in GSE89076, where only five adenomas were available; all five were overexpressed in published stool RNA-seq of CRC patients. Conclusions: A five-gene core, TRIP13, CEMIP, PUS7, RPGRIP1L, and SLC22A3, discriminates colorectal tumor tissue from non-tumor in repositories external to its selection, with elevation already present in premalignant adenoma. Having been reached by two routes that share neither criterion nor starting point, these five genes are candidates for experimental validation and for evaluation in material accessible without biopsy.