A Robust Cell-Free RNA Approach for the Early Detection of Colorectal Cancer
Monteagudo-Mesas, P.; Sanchez, L.; Asole, G.; Neto, B.; Tuni-Dominguez, C.; Gonzalez, L.; Rusu, E. C.; Cabus, L.; Panadero-Fajardo, S.; Catalina, P.; Garcia, S.; Simon-Extremera, P.; Padilla Garcia, L.; Lagarde, J.; Sanders, P.; Weber, M.
Show abstract
Colorectal cancer (CRC) screening remains limited by patient adherence and sub-optimal sensitivity for early-stage disease. While liquid biopsy has revolutionized cancer diagnostics, cfDNA-based methods often struggle with early-stage detection due to low analyte levels. Here, we present a robust cell-free RNA (cfRNA) platform for the early detection of CRC. Using a retrospective cohort of 255 healthy controls and 250 CRC patients, we implemented an optimized workflow featuring a RUVg-based normalization strategy to remove platelet-driven transcriptomic noise. We identified differentially expressed genes enriched in key CRC-associated biological pathways, including inflammation, EMT, and metabolic dysregulation. An XGBoost classifier trained on these features achieved a mean AUC of 0.92 in cross-validation and 0.89 in a validation cohort, demonstrating 67% sensitivity at 90% specificity. Notably, our platform showed particular efficacy in identifying early stage cancer (stage I and II), achieving 73.7% sensitivity at 90% specificity. These findings suggest that cfRNA profiling offers a powerful, non-invasive orthogonal approach to CRC screening, capable of overcoming the sensitivity limitations of DNA-based assays in early-stage disease.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients' plasma 94%
- Genome profiles of lymphovascular breast cancer cells reveal multiple clonally differentiated outcomes with multi-regional LCM and G&T-seq 94%
- Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19 93%
Similar papers in this journal
- Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells 95%
- Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data. 94%
- Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology 93%
Similar papers in this journal
Similar papers in this journal
- Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples 94%
- Cross-dataset pan-cancer detection: Correlating cell-free DNA fragment coverage with open chromatin sites across cell types 94%
- Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer 94%
Similar papers in this journal
- Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector 93%
- Joint processing of long- and short-read sequencing data with deep learning improves variant calling. 93%
- UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.