Insights into early-onset colorectal cancer from a single-nucleus RNA-seq atlas of colorectal cancer across the age continuum

The incidence of early-onset colorectal cancer (EO-CRC; diagnosed before age 50 years) is increasing worldwide. Although current data indicate that EO-CRC may be biologically distinct from average-onset CRC (AO-CRC; diagnosed at age ≥50 years), molecular differences remain poorly defined. To address this knowledge gap, we generated a single-nucleus RNA sequencing (snRNA-seq) atlas from 189 primary CRC tumors (54 EO-CRC, 135 AO-CRC) spanning eight decades of life, with at least 20 tumors in most age decades. Our analyses stratified tumors by microsatellite status and accounted for tumor sidedness, stage, patient sex and neoadjuvant treatment history, modeling age continuously or categorically (EO-CRC versus AO-CRC). Among microsatellite-stable (MSS) tumors, those from younger patients were characterized by increased stromal and decreased epithelial proportions, which we confirmed using multispectral immunofluorescence and machine learning in an external cohort of 712 MSS CRC tumors (18 EO-CRC, 694 AO-CRC). Tumor epithelial cells from young patients exhibited increased expression of long noncoding RNAs and FN1, with a trend toward increased heterogeneity in copy number alterations. MSS left-sided EO-CRC tumors had more cell–cell interactions, with epithelial-to-mesenchymal transition-related signaling pathways (FN1/GDF/ACTIVIN) showing increased, cell type-specific interactions. Our large high-resolution snRNA-seq atlas uncovers age-associated features of CRC and provides a resource for the community to understand EO-CRC biology. A high-resolution snRNA-seq atlas of 189 colorectal tumors from patients aged 20–90+ years uncovers age-associated features of colorectal cancer.