To what extent stromal cells in the tumor microenvironment (TME) are transformed by colorectal cancer (CRC) cells is unexplored. To dissect alterations in these non-malignant cells, we performed single-cell multiomics sequencing of 21 patients with microsatellite-stable CRCs and 6 cancer-free, elderly individuals. Surprisingly, somatic copy number alterations (SCNAs) are prevalent in immune cells, fibroblasts, and endothelial cells in both the TME and the normal tissues of each individual. Moreover, the proportions of fibroblasts with SCNAs in tumors (11.1%–47.7%) are much higher than those in adjacent normal tissues (1.1%–10.6%), with gain of chromosome 7 strongly enriched in the TME, clearly indicating clonal expansion. Furthermore, five genes (BGN, RCN3, TAGLN, MYL9, and TPM2) are identified as fibroblast-specific biomarkers of poorer prognosis of CRC. Our study provides evidence and functional relevance of pervasive genomic alterations in the stromal cells of TME in CRC.

尚未探索肿瘤微环境（TME）中的基质细胞被结直肠癌（CRC）转化到何种程度。为了剖析这些非恶性细胞的变化，我们对21例微卫星稳定CRC和6名无癌老年患者进行了单细胞多组学测序。令人惊讶的是，体细胞拷贝数改变（SCNA）在TME和每个个体的正常组织中的免疫细胞，成纤维细胞和内皮细胞中普遍存在。此外，肿瘤中SCNA的成纤维细胞比例（11.1％至47.7％）远高于邻近正常组织中的比例（1.1％至10.6％），其中第7号染色体的增益在TME中高度富集，清楚地表明了克隆扩增。此外，还有五个基因（BGN，RCN3，TAGLN，MYL9和TPM2）被鉴定为CRC预后较差的成纤维细胞特异性生物标志物。我们的研究提供了CRC中TME基质细胞中普遍的基因组改变的证据和功能相关性。