单细胞RNA测序(scRNA-seq),研究肿瘤微环境(TME)的强大工具,不保存/提供关于组织形态和细胞相互作用的空间信息。要了解TME中邻近的不同蜂窝组件之间的串扰,我们进行了scRNA-seq和空间转录组(ST)分析,分析了来自3个结直肠癌(CRC)肿瘤-正常血液对的41,700个细胞.独立的scRNA-seq分析揭示了八个主要的细胞群体,包括B细胞,T细胞,单核细胞,NK细胞,上皮细胞,成纤维细胞,肥大细胞,内皮细胞。从上皮细胞中鉴定出恶性细胞后,我们观察到7种反映肿瘤异质性状态的恶性细胞亚型,包括肿瘤_CAV1,肿瘤_ATF3_JUN|FOS,肿瘤_ZEB2,肿瘤_VIM,肿瘤_WSB1,肿瘤_LXN,和肿瘤_PGM1。通过将scRNA-seq获得的细胞注释转移到ST点,我们注释了CRC患者冷冻切片中的四个区域,包括肿瘤,基质,免疫浸润,和结肠上皮区域。此外,我们观察到间质和肿瘤区域之间的强烈细胞间相互作用,这些区域在冷冻切片中非常近。特别是,推断一对配体和受体(C5AR1和RPS19)在基质和肿瘤区域的串扰中起关键作用。对于肿瘤区域,确定了TMSB4X高表达的典型特征,这可能是CRC的潜在标志物。发现基质区以VIM高表达为特征,这表明它在TME中培育了一个基质生态位。总的来说,我们研究中的单细胞和空间分析揭示了CRCTME中的肿瘤异质性和分子相互作用,这提供了对CRC进展的潜在机制的见解,并可能有助于开发靶向非肿瘤成分的抗癌疗法,例如CRC中的细胞外基质(ECM)。我们鉴定的典型基因可能有助于CRC的新分子亚型。
Single cell RNA sequencing (scRNA-seq), a powerful tool for studying the tumor microenvironment (TME), does not preserve/provide spatial information on tissue morphology and cellular interactions. To understand the crosstalk between diverse cellular components in proximity in the TME, we performed scRNA-seq coupled with spatial transcriptomic (ST) assay to profile 41,700 cells from three colorectal cancer (CRC) tumor-normal-blood pairs. Standalone scRNA-seq analyses revealed eight major cell populations, including B cells, T cells, Monocytes, NK cells, Epithelial cells, Fibroblasts, Mast cells, Endothelial cells. After the identification of malignant cells from epithelial cells, we observed seven subtypes of malignant cells that reflect heterogeneous status in tumor, including tumor_CAV1, tumor_ATF3_JUN | FOS, tumor_ZEB2, tumor_VIM, tumor_WSB1, tumor_LXN, and tumor_PGM1. By transferring the cellular annotations obtained by scRNA-seq to ST spots, we annotated four regions in a cryosection from CRC patients, including tumor, stroma, immune infiltration, and colon epithelium regions. Furthermore, we observed intensive intercellular interactions between stroma and tumor regions which were extremely proximal in the cryosection. In particular, one pair of ligands and receptors (C5AR1 and RPS19) was inferred to play key roles in the crosstalk of stroma and tumor regions. For the tumor region, a typical feature of TMSB4X-high expression was identified, which could be a potential marker of CRC. The stroma region was found to be characterized by VIM-high expression, suggesting it fostered a stromal niche in the TME. Collectively, single cell and spatial analysis in our study reveal the tumor heterogeneity and molecular interactions in CRC TME, which provides insights into the mechanisms underlying CRC progression and may contribute to the development of anticancer therapies targeting on non-tumor components, such as the extracellular matrix (ECM) in CRC. The typical genes we identified may facilitate to new molecular subtypes of CRC.