Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
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DOI：
10.1038/ng.3818
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发表时间：
2017-05-01
期刊：
影响因子：
30.8
通讯作者：
Prabhakar, Shyam
中科院分区：
文献类型：
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作者：
Li, Huipeng;Courtois, Elise T.;Prabhakar, Shyam
肿瘤内异质性是癌症治疗的主要障碍，也是大体积肿瘤分析中的一个重要混杂因素。我们使用 11 个原发性结直肠肿瘤和匹配的正常粘膜的单细胞 RNA-seq 对结直肠肿瘤及其微环境中的转录异质性进行了公正的分析。为了对单细胞转录组进行稳健聚类，我们开发了参考成分分析 (RCA)，这是一种可大幅提高聚类准确性的算法。使用 RCA，我们鉴定了两种不同的癌症相关成纤维细胞 (CAF) 亚型。此外，发现上皮间质转化 (EMT) 相关基因仅在肿瘤样本的 CAF 亚群中上调。值得注意的是，之前根据大量转录组学分配给单一亚型的结直肠肿瘤可以通过使用单细胞特征分为具有不同生存概率的亚组，从而强调了我们方法的预后价值。总体而言，我们的结果表明，肿瘤和匹配的正常样本的无偏单细胞 RNA-seq 分析为表征肿瘤内的异常细胞状态提供了独特的机会。
Intratumoral heterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs). Additionally, epithelial-mesenchymal transition (EMT)-related genes were found to be upregulated only in the CAF subpopulation of tumor samples. Notably, colorectal tumors previously assigned to a single subtype on the basis of bulk transcriptomics could be divided into subgroups with divergent survival probability by using single-cell signatures, thus underscoring the prognostic value of our approach. Overall, our results demonstrate that unbiased single-cell RNA-seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor.