School of Clinical Medicine, Qingdao University, Qingdao, Shandong 266000, P.R. China.
Department of Gastroenterology, Qingdao Municipal Hospital, Shinan, Qingdao, Shandong 266071, P.R. China.
Mol Med Rep. 2022 Nov;26(5). doi: 10.3892/mmr.2022.12855. Epub 2022 Sep 16.
Single‑nucleus RNA sequencing (snRNA‑seq) is a method used to analyze gene expression in cells for which isolation is complex, such as those in hepatocellular carcinoma (HCC) tissues. It constitutes an alternative to single‑cell RNA sequencing (scRNA‑seq) by analyzing the nucleus rather than the whole cell; however, whether it can completely replace scRNA‑seq in HCC remains to be clarified. In the present study, scRNA‑seq was compared with snRNA‑seq in tumor tissue obtained from patients with HCC, using the 10X Genomics Chromium platform. Seurat was also used to process the data and compare the differences between the two sequencing methods in identifying different cell types. In the present study, the transcriptomes of 14,349 single nuclei and 9,504 single cells were obtained from the aforementioned HCC tissue. A total of 21 discrete cell clusters, including hepatocytes, endothelial cells, fibroblasts, B cells, T cells, natural killer cells and macrophages were identified. Notably, a high number of hepatocytes were detected using snRNA‑seq, while an increased number of immunocytes were identified in the tumor microenvironment using scRNA‑seq. Results of the present study provided a comprehensive image of human HCC at a single‑cell resolution. Moreover, results of the present study further demonstrated that snRNA‑seq may be adequate in replacing scRNA‑seq in certain cases, and snRNA‑seq performs at an improved level in hepatocyte sequencing. Combined use of the two sequencing methods may contribute to the study of intercellular interactions.
单细胞 RNA 测序 (snRNA-seq) 是一种用于分析分离复杂的细胞基因表达的方法，例如肝癌 (HCC) 组织中的细胞。它通过分析细胞核而不是整个细胞，构成了对单细胞 RNA 测序 (scRNA-seq) 的替代方法；然而，它是否可以完全替代 HCC 中的 scRNA-seq 仍需阐明。在本研究中，使用 10X Genomics Chromium 平台，在 HCC 患者的肿瘤组织中比较了 scRNA-seq 和 snRNA-seq。还使用了 Seurat 来处理数据，并比较了两种测序方法在识别不同细胞类型方面的差异。在本研究中，从上述 HCC 组织中获得了 14349 个单个核和 9504 个单个细胞的转录组。总共鉴定出 21 个离散的细胞簇，包括肝细胞、内皮细胞、成纤维细胞、B 细胞、T 细胞、自然杀伤细胞和巨噬细胞。值得注意的是，使用 snRNA-seq 检测到大量的肝细胞，而使用 scRNA-seq 在肿瘤微环境中鉴定到更多的免疫细胞。本研究的结果提供了人类 HCC 在单细胞分辨率下的全面图像。此外，本研究的结果进一步表明，在某些情况下，snRNA-seq 可能足以替代 scRNA-seq，并且 snRNA-seq 在肝细胞测序方面表现出更高的水平。两种测序方法的联合使用可能有助于研究细胞间相互作用。
