scRNA-seq analysis of hepatocellular carcinoma with microvascular invasion.

Published: 13 August 2023| Version 1 | DOI: 10.17632/j877fyr2pp.1


Microvascular invasion (MVI) is a significant pathological feature of hepatocellular carcinoma (HCC) associated with poor outcomes, early recurrence and intrahepatic metastasis in post-surgical resection and transplant patients. However, the intricate tumor microenvironment (TME) and transcriptional programs underlying MVI in HCC remain poorly understood. We conducted single-cell RNA sequencing of 46,789 individual cells from 10 samples of MVI+ (MVI present) and MVI- (MVI absent) HCC patients. By examining the cellular and molecular features associated with MVI, we conducted comprehensive analyses and validated key findings.


Steps to reproduce

Single-cell suspensions (2×105 cells/ml) with PBS (HyClone) were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads, which captured the mRNA, were subsequently collected from the microwell chip. The captured mRNA was subjected to reverse transcription to obtain cDNA, followed by PCR amplification. The amplified cDNA was then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (22). The individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired-end reads.


First Affiliated Hospital of Harbin Medical University, Wenzhou Medical University Eye Hospital


Single-Cell RNA Sequencing