Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival

Abstract

Background Hepatocellular carcinoma (HCC) is a common primary liver cancer with poor overall survival. We hypothesized that there are HCC-associated cell-types that impact patient survival. Methods We combined liver single nucleus (snRNA-seq), single cell (scRNA-seq), and bulk RNA-sequencing (RNA-seq) data to search for cell-type differences in HCC. To first identify cell-types in HCC, adjacent non-tumor tissue, and normal liver, we integrated single-cell level data from a healthy liver cohort (n = 9 non-HCC samples) collected in the Strasbourg University Hospital; an HCC cohort (n = 1 non-HCC, n = 14 HCC-tumor, and n = 14 adjacent non-tumor samples) collected in the Singapore General Hospital and National University; and another HCC cohort (n = 3 HCC-tumor and n = 3 adjacent non-tumor samples) collected in the Dumont-UCLA Liver Cancer Center. We then leveraged these single cell level data to decompose the cell-types in liver bulk RNA-seq data from HCC patients’ tumor (n = 361) and adjacent non-tumor tissue (n = 49) from the Cancer Genome Atlas (TCGA) multi-center cohort. For replication, we decomposed 221 HCC and 209 adjacent non-tumor liver microarray samples from the Liver Cancer Institute (LCI) cohort collected by the Liver Cancer Institute and Zhongshan Hospital of Fudan University. Results We discovered a tumor-associated proliferative cell-type, Prol (80.4% tumor cells), enriched for cell cycle and mitosis genes. In the liver bulk tissue from the TCGA cohort, the proportion of the Prol cell-type is significantly increased in HCC and associates with a worse overall survival. Independently from our decomposition analysis, we reciprocally show that Prol nuclei/cells significantly over-express both tumor-elevated and survival-decreasing genes obtained from the bulk tissue. Our replication analysis in the LCI cohort confirmed that an increased estimated proportion of the Prol cell-type in HCC is a significant marker for a shorter overall survival. Finally, we show that somatic mutations in the tumor suppressor genes TP53 and RB1 are linked to an increase of the Prol cell-type in HCC. Conclusions By integrating liver single cell, single nucleus, and bulk expression data from multiple cohorts we identified a proliferating cell-type (Prol) enriched in HCC tumors, associated with a decreased overall survival, and linked to TP53 and RB1 somatic mutations.

A CD8+ T cell‐related genes prognostic model for hepatocellular carcinoma patients

“…Several previous analyses have also indicated that some tumour prognostic models may predict HCC patient survival. However, the identification of tumour subtype needs whole‐transcriptome sequencing data, which may be challenging in real‐world practice 30,31 . We established a new CD8T‐RGPI from CD8 + T cell infiltration‐associated genes by calculating the risk score, which had same prediction abilities for prognostic outcomes of HCC patients compared with other prognostic models 32,33 .…”

“…However, the identification of tumour subtype needs whole-transcriptome sequencing data, which may be challenging in real-world practice. 30,31 We established a new CD8T-RGPI from CD8 + T cell infiltration-associated genes by calculating the risk score, which had same prediction abilities for prognostic outcomes of HCC patients compared with other prognostic models. 32,33 Based on the characteristics of HCC patients, CD8T-RGPI exhibited a differential expression pattern.…”

Hepatocellular carcinoma after treatment of hepatitis C with direct-acting antivirals: a critical re-appraisal

“…The single-cell analysis demonstrated that an upregulation of the inhibitor of apoptosis MLX interacting protein-like (MLXIPL) was related to poor survival in HCC [148] . HCC survival was also deceased in association with a proliferating cell type identified in HCC tumors [149] .…”

Metabolic crosstalk between skeletal muscle and liver through IRF4-FSTL1 in NASH

“…According to sc-RNAseq from human and mouse liver, these 12 receptors expressed different patterns in different cell types (Extended Data Fig. 5a-d) 35,36,37,38 . We then measured expression of these receptors in our models.…”