# Single-cell RNAseq reveals adverse metabolic transcriptional program in intrahepatic cholangiocarcinoma malignant cells

## TL;DR

This study identifies a harmful metabolic gene pattern in liver cancer cells that predicts worse patient outcomes, independent of other factors.

## Contribution

The study reveals a novel metabolic transcriptional program in ICA malignant cells linked to poor prognosis.

## Key findings

- 16 metabolic genes are overexpressed in ICA patients with poor survival.
- A metabolic gene score predicts worse overall survival independent of fibrosis and tumor stage.
- Seven key metabolic genes are mainly expressed in malignant cells and mark the proliferative ICA subclass.

## Abstract

Intrahepatic cholangiocarcinoma (ICA) is a highly aggressive primary liver cancer, which originates from the epithelial cells of the bile ducts. The transcriptional profile of metabolic enzymes was investigated at both bulk and single-cell levels in tumor samples from distinct ICA cohorts. In a training cohort (TCGA consortium), 16 genes encoding for metabolic enzymes were found overexpressed in cases with poor survival. A computed metabolic gene expression score was significantly associated with worse ICA prognosis at the univariate level (overall survival [OS] log-rank p = 8.2e-4). After adjusting for Ishak fibrosis score and tumor staging, the metabolic expression remained an independent predictor of poor prognosis (multivariate OS log-rank p = 0.01). Seven genes encoding key enzymes (FH, MAT2B, PLOD2, PLOD1, PDE6D, ALDOC, and NT5DC3) were validated as markers of the proliferative subclass of ICA in the GSE32225 dataset, related to poor prognosis. The metabolic score was significantly different between the inflammatory and proliferative subclasses in the validation cohort (p < 2.2e-16). At the single-cell level, in the tumor microenvironment of 10 ICA patients, these seven enzymes were predominantly expressed by malignant cells. The single-cell metabolic score was thus higher in malignant cells. This study identifies a metabolic transcriptional program linked to poor prognosis in ICA, independent of fibrosis and tumor staging.

•Metabolic transcriptional program linked to poor prognosis identified in intrahepatic cholangiocarcinoma (ICA).•16 metabolic enzymes were overexpressed in ICA patients with poor survival in the TCGA cohort.•A metabolic gene score predicts worse OS, independent of fibrosis and tumor stage.•Seven metabolic genes mark the proliferative ICA subclass.•Single-cell analysis shows these enzymes are mainly in malignant tumor cells.•The metabolic gene expression score was significantly higher in proliferative ICA subclass, linking it to poor prognosis.

Metabolic transcriptional program linked to poor prognosis identified in intrahepatic cholangiocarcinoma (ICA).

16 metabolic enzymes were overexpressed in ICA patients with poor survival in the TCGA cohort.

A metabolic gene score predicts worse OS, independent of fibrosis and tumor stage.

Seven metabolic genes mark the proliferative ICA subclass.

Single-cell analysis shows these enzymes are mainly in malignant tumor cells.

The metabolic gene expression score was significantly higher in proliferative ICA subclass, linking it to poor prognosis.