Integration of single-cell and bulk RNA-sequencing to analyze the heterogeneity of hepatocellular carcinoma and establish a prognostic model.

ABSTRACT:

Background

The highly heterogeneous nature of hepatocellular carcinoma (HCC) results in different responses and prognoses to the same treatment in patients with similar clinical stages.

Aims

Thus, it is imperative to investigate the association between HCC tumor heterogeneity and treatment response and prognosis.

Methods and results

At first, we downloaded scRNA-seq, bulk RNA-seq, and clinical data from TCGA and GEO databases. We conducted quality control, normalization using SCTransform, dimensionality reduction using PCA, batch effect removal using Harmony, dimensionality reduction using UMAP, and cell annotation-based marker genes on the scRNA-seq data. We recognized tumor cells, identified tumor-related genes (TRGs), and performed cell communication analysis. Next

SUBMITTER: Mu Y 

PROVIDER: S-EPMC10809200 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature