Integrated Machine Learning and Bioinformatic Analyses Constructed a Novel Stemness-Related Classifier to Predict Prognosis and Immunotherapy Responses for Hepatocellular Carcinoma Patients

Immunotherapy has made great progress in hepatocellular carcinoma (HCC), yet there is still a lack of biomarkers for predicting response to it. Cancer stem cells (CSCs) are the primary cause of the tumorigenesis, metastasis, and multi-drug resistance of HCC. This study aimed to propose a novel CSCs-related cluster of HCC to predict patients' response to immunotherapy. Based on RNA-seq datasets from The Cancer Genome Atlas (TCGA) and Progenitor Cell Biology Consortium (PCBC), one-class logistic regression (OCLR) algorithm was applied to compute the stemness index (mRNAsi) of HCC patients. Unsupervised consensus clustering was performed to categorize HCC patients into two stemness subtypes which further proved to be a predictor of tumor immune microenvironment (TIME) status, immunogenomic expressions and sensitivity to neoadjuvant therapies. Finally, four machine learning algorithms (LASSO, RF, SVM-RFE and XGboost) were applied to distinguish different stemness subtypes. Thus, a five-hub-gene based classifier was constructed in TCGA and ICGC HCC datasets to predict patients' stemness subtype in a more convenient and applicable way, and this novel stemness-based classification system could facilitate the prognostic prediction and guide clinical strategies of immunotherapy and targeted therapy in HCC.

Automated summary

This study proposes a novel classification system for hepatocellular carcinoma (HCC) based on cancer stem cells (CSCs) that can predict patients' response to immunotherapy. Using RNA-seq datasets and machine learning algorithms, the study computes a stemness index (mRNAsi) and performs clustering analysis to categorize HCC patients into different stemness subtypes. This stemness-based classification system can facilitate prognostic prediction and guide clinical strategies for immunotherapy and targeted therapy in HCC.