Analysis of m6A-Related lncRNAs for Prognosis Value and Response to Immune Checkpoint Inhibitors Therapy in Hepatocellular Carcinoma

Abstract

Introduction

N6-methyladenosine (m6A) modification and long non-coding RNAs (lncRNAs) play pivotal roles in the progression of hepatocellular carcinoma (HCC). However, how their interaction is involved in the prognostic value of HCC and immune checkpoint inhibitors (ICIs) therapy remains unclear.

Methods

The RNA sequencing and clinical data of HCC patients were collected from TCGA database. The prognostic m6A-related lncRNAs were screened out with Pearson correlation test, univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. Patients with HCC were classified into 2 subtypes by consensus clustering. Survival analyses were performed to assess the prognostic value of different clusters and risk models. Potential tumor correlated biological pathways correlated with different clusters were explored through gene set enrichment analysis. We also identified the relationship of the risk model and clusters with response to immune checkpoint inhibitors (ICIs) therapy and tumor microenvironment (TME). Furthermore, the prognostic value of the 9 m6A-related lncRNAs was validated in the external cohort. Finally, the role of SNHG4 was explored by silencing and overexpression of SNHG4 through conducting proliferation, migration and invasion experiments.

Results

Patients from 2 clusters and different risk groups based on m6A-related lncRNAs had significantly different clinicopathological characteristics and overall survival outcomes. Tumor-correlated biological pathways were found to be correlated with Cluster 2 through GSEA. Moreover, we found that patients from different clusters and risk groups expressed higher levels of immune checkpoint genes and had distinct TME and different responses for ICIs therapy. Prognostic value of this risk model was further confirmed in the external cohort. Finally, consistent with the discovery, SNHG4 played an oncogenic role in vitro.

Conclusion

Our study demonstrated that the 9 m6A-related lncRNA signature may serve as a novel predictor in the prognosis of HCC and optimize (ICIs) therapy. SNHG4 plays an oncogenic role in HCC.

Keywords:

• N6-methyladenosine
• long non-coding RNAs
• prognosis
• immune checkpoints inhibitors therapy
• hepatocellular carcinoma

Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China (grant number 91859107), the Shanghai Science and Technology Committee (grant number 18DZ1930102, grand number 19411965500), the Shanghai Municipal Key Clinical Specialty (shslczdzk03202), the Clinical Research Plan of SHDC (SHDC2020CR1029B), Zhongshan Hospital, Fudan University (grant number 2018ZSLC22, 2020ZSLC61) and Clinical Research Plan of SHDC (SHDC2020CR1029B).

Data Sharing Statement

A publicly available database was analyzed in this study; it can be found in the The Cancer Genome Atlas (https://portal.gdc.cancer.gov/).

Ethics Statement

This study protocol which involved human participants was approved by the Clinical Research Ethics Committee of Zhongshan Hospital of Fudan University (B2018-236), and informed consent was obtained from all of the patients. All the analyses of data and material have been performed in accordance with the Declaration of Helsinki.

Disclosure

All authors state that they have no conflicts of interest.