Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer

Junliang Chen; Zhihao Liu; Zhiyuan Wu; Wenjun Li; Xiaodong Tan

doi:10.3389/fonc.2023.1132424

Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer

Front Oncol. 2023 May 12:13:1132424. doi: 10.3389/fonc.2023.1132424. eCollection 2023.

Authors

Junliang Chen¹, Zhihao Liu¹, Zhiyuan Wu¹, Wenjun Li¹, Xiaodong Tan¹

Affiliation

¹ Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.

Abstract

Background: Chemoresistance is a major hurdle to improving the prognosis of pancreatic cancer (PC). This study aimed to identify key genes regulating chemoresistance and develop a chemoresistance-related gene signature for prognosis prediction.

Methods: A total of 30 PC cell lines were subtyped according to gemcitabine sensitivity data from the Cancer Therapeutics Response Portal (CTRP v2). Differentially expressed genes (DEGs) between gemcitabine-resistant and gemcitabine-sensitive cells were subsequently identified. These upregulated DEGs associated with prognostic values were incorporated to build a LASSO Cox risk model for The Cancer Genome Atlas (TCGA) cohort. Four datasets (GSE28735, GSE62452, GSE85916, and GSE102238) from the Gene Expression Omnibus (GEO) were used as an external validation cohort. Then, a nomogram was developed based on independent prognostic factors. The responses to multiple anti-PC chemotherapeutics were estimated by the "oncoPredict" method. Tumor mutation burden (TMB) was calculated using the "TCGAbiolinks" package. Analysis of the tumor microenvironment (TME) was performed using the "IOBR" package, while the TIDE and "easier" algorithms were employed to estimate immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducted to validate the expression and functions of ALDH3B1 and NCEH1.

Results: A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1. Bulk and single-cell RNA sequencing analyses indicated that all five genes were highly expressed in tumor samples. This gene signature was not only an independent prognostic factor but also a biomarker forecasting chemoresistance, TMB, and immune cells. In vitro experiments suggested that ALDH3B1 and NCEH1 were involved in PC progression and gemcitabine chemoresistance.

Conclusion: This chemoresistance-related gene signature links prognosis with chemoresistance, TMB, and immune features. ALDH3B1 and NCEH1 are two promising targets for treating PC.

Keywords: chemoresistance; gemcitabine; immunotherapy; pancreatic cancer; prognosis; tumor microenvironment; tumor mutation burden.

Grants and funding

This work was supported by the National Natural Science Foundation of China (No. 180530068), the Special Project of Provincial Science and Technology Development from National Guidance (No. 2020JH6/10500055), the Key Research and Development Program of Liaoning Province (2020JH2/10300130), and the 345 Talent Project of Shengjing Hospital of China Medical University.