Autophagy-Mediated Neuroendocrine Reprogramming by Trehalose in H841 Cells: Insights from Differential Gene Expression in Small Cell Lung Cancer

Abstract

Introduction: Small Cell Lung Cancer (SCLC) is a highly aggressive neuroendocrine carcinoma known for its rapid progression, high relapse rate, and pronounced phenotypic plasticity. The ability of SCLC cells to transition between neuroendocrine (NE) and non-NE states contributes to therapy resistance and tumor heterogeneity. Autophagy, a cellular degradation and recycling process, may influence this plasticity. Trehalose, a naturally occurring mTOR-independent autophagy enhancer.

Objective: This study aims to identify differentially expressed genes (DEGs) between trehalose-treated and untreated H841 SCLC cells using RNA sequencing, and to perform functional annotation and gene ontology (GO) analysis of these DEGs to understand the biological impact of autophagy.

B This study used the H841 SCLC cell line to investigate transcriptional changes following trehalose-induced autophagy. Public RNA-seq data (BioProject PRJNA1198304, GEO GSE284267) comprising three replicates each of control and trehalose-treated samples were processed using the Galaxy Europe platform. Quality control was performed using FastQC and Fastp; alignment to the human genome (GRCh38) was conducted with RNA STAR, and gene quantification with HTSeq-count. Differential expression analysis was carried out using DESeq2, and functional annotation via Metascape, DAVID, KEGG, and Cytoscape.

Results: A total of 12,132 DEGs were identified, including 7,041 upregulated and 5,091 downregulated genes. Key upregulated genes included GABARAP and NFE2L3, associated with autophagy and stress adaptation. KEGG analysis revealed downregulation of cell cycle-related pathways (e.g., ESCO1), while GO analysis highlighted enrichment in RNA processing, chromatin organization, and translation initiation. PCA and heatmap analyses confirmed distinct clustering of treated versus control samples, supporting a strong transcriptional response to trehalose.

Conclusion: Trehalose-induced autophagy significantly alters the transcriptome of SCLC cells by downregulating proliferation-associated genes and upregulating differentiation pathways, suggesting its potential role in modulating neuroendocrine plasticity, stress adaptation, and therapeutic response in aggressive tumor phenotypes.