Identification of Hub Genes and Pathways in Preinfusion Chimeric Antigen Receptor (CAR) T-cell Products Associated...

Chimeric antigen receptor (CAR) T-cell therapy has transformed cancer management over the past decades, offering new hope to many patients. However, its effectiveness is often limited due to cytokine release syndrome (CRS), a life-threatening inflammatory response. Despite its clinical relevance, the molecular mechanisms underlying CRS, specifically in CAR T-cell products, remain poorly understood. This study aims to identify hub genes and pathways in preinfusion CAR T-cell products associated with CRS development and evaluate their potential as therapeutic targets through drug-gene interaction analysis and immune cell correlation profiling.

We examined gene expression data from 43 preinfusion clusters of differentiation 22 of CAR T-cell samples (CD22+), sourced from the Gene Expression Omnibus dataset GSE200296. Using the linear models for microarray data package, we identified differences in gene expression and conducted enrichment analyses to explore relevant biological pathways, including Kyoto Encyclopedia of Genes and Genomes and Gene Ontology terms. We built protein-protein interaction networks using the Search Tool for Retrieval of Interacting Genes/Proteins database to understand how these genes interact and pinpointed central "hub genes" with Cytoscape and the cytoHubba plugin. Our findings were validated using the GeneCards database (Weizmann Institute of Science, Israel) and an independent CRS-related dataset (GSE164805). Additionally, we analyzed immune cell populations and explored potential drug-gene interactions.

Our study identified 24 genes with changed expression levels: 16 were downregulated and eight were upregulated. We identified five hub genes, interleukin (IL)1B, IL15, CD276, NCR2, and CCL17, as key contributors in CRS, which were primarily implicated in immune-related pathways, including cytokine-cytokine receptor interactions, IL17 signaling, and TNF signaling. These genes were especially expressed in monocytes, macrophages, and dendritic cells, confirming that those immune cell types play a critical role in CRS development. Through drug-gene interaction analysis, we found prospective therapies, such as enoblituzumab (targeting CD276) and canakinumab (targeting IL1B), which might assist in reducing CRS severity.

The study highlights IL1B, IL15, CD276, NCR2, and CCL17 as key CRS genes in preinfusion CAR T-cell products. Their dysregulation activity may contribute to the increased inflammation noted in CRS, pointing to a loss of regulatory control. Bringing us closer to better patient outcomes, these findings not only suggest that these genes could serve as valuable biomarkers for predicting CRS but also open the way for the development of more precise treatments such as combining drugs such as enoblituzumab and canakinumab, which might assist in reducing CRS severity and making CAR T-cell therapy safer and more effective, ultimately improving patient lives.