Integrative analysis identifies Hspa5 as a key regulator of the ERS/UPR-immune axis in spinal cord injury

Endoplasmic reticulum stress (ERS) and the unfolded protein response (UPR) are critical in secondary spinal cord injury (SCI), but their systematic characterization and link to immune infiltration remain unclear. This study aimed to identify key ERS/UPR-related genes and their association with the immune microenvironment to find robust biomarkers for SCI.

We analyzed bulk RNA-seq data (GSE151371) to identify differentially expressed genes (DEGs), followed by pathway enrichment analyses. Machine learning (SVM-RFE) and protein-protein interaction networks were used to screen for hub genes. The identified hub genes were validated using an independent cohort (GSE5296), single-cell sequencing data (GSE213240), and qRT-PCR in a murine SCI model.

We identified 17 ERS-related and 27 UPR-related DEGs, primarily enriched in neuron death pathways. SCI samples showed elevated ERS/UPR phenotype scores that positively correlated with myeloid cell infiltration. PPI analysis pinpointed Dnajc3 and Hspa5 as central hub genes. However, multi-level validation confirmed that while Hspa5 was consistently and significantly upregulated across all platforms, Dnajc3 did not show significant differential expression in single-cell sequencing and qRT-PCR validation, thereby limiting its credibility as a direct transcriptional biomarker. A diagnostic nomogram incorporating both genes achieved an AUC of 0.745.

ERS/UPR activation is a critical component of the post-SCI transcriptomic response and is closely linked to immune remodeling. Hspa5 emerges as a robust and dominant hub gene, representing a promising therapeutic target for SCI.