Gene expression and alternative splicing are observed to shift in different ways after binding of naringenin chalcone and HRH2 in 293T cells

Histamine H2 receptor (HRH2) is a key mediator of histamine signaling, regulating gastric acid secretion and contributing to immune modulation. Naringenin chalcone is a natural chalcone compound and an important synthetic intermediate. Previous work showed that naringenin chalcone binds HRH2 and suppresses HRH2-induced cAMP production. Here, we used RNA sequencing to characterize transcriptomic and alternative splicing changes triggered by HRH2 activation and to assess how these responses are modulated by naringenin chalcone. HRH2 activation by histamine induced 11,507 differentially expressed genes (DEGs), primarily enriched in cytoplasmic translation and oxidative phosphorylation. Low-dose naringenin chalcone shifted enrichment toward centriole assembly and synaptic signaling, whereas high-dose treatment produced patterns similar to histamine alone, suggesting concentration-dependent effects. Compared with histamine alone, high-dose naringenin chalcone altered the expressions of 2794 genes, strongly enriched in RNA-splicing-related processes. We further analyzed genes with differential transcript usage (gDTUs). Under histamine treatment, gDTUs were enriched in nuclear matrix and histone methyltransferase activity, while naringenin chalcone redirected enrichment toward RNA splicing and its regulation, a pattern consistent with the DEG-based results. When compared with baseline 293T cells, over 60% of gDTUs overlapped with DEGs; however, when examining the specific influence of naringenin chalcone, the overlap dropped below 20%. These findings suggest that naringenin chalcone differentially affects gene expression and alternative splicing, although these regulatory layers may converge on related biological outcomes. Overall, our study provides new insights into the molecular interplay between naringenin chalcone and HRH2 and offers a reference for further mechanistic investigation.