Multi-omics data reveal B cell regulated immune heterogeneity of MIF signaling pathway in uveal melanoma

Tebentafusp, a T-cell receptor (TCR)-based therapeutic agent, has emerged as a groundbreaking treatment for uveal melanoma (UM), particularly in cases of metastatic UM. While this innovation has significantly improved patient prognosis, the development of additional therapeutic strategies remains crucial. This study aims to explore the role of the B-cell receptor (BCR) in the pathogenesis of UM, with the goal of identifying it as a potential target for future treatments. Both bulk RNA-seq and single-cell RNA-seq (scRNA-seq) datasets were collected for comprehensive analysis. The TRUST4 algorithm was employed to reconstruct and analyze the BCR repertoire in UM samples, enabling the evaluation of BCR clonal diversity in the bulk RNA-seq analysis. Additionally, blood samples from a UM cohort at Beijing Tongren Hospital, comprising 5 primary and 5 metastatic UM patients, were collected and subjected to proteomic analysis. In the clinical cohort and the scRNA-seq analyses, a combination of differentially expressed gene (DEG) identification, gene set enrichment analysis (GSEA), and cell-cell communication network analysis was utilized to elucidate key signaling pathways involved in UM progression. UM cell lines were adopted to verify the role of Migration Inhibitory Factor (MIF)-CD74 in the tumor. Analysis using the TRUST4 algorithm revealed that UM samples exhibited lower clonal diversity, as indicated by various diversity indices. Notably, certain IGK, IGH, IGL-V, and J genes were significantly highly expressed in UM samples, suggesting a critical role of BCR in UM pathogenesis (P < 0.05). Clinically, patients with primary UM demonstrated a smaller largest basal diameter (11.3 ± 1.2 mm vs. 13.4 ± 2.8 mm) and reduced tumor height (7.1 ± 2.2 mm vs. 8.2 ± 2.1 mm) compared to metastatic cases. Proteomic analysis of blood samples identified a total of 3,188 proteins, with 164 upregulated and 232 downregulated (P < 0.05). Functional enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) highlighted the enrichment of BCR-related signaling pathways in UM blood samples. Furthermore, scRNA-seq analysis confirmed differential expression of V and J genes across B-cell subtypes. Specifically, plasma B cells were found to regulate the MIF signaling pathway through interactions between the receptor CXCR4 and CD74 in metastatic UM. Downregulating MIF-CD74 could relief tumor cell proliferation in primary and metastatic UM cells. Our findings demonstrate that specific V and J genes within the BCR repertoire provide new insights into the underlying mechanisms of UM, particularly in metastatic UM. Both proteomic and scRNA-seq analyses revealed activation of the MIF signaling pathway in metastatic UM samples, mediated through the interaction with CD74, which has been verified in UM cell lines. These discoveries shed light on potential novel therapeutic strategies for UM, offering promising directions for future treatment development.