Shared Immune and Epigenetic Pathways in Systemic Lupus Erythematosus and Melanoma Immunotherapy: A Cross-Disease Analysis with Prognostic and Therapeutic Implications

Abstract

Systemic lupus erythematosus (SLE) and melanoma both involve dysregulated immune pathways, yet their molecular convergence remains poorly understood. We performed a cross-disease transcriptomic analysis of melanoma (GSE168204) and SLE (GSE211700) datasets to identify shared signatures of immune activation and immune checkpoint blockade (ICB) response. Differential expression analysis revealed two distinct signatures: (i) an immune signatures upregulated in melanoma responders and SLE (n = 147 genes), enriched in interferon signaling and epigenetic regulators such as ASF1B and EZH2 [4, 7, 52]; and (ii) a cell cycle signatures upregulated in melanoma non-responders and SLE (n = 157 genes), dominated by CDK1 and CCNB1 [39]. Pathway enrichment and protein-protein interaction analyses confirmed that immune activation and epigenetic remodeling drive convergence between SLE and melanoma responders, while cell cycle upregulation is specific to ICB resistance [13, 53]. Validation in independent datasets (GSE91061, GSE261866) supported the immune signatures relevance (AUC = 0.780, p = 0.0456) and the cell cycle signatures specificity to melanoma (p = 0.2414 in SLE) [17, 18].In TCGA-SKCM survival analysis, the cell cycle signature demonstrated strong prognostic value, predicting dramatically worse overall survival (OS HR = 15.634, 95% CI: 1.898 - 128.761, p = 0.011) and progression-free survival (PFS HR = 8.484, 95% CI: 1.420 - 50.688, p = 0.019). The immune signature showed protective trends for both OS (HR = 0.259, p = 0.121) and PFS (HR = 0.656, p = 0.585), while a composite score integrating both signatures achieved significant prognostic utility (OS HR = 0.141, p = 0.004; PFS HR = 0.324, p = 0.053) [40]. Connectivity Map analysis identified mTOR inhibitors, proteasome inhibitors, HDAC inhibitors, and statins as candidate therapeutics targeting these pathways [45, 50]. Limitations include reliance on transcriptomic data, moderate biomarker performance (AUC = 0.6567 - 0.780), and lack of functional validation. Future studies should validate these signatures in ICB-treated cohorts, integrate multi-omics, and test proposed therapeutics preclinically. Overall, this cross-disease analysis highlights immune-epigenetic convergence linking SLE and melanoma, with implications for biomarker development and therapeutic repurposing [6, 12].