整合bulk与单细胞转录组学揭示PARL作为线粒体调控因子与肺鳞状细胞癌的免疫代谢重编程及良好预后相关

Background: Lung squamous cell carcinoma (LUSC) lacks reliable prognostic biomarkers. Given the growing recognition of mitochondrial dysfunction as a driver of cancer metabolism and immune regulation, we investigated the mitochondrial protease presenilin-associated rhomboid-like (PARL) gene expression as a potential modulator of tumor progression and immune microenvironment in LUSC. ​ Methods: TCGA-LUSC bulk RNA-seq was analyzed with DESeq2 to evaluate PARL differential expression. Univariate and multivariate Cox models were performed to evaluate association with overall survival (OS). Limma was used to assess pathway-level differences using Hallmark MSigDB gene sets. Functional enrichment was performed using GO and GSEA. CIBERSORTx was utilized to assess immune infiltration. Single-cell analysis of the 10x Genomics NSCLC Tumor 1 dataset included quality control, normalization, clustering, automated annotation (SingleR), and pseudotime trajectory analysis to examine lineage-specific PARL patterns. Results: Low PARL expression correlated with shorter OS (median OS: 39 vs. 61 months; log-rank p = 0.008) and remained an independent favorable prognostic factor (HR = 0.75, p = 0.003). The survival benefit of high PARL expression persisted across early and late disease stages. Functional enrichment analysis indicated that high- PARL tumors were enriched for mitochondrial organization, oxidative phosphorylation, and apoptotic regulation, whereas PARL -low tumors favored proliferative and cell cycle pathways. Key pathways downregulated in high- PARL tumors included KRAS signaling, complement, IL6/JAK/STAT3, and TGF-beta signaling, while DNA repair, MYC targets, Oxidative Phosphorylation, and G2M checkpoint pathways were upregulated, suggesting enhanced metabolic activity and cell cycle regulation. Furthermore, Pearson's chi-squared test showed a significant association between PARL expression and TP53 mutations (χ ² = 8.04, p = 0.0046). CIBERSORTx analysis revealed that PARL -high tumors exhibited lower infiltration of immunosuppressive and pro-inflammatory cells, including Tregs, M2 macrophages, and neutrophils suggesting a role for PARL in shaping a less suppressive immune microenvironment. Single-cell trajectory analysis revealed PARL expression peaked in progenitor and stromal populations, implying an early role in mitochondrial quality control and immune differentiation, influencing tumor-immune dynamics and clinical outcomes. Conclusions: PARL emerges as a candidate gene expression-based biomarker associated with mitochondrial homeostasis, reduced immunosuppression and favorable prognosis in LUSC. These findings highlight a potential role of PARL in immune metabolic adaptation and support further validation to establish its clinical relevance.