Integrating bulk RNA-seq, scRNA-seq, Mendelian randomization, and meta-analysis to identify the peroxisome-associated genes FLOT1, NMI, and LY9 as potential biomarkers for sepsis

Background Accumulating evidence suggests a close association between peroxisomes and sepsis, yet the contribution of peroxisome-related genes (PRGs) remains unclear. This study aimed to identify and validate PRG-associated biomarkers involved in sepsis. Results Sepsis transcriptomic datasets were integrated with PRGs, and candidate biomarkers were screened using single-cell RNA sequencing, differential expression analysis, Mendelian randomization, and machine-learning approaches, followed by validation. Three PRG-associated biomarkers (FLOT1, NMI, and LY9) were identified. LY9 acted as a protective factor, whereas FLOT1 and NMI were associated with increased sepsis risk. Enrichment analyses indicated shared involvement in aminoacyl-tRNA biosynthesis and proteasome-related pathways. Immune infiltration analysis showed that neutrophils were negatively correlated with LY9 expression and positively correlated with FLOT1 expression. MXI1 was identified as a common transcriptional regulator of all three biomarkers, and eight literature-associated compounds were identified for hypothesis generation. Exploratory single-cell analysis suggested potential monocyte differentiation states accompanied by dynamic biomarker expression. Meta-analysis confirmed that elevated FLOT1 and NMI increased sepsis susceptibility, while higher LY9 reduced risk. Preliminary RT‒qPCR analysis showed NMI upregulation and LY9 downregulation in sepsis patients compared with nonsepsis controls. Conclusions FLOT1, NMI, and LY9 may serve as candidate peroxisome-related biomarkers associated with sepsis, providing preliminary clues for future mechanistic and validation studies.