Single‐Cell and Bulk RNA Sequencing Reveal MCL1 as a Key Regulator of Mitochondrial Function in Liver Ischemia–Reperfusion Injury

ABSTRACT Liver ischemia–reperfusion injury (LIRI), a significant complication following liver transplantation and surgical procedures, remains inadequately addressed due to the limited therapeutic options available. This study aims to elucidate the pivotal regulators underlying the maladaptive immune responses and mitochondrial dysfunction associated with LIRI. By integrating multiple microarray datasets (GSE12720, GSE112713, GSE23649, and GSE151648) and single‐cell RNA sequencing (scRNA‐seq) data (GSE171539), we employed weighted gene co‐expression network analysis (WGCNA) alongside four machine learning algorithms (SVM, LASSO, RF, and XGBoost) to identify hub genes. Our analyzes highlighted MCL1 as a critical hub gene linked to mitochondrial function, exhibiting significantly elevated expression levels in LIRI, coupled with strong diagnostic accuracy. Further single‐cell analysis revealed MCL1's specific enrichment in endothelial cells (ECs) and macrophages (MCs), along with the identification of a novel macrophage subset (CSF1R + IL‐1B + MCL1 + ) characterized by a dual pro‐inflammatory and pro‐survival phenotype. This finding suggests enhanced intercellular crosstalk involving key pathways such as NF‐κB, apoptosis, and cytokine signaling, while in silico knockout of MCL1 markedly disrupted immune‐related gene networks. Validation studies confirmed MCL1 upregulation and the presence of the macrophage subset in a murine LIRI model. In conclusion, our findings position MCL1 as a vital regulator linking immune inflammation and mitochondrial dysfunction in LIRI, proposing it as a promising diagnostic biomarker and therapeutic target for managing this condition, though its optimal therapeutic direction requires further investigation.