Multi-Omics Analysis Reveals Differentially Expressed Proteins and Metabolites in Malignant Pleural Effusion

Malignant pleural effusion (MPE) is a common manifestation in advanced malignancies. However, its differentiation from benign pleural effusions, such as parapneumonic effusion (PPE) and tuberculous pleural effusion (TPE), remains challenging. This study aimed to profile differentially expressed proteins and metabolites between MPE, PPE, and TPE.

Pleural effusion samples from patients with MPE, PPE, and TPE were collected and subjected to proteomic and metabolomic profiling. Differentially expressed proteins (DEPs) and differentially abundant metabolites (DAMs) were identified, followed by functional enrichment analyzes. Integrated proteome-metabolome analysis was performed to construct protein-metabolite interaction networks and reveal key pathways associated with malignant and benign pleural effusions.

Proteomic and metabolomic profiles differed significantly between MPE and non-MPE. Arginine-proline and glutamate metabolism were commonly enriched at both protein and metabolite levels in MPE versus PPE and TPE. At the protein level, Isocitrate Dehydrogenase 1 (IDH1) was significantly upregulated in MPE compared with both PPE and TPE. At the metabolite level, sarcosine and l-glutamine were markedly elevated, while creatine was significantly decreased in MPE. Integrated analysis further indicated that these four molecules play important roles in distinguishing MPE from PPE and TPE.

Combined proteomic and metabolomic analyzes revealed the critical involvement of IDH1 in glutamate metabolism and arginine and proline metabolic pathways during MPE metabolic reprogramming. Identified molecules, including IDH1, l-glutamine, creatine, and sarcosine, may serve as potential diagnostic biomarkers for differentiating malignant from benign pleural effusions.