Integrated Metabolic and Immune Molecular Subtyping and a Molecular Classification Score for Revealing Disease Heterogeneity in Pulmonary Arterial Hypertension

Objectives: Despite the central role of metabolic–immune crosstalk in pulmonary arterial hypertension (PAH), integrative quantitative tools remain lacking. We aimed to construct and validate a metabolic–immune molecular classification score (MIRS) as a quantitative metric to capture the inflammation–metabolism balance and to assess its discriminatory performance for molecular subtyping, cross-cohort applicability, and biological implications. Methods: We integrated five PAH lung tissue transcriptomic datasets from the Gene Expression Omnibus (GEO). A training set was used to identify differentially expressed genes and to derive MIRS as the first principal component of 20 core genes. MIRS was projected onto independent validation cohorts. Immune microenvironment, pathway activities, protein–protein interaction, and drug repositioning analyses were performed. Results: MIRS significantly distinguished Non-IPAH from IPAH in GSE117261 (AUC = 0.718, p = 0.010) and revealed internal heterogeneity in SSc-PAH. MIRS-related gene expression patterns showed significant differences across COPD and ILD lung tissues in independent datasets. A unified fixed PCA projection pipeline with mean imputation for missing core genes was applied to all pulmonary disease datasets, enabling consistent numerical quantification of MIRS across cohorts under the same mathematical framework. MIRS failed to discriminate PAH from controls in PBMCs, indicating that this tissue-derived signature is not readily detectable in peripheral blood—a limitation that restricts its applicability to lung tissue specimens and highlights challenges for blood-based biomarker development in PAH. Higher MIRS correlated with increased immune scores and myeloid cell infiltration in Non-IPAH. Drug prediction identified sirolimus and tocilizumab as top candidates, with MIRS-stratified sensitivity patterns aligning with pathway loading directions. Conclusions: MIRS is a quantitative, tissue-restricted metric that captures metabolic–immune activation in PAH, with exploratory observations in other pulmonary diseases that warrant further validation. It provides a molecular stratification basis for subtype discrimination and a hypothesis-generating framework for future therapeutic investigations.