Multi-Omics Brings New Clarity to the REHAB-PH Trial

Pulmonary arterial hypertension (PAH) is one of the most biologically heterogeneous cardiovascular diseases, making it difficult to identify therapies that consistently benefit broad patient populations. In a post hoc analysis of the REHAB-PH trial, investigators explored whether longitudinal metabolomic and proteomic profiling could provide deeper insight into treatment response, even when a clinical trial fails to meet its primary endpoints. Their findings suggest that multi-omics may offer valuable biological context that conventional clinical outcomes alone cannot capture.

REHAB-PH was a single-center, randomized, double-blind, placebo-controlled trial evaluating the histamine H2 receptor antagonist famotidine in adults with PAH. Seventy-nine participants were randomized to receive either famotidine 20 mg daily (n=40) or placebo (n=39) for 24 weeks. Plasma samples were collected at baseline and study completion for comprehensive metabolomic and proteomic analysis. Seventy-one participants ultimately contributed paired molecular data for longitudinal analyses.

The investigators used advanced molecular profiling platforms to measure 1,118 circulating metabolites and 7,289 plasma proteins. Metabolomics characterizes small molecules that reflect ongoing cellular metabolism, while proteomics quantifies proteins that participate in signaling pathways, tissue remodeling, inflammation, and other biological processes. Together, these approaches can reveal treatment-related molecular changes that may not be apparent through clinical measures alone.

Baseline metabolomic and proteomic signatures showed substantial overlap between treatment groups, with no significant differences detected among individual analytes or biological pathways. Dimensionality reduction analyses demonstrated near-identical molecular distributions between arms, supporting the integrity of the trial design despite its relatively modest sample size.

Stable Molecular Signatures in the Absence of Intervention

The placebo arm provided a unique opportunity to evaluate the natural stability of circulating molecular markers over time. Over the 24-week study period, 65.7% of metabolites and 69.7% of proteins demonstrated moderate-to-high longitudinal stability, defined by intraclass correlation coefficients (ICCs) greater than 0.40. Only 7.7% of metabolites and 9.3% of proteins exhibited substantial variability (ICC <0.10).

These findings are important because they suggest that most circulating metabolites and proteins remain relatively stable in clinically stable PAH, supporting their potential use as longitudinal biomarkers in future interventional studies.

Proteomics Revealed Biological Activity Despite Clinical Neutrality

Although the parent REHAB-PH trial found no significant clinical benefit with famotidine, molecular analyses told a more nuanced story. No individual metabolites or proteins remained statistically significant after correction for multiple testing, and no metabolomic pathways reached significance. However, proteomic pathway analysis identified significant changes in 191 pathways, including 171 upregulated and 20 downregulated pathways.

Several affected pathways were linked to cell-cycle regulation, transforming growth factor-beta signaling, vesicle transport, and cellular signaling networks. Conversely, pathways involving glycosylation and transmembrane receptor tyrosine kinase activity were downregulated. The latter observation is particularly intriguing because histamine H2 receptor signaling may interact with receptor tyrosine kinase pathways involved in endothelial function, vascular remodeling, and cardiac adaptation.

Proteomic variability also increased in the famotidine arm. While only 9.8% of metabolites displayed high variability during treatment, 19.4% of proteins showed substantial variability, approximately twice the rate observed in the placebo group. This finding suggests that the proteome may be more sensitive than the metabolome for detecting the biological effects of certain pharmacologic interventions.

Molecular Endotypes May Influence Drug Response

Exploratory network analyses identified two proteomic endotypes that appeared to correlate with differential responses to famotidine. One protein module was associated with worsening clinical measures, including rising BNP levels, worsening right ventricular dilation, reduced 6-minute walk distance, and lower tricuspid annular plane systolic excursion (all Pearson correlation p<0.05). A second module correlated with improvements in 6-minute walk distance and right ventricular dilation (Pearson correlation p<0.05). These associations were not observed in the placebo arm.

While exploratory, these findings raise the possibility that biologically distinct PAH subgroups may respond differently to targeted therapies, highlighting a potential role for molecular endotyping in future precision medicine strategies.

Looking Ahead

This analysis demonstrates that integrating metabolomics and proteomics into prospective PAH trials is both feasible and informative. Even when a therapy fails to improve conventional clinical outcomes, multi-omic profiling can reveal underlying biological activity, identify candidate response signatures, and improve understanding of disease heterogeneity. The study ultimately highlights how molecular data may help extract meaningful insights from otherwise negative trials and guide the development of more personalized therapeutic approaches in PAH.

Reference:

Pi H, Xia L, Rayner SG, et al. Harnessing metabolomics and proteomics in a clinical trial for pulmonary arterial hypertension: insights from post-hoc analysis of the REHAB-PH trial. EBioMedicine. 2026;126:106191. doi:10.1016/j.ebiom.2026.106191