Myocardial Gene Expression Signatures in Human Heart Failure With Preserved Ejection Fraction

Abstract

Background: Heart failure with preserved ejection fraction (HFpEF) constitutes half of all HF yet lacks effective therapy. Understanding its myocardial biology remains limited due to a paucity of heart tissue molecular analysis. Methods: We performed RNA sequencing on right ventricular septal endomyocardial biopsies prospectively obtained from patients with consensus criteria for HFpEF (n=41) and contrasted to RV-septal tissue from HF with reduced EF (HFrEF, n=30) and donor controls (CON, n=24). Principal component analysis (PCA) and hierarchical clustering tested for transcriptomic distinctiveness between groups and impact of co-morbidities, and differential gene expression with pathway enrichment contrasted HF groups to CON. Within HFpEF, non-negative matrix factorization (NMF) and weighted gene co-expression analysis (WGCNA) identified molecular subgroups and the resulting clusters were correlated with hemodynamic and clinical data. Results: HFpEF patients were more often women (59%), African American (68%), obese (median BMI 41), and hypertensive (98%), with clinical HF characterized by 65% NYHA III-IV, nearly all on a loop diuretic, and 70% with a HF hospitalization in the prior year. PCA separated HFpEF from HFrEF and CON with minimal overlap and this persisted after adjusting for primary co-morbidities: BMI, sex, age, diabetes, and renal function. Hierarchical clustering confirmed group separation. Nearly half the significantly altered genes in HFpEF versus CON (1882 up, 2593 down) changed in the same direction in HFrEF; however, 5745 genes were uniquely altered between HF groups. Compared to CON, uniquely upregulated genes in HFpEF were enriched in mitochondrial ATP synthesis/electron transport, pathways downregulated in HFrEF. HFpEF-specific down-regulated genes engaged endoplasmic reticulum stress, autophagy, and angiogenesis. BMI differences largely accounted for HFpEF upregulated genes whereas neither this nor broader co-morbidity adjustment altered pathways enriched in downregulated genes. NMF identified three HFpEF transcriptomic subgroups with distinctive pathways and clinical correlates, including a group closest to HFrEF with higher mortality, and a mostly female group with smaller hearts and pro-inflammatory signaling. These groupings remained after sex adjustment. WGCNA analysis yielded analogous gene-clusters and clinical groupings. Conclusions: HFpEF exhibits distinctive broad transcriptomic signatures and molecular subgroupings with particular clinical features and outcomes. The data reveal new signaling targets to consider for precision therapeutics.

PDE9 Inhibition Activates PPARα to Stimulate Mitochondrial Fat Metabolism and Reduce Cardiometabolic Syndrome

“…Group 1 had fewer patients with diabetes, their left ventricles were smaller with less hypertrophy, and plasma natriuretic peptide levels lower as compared to Group 2. Interestingly, Group 1 overlaps with a HFpEF subgroup we had previously identified using agnostic non-negative matrix factorization and the broad transcriptome (35) , that contained mostly females with smaller hearts and pro-inflammatory signaling (Table S1). Group 2 overlaps with a second sub-group whose hearts display expression profiles closest to that for HF with low EF (35) .…”

“…Interestingly, Group 1 overlaps with a HFpEF subgroup we had previously identified using agnostic non-negative matrix factorization and the broad transcriptome (35) , that contained mostly females with smaller hearts and pro-inflammatory signaling (Table S1). Group 2 overlaps with a second sub-group whose hearts display expression profiles closest to that for HF with low EF (35) . These results support the relevance of PPARA downregulation in HFpEF and reveal a subgroup that may be particularly responsive to enhancement by PDE9-I.…”

“…Among the most prominent clinical syndromes combining morbid obesity and CMS is HFpEF, which now affects over half of all patients with heart failure (11) . Our RNAseq analysis of differentially expressed genes in myocardium from human HFpEF versus controls found the transcriptome is potently influenced by BMI, and identified patient subgroups with distinct signaling pathway and clinical characteristics (35) . Using this database, we now show mRNA abundance for PPARA, PPARG , and PPARGC1A is reduced by ∼40% (adjusted q-score, p<1e -6 for each, Figure 6a) in HFpEF versus controls.…”

Xbp1s-FoxO1 axis governs lipid accumulation and contractile performance in heart failure with preserved ejection fraction

“…Similarly, in two models of reduced cardiac lipid accumulation in HFpEF (Xbp1 overexpression and FoxO1 deletion) we did not observe an increase in FA oxidation in cardiomyocytes, suggesting that the prevalent mechanisms of lipid accumulation in HFpEF cardiomyocytes are activation of FA uptake/biogenesis pathways. Dysregulation of the UPR pathway has emerged as a hallmark of cardiac alterations in HFpEF 31,32 . We have previously demonstrated, in both clinical and experimental HFpEF, inflammationdependent suppression of the IRE1α/Xbp1s arm of the UPR 9 .…”

Phenotyping heart failure using model-based analysis and physiology-informed machine learning

“…The distinct HFpEF populations found here are consistent with the recent studies describing HFpEF as a disparate phenotype. In one such study, analysis of RNA sequencing of right ventricular septal endocardial biopsies on control, HFrEF, and HFpEF patients through unsupervised machine learning identified three HFpEF transcriptome subgroups with distinctive pathways and clinical correlations (Hahn et al, 2021). These HFpEF subgroups included: a hemodynamic-driven HFpEF group close to HFrEF showing the worst clinical outcomes; a HFpEF cohort with smaller hearts and inflammatory and matrix signatures; and a third heterogeneous phenotype with worse HF symptoms but lower NT-proBNP and smaller hearts that remains distinct from HFrEFs.…”