Kuku, Kayode O.

BACKGROUND: Heart failure (HF) is a heterogeneous syndrome with high mortality. The need for a new taxonomy of HF is recognized; up to now, such phenomapping efforts have primarily used clinical data. Proteomics offers potential for more precise phenotypic identification and mechanistic insights. However, few phenomapping studies have used this approach, and all have focused on targeted cardiovascular proteomics panels and a restricted HF ejection fraction group. METHODS: We measured over 7000 plasma proteins in a population-based cohort of 1351 patients with HF, used k-means clustering to identify distinct phenogroups, and compared their clinical characteristics and all-cause mortality. RESULTS: Three proteomics-defined phenogroups were identified, with substantial differences in survival (phenogroup 1 5-year survival probability, 65% [95% CI, 61%–68%]; phenogroup 2, 45% [40%–51%]; phenogroup 3, 26% [22%–30%]), independent of clinical characteristics. Phenogroups also exhibited differences in several measures suggesting poorer health, including NT-proBNP (N-terminal pro-B-type natriuretic peptide), kidney function, and Meta-Analysis Global Group in Chronic Heart Failure scores, but did not differ by ejection fraction or New York Heart Association class. CONCLUSIONS: Our study demonstrates that molecular phenomapping can stratify patients with HF into distinct subgroups that go beyond predefined clinical classifications.

Background: Heart failure (HF) is a heterogeneous syndrome with high mortality. Previous work characterizing HF subgroups primarily relied on clinical data to cluster patients, an approach constrained by the boundaries of documented clinical features. Clustering based on biomarker data, such as proteomics, may provide insights into underlying molecular processes. However, few studies have used this approach, and all used targeted cardiovascular proteomics panels and a restricted HF ejection fraction group. Hypothesis: We used unsupervised clustering analysis to characterize molecular phenogroups in a population-based HF cohort using a large-scale array of circulating plasma proteins. We hypothesized that distinct proteomic-defined phenogroups would exhibit differences in clinical characteristics, mortality, and protein expression. Methods: We measured 7151 SOMAmers (Slow off-rate modified aptamers) targeting human proteins via the SomaLogic 7K SomaScan assay in 1351 HF patients. After feature selection, 831 SOMAmers were used in k-means clustering of patients via R package “ConsensusClusterPlus.” Phenogroups were compared for clinical characteristics, all-cause mortality, and protein expression. Results: Three phenogroups were identified, exhibiting different clinical characteristics ( Table 1 ) and survival probabilities (5-year survival probability in phenogroup 1: 65% [61%, 68%], phenogroup 2: 45% [40%, 51%], and phenogroup 3: 26% [22%, 30%]). In covariate-adjusted Cox models, membership in phenogroups 2 and 3 was significantly associated with increased rate of mortality compared to phenogroup 1. Phenogroups did not differ by ejection fraction or New York Heart Association class. Pathway overrepresentation analysis of differentially expressed SOMAmers identified pathways associated with inflammatory response and immune cell trafficking. Conclusions: Unsupervised clustering analysis using large-scale proteomics data identified three HF phenogroups with different proteomic signatures, clinical characteristics, and outcomes. Future work is necessary to elucidate how molecular differences contribute to heterogeneity in HF to improve risk stratification beyond current recommended clinical guidelines.

Introduction: Coronary disease is the most common cause of heart failure (HF). HF is classified as ischemic (IHF) or non-ischemic (NIHF) based on this etiology. IHF and NIHF have distinct mechanisms not accounted for by ejection fraction (EF) and an improved understanding of the differences could drive the discovery of novel therapeutic targets. We therefore sought to identify proteomic signatures between IHF and NIHF. Methods: Proteomic profiling using the SomaScan®1.7K was performed using plasma samples from HF patients in a community cohort (Rochester Epidemiology Project, 2003-2012). IHF was defined by prior myocardial infarction, percutaneous coronary intervention or coronary artery bypass graft, or obstructive disease in at least 1 vessel on coronary angiography. We compared the protein expression levels between IHF and NIHF using t-test and applied the Benjamini-Hochberg false-discovery rate (FDR) procedure for multiple comparisons. We explored pathway analysis for functional annotations using the biological process component of the Gene Ontology Resource (Panther 17v). Results: Among 1,388 patients, there were 518 IHF patients (age: 75±12years, 39.4% female, NYHA Class III/IV: 72.5%, EF:45±15%), and 870 NIHF patients (age: 75±14years, 53.6% female, NYHA Class III/IV: 66.9%, EF:49±17%). Among 7335 plasma proteins quantified, 63 unique proteins (FDR < 0.05) were differentially expressed between IHF and NIHF. Thirty-seven proteins including Troponin-I and T, and Myoglobin showed increased expression in IHF compared to NIHF and 26 including IGFBP-3 showed decreased expression. Pathophysiologic pathways including angiogenesis, coagulation, and lipid metabolism were represented in IHF, while inflammation and remodeling signaling pathways were dominant in relation to NIHF. Conclusions: High-throughput proteomic techniques are able to delineate IHF versus NIHF patients based on distinct biomarkers and pathophysiologic processes.

Introduction: Heart failure (HF) is a complex syndrome with high mortality often associated with impaired kidney function. Estimated glomerular filtration rate (eGFR) is central to kidney function assessment in HF. However, novel proteins related to kidney function (lipocalin 2 [LCN2], macrophage inhibitory cytokine 1 [MIC1], T cell immunoglobulin and mucin domain 1 [TIM1]) may improve risk stratification of HF patients, beyond eGFR. Their prognostic contribution remain to be fully explored. Hypothesis: Proteomic assessment of kidney function biomarkers improves risk stratification in HF. Methods: Clinical data and biospecimens were collected from a HF community cohort in Southeastern Minnesota from 2003-2012. Serum creatinine was measured in 1,388 patients and eGFR was calculated with the 2021 Chronic Kidney Disease (CKD) Epidemiology Collaboration equation. CKD was defined as an eGFR <60 mL/min/1.73m 2 . Plasma proteins were measured using the SomaLogic aptamer-based technology SomaScan®. In HF patients with and without CKD, Cox proportional hazard models were used to estimate the association between kidney function biomarkers and mortality, after adjustment for Meta-Analysis Global Group in Chronic HF (MAGGIC) risk score. Results: At HF index, patients were on average 75±13 years of age and 48% female. Patients had a median eGFR of 57 mL/min/1.73m 2 and 64% had CKD. Adjusted geometric mean levels of LCN2, MIC1, and TIM1 levels were 20-30% higher in patients with CKD. Patients with CKD were at higher risk of dying (HR 1.6, 95% CI 1.4-1.8). Patients with above median levels of LCN2, TIM1, MIC1 were at higher risk of dying, irrespective of CKD (See Figure). Conclusions: In a HF community cohort, several novel kidney function biomarkers provided further risk stratification in patients with and without CKD.

Introduction: Heart Failure (HF) is a syndrome of high comorbidity and mortality. The impact of comorbidities on life expectancy in HF is well studied, but guideline-recommended disease-centric risk scores such as the Meta-analysis Global Group in Chronic Heart Failure (MAGGIC) score may not fully account for the effect of comorbidities. The Charlson Comorbidity Index (Charlson) is a validated measure that quantifies the prognostic impact of comorbidities. Objective: To examine the incremental value of Charlson over MAGGIC in predicting death in HF. Methods: In a population-based HF cohort, we computed MAGGIC and Charlson scores using electronically linked medical records. Patients were divided based on ejection fraction (EF) into reduced [EF <50%, HFrEF] or preserved [EF ≥50%, HFpEF]. Cox regression was performed to assess the association between the risk scores and mortality. The incremental value of Charlson over MAGGIC was tested by calculating the area under the ROC [receiver operating characteristic] curves (AUCs) with 95% confidence interval (CI). Results: We studied 1,388 patients with HF validated using the Framingham criteria (mean age, 75±13 years, 48% female, mean EF, 49±17%). The median Charlson was 7.0 (interquartile range 5.0-9.0) and was higher in HFpEF than HFrEF (7.0 [5.0-9.0] vs. 6.0 [4.0-8.3] respectively. Over a median follow-up of 13.9 years (13.3-14.2), mortality was 17.4% (95% CI, 15.4 -19.3%) and 36.8% (95% CI, 34.2-39.3%) at 1, and 3 years respectively. In regression analysis, increasing MAGGIC and Charlson were independently associated with death (HR 1.09, 95% CI 1.08-1.11 and HR,1.22, 95% CI 1.20-1.24, both p <0.001) irrespective of EF. Discrimination ability was improved by adding Charlson over MAGGIC (Table), reaching statistical significance at 3 years. Conclusion: In this HF cohort, the Charlson index provided an added value over MAGGIC in predicting the risk of death at 3 years. These findings emphasize the importance of accounting for comorbidities in mid-term risk stratification in HF.

Introduction: Over six million U.S. adults have heart failure (HF). Evaluation of kidney function is critical to the care of patients with HF but may not be fully captured by traditional measures, such as estimated glomerular filtration rate (eGFR) or the Meta-Analysis Global Group in Chronic HF (MAGGIC) risk score. Identifying patients at highest risk of progressive chronic renal insufficiency (PCRI) may improve risk stratification in HF, beyond these traditional measures. High-throughput proteomics has allowed for the development of PCRI risk scores based on novel kidney function biomarkers. However, the prognostic value of a proteomic-based PCRI risk score in HF has not been explored. Hypothesis: Proteomic-based PCRI risk scores will improve risk stratification in HF. Methods: Clinical data and plasma were collected from 1,389 patients in a HF community cohort from Southeastern Minnesota (2003-2012). Results from the aptamer-based technology SomaScan® were used to derive PCRI risk scores using the SomaSignal™ Kidney Prognosis test, a protein-based algorithm developed to predict risk of PCRI within four years. Cox proportional hazard models were used to estimate the association between quintiles of PCRI and mortality, after adjustment for the MAGGIC score. Results: PCRI risk scores were available for 1,349 patients who were on average 75±13 years of age, 48% female, and had a median eGFR of 57 mL/min/1.73m 2 . There was a positive association with mortality across PCRI risk quintiles, after adjustment for the MAGGIC score. (Figure). Overall, the highest quintile was associated over a two-fold higher risk of mortality compared with the lowest quintile (HR 2.3, 95% CI 1.8,2.8). The higher risk of mortality remained in analyses stratified by patients with (HR 1.5, 95% CI 1.1,2.1) and without (HR 2.2, 95% CI 1.4,3.5) an eGFR <60 mL/min/1.73 m 2 . Conclusions: In this community HF cohort, proteomic-based PCRI risk scores improve risk stratification, independent of traditional measures of kidney function.

Abstract Background Heart failure (HF) is a complex clinical syndrome that affects over 60 million persons worldwide.1 The 5-year survival rate of HF is less than 50% irrespective of ejection fraction (EF) and the limitations of EF in sufficiently phenotyping HF are recognized.2,3 High throughput proteomics assays are an attractive option for precision phenotyping.4 Purpose To explore the proteomic profiles and biomarker pathways associated with death in an HF community cohort. Methods We measured proteomics in plasma specimens collected from an HF cohort (2003–2012) of patients predominantly of European Ancestry (92%). The relative concentrations of circulating plasma proteins were measured using an aptamer-based assay containing 7335 human protein targets. Proteins significantly associated with mortality were selected while adjusting for age, sex, and eGFR. These proteins were employed in clustering analysis and subjected to 10-fold cross-validation. We quantified and corrected the clustering bias via bootstrapping and subsequently validated the results via semi-supervised clustering. Multivariable Cox regression was implemented for the cluster variable while adjusting for the Meta-analysis Global Group in Chronic Heart Failure (MAGGIC) risk score. Additionally, we performed enrichment and pathway analysis of the outcome-associated proteins considering significance thresholds of −log10(P-value) &gt;2, FDR corrected P&lt;0.05 (regulator analysis) and Z-scores of &gt;2 and &lt;−2 as thresholds for activation and inhibition of proteins/pathways. Results From a total of 1,388 patients (mean age 75±13; 52% male), 2 distinct clusters, (HR: 2.04; 95% CI [1.78–2.34]; p-value: &lt;0.0001 independent of MAGGIC) were identified, cluster 1; n=722, mean age 72±14; NYHA class III/IV: 41%/26%; EF: 47%±17 and cluster 2; n=666, mean age 79±11; NYHA class III/IV: 41%/31%, EF: 48%±16 based on the 447 proteins [354 positively and 93 negatively] significantly associated with mortality (1,158 events). Gene-set enrichment analysis of all 447 proteins revealed cell adhesion, extracellular matrix organization, enzyme-linked protein/tyrosine kinase signaling pathways, humoral immune response, tissue development, growth factor signaling, post-translational protein modification, and platelet degranulation as the dominant biological themes. Finally, we found 18 upstream regulators predicted to be driving the expressions of the proteins in the dataset including a predicted outcome-associated protein-Transforming Growth Factor Beta 1 – TGFB1 (p=7.46E-09), Interleukin 1B, IL1B (p=9.40E-08), and oncostatin M, OSM (p=6.61E-05) as the top 3 regulators (predicted activation) based on FDR-corrected statistical significance of P&lt;0.05 (Figure 1) Conclusion We identified distinct clusters based on proteomic profiles associated with HF mortality independently of clinical prognostic makers. Further, we delineated protein regulators driving the major pathways associated with HF survival. Funding Acknowledgement Type of funding sources: Public Institution(s). Main funding source(s): Department of Intramural Research, NIH/NHLBI