Publications

Proteomic profiling may provide insights into new biomarkers and pathways in coronary heart disease (CHD). We profiled ∼1,300 proteins in 1,967 Black individuals in the Jackson Heart Study and found Secreted and Transmembrane Protein 1 (SECTM1), a monocyte chemoattractant, to be our top novel finding associated with incident CHD. We validated our findings in the Cardiovascular Health Study. The top variant (rs116473040) associated with SECTM1 was associated with circulating monocyte percentage of white blood cells in a genomic database. In vivo studies demonstrated that recombinant SECTM1a increased the proportion of proatherogenic Ly6Chi monocytes, suggesting a pathway by which SECTM1 may contribute to CHD.

BACKGROUND: Substantial efforts have been dedicated to exploring the link between genetic regulation and the proteome, informing studies of complex trait mechanisms. Most of these efforts have been limited to populations of European ancestry.

RESULTS: We conduct an Olink protein quantitative trait locus (pQTL) analysis on 1245 proteins involving 1033 self-identified African American (AA) and 1764 non-Hispanic White (NHW) participants from the Women's Health Initiative and Framingham Heart Study. For replication of candidate pQTLs, we use data from 534 self-identified AA adults from the Jackson Heart Study and protein genome-wide association analysis statistics from the UK Biobank Pharma Proteomics Project, including 54,219 participants, of whom 931 are of African ancestry. In total, we identify and validate 5103 pQTLs (4496 or 88% cis- and 602 or 12% trans-pQTLs) for 983 proteins. Among these, 195 are previously unreported, with most (166 or 85%) identified in our AA sample, many of which were essentially monomorphic in European reference populations. Several of these newly identified African ancestry-specific pQTLs have been reported in ClinVar; our results suggest impact on circulating protein levels, potentially bolstering evidence for clinical significance. We identify a "cis pQTL hotspot" within the leukocyte receptor gene cluster on human chromosome 19q13.4. We also provide examples where a particular cis-pQTL, identified through conditional analysis, offers biological insights into an overlapping GWAS signal for disease susceptibility.

CONCLUSIONS: The identification of previously undescribed African ancestry-specific pQTLs contributes to understanding protein genetic regulation and highlights the significance of proteomic analysis in diverse populations.

BACKGROUND: Pathogenic variants in the lamin A/C (LMNA) gene cause an aggressive form of dilated cardiomyopathy (DCM), marked by higher rates of advanced conduction disease, malignant ventricular tachyarrhythmias, and advanced heart failure compared with other causes of nonischemic cardiomyopathy. However, the mechanisms that drive the development and progression of LMNA DCM are incompletely understood.

METHODS: To identify proteins and biological pathways associated with likely pathogenic/pathogenic LMNA variants, we measured ≈3000 plasma proteins using the OLINK platform in a genetic DCM cohort consisting of LMNA (n=41) and sarcomeric (n=18) DCM, along with phenotype-negative individuals from family-based cascade screening (n=55) with (LMNA, n=16; sarcomere, n=12) or without the family variant (genotype negative, n=27).

RESULTS: We identified several novel proteins associated with LMNA DCM compared with sarcomeric DCM, including EDA2R (ectodysplasin A2 receptor; per log2 fold change in relative protein abundance, β=3.0; P=4×10-³) and MYL4 (myosin light chain 4; β=2.32; P=5×10-³). Among the proteins associated with LMNA DCM, 26 showed concordant differential gene expression from single-cell sequencing in cardiomyocytes from myocardial biopsies in advanced LMNA heart failure compared with control hearts (false discovery rate, <5%). We performed principal component analyses on these 26 proteins to identify proteomic signatures of LMNA DCM and found the first principal component to be associated with left ventricular ejection fraction and complete heart block in the LMNA DCM cohort. Six proteins-EDA2R, MYL4, CRIM1 (cysteine-rich transmembrane bone morphogenetic protein regulator 1), TPR (translocated promoter region), FSTL3 (follistatin-like 3), and NFYA (nuclear transcription factor Y)-were associated with LMNA pathogenic variants across phenotype-negative individuals, DCM, and their respective cardiomyocyte RNA expression profiles in advanced heart failure.

CONCLUSIONS: Proteomic profiling in individuals with likely pathogenic/pathogenic LMNA variants illuminated integral pathways across the spectrum of LMNA DCM. These findings may help advance genotype-driven biomarker discovery and tailored therapeutic development in LMNA DCM.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) exhibits marked heterogeneity in lung function decline, mortality, exacerbations, and other disease-related outcomes. Omic risk scores (ORS) estimate the cumulative contribution of omics, such as the transcriptome, proteome, and metabolome, to a particular trait. This study evaluates the predictive value of ORS for COPD-related traits in both smoking-enriched and general population cohorts.

METHODS: ORS were developed and tested in 3,339 participants of Genetic Epidemiology of COPD (COPDGene) with blood RNA-sequencing, proteomic, and metabolomic. Single- and multi-omic risk scores were trained 24 cross-sectional and five longitudinal traits using 80% of the data, focusing on disease severity, exacerbations, and traits from spirometry and computed tomography scans. Multivariable models were used to test ORS associations with outcomes in remaining COPDGene participants and externally validated in SubPopulations and InteRmediate Outcome Measures in COPD Study (SPIROMICS) (n = 2,177) and Multi-Ethnic Study of Atherosclerosis (MESA) (n = 1,000).

RESULTS: In the COPDGene testing set, 69 of 72 single-omic ORS showed significant associations with 24 cross-sectional traits (adjusted p-value < 0·05). One of 15 longitudinal ORS was associated with changes in trait values between COPDGene visits. Significant associations were observed for all 38 cross-sectional ORS tested in SPIROMICS and for 16 of 24 in MESA. Proteomic and metabolomic risk scores generally displayed stronger associations than transcriptomic scores.

DISCUSSION: Blood-based ORS can predict cross-sectional and future COPD-related traits in both smoking-enriched and general population cohorts.

BACKGROUND: In hypertrophic cardiomyopathy (HCM), the mechanisms through which pathogenic sarcomere variants (G+) lead to left ventricular hypertrophy (LVH) are not understood.

METHODS: VANISH (Valsartan for Attenuating Disease Evolution in Early Sarcomeric Hypertrophic Cardiomyopathy) was a multicenter, double-blind, placebo-controlled, randomized trial testing valsartan's ability to attenuate phenotypic progression in early sarcomeric (G+LVH+) and subclinical HCM (G+LVH‒). The outcome was a composite z-score reflecting change in cardiac remodeling from baseline to year 2 (end of study). Baseline and year 2 blood samples were used to quantify 276 proteins using a proximity extension assay (Olink, Sweden). We explored relative differences in protein abundance between early and subclinical HCM at baseline. In addition, we compared proteomic changes between baseline and year 2 in subclinical HCM participants who experienced phenotypic conversion to early HCM (convertors) versus nonconvertors; early HCM participants receiving valsartan versus placebo; and in association with changes in the phenotypic progression z-score. Comparisons were made using the t-test, Mann-Whitney U test, linear mixed models, and generalized linear models, correcting for multiple testing using a 5% false discovery rate.

RESULTS: Circulating proteins were analyzed in 192 participants (32 subclinical and 160 early HCM [81 allocated to valsartan]). NT-proBNP (N-terminal pro-B-type natriuretic peptide) differentiated early from subclinical HCM and tracked with phenotypic progression in early HCM (1-unit worsening in z-score associated with a 27% increase in NT-proBNP [95% CI, 17-37%]). Some extracellular matrix remodeling proteins showed a higher abundance (eg, tissue-type plasminogen activator) in early compared with subclinical HCM or tracked with disease progression (decorin) in early HCM. Some growth factors had a higher relative abundance in early HCM (eg, fibroblast growth factor-21). While no individual protein was able to distinguish phenotypic convertors from nonconvertors, multiprotein panels including lipocalin 2, lectin-like oxidized low-density lipoprotein receptor 1, and either NT-proBNP or interleukin-17 receptor A, could distinguish these groups.

CONCLUSIONS: NT-proBNP was the most informative protein, showing a higher abundance in early compared with subclinical HCM and tracking with the phenotypic progression z-score in early-stage HCM. Studying pathways involving growth factors and extracellular matrix remodeling may yield additional insights into the mechanisms behind disease progression in sarcomevere variant carriers and early HCM.

REGISTRATION: URL: https://www.clinicaltrials.gov; Unique identifier: NCT01912534.

Measures from affinity-proteomics platforms often correlate poorly, challenging interpretation of protein associations with genetic variants (pQTL) and phenotypes. Here, we examined 2,157 proteins measured on both SomaScan 7k and Olink Explore 3072 across 1,930 participants with genetic similarity to European, African, East Asian, and Admixed American ancestry references. Inter-platform correlation coefficients for these 2,157 proteins followed a bimodal distribution (median r=0.30). Protein measures from each platform were associated with genetic variants (pQTLs), and one-third of the pQTL signals were driven by protein-altering variants (PAVs). We highlight 80 proteins that correlate differently across ancestry groups likely due to differing PAV frequencies by ancestry. Furthermore, adjustment for PAVs with opposite directions of effect by platform improved inter-platform protein measure correlation and resulted in more concordant genetic and phenotypic associations. Hence, PAVs need to be accounted for across ancestries to facilitate platform-concordant and accurate protein measurement.

AIMS: Inflammation has been implicated in the pathogenesis of desmoplakin (DSP) cardiomyopathy, and retrospective studies have described abnormal myocardial fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) findings in symptomatic patients eventually diagnosed with DSP cardiomyopathy. We aimed to prospectively investigate if ambulatory patients with DSP cardiomyopathy had myocardial FDG uptake PET/CT imaging indicative of myocardial inflammation and if they had circulating biomarker evidence of inflammation.

METHODS: We prospectively recruited participants with DSP cardiomyopathy and participants with titin cardiomyopathy as a comparator group. Blood samples for clinical labs and proteomic profiling, myocardial perfusion single-photon emission computed tomography (SPECT) and myocardial FDG PET/CT were obtained for all participants.

RESULTS: Ten participants with DSP cardiomyopathy (median age 36.5 years (28, 60); 80% female; 100% White and non-Hispanic) and four participants with titin cardiomyopathy (median age 55.5 years [38.5, 64]; 50% female; 100% White and non-Hispanic) were recruited. There were no significant differences between the groups in white blood cell count, ESR, hsCRP or hsTn. Three participants with DSP cardiomyopathy and two participants with titin cardiomyopathy had non-specific myocardial FDG uptake on PET/CT. All other participants had no myocardial FDG uptake. Integration of miRNA differential expression and their predicted targets from the differential expression proteomics data identified a total of 11 inverse miRNA-mRNA pairs potentially involved in the regulation of top 20 significantly enriched pathways, including pathways involved in metabolism, inflammasome/inflammatory signalling and cell death/pyroptosis.

CONCLUSIONS: In a group of ambulatory patients with DSP and titin cardiomyopathy, we found no differences in FDG PET/CT findings or clinical circulating biomarkers of inflammation. However, miRNA-seq/proteomics analyses identified several enriched pathways and unique miRNA-protein pairs between DSP and titin cardiomyopathy, including pathways involved in inflammasome/inflammatory signalling. Future work will centre on evaluation during myocarditis-like episodes.

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a heterogeneous condition that can lead to atrial fibrillation, heart failure, and sudden cardiac death in many individuals but mild clinical impact in others. The mechanisms underlying this phenotypic heterogeneity are not well defined. The aim of this study was to use plasma proteomic profiling to help illuminate biomarkers that reflect or inform the heterogeneity observed in HCM.

METHODS: The Olink antibody-based proteomic platform was used to measure plasma proteins in patients with genotype positive (sarcomeric) HCM participating in the HCM Registry. We assessed associations between plasma protein levels with clinical features, cardiac magnetic resonance imaging metrics, and the development of atrial fibrillation.

RESULTS: We measured 275 proteins in 701 patients with sarcomeric HCM. There were associations between late gadolinium enhancement with proteins reflecting neurohormonal activation (NT-proBNP [N-terminal pro-B-type natriuretic peptide] and ACE2 [angiotensin-converting enzyme 2]). Metrics of left ventricular remodeling had novel associations with proteins involved in vascular development and homeostasis (vascular endothelial growth factor-D and TM [thrombomodulin]). Assessing clinical features, the European Society of Cardiology sudden cardiac death risk score was inversely associated with SCF (stem cell factor). Incident atrial fibrillation was associated with mediators of inflammation and fibrosis (MMP2 [matrix metalloproteinase 2] and SPON1 [spondin 1]).

CONCLUSIONS: Proteomic profiling of sarcomeric HCM identified biomarkers associated with adverse imaging and clinical phenotypes. These circulating proteins are part of both established pathways, including neurohormonal activation and fibrosis, and less familiar pathways, including endothelial function and inflammatory proteins less well characterized in HCM. These findings highlight the value of plasma profiling to identify biomarkers of risk and to gain further insights into the pathophysiology of HCM.

Plasma proteomic profiles associated with subclinical somatic mutations in blood cells may offer novel insights into downstream clinical consequences. Here, we explore such patterns in clonal hematopoiesis of indeterminate potential (CHIP), which is linked to several cancer and non-cancer outcomes, including coronary artery disease (CAD). Among 61,833 ancestrally diverse participants (3,881 with CHIP) from NHLBI TOPMed and UK Biobank with blood-based DNA sequencing and proteomic measurements (1,148 proteins by SomaScan in TOPMed and 2,917 proteins by Olink in UK Biobank), we identified 32 and 345 unique proteins from TOPMed and UK Biobank, respectively, associated with the most prevalent driver genes (DNMT3A, TET2, and ASXL1). These associations showed substantial heterogeneity by driver genes, sex, and race, and were enriched for immune response and inflammation pathways. Mendelian randomization in humans, coupled with ELISA in hematopoietic Tet2-/- vs wild-type mice validation, disentangled causal proteomic perturbations from TET2 CHIP. Lastly, we identified plasma proteins shared between CHIP and CAD.