Use of a proximity extension assay proteomics chip to discover new biomarkers for human atherosclerosis

Lind, Lars; Ärnlöv, Johan; Lindahl, Bertil; Siegbahn, Agneta; Sundström, Johan; Ingelsson, Erik

doi:10.1016/j.atherosclerosis.2015.07.023

Cited by 121 publications

(100 citation statements)

References 28 publications

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“…43 To note is that of the 16 proteins that showed a false discovery rate <0.05 about incident ischemic stroke in the PIVUS sample in this study, only MMP-12, osteoprotegrin, and GDF-15 were identified to be related to carotid artery atherosclerosis by guest on May 8, 2018 http://stroke.ahajournals.org/ in the same sample in the recently published study. Because an atherosclerotic ischemic event is a combination of plaque presence, plaque rupture and prothrombotic/nonfibrinolytic blood MMP-12, osteoprotegrin, and GDF-15 are most likely related to plaque presence, whereas other proteins identified in this study are more likely to be related to these other events in the atherosclerotic ischemic event chain.…”

Section: Ischemic Stroke and Atherosclerosismentioning

confidence: 75%

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Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip

Lind

Siegbahn

Lindahl

et al. 2015

Stroke

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Eligible subjects were 70 years of age and living in the city of Uppsala, Sweden. Subjects were chosen at random from the Total Background and Purpose-Emerging technologies have made it possible to simultaneously evaluate a large number of circulating proteins as potential new stroke risk markers. Methods-We explored associations between 85 cardiovascular proteins, assessed by a proteomics chip, and incident ischemic stroke in 2 independent cohorts of elderly (Prospective Investigation of the Vasculature in Uppsala Seniors [PIVUS]: n=977; 50% women, mean age=70.1 years, 71 fatal/nonfatal ischemic stroke events during 10.0 years; and Uppsala Longitudinal Study in Adult Men [ULSAM]: n=720, mean age=77.5 years, 75 ischemic stroke events during 9.5 years). The proteomics chip uses 2 antibodies for each protein and a polymerase chain reaction step to achieve a highspecific binding and the possibility to measure multiple proteins in parallel, but gives no absolute concentrations. Results-In PIVUS, 16 proteins were related to incident ischemic stroke using a false discovery rate of 5%. Of these, N-terminal pro-B-type natriuretic peptide (P=0.0032), adrenomedullin (P=0.018), and eosinophil cationic protein (P=0.0071) were replicated in ULSAM after adjustment for established stroke risk factors. In predefined secondary metaanalyses of individual data, interleukin-27 subunit α, growth/differentiation factor 15, urokinase plasminogen activator surface receptor, tumor necrosis factor receptor superfamily member 6, macrophage colony-stimulating factor 1, and matrix metalloproteinase-7 were also potential risk markers for ischemic stroke after adjustment for multiple comparisons (P<0.0006). The addition of N-terminal pro-B-type natriuretic peptide, adrenomedullin, and eosinophil cationic protein to a model with established risk factors increased the C-statistic from 0.629 to 0.689 (P=0.001). Conclusions-Our data suggest that large-scale proteomics analysis is a promising way of discovering novel biomarkers that could substantially improve the prediction of ischemic stroke. Lind et al New Risk Markers for Ischemic Stroke 3341Population Register. In total, 1016 individuals of 2025 invited took part in the investigation (50.1%) at age 70 years when also the blood sample for proteomics was collected. 12 A follow-up of incident ischemic stroke was performed after 10 years, without any loss of follow-up. After exclusion of the 39 individuals with stroke before the baseline investigation in Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS), 71 of remaining 977 subjects experienced an ischemic stroke during a median follow-up of 10.0 years (range, 0.04-10.9 years), resulting in an incidence rate of 7.9 per 1000 person years at risk. ULSAM StudyUppsala Longitudinal Study in Adult Men (ULSAM) is a longitudinal population-based study including men born between 1920 and 1924 in Uppsala County, Sweden, being invited for the first time at age 50 years (n=2322). 13 This study used the 77-year examination cycle as base...

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Section: Ischemic Stroke and Atherosclerosismentioning

confidence: 75%

Section: Ischemic Stroke and Atherosclerosismentioning

confidence: 99%

Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip

Lind

Siegbahn

Lindahl

et al. 2015

Stroke

Self Cite

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“…In a population-based study of elderly men, it was used to identify seven proteins associated with carotid plaque burden 98 and three proteins associated with ischemic stroke, 99 of which the latter were replicated in an independent cohort and resulted in a modest improvement in predictive accuracy.…”

Section: Recent Progress In Plasma Proteomics Of Cardiovascular Diseasementioning

confidence: 99%

Emerging Affinity-Based Proteomic Technologies for Large-Scale Plasma Profiling in Cardiovascular Disease

Smith¹,

2017

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Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision-making. Routinely used plasma biomarkers include troponins, natriuretic peptides and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, as well as the broad range of abundance levels. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages limiting sample throughput. Multiplexing of targeted methods based on capture and detection of specific proteins are therefore receiving increasing attention in plasma proteomics. Immunoaffinity assays are the workhorse for measuring individual proteins but have been limited for proteomic applications by long development times, cross-reactivity preventing multiplexing, specificity issues, and incomplete sensitivity to detect proteins in the lower range of the abundance spectrum (below picograms per milliliter). Emerging technologies to address these issues include nucleotide-labeled immunoassays and aptamer reagents which can be automated for efficient multiplexing of thousands of proteins at high sample throughput, coupling of affinity capture methods to mass spectrometry for improved specificity, and ultrasensitive detection systems to measure low-abundance proteins. In addition, proteomics can now be integrated with modern genomics tools to comprehensively relate proteomic profiles to genetic variants, which may both influence binding of affinity reagents and serve to validate the target specificity of affinity assays. The application of deep quantitative proteomic profiling to large cohorts has thus become increasingly feasible with emerging affinity methods. The aims of this article are to provide the broad readership of Circulation with a timely overview of emerging methods for affinity proteomics and recent progress in cardiovascular medicine based on such methods.

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“…14 Recently, Lind et al found an association between Tim-1 and plaque occurrence in carotid arteries in a human population-based study using proteomic arrays. 15 Interestingly, a SNP in the TIM-4 encoding gene TIMD4 is associated with lowered LDL, triglycerides and cardiovascular disease. 16, 17 However, it is not known if this SNP affects the expression or function of Tim-4.…”

Section: Introductionmentioning

confidence: 99%

Blockade of Tim-1 and Tim-4 Enhances Atherosclerosis in Low-Density Lipoprotein Receptor–Deficient Mice

Foks

Engelbertsen

Kuperwaser

et al. 2016

ATVB

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Objective T cell immunoglobulin and mucin domain (Tim) proteins are expressed by numerous immune cells, recognize phosphatidylserine (PS) on apoptotic cells and function as costimulators or coinhibitors. Tim-1 is expressed by activated T cells but is also found on dendritic cells and B cells. Tim-4, present on macrophages and dendritic cells, plays a critical role in apoptotic cell clearance, regulates the number of PS-expressing activated T cells and is genetically associated with low LDL and triglyceride levels. Since these functions of Tim-1 and Tim-4 could affect atherosclerosis, their modulation has potential therapeutic value in cardiovascular disease. Approach and Results ldlr−/− mice were fed a high-fat diet for 4 weeks while being treated with control (rat IgG1) or anti-Tim-1 (3D10) or -Tim-4 (21H12) mAbs that block PS recognition and phagocytosis. Both anti-Tim-1 and anti-Tim-4 treatments enhance atherosclerosis by 45% compared with controls by impairment of efferocytosis and increasing aortic CD4+T cells. Consistently, anti-Tim-4-treated mice show increased percentages of activated T cells and 'late' apoptotic cells in the circulation. Moreover, in vitro blockade of Tim-4 inhibited efferocytosis of oxLDL-induced apoptotic macrophages. Whereas anti-Tim-4 treatment increased Th1 and Th2 responses, anti-Tim-1 induced Th2 responses but dramatically reduced the percentage of Tregs. Finally, combined blockade of Tim-1 and Tim-4 increased atherosclerotic lesion size by 59%. Conclusion Blockade of Tim-4 aggravates atherosclerosis likely by prevention of phagocytosis of PS-expressing apoptotic cells and activated T cells by Tim-4-expressing cells, whereas Tim-1-associated effects on atherosclerosis are related to changes in Th1/Th2 balance and reduced circulating Tregs.

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Use of a proximity extension assay proteomics chip to discover new biomarkers for human atherosclerosis

Cited by 121 publications

References 28 publications

Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip

Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip

Emerging Affinity-Based Proteomic Technologies for Large-Scale Plasma Profiling in Cardiovascular Disease

Blockade of Tim-1 and Tim-4 Enhances Atherosclerosis in Low-Density Lipoprotein Receptor–Deficient Mice

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