Comparative RNA expression analyses from small-scale, single-donor platelet samples

Human platelet microRNA-mRNA networks associated with age and gender revealed by integrated plateletomics

There is little data considering relationships among human RNA, demographic variables, and primary human cell physiology. The platelet RNA and expression-1 study measured platelet aggregation to arachidonic acid, ADP, protease-activated receptor (PAR) 1 activation peptide (PAR1-AP), and PAR4-AP, as well as mRNA and microRNA (miRNA) levels in platelets from 84 white and 70 black healthy subjects. A total of 5911 uniquely mapped mRNAs and 181 miRNAs were commonly expressed and validated in a separate cohort. One hundred twenty-nine mRNAs and 15 miRNAs were differentially expressed (DE) by age, and targets of these miRNAs were over-represented among these mRNAs. Fifty-four mRNAs and 9 miRNAs were DE by gender. Networks of miRNAs targeting mRNAs, both DE by age and gender, were identified. The inverse relationship in these RNA pairs suggests miRNAs regulate mRNA levels on aging and between genders. A simple, interactive public web tool (www.plateletomics.com) was developed that permits queries of RNA levels and associations among RNA, platelet aggregation and demographic variables. Access to these data will facilitate discovery of mechanisms of miRNA regulation of gene expression. These results provide new insights into aging and gender, and future platelet RNA association studies must account for age and gender.

Reverse transcription-PCR methods significantly impact richness and composition measures of expressed fungal cellobiohydrolase I genes in soil and litter

The importance of soil fungi in complex carbon degradation and the recent identification of genes involved in this process have sparked considerable interest in examining fungal gene expression in situ. Expression of target eukaryotic genes is commonly examined using reverse transcription (RT)-PCR, during which single-stranded (ss) complementary DNA (cDNA) is synthesized from an oligo (dT) primer and the gene of interest is subsequently amplified by PCR using gene specific primers. Another method that is being increasingly employed in environmental gene expression studies is SMART PCR, which generates and amplifies double-stranded (ds) complementary DNA (cDNA) from sscDNA using PCR, prior to gene-specific PCR. We performed a replicated comparison of these two methods using RNA extracted from forest soil and litter to determine if the two approaches yielded comparable results. Richness, composition and reproducibility of gene expression profiles of the fungal glycosyl hydrolase family 7 (GH7) cellobiohydrolase I gene (cbhI) were examined when amplified from sscDNA or dscDNA synthesized using SMART PCR. In the dscDNA libraries from soil or litter samples, richness was significantly reduced and the composition was altered relative to sscDNA libraries. Library composition was significantly more reproducible among replicate sscDNA libraries than among parallel dscDNA libraries from litter. In sum, the reduced richness and altered composition produced in the dscDNA libraries could substantially influence ecological interpretations of the data. Defining the factors underpinning the methodological biases will potentially aid in optimizing the design of gene expression studies in soils and other complex environmental samples.

Relationship between circulating platelet counts and ductus arteriosus patency after indomethacin treatment

OBJECTIVE

To determine whether low platelet counts are related to the incidence of patent ductus arteriosus (PDA) after indomethacin treatment in preterm human infants.

STUDY DESIGN

Multivariable logistic regression modeling was used for a cohort of 497 infants, who received indomethacin (within 15 hours of birth).

RESULTS

Platelet counts were not related to the incidence of permanent closure after indomethacin constriction. There was a relationship between platelet counts and the initial degree of constriction; however, this relationship appeared to be primarily influenced by the high end of the platelet distribution curve. PDA incidence was similar in infants with platelet counts < 50 × 10⁹/L and those with platelet counts above this range. Only when platelet counts were consistently >230 ×10⁹/L was there a decrease in PDA incidence.

CONCLUSION

In contrast to the evidence in mice, low circulating platelet counts do not affect permanent ductus closure (or ductus reopening) in human preterm infants.

Gene expression profiling reveals multiple differences in platelets from patients with stable angina or non-ST elevation acute coronary syndrome

INTRODUCTION

Platelets play a key role in coronary artery disease. They have the capacity of protein synthesis through translation of megakaryocyte-derived mRNAs, which may influence pathophysiological functions. The present study aimed to prove the concept that platelets from patients with non-ST elevation acute coronary syndrome (NSTE-ACS) have differential mRNA expression profiles, in the hypothesis that this may influence their thrombogenicity.

MATERIALS AND METHODS

Gene expression profiles were determined in RNA pools from resting platelets of patients with stable angina (SA, n = 14) or NSTE-ACS (n = 15) using a glass microarray platform. Validation was done by real-time PCR and immunoblot analyses in independent sets of individual samples (26 SA and 17 NSTE-ACS patients, in total). Parallel comparison with healthy subjects was performed to relate the relative abundance of validated genes in CAD patients to a control expression level.

RESULTS

Microarray analysis identified 45 transcripts with a significant ≥ ± 2.0-fold difference in expression between NSTE-ACS and SA platelet pools. Thus, gene expression profiles at least partially discriminate unstable from stable CAD. Validation confirmed a significant over-expression of 3 genes in NSTE-ACS at both mRNA and protein level. In particular, the glycoprotein Ib β-polypeptide (GP1BB) was increased in NSTE-ACS also in comparison with healthy subjects.

CONCLUSION

This study provides evidence that NSTE-ACS platelets are potentially preconditioned to a higher degree of reactivity on the transcriptional level. Our data suggest that a different composition of the mRNA pool might mediate an increased platelet prothrombotic potential in NSTE-ACS patients.

The platelet proteome

PURPOSE OF REVIEW

The proteome is the pool of proteins expressed at a given time and circumstance. The word 'proteomics' summarizes several technologies for visualization, quantitation and identification of these proteins. Recent advances in these techniques are helping to elucidate platelet processes which are relevant to bleeding and clotting disorders, transfusion medicine and regulation of angiogenesis.

RECENT FINDINGS

Over 1100 platelet proteins have been identified using proteomic techniques. Various subproteomes have been characterized, including platelet releasates (the 'secretome'), alpha and dense granules, membrane and cytoskeletal proteins, platelet-derived microparticles, and the platelet 'phosphoproteome'. Proteomic data about platelets have become increasingly available in integrated databases.

SUMMARY

Proteomic experiments in resting and activated platelets have identified novel signaling pathways and secreted proteins which may represent therapeutic targets, as well as potential cancer biomarkers.

P-selectin mRNA is maintained in platelet concentrates stored at 4 degrees C

BACKGROUND

Platelets (PLTs) contain mRNA and synthesize proteins in response to activation. Most guidelines for PLT concentrates (PCs) recommend ambient temperature for storage but the impact of the storage temperature on PLT mRNA content has not yet been investigated.

STUDY DESIGN AND METHODS

Ten leukoreduced apheresis PCs were split and stored at 22 and 4 degrees C. P-selectin mRNA, its expression on PLTs, and its soluble form were quantified. In parallel, cellular (cell count, mean PLT volume), metabolic (pH, pO(2), pCO(2), HCO(3), glucose), and functional markers (swirling, hypotonic shock response, aggregation to collagen) were analyzed. Rotation thrombelastography was used to monitor the hemostatic potential of PLTs. All measurements were performed on Days 1 and 5 of storage.

RESULTS

After 5 days of storage at 4 degrees C, only 31 +/- 27 percent of P-selectin mRNA and 29 +/- 41 percent of glyceraldehyde-3-phosphate dehydrogenase mRNA were lost, while minute amounts of the mRNAs were detectable at 22 degrees C. In PCs stored at 4 degrees C the percentage of P-selectin-positive PLTs was significantly higher when compared to PCs stored at 22 degrees C. Soluble P-selectin concentrations did not significantly differ between both storage temperatures. Thrombelastography revealed significantly shorter reaction times in PLTs kept at 4 degrees C.

CONCLUSION

Our data indicate that storage at 4 degrees C is accompanied by maintained mRNA levels. PLTs with intact mRNA levels and short reaction times in thrombelastography might be functionally superior to PLTs that are devoid of mRNA and show less augmented P-selectin surface expression. In therapeutic applications, that is, if PLTs are transfused to control acute bleeding, PLTs kept at 4 degrees C may be advantageous.

Sepsis alters the megakaryocyte-platelet transcriptional axis resulting in granzyme B-mediated lymphotoxicity

RATIONALE

Sepsis-related mortality results in part from immunodeficiency secondary to profound lymphoid apoptosis. The biological mechanisms responsible are not understood.

OBJECTIVES

Because recent evidence shows that platelets are involved in microvascular inflammation and that they accumulate in lymphoid microvasculature in sepsis, we hypothesized a direct role for platelets in sepsis-related lymphoid apoptosis.

METHODS

We studied megakaryocytes and platelets from a murine-induced sepsis model, with validation in septic children, which showed induction of the cytotoxic serine protease granzyme B.

MEASUREMENTS AND MAIN RESULTS

Platelets from septic mice induced marked apoptosis of healthy splenocytes ex vivo. Platelets from septic granzyme B null (-/-) mice showed no lymphotoxicity.

CONCLUSIONS

Our findings establish a conceptual advance in sepsis: Septic megakaryocytes produce platelets with acutely altered mRNA profiles, and these platelets mediate lymphotoxicity via granzyme B. Given the contribution of lymphoid apoptosis to sepsis-related mortality, modulation of platelet granzyme B becomes an important new target for investigation and therapy.

Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE)

Platelets are anucleated cells that are generated from megakaryocytes via thrombopoiesis. They lack genomic DNA but have a pool of individual mRNA transcripts. Taken together, these mRNAs constitute a platelet transcriptome. Platelets have a unique and reproducible transcript profile, which includes approximately 1,600-3,000 individual transcripts. In this chapter, we will focus on platelet purification and on transcript profiling using an Affymetrix microarray platform and serial analysis of gene expression (SAGE). Platelet purification is described in detail. Large-scale platelet purification schema is designed to purify platelets from apheresis platelet bags (approximately 3-5 x 10(11) platelets/bag). Modification of this schema --small-scale platelet purification--is designed to isolate platelets from 20 ml of peripheral blood. This chapter provides detailed protocols for microarray and SAGE transcript profiling. We also discuss peculiarities of platelet purification, RNA isolation, and transcript profiling.

cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR

The comparison of two RNA populations that differ from the effects of a single-independent variable, such as a drug treatment or a specific genetic defect, can identify differences in the abundance of specific transcripts that vary in a population-dependent manner. There are a variety of methods for identifying differentially expressed genes, including microarray, SAGE, qRT-PCR, and DDGE. This protocol describes a potentially less sensitive yet relatively easy and cost-effective alternative that does not require prior knowledge of the transcriptomes under investigation and is particularly applicable when minimal levels of starting material, RNA, are available. RNA input can often be a limiting factor when analyzing RNA from, for example, rigorously purified blood cells. This protocol describes the use of SMART-PCR to amplify cDNA from sub-microgram levels of RNA. The amplified cDNA populations under comparison are then subjected to suppression subtractive hybridization (SSH-PCR), a technique that couples subtractive hybridization with suppression PCR to selectively amplify fragments of differentially expressed genes. The final products are cDNA populations enriched for significantly over-represented transcripts in either of the two input RNA preparations. These cDNA populations may then be cloned to make subtracted cDNA libraries and/or used as probes to screen subtracted cDNA, global cDNA, or genomic DNA libraries.

Platelet transcriptome and cardiovascular disease

Platelet hyper-reactivity is likely to play a role in cardiovascular disease, but there are no standardized tests to evaluate platelet responsiveness. A 'platelet chip' (a synthetic oligonucleotide microarray representing all platelet-restricted genes) is under development as a tool for high-throughput characterization of platelet-based bleeding and clotting disorders. In future, platelet gene profiling may be used to improve thrombohemorrhagic risk assessment and to guide antiplatelet therapy for patients at risk of cardiovascular disease.

Bioinformatic discovery of novel bioactive peptides

Short synthetic oligopeptides based on regions of human proteins that encompass functional motifs are versatile reagents for understanding protein signaling and interactions. They can either mimic or inhibit the parent protein's activity and have been used in drug development. Peptide studies typically either derive peptides from a single identified protein or (at the other extreme) screen random combinatorial peptides, often without knowledge of the signaling pathways targeted. Our objective was to determine whether rational bioinformatic design of oligopeptides specifically targeted to potentially signaling-rich juxtamembrane regions could identify modulators of human platelet function. High-throughput in vitro platelet function assays of palmitylated cell-permeable oligopeptides corresponding to these regions identified many agonists and antagonists of platelet function. Many bioactive peptides were from adhesion molecules, including a specific CD226-derived inhibitor of inside-out platelet signaling. Systematic screens of this nature are highly efficient tools for discovering short signaling motifs in molecular signaling pathways.