Modeling of clinical phenotypes in systemic lupus erythematosus based on the platelet transcriptome and FCGR2a genotype.

BACKGROUND: The clinical heterogeneity of SLE with its complex pathogenesis remains challenging as we strive to provide optimal management. The contribution of platelets to endovascular homeostasis, inflammation and immune regulation highlights their potential importance in SLE. Prior work from our group showed that the Fcγ receptor type IIa (FcγRIIa)-R/H131 biallelic polymorphism is associated with increased platelet activity and cardiovascular risk in SLE. The study was initiated to investigate the platelet transcriptome in patients with SLE and evaluate its association across FcγRIIa genotypes and distinct clinical features. METHODS: Fifty-one patients fulfilling established criteria for SLE (mean age = 41.1 ± 12.3, 100% female, 45% Hispanic, 24% black, 22% Asian, 51% white, mean SLEDAI = 4.4 ± 4.2 at baseline) were enrolled and compared with 18 demographically matched control samples. The FCGR2a receptor was genotyped for each sample, and RNA-seq was performed on isolated, leukocyte-depleted platelets. Transcriptomic data were used to create a modular landscape to explore the differences between SLE patients and controls and various clinical parameters in the context of FCGR2a genotypes. RESULTS: There were 2290 differentially expressed genes enriched for pathways involved in interferon signaling, immune activation, and coagulation when comparing SLE samples vs controls. When analyzing patients with proteinuria, modules associated with oxidative phosphorylation and platelet activity were unexpectedly decreased. Furthermore, genes that were increased in SLE and in patients with proteinuria were enriched for immune effector processes, while genes increased in SLE but decreased in proteinuria were enriched for coagulation and cell adhesion. A low-binding FCG2Ra allele (R131) was associated with decreases in FCR activation, which further correlated with increases in platelet and immune activation pathways. Finally, we were able to create a transcriptomic signature of clinically active disease that performed significantly well in discerning SLE patients with active clinical disease form those with inactive clinical disease. CONCLUSIONS: In aggregate, these data demonstrate the platelet transcriptome provides insight into lupus pathogenesis and disease activity, and shows potential use as means of assessing this complex disease using a liquid biopsy.

An inflammatory transcriptomic signature in psoriasis associates with future cardiovascular events.

BACKGROUND: Psoriasis is an inflammatory skin disease associated with increased cardiovascular (CV) risk, whose pathogenesis is not fully known. OBJECTIVE: We identified a transcriptomic signature in psoriasis and investigated its association with prevalent and future risk of a CV event to understand the connection between psoriasis and CV disease (CVD). METHODS: Psoriasis patients (n = 37) with a history of moderate-severe skin disease without CVD and 11 matched controls underwent whole blood RNA sequencing. This transcriptomic signature in psoriasis versus controls was evaluated in two CVD cohorts: Women referred for cardiac catheterization with (n = 76) versus without (n = 97) myocardial infarction (MI), and patients with peripheral artery disease (n = 106) followed over 2.5 years for major adverse CV or limb events (MACLE). The association between genes differentially expressed in psoriasis and prevalent and incident CV events was assed. RESULTS: In psoriasis, median age was 44 (IQR; 34-51) years, 49% male and ACC/AHA ASCVD Risk Score of 1.0% (0.6-3.4) with no significant difference versus controls. The median psoriasis area and severity index score (PASI) was 4.0 (IQR 2.9-8.2) with 36% on biologic therapy. Overall, 247 whole blood genes were upregulated and 228 downregulated in psoriasis versus controls (p < 0.05), and 1302 genes positively and 1244 genes negatively correlated with PASI (p < 0.05). Seventy-three genes overlapped between psoriasis prevalence and PASI with key regulators identified as IL-6, IL-1ß and interferon gamma. In the CVD cohorts, 50 of 73 genes (68%) identified in psoriasis associated with prevalent MI, and 29 (40%) with incident MACLE. Key regulator transcripts identified in psoriasis and CVD cohorts included SOCS3, BCL3, OSM, PIM2, PIM3 and STAT5A. CONCLUSIONS: A whole blood transcriptomic signature of psoriasis diagnosis and severity associated with prevalent MI and incident MACLE. These data have implications for better understanding the link between psoriasis, systemic inflammation and CVD.

Gene Expression Signature in Patients With Symptomatic Peripheral Artery Disease.

[Figure: see text].

Circulating inflammatory and atherogenic biomarkers are not increased following single meals of dairy foods.

BACKGROUND/OBJECTIVES: Inflammation characterizes obesity and is nutritionally modifiable. The hypothesis of this study is that full-fat dairy foods influence circulating inflammatory and atherogenic biomarkers according to fermentation status. SUBJECTS/METHODS: Thirteen overweight subjects participated in five test meals. Single breakfasts containing control low-fat milk or 45 g fat from butter, cream, yoghurt or cheese were tested over 3 weeks. Plasmas obtained 3 and 6 h were later analyzed for inflammatory markers interleukin (IL)-6, IL-1ß, tumor necrosis factor-α and high-sensitive C-reactive protein, and atherogenesis-related markers monocyte chemoattractant protein-1, macrophage inflammatory protein-1α, intercellular adhesion molecule-1 and vascular cell adhesion molecule-1. A 4-week study in 12 subjects compared the effects on these biomarkers of diets containing ≈50 g dairy fat daily as either butter, cream and ice cream (non-fermented) or cheese plus yoghurt (fermented) dairy foods. RESULTS: In single-meal study, one outlier subject showed marked increments in biomarkers, hence the following results apply to 12. Within group analysis includes significant falls at 3 h in four inflammatory markers after cream, butter and low fat, and three atherogenesis-related biomarkers after cream. Changes were few after cheese and yoghurt. By 6 h, most values returned to baseline. However, between group analysis showed no differences between the five meals. The 4-week study showed no significant differences in fasting biomarker concentrations between non-fermented and fermented dairy diets. CONCLUSIONS: Single high-fat meals containing sequentially four different full-fat dairy foods did not increase eight circulating biomarkers related to inflammation or atherogenesis. Among subjects, significant falls occurred at 3 h in inflammatory biomarkers after cream and butter but were not specific for full-fat dairy foods. We could not confirm the reported increments in inflammation after fat meals.

What is the economic threshold of soybean aphids (Hemiptera: Aphididae) in enemy-free space?

Soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is a serious pest of soybean, Glycine max (L.) Merr., in the North Central United States. Current management recommendations rely on the application of insecticides based on an economic threshold (ET) of 250 aphids per plant. Natural enemies are important in slowing the increase of aphid populations and can prevent them from reaching levels that can cause economic losses. However, biological control of A. glycines is inconsistent and can be affected negatively by the intensity of agricultural activity. We measured the impact of a natural-enemy-free environment on the capacity of the current ET to limit yield loss. In 2008 and 2009, caged microplots were assigned to one of three treatments: plants kept aphid-free (referred to as the control), plants that experienced a population of 250 aphids per plant (integrated pest management [IPM]), and plants that experienced unlimited aphid population growth (unlimited). The population growth rate of aphids in the unlimited treatment for the 10 d after the application of insecticides to the IPM treatment was calculated using linear regression. The linear equation was solved to determine the mean number of days between the ET and the EIL for an aphid population in absence of predators. The number of days was determined to be 6.97 +/- 1.11 d. The 2-yr average yield for the IPM treatment was 99.93% of the control treatment. Our study suggests the current soybean aphid ET of 250 aphids per plant can effectively protect yield even if the impact of natural enemies is reduced.

Sucrose increases calcium-dependent protein kinase and phosphatase activities in potato plants.

The effect of sucrose on tuber formation, calcium-dependent protein kinase (CDPK) and phosphatase activities was analysed using in vitro cultured potato plants. In short treatments, sucrose induced CDPK and phosphatase activities. In long treatments, sucrose induced tuber formation in the absence of other tuber inducing stimuli. Sorbitol caused a minor increase in CDPK activity and affected plant morphology but did not induce tuber development. The addition of the protein kinase inhibitor Staurosporine precluded sucrose-induced tuberization. Altogether, our results suggest that phosphorylation/dephosphorylation events are involved in sucrose-induced tuber development.

A randomised, crossover, multicentre study to compare the performance of 0.1% (w/v) sodium hyaluronate with 1.4% (w/v) polyvinyl alcohol in the alleviation of symptoms associated with dry eye syndrome.

AIMS: To assess the safety and performance of a 0.1% (w/v) solution of sodium hyaluronate (HA, Fermavisc, in the alleviation of symptoms of severe dry eye in comparison with a 1.4% (w/v) solution of polyvinyl alcohol. METHODS: A randomised, crossover, multicentre study carried out at eight centres in the UK. Eligible patients giving written informed consent were randomised to the order in which they would receive the two study products. Each treatment period lasted for 4 weeks, then the patient crossed over to the other study product. Symptoms of burning and grittiness were assessed by visual analogue scale (VAS) at each study visit and other objective clinical assessments of ocular structure and function were carried out at baseline and the end of each treatment period. RESULTS: Thirty-nine patients were entered into the study and 32 completed both treatment periods and were included in the statistical analyses. A significant improvement in the patients' VAS assessment of burning was seen after treatment with HA (P = 0.03, 95% Confidence Interval: -23.5 to -1.1). This treatment also resulted in a significantly lower rose bengal staining score (P = 0.04, 95% Confidence Interval: -1.62 to -0.05 for the right eye). CONCLUSION: The results show a significant clinical benefit in terms of relief of the symptom of burning when HA is applied topically to the eye three or four times per day or as required. HA also appears to have a protective effect on the corneal epithelium, as shown by a reduction in the level of staining of corneal epithelial cells by rose bengal. This study confirms that Fermavisc is a safe and effective product for use in the alleviation of symptoms of severe dry eye syndrome.

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs.

Sequencing of the Arabidopsis genome has led to the identification of thousands of new putative genes based on the predicted proteins they encode. Genes encoding tRNAs, ribosomal RNAs, and small nucleolar RNAs have also been annotated; however, a potentially important class of genes has largely escaped previous annotation efforts. These genes correspond to RNAs that lack significant open reading frames and encode RNA as their final product. Accumulating evidence indicates that such "non-coding RNAs" (ncRNAs) can play critical roles in a wide range of cellular processes, including chromosomal silencing, transcriptional regulation, developmental control, and responses to stress. Approximately 15 putative Arabidopsis ncRNAs have been reported in the literature or have been annotated. Although several have homologs in other plant species, all appear to be plant specific, with the exception of signal recognition particle RNA. Conversely, none of the ncRNAs reported from yeast or animal systems have homologs in Arabidopsis or other plants. To identify additional genes that are likely to encode ncRNAs, we used computational tools to filter protein-coding genes from genes corresponding to 20,000 expressed sequence tag clones. Using this strategy, we identified 19 clones with characteristics of ncRNAs, nine putative peptide-coding RNAs with open reading frames smaller than 100 amino acids, and 11 that could not be differentiated between the two categories. Again, none of these clones had homologs outside the plant kingdom, suggesting that most Arabidopsis ncRNAs are likely plant specific. These data indicate that ncRNAs represent a significant and underdeveloped aspect of Arabidopsis genomics that deserves further study.

Characterization of Rny1, the Saccharomyces cerevisiae member of the T2 RNase family of RNases: unexpected functions for ancient enzymes?

The T(2) family of nonspecific endoribonucleases (EC ) is a widespread family of RNases found in every organism examined thus far. Most T(2) enzymes are secretory RNases and therefore are found extracellularly or in compartments of the endomembrane system that would minimize their contact with cellular RNA. Although the biological functions of various T(2) RNases have been postulated on the basis of enzyme location or gene expression patterns, the cellular roles of these enzymes are generally unknown. In the present work, we characterized Rny1, the only T(2) RNase in Saccharomyces cerevisiae. Rny1 was found to be an active, secreted RNase whose gene expression is controlled by heat shock and osmotic stress. Inactivation of RNY1 leads to unusually large cells that are temperature-sensitive for growth. These phenotypes can be complemented not only by RNY1 but also by both structurally related and unrelated secretory RNases. Additionally, the complementation depends on RNase activity. When coupled with a recent report on the effect of specific RNAs on membrane permeability [Khvorova, A., Kwak, Y-G., Tamkun, M., Majerfeld, I. & Yarus, M. (1999) Proc. Natl. Acad. Sci. USA 96, 10649-10654], our work suggests an unexpected role for Rny1 and possibly other secretory RNases. These enzymes may regulate membrane permeability or stability, a hypothesis that could present an alternative perspective for understanding their functions.

Regulation of S-like ribonuclease levels in Arabidopsis. Antisense inhibition of RNS1 or RNS2 elevates anthocyanin accumulation.

The S-like ribonucleases (RNases) RNS1 and RNS2 of Arabidopsis are members of the widespread T2 ribonuclease family, whose members also include the S-RNases, involved in gametophytic self-incompatibility in plants. Both RNS1 and RNS2 mRNAs have been shown previously to be induced by inorganic phosphate (Pi) starvation. In our study we examined this regulation at the protein level and determined the effects of diminishing RNS1 and RNS2 expression using antisense techniques. The Pi-starvation control of RNS1 and RNS2 was confirmed using antibodies specific for each protein. These specific antibodies also demonstrated that RNS1 is secreted, whereas RNS2 is intracellular. By introducing antisense constructs, mRNA accumulation was inhibited by up to 90% for RNS1 and up to 65% for RNS2. These plants contained abnormally high levels of anthocyanins, the production of which is often associated with several forms of stress, including Pi starvation. This effect demonstrates that diminishing the amounts of either RNS1 or RNS2 leads to effects that cannot be compensated for by the actions of other RNases, even though Arabidopsis contains a large number of different RNase activities. These results, together with the differential localization of the proteins, imply that RNS1 and RNS2 have distinct functions in the plant.

Stage-specific substrate phosphorylation by a Ca2+/calmodulin-dependent protein kinase in Trypanosoma cruzi.

The presence of Ca2+/calmodulin (Ca2+/CaM)-dependent protein kinase (TcCaM K) and some stage-specific substrates that appeared during morphogenesis of the parasite Trypanosoma cruzi were identified. Western blot analysis using a polyclonal antibody against rat brain CaM K type 11 recognized the same subunit composition (52, 59/62 kDa) observed for the mammalian enzyme, as well as the previously characterized TcCaM K found in epimastigote forms. Differential protein phosphorylation profiles were observed after enzyme activation in the stages of T. cruzi. Co-immunoprecipitation of stage-specific substrates with the TcCaM K suggested that the enzyme might be involved in the phosphorylation of a different set of proteins through the life cycle. Three phosphoproteins, pp105 and pp87 from epimastigotes and pp23 from trypomastigotes were identified as potential substrates for TcCaM K. The characterization of these endogenous stage markers might be a useful tool to understand the developmental cycles of these pathogenic protozoa.

Changes in Calcium-Dependent Protein Kinase Activity during in Vitro Tuberization in Potato.

A soluble Ca2+-dependent protein kinase (CDPK) was purified to homogeneity in potato (Solanum tuberosum L.) plants. Potato CDPK was strictly dependent on Ca2+ (one-half maximal activation 0.6 [mu]M) and phosphorylated a wide diversity of substrates, in which Syntide 2 was the best phosphate acceptor (Michaelis constant = 30 [mu]M). The kinase was inhibited by Ca2+-chelating agents, phenotiazine derivatives, and N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (one-half maximal inhibition = 0.25 mM). Polyclonal antibodies directed against the regulatory region of the soybean CDPK recognized a 53-kD polypeptide. In an autophosphorylation assay, this same band was strongly labeled with [[gamma]-32P]ATP in the presence of Ca2+. CDPK activity was high in nontuberized plants, but increased 2.5-fold at the onset of tuber development and was reduced to one-half of its original activity when the tuber had completed formation. In the early stages of tuberization, Ca2+-dependent phosphorylation of endogenous targets (specific bands of 68, 51, and 46 kD) was observed. These polypeptides were not labeled in nontuberizing plants or in completely formed tubers, indicating that this phosphorylation is a stage-specific event. In addition, dephosphorylation of specific polypeptides was detected in tuberizing plants, suggesting the involvement of a phosphatase. Preincubation of crude extracts with phosphatase inhibitors rendered a 100% increase in CDPK activity.