Abstract The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application ( http://STARGEO.org ) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis. In this paper, we target a small group of biomedical graduate students to show rapid crowd-curation of precise sample annotations across all phenotypes, and we demonstrate the biological validity of these crowd-curated annotations for breast cancer. STARGEO.org makes GEO data findable, accessible, interoperable and reusable (i.e., FAIR) to ultimately facilitate knowledge discovery. Our work demonstrates the utility of crowd-curation and interpretation of open ‘big data’ under FAIR principles as a first step towards realizing an ideal paradigm of precision medicine.
Background: Malaria accounts for a considerable amount of mortality around the world, especially among young children. Artemisinin Combination Therapies (ACTs) remain the most potent treatment for uncomplicated cases of malaria. Early signs of drug resistance have emerged in the form of delayed clearance of the parasite in Southeast Asia. There is a high demand for newer drugs and vaccines to help control the worldwide malaria burden pending complete drug resistance to ACTs. The aim of this study is to characterize the disease signature of a malaria infection using meta-analysis of microarray data, and use this data to facilitate the pursuit of newer drugs and vaccines to fight malaria worldwide. Methods: Through a unique collaboration between medical students and computer scientists in systems biology, Search Tag & Analyze Resource (STAR) is a platform that was created that allows us to easily analyze gene signatures through meta-analyses of series in the Gene Expression Omnibus (GEO). Experiment samples within the database are annotated with tags and run through meta-analysis. Results: Using STAR, we generated one preliminary gene signature using samples on GEO: whole blood samples from malaria infections versus blood samples from health controls. We have found LGR4 and p70-S6k to be the top upstream regulators (p=0.002 for both). GBA and C15orf48 were the top significantly up-regulated genes. LEF1, PDCD4, and CNST were the top significantly down-regulated genes. GBA, LEF1, and the p70-S6k pathway have all been reported before as associated with malaria disease expression, the other genes have not. Conclusion: These preliminary results are proof-of-concept to the potential of STAR. With the collaboration fully functional, thousands of samples will be added to improve the gene signature of malaria infection. The study will also include parasite gene expression run with the same meta-analysis. We report here a first step towards novel transitional opportunities for better biomarkers and drugs for infectious diseases like malaria and beyond.
Earlier, we have shown that GM-CSF derived bone marrow (BM) dendritic cells (G-BMDCs) can expand Foxp3+ regulatory T-cells (Tregs) through a TCR-independent, but IL-2 dependent mechanism that required OX40L/OX40 interaction. While some reports have shown suppression of autoimmunity upon treatment with an OX40 agonist, others have shown exacerbation of autoimmune disease instead. To better understand the basis for these differing outcomes, we compared the effects of OX40L treatment in 6-week-old pre-diabetic and 12-week-old near diabetic NOD mice. Upon treatment with OX40L, 6-week-old NOD mice remained normoglycemic and showed a significant increase in Tregs in their spleen and lymph nodes, while 12-week-old NOD mice very rapidly developed hyperglycemia and failed to show Treg increase in spleen or LN. Interestingly, OX40L treatment increased Tregs in the thymus of both age groups. However, it induced Foxp3+CD103+CD38− stable-phenotype Tregs in the thymus and reduced the frequency of autoreactive Teff cells in 6-week-old mice; while it induced Foxp3+CD103−CD38+ labile-phenotype Tregs in the thymus and increased autoreactive CD4+ T cells in the periphery of 12-week-old mice. This increase in autoreactive CD4+ T cells was likely due to either a poor suppressive function or conversion of labile Tregs into Teff cells. Using ex vivo cultures, we found that the reduction in Treg numbers in 12-week-old mice was likely due to IL-2 deficit, and their numbers could be increased upon addition of exogenous IL-2. The observed divergent effects of OX40L treatment were likely due to differences in the ability of 6- and 12-week-old NOD mice to produce IL-2.
The goal of sugar-sweetened beverage (SSB) taxes is to raise the prices of SSBs to decrease consumption. Price promotions play an important role in the sales of SSBs and could potentially be used by manufacturers to weaken the impact of such taxes. The purpose of this study is to determine how price promotions changed after the introduction of the 2017 Oakland SSB tax. A difference-in-differences study design was used to compare changes in prices and the prevalence and amount of price promotions for beverages in Oakland, California, relative to Sacramento, California, using two different datasets. Nielsen Retail Scanner data included price promotions for beverages sold and store audit data included price promotions offered by retailers. Changes were analyzed for SSBs, noncalorically sweetened beverages, and unsweetened beverages. After the implementation of the tax, the prevalence of price promotions for SSBs did not change significantly in Oakland relative to the comparison site of Sacramento. However, the depth of price promotions increased by an estimated 0.35 cents per ounce (P<0.001) based on the Nielsen retail scanner data and by 0.39 cents per ounce (P<0.001) based on the store audit data. This increase in the amount by which SSBs were price promoted following the introduction of the Oakland SSB tax may reflect a strategy by manufacturers to weaken the tax and/or retailers to bolster demand.
We have previously shown that OX40L/OX40 interaction is critical for TCR-independent selective proliferation of Foxp3+ Tregs, but not Foxp3- effector T-cells (Teff), when CD4+ T-cells are co-cultured with GM-CSF derived bone marrow dendritic cells (G-BMDCs). Events downstream of OX40L/OX40 interaction in Tregs responsible for this novel mechanism are not understood. Earlier, OX40L/OX40 interaction has been shown to stimulate CD4+ T-cells through the formation of a signalosome involving TRAF2/PKC-Ѳ leading to NF-kB activation. In this study, using CD4+ T-cells from WT and OX40-/- mice we first established that OX40 mediated activation of NF-kB was critical for this Treg proliferation. Although CD4+ T-cells from PKC-Ѳ-/- mice were also defective in G-BMDC induced Treg proliferation ex vivo, this defect could be readily corrected by adding exogenous IL-2 to the co-cultures. Furthermore, by treating WT, OX40-/-, and PKC-Ѳ-/- mice with soluble OX40L we established that OX40L/OX40 interaction was required and sufficient to induce Treg proliferation in vivo independent of PKC-Ѳ status. Although PKC-Ѳ is dispensable for TCR-independent Treg proliferation per se, it is essential for optimum IL-2 production by Teff cells. Finally, our findings suggest that OX40L binding to OX40 likely results in recruitment of TRAF1 for downstream signalling.
Deep-vein thrombosis (DVT) resolves via a sterile inflammatory response. Defining the inflammatory response of DVT may allow for new therapies that do not involve anticoagulation. Previously, we have shown that Toll-like receptor 9 (Tlr9) gene deleted mice had impaired venous thrombosis (VT) resolution. Here, we further characterise the role of Tlr9 signalling and sterile inflammation in chronic VT and vein wall responses. First, we found a human precedent exists with Tlr9+ cells present in chronic post thrombotic intraluminal tissue. Second, in a stasis VT mouse model, endogenous danger signal mediators of uric acid, HMGB-1, and neutrophil extracellular traps marker of citrullinated histone-3 (and extracellular DNA) were greater in Tlr9-/- thrombi as compared with wild-type (WT), corresponding with larger VT at 8 and 21 days. Fewer M1 type (CCR2+) monocyte/macrophages (MØ) were present in Tlr9-/- thrombi than WT controls at 8 days, suggesting an impaired inflammatory cell influx. Using bone marrow-derived monocyte (BMMØ) cell culture, we found decreased fibrinolytic gene expression with exposure to several endogenous danger signals. Next, adoptive transfer of cultured Tlr9+/+ BMMØ to Tlr9-/- mice normalised VT resolution at 8 days. Lastly, although the VT size was larger at 21 days in Tlr9-/- mice and correlated with decreased endothelial antigen markers, no difference in fibrosis was found. These data suggest that Tlr9 signalling in MØ is critical for later VT resolution, is associated with necrosis clearance, but does not affect later vein wall fibrosis. These findings provide insight into the Tlr9 MØ mechanisms of sterile inflammation in this disease process.
