Citations

Abstract IL-17 is known to play important roles in immune and inflammatory disease, such as in asthma, but its functions in allergic airway inflammation are still controversial, and the molecular mechanisms mediating these functions remain unclear. Increased production of eosinophils in bone marrow and their emergence in the airway have been linked to the onset and progression of allergic asthma. In this study, we investigated the effects of exogenous IL-17 on allergic airway inflammation and explored the underlying molecular mechanisms through eosinophil generation. Exogenous IL-17 significantly attenuated the features of allergic inflammation induced by ovalbumin in mice. It inhibited eosinophil differentiation both in vivo and in vitro, accompanied by down-regulated expression of CC chemokine receptor 3, GATA binding protein 1 (GATA-1), and GATA binding protein 2 (GATA-2), as well as reduced formation of common myeloid progenitors and eosinophil progenitors, but without influencing eosinophil apoptosis. IL-17 also significantly decreased the number of eosinophils in IL-5–transgenic mice, although it notably increased the levels of IL-3, IL-5, and granulocyte/macrophage colony–stimulating factor. In addition, IL-17 had little effect on secretion of the inflammatory cytokines by eosinophils. Neutralization of endogenous IL-17 significantly augmented eosinophil recruitment in the airways. Together, these findings suggest that exogenous IL-17 protects against allergic airway inflammation, most likely through inhibition of the eosinophil differentiation in bone marrow.

Abstract Motivation: RNA-seq has become the method of choice to quantify genes and exons, discover novel transcripts and detect fusion genes. However, reliable variant identification from RNA-seq data remains challenging because of the complexities of the transcriptome, the challenges of accurately mapping exon boundary spanning reads and the bias introduced during the sequencing library preparation. Method: We developed RVboost, a novel method specific for RNA variant prioritization. RVboost uses several attributes unique in the process of RNA library preparation, sequencing and RNA-seq data analyses. It uses a boosting method to train a model of ‘good quality’ variants using common variants from HapMap, and prioritizes and calls the RNA variants based on the trained model. We packaged RVboost in a comprehensive workflow, which integrates tools of variant calling, annotation and filtering. Results: RVboost consistently outperforms the variant quality score recalibration from the Genome Analysis Tool Kit and the RNA-seq variant-calling pipeline SNPiR in 12 RNA-seq samples using ground-truth variants from paired exome sequencing data. Several RNA-seq–specific attributes were identified as critical to differentiate true and false variants, including the distance of the variant positions to exon boundaries, and the percent of the reads supporting the variant in the first six base pairs. The latter identifies false variants introduced by the random hexamer priming during the library construction. Availability and implementation: The RVboost package is implemented to readily run in Mac or Linux environments. The software and user manual are available at http://bioinformaticstools.mayo.edu/research/rvboost/. Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract Pneumonia remains a leading cause of morbidity and mortality despite advances in treatment and therapy. The “Pneumonia: Treatment and Diagnosis” session of the Pittsburgh International Lung Conference examined topics related to improving care of patients with pneumonia. These topics included the process and quality of care for community-acquired pneumonia (CAP), diagnosis and treatment of emerging fungal pathogens, an overview of the strengths and weaknesses of different diagnostic modalities, and an example of how basic science is exploring immunomodulatory strategies for pneumonia treatment. Systematic health care provider and institutional improvements can decrease mortality rates in CAP, particularly in patients with increasingly complex comorbidities. Aspects of current guidelines for the diagnosis and treatment of fungal pneumonia were reviewed through a series of case presentations. Proper treatment of pneumonia hinges on correct pathogen identification but is complicated by the variety of diagnostic assays with variable specificity, sensitivity, and interpretation. In addressing this topic, Dr. Patrick Murray, Ph.D., discussed a range of diagnostic tests for a variety of pathogens and guidelines for their use. In addition to the current state of CAP treatment, Bill (Beibei) Chen, M.D., Ph.D., presented a new potential therapeutic agent called forsythin, an immunomodulatory compound derived from a plant used in traditional Chinese medicine. These topics, ranging from institution-sized policy to interactions at the molecular scale, paint a broad perspective of the efforts against pneumonia.

SummaryThis single institution, open label Phase I‐II dose escalation trial evaluated the safety and efficacy of the combination of lenalidomide (Revlimid®), cyclophosphamide and prednisone (CPR) in patients with relapsed/refractory multiple myeloma. The maximal administered dose of CPR consisted of cyclophosphamide 300 mg/m2 on day 1, 8, and 15, lenalidomide 25 mg on d 1–21 and prednisone 100 mg every other day in a 28‐d cycle. Between November 2007 and June 2009, 32 patients were entered in cohorts of three at three dose levels. The median age was 64 years, 59% were male, with a median two prior regimens. Responding patients could stay on treatment until progression. The full‐dose CPR regimen produced no dose‐limiting toxicity and was delivered for a median of 16 months (3·5–65 months) with acceptable safety and tolerance. The overall response rate (≥ partial response) was 94% at a median follow up of 28 months. The median progression‐free survival was 16·1 months [95% confidence interval (CI); 10·9–22·5 months], while the median overall survival was 27·6 months (95% CI; 16·8–36·6 months). Only the beta‐2 microglobulin level at protocol entry correlated with a better survival (P = 0·047). These observations compare favourably with other 2‐ and 3‐ drug combinations for relapsed/refractory myeloma, and suggest that CPR should be evaluated further in the setting of relapsed/refractory disease, or in newly diagnosed patients.

Abstract The Polycomb repressive complex 2 (PRC2) is important for maintenance of stem cell pluripotency and suppression of cell differentiation by promoting histone H3 lysine 27 trimethylation (H3K27me3) and transcriptional repression of differentiation regulatory genes. Here we show that the tumor suppressor protein BRCA1 interacts with EZH2 and other components of PRC2 in mouse embryonic stem (ES) and human breast cancer cells. The BRCA1-binding region in EZH2 overlaps with the non-coding RNA (ncRNA)-binding domain, and BRCA1 expression inhibits the binding of EZH2 to the HOTAIR ncRNA. Decreased expression of BRCA1 causes EZH2 re-targeting genome wide and elevates H3K27me3 levels at PRC2 target loci in both mouse ES and human breast cancer cells. BRCA1 deficiency blocks ES cell differentiation and enhances breast cancer migration and invasion in an EZH2-dependent manner. These results reveal that BRCA1 is a key negative modulator of PRC2 and that loss of BRCA1 inhibits ES cell differentiation and enhances cancer aggressive phenotypes via augmented PRC2 function. Citation Format: Xianzhou Zeng, Shuai Chen, Lan Wang, Haojie Huang. BRCA1 is a negative modulator of the PRC2 complex. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5358. doi:10.1158/1538-7445.AM2013-5358

Abstract Background: Variation in mitochondrial genes in cancer cells alters the mitochondrial bioenergetic and biosynthetic state, which mediates cross-talk between mitochondria and the nucleus to modulate many cellular processes. The objective of this study was to comprehensively evaluate mitochondria-nuclear cross-talk in terms of SNP-SNP interactions associated with invasive epithelial ovarian cancer (EOC) risk, which may play an important role in unveiling the underlying mechanism of this complex lethal disease. Methods: Our analyses were based on 1,938 invasive EOC cases and 2,009 controls with greater than 80% European ancestry from five case-control studies genotyped using the Illumina 610quad chip. We evaluated 2,488 SNPs in over 1,500 genes in eight mitochondria-related pathways (apoptosis, oxidation-reduction, epithelial-mesenchymal transition, immunomoduation, transmembrane transport, small GTPases, BRCA1-interactors and circadian rhythm). SNPs with strong linkage disequilibrium of r2 > 0.8 were excluded. We examined 2-way SNP-SNP interactions associated with invasive EOC risk using the two-stage Random Forests plus Multivariate Adaptive Regression Splines (TRM) approach. Bootstrapping was further performed to select important variables and reduce false positive findings. Based on the scree plot using 1,000 bootstrap samples, the factors with more than 4% of bootstrap frequency were defined as significant factors. We then included each identified factors separately in model adjusting for study site and first principal component representing European ancestry. Results: Five significant SNP-SNP interactions were observed: (rs2270799 in IQSEC3 (12p13.33) + rs933305 in CUX2 (12q24.3), (p= 6.3x10−5); rs6063251 in PREX1 (20q13.3) + rs9705 in SLC39A8 (4q22-q24), (p= 3.5x10−5); rs933305 in CUX2 (12q24.3) + rs1712957 in ARHGAP15 (2q22.2-q22.3), (p=4.2x10−7), rs2861828 in SLIT1 (10q23.3-q24) + rs6063251 in PREX1 (20q13.3), (p=2.5x10−7); rs10954593 in SEMA3C (7q21-q31) + rs933305 in CUX2 (12q24.3), (p=2.8x10−3). Four of the five interactions involved SNPs from genes in the small GTPases pathway (IQSEC3; PREX1 (twice) and ARHGAP15). In addition, three of the five interaction pairs involved the CUX2 gene. This gene encodes a protein which contains three CUT domains and a homeodomain, which are DNA-binding motifs. The main mitochondrial SNP-SNP interaction involved the nuclear mitochondria gene SLC39A8. Conclusions: Our results suggest that genetic variation in mitochondrial-related pathways may be associated with invasive EOC risk. These findings highlight important genes/pathways that may interact as a network to influence invasive EOC risk and may generate novel therapeutic targets. External validation will be done using other independent studies for future analyses. Citation Format: Hui-Yi Lin, Ya-Yu Tsai, Y. Ann Chen, Zhihua Chen, Xiaotao Qu, Ellen L. Goode, Joellen Schildkraut, Edwin Iversen, Steven A. Narod, Thomas A. Sellers, Catherine M. Phelan. SNP-SNP interactions in mitochondria-related pathways are associated with invasive Epithelial Ovarian Cancer (EOC) risk . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4839. doi:10.1158/1538-7445.AM2013-4839