Functional genomics and rheumatoid arthritis: where have we been and where should we go?

Studies in model organisms and humans have begun to reveal the complexity of the transcriptome. In addition to serving as passive templates from which genes are translated, RNA molecules are active, functional elements of the cell whose products can detect, interact with, and modify other transcripts. Gene expression profiling is the method most commonly used thus far to enrich our understanding of the molecular basis of rheumatoid arthritis in adults and juvenile idiopathic arthritis in children. The feasibility of this approach for patient classification (for example, active versus inactive disease, disease subsets) and improving prognosis (for example, response to therapy) has been demonstrated over the past 7 years. Mechanistic understanding of disease-related differences in gene expression must be interpreted in the context of interactions with transcriptional regulatory molecules and epigenetic alterations of the genome. Ongoing work regarding such functional complexities in the human genome will likely bring both insight and surprise to our understanding of rheumatoid arthritis

Using Chromatin Architecture to Understand the Genetics and Transcriptomics of Juvenile Idiopathic Arthritis

The presence of abnormal gene expression signatures is a well-described feature of the oligoarticular and polyarticular forms of juvenile idiopathic arthritis. In this review, we discuss how new insights into genetic risk for JIA and the three dimensional architecture of the genome may be used to develop a better understanding of the mechanisms driving these gene expression patterns

Plasma exosomes from children with juvenile dermatomyositis are taken up by human aortic endothelial cells and are associated with altered gene expression in those cells

BACKGROUND: The pathology of juvenile dermatomyositis (JDM) is characterized by prominent vessel wall and perivascular inflammation. This feature of the disease has remained unexplained and under-investigated. We have hypothesized that plasma exosomes, which play an important role in inter-cellular communication, may play a role in the vascular injury associated with JDM. OBJECTIVE: To characterize the circulating exosomes of children with JDM and determine whether the small RNA cargoes within those exosomes are capable of altering transcriptional programs within endothelial cells. DESIGN/METHODS: We purified exosomes from plasma samples of children with active, untreated JDM (n = 6) and healthy controls (n = 9). We characterized the small RNA cargoes in JDM and control exosomes by RNA sequencing using the Illumina HiSeq 2500 platform. We then incubated isolated exosomes from healthy controls and children with JDM with cultured human aortic endothelial cells (HAEC) for 24 h. Fluorescence microscopy was used to confirm that both control and JDM exosomes were taken up by HAEC. RNA was then purified from HAEC that had been incubated with either control or JDM exosomes and sequenced on the Illumina platform. Differential expression of mRNAs from HAEC incubated with control or JDM exosomes was ascertained using standard computational methods. Finally, we assessed the degree to which differential gene expression in HAEC could be attributed to the different small RNA cargoes in JDM vs control exosomes using conventional and novel analytic methods. RESULTS: We identified 10 small RNA molecules that showed differential abundance when we compared JDM and healthy control exosomes. Fluorescence microscopy of labeled exosomes confirmed that both JDM and control exosomes were taken up by HAEC. Differential gene expression analysis revealed 59 genes that showed differential expression between HAEC incubated with JDM exosomes vs HAEC incubated with exosomes from controls. Statistical analysis of gene expression data demonstrated that multiple miRNAs exerted transcriptional control on multiple genes with HAEC. CONCLUSIONS: Plasma exosomes from children with active, untreated JDM are taken up by HAEC and are associated with alterations in gene expression in those cells. These findings provide new insight into potential mechanisms leading to the targeting of vascular tissue by the immune system in JDM

HIV-associated Cryptococcal Meningitis: a Review of Novel Short-Course and Oral Therapies

Abstract Purpose of review HIV-associated cryptococcal meningitis remains a significant public health problem in parts of Africa and Asia and a major cause of AIDS-related mortality, accounting for 15% of all AIDS-related deaths worldwide. Cryptococcal meningitis is uniformly fatal if untreated, and access to antifungal therapy in regions with the highest burden is often limited. Outcomes with fluconazole monotherapy are poor, and induction treatment with amphotericin B and high-dose fluconazole for 2 weeks is associated with significant drug-related toxicities and prolonged hospital admissions. This review focuses on the potential of novel short-course and oral combination therapies for cryptococcal meningitis. Recent findings Recent clinical trials have shown that shorter courses of amphotericin, if paired with oral flucytosine, rather than fluconazole, can achieve non-inferior mortality outcomes. In addition, an oral combination of fluconazole and flucytosine is a potential alternative. Liposomal amphotericin B may further simplify treatment; it is associated with fewer drug-related toxicities, and a recent phase II randomised controlled trial demonstrated that a single, high dose of liposomal amphotericin is non-inferior to 14 standard daily doses at clearing Cryptococcus from cerebrospinal fluid. This has been taken forward to an ongoing phase III, clinical endpoint study. Summary The incidence and mortality associated with cryptococcal meningitis is still unacceptably high. There is evidence supporting the use of short-course amphotericin B and oral combination antifungal treatment regimens for cryptococcal meningitis (CM). Ongoing research into short-course, high-dose treatment with liposomal amphotericin may also help reduce the impact of this devastating disease. </jats:sec

Postactivation potentiation and change of direction speed in elite academy rugby players

This study investigated the effect of preceding pro-agility sprints with maximal isometric squats to determine if postactivation potentiation (PAP) could be harnessed in change of direction speed. Sixteen elite under-17 rugby union players (age: 16 +/- 0.41yrs; body mass: 88.7 +/- 12.1kg, height: 1.83 +/- 0.07m) from an Aviva Premiership rugby club were tested. Subjects performed a change of direction specific warm-up, followed by two baseline pro-agility tests. After 10 minutes recovery, 3 x 3-second maximal isometric squats with a 2 minute recovery between sets were completed as a conditioning activity (CA) on a force plate where peak force and mean rate of force development over 300 milliseconds were measured. The pro-agility test was repeated at set time intervals of 1, 3, 5 and 7 minutes following the CA. Overall pro-agility times were significantly slower (p < 0.05) at 1-minute post-CA compared to the baseline (3.3%), with no significant differences occurring at 3, 5 or 7 minutes post-CA. Therefore, it appears that performing multiple sets of maximal isometric squats do not enhance pro-agility performance

Increase in CD5+ B Cells in Juvenile Rheumatoid Arthritis

Objective. To investigate the association between CD5+ B cell expression and IgM rheumatoid factor (IgM-RF) in juvenile rheumatoid arthritis (JRA). Methods. CD5+ B cell levels analyzed by flow cytometry and IgM-RF expression determined by enzymelinked immunosorbent assay were compared in children with JRA, children with other collagen vascular diseases, and healthy controls. Results. Children with polyarticular JRA had expanded populations of CD5+ B cells, and expansion of CD5+ B cells and IgM-RF both correlated with disease activity. Conclusion. The results indicate that an expanded CD5+ B cell population leads to IgM-RF production in patients with polyarticular JRA, as well as patients with RA.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/37790/1/1780350213_ftp.pd

Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts.

The studies proposed here were undertaken to test the hypothesis that, under specific circumstances (e.g., a strong enough inflammatory stimulus), genes that are repressed at the maternal-fetal interface via DNA methylation might be de-methylated, allowing either a maternal immune response to the semi-allogenic fetus or the onset of early labor. Chorionic trophoblasts (CT) were isolated from fetal membranes, followed by incubation with medium from LPS-activated PBMC or resting PBMC medium for 2 h. RNA and DNA were isolated from the cells for RNA-seq and DNA methylation studies. Two hrs after being exposed to conditioned medium from LPS-activated PBMC, CT showed differential expression of 114 genes, all but 2 of which showed higher expression in the stimulated cells than is the unstimulated cells. We also identified 318 differentially methylated regions (DMRs) that associated with 306 genes (155 protein coding genes) in the two groups, but the observed methylation changes had negligible impact on the observed transcriptional changes in CT. CT display complex patterns of transcription in response to inflammation. DNA methylation does not appear to be an important regulator of the observed transcriptional changes

Advances in Epigenetics and Integration of Omics in Lupus

Systemic lupus erythematosus (SLE) is a chronic, multi-organ disease that predominantly affects young women of childbearing age. It is also a disease in which epigenetic modulation is emerging as an important mechanism for understanding how the environment interacts with inherited genes to produce disease. Much of the genetic risk for SLE identified in genome-wide association studies has been shown to lie in the non-coding genome, where epigenetic modifications of DNA and histone proteins regulate and co-ordinate transcription on a genome-wide basis. Novel methodologies, including high-throughput sequencing of open chromatin, RNA sequencing, protein microarrays, and gas chromatography-mass spectrometry, have revealed intriguing insights into the pathogenesis of SLE. We review these recent data and their potential contribution to more accurate diagnoses and the development of new therapeutic agents to improve patient outcomes

RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states

Background The transcriptional complexity of mammalian cells suggests that they have broad abilities to respond to specific environmental stimuli and physiologic contexts. These abilities were not apparent a priori from the structure of mammalian genomes, but have been identified through detailed transcriptome analyses. In this study, we examined the transcriptomes of cells of the innate immune system, human neutrophils, using RNA sequencing (RNAseq). Methods We sequenced poly-A RNA from nine individual samples corresponding to specific phenotypes: three children with active, untreated juvenile idiopathic arthritis (JIA)(AD), three children with the same disease whose disease was inactive on medication (CRM), and three children with cystic fibrosis (CF). Results We demonstrate that transcriptomes of neutrophils, typically considered non-specific in their responses and functions, display considerable specificity in their transcriptional repertoires dependent on the pathologic context, and included genes, gene isoforms, and long non-coding RNA transcripts. Furthermore, despite the small sample numbers, these findings demonstrate the potential of RNAseq approaches to biomarker development in rheumatic diseases. Conclusions These data demonstrate the capacity of cells previously considered non-specific in function to adapt their transcriptomes to specific biologic contexts. These data also provide insight into previously unrecognized pathological pathways and show considerable promise for elucidating disease and disease-state specific regulatory networks

Design Considerations for Attitude State Awareness and Prevention of Entry into Unusual Attitudes

Loss of control - inflight (LOC-I) has historically represented the largest category of commercial aviation fatal accidents. A review of the worldwide transport airplane accidents (2001-2010) evinced that loss of attitude or energy state awareness was responsible for a large majority of the LOC-I events. A Commercial Aviation Safety Team (CAST) study of 18 worldwide loss-of-control accidents and incidents determined that flight crew loss of attitude awareness or energy state awareness due to lack of external visual reference cues was a significant causal factor in 17 of the 18 reviewed flights. CAST recommended that "Virtual Day-Visual Meteorological Condition" (Virtual Day-VMC) displays be developed to provide the visual cues necessary to prevent loss-of-control resulting from flight crew spatial disorientation and loss of energy state awareness. Synthetic vision or equivalent systems (SVS) were identified for a design "safety enhancement" (SE-200). Part of this SE involves the conduct of research for developing minimum aviation system performance standards (MASPS) for these flight deck display technologies to aid flight crew attitude and energy state awareness similar to that of a virtual day-VMC-like environment. This paper will describe a novel experimental approach to evaluating a flight crew's ability to maintain attitude awareness and to prevent entry into unusual attitudes across several SVS optical flow design considerations. Flight crews were subjected to compound-event scenarios designed to elicit channelized attention and startle/surprise within the crew. These high-fidelity scenarios, designed from real-world events, enable evaluation of the efficacy of SVS at improving flight crew attitude awareness to reduce the occurrence of LOC-I incidents in commercial flight operations