Integrative Omics Analysis of Rheumatoid Arthritis Identifies Non-Obvious Therapeutic Targets

Identifying novel therapeutic targets for the treatment of disease is challenging. To this end, we developed a genome-wide approach of candidate gene prioritization. We independently collocated sets of genes that were implicated in rheumatoid arthritis (RA) pathogenicity through three genome-wide assays: (i) genome-wide association studies (GWAS), (ii) differentially expression in RA fibroblast-like synoviocytes (FLS), and (iii) differentially methylation in RA FLS. Integrated analysis of these complementary data sets identified a significant enrichment of multi-evidence genes (MEGs) within pathways relating to RA pathogenicity. One MEG is Engulfment and Cell Motility Protein-1 (ELMO1), a gene not previously considered as a therapeutic target in RA FLS. We demonstrated in RA FLS that ELMO1 is: (i) expressed, (ii) promotes cell migration and invasion, and (iii) regulates Rac1 activity. Thus, we created links between ELMO1 and RA pathogenicity, which in turn validates ELMO1 as a potential RA therapeutic target. This study illustrated the power of MEG-based approaches for therapeutic target identification.     

Phase-dependent changes in local dynamic stability of human gait

Several methods derived from nonlinear time series analysis have been suggested to quantify stability in human gait kinematics. One of these methods is the definition of the maximum finite time Lyapunov exponent (λ) that quantifies how the system responds to infinitesimal perturbations. However, there are fundamental limitations to the conventional definition of λ for gait kinematics. First, exponential increase in initial perturbations cannot be assumed since real-life perturbations of gait kinematics are finite sized. Second, the transitions between single and double support phase within each stride cycle define two distinct dynamical regimes that may not be captured by a single λ. The present article presents a new method to quantify intra-stride changes λ(t) in local dynamical stability and employs the method to 3D lower extremity gait kinematics in 10 healthy adults walking on a treadmill at 3 different speeds. All participants showed an intra-stride change in λ(t) in the transition between single and double support phase. The intra-stride change reflected an both a increase and decrease in λ(t) at heel strike and toe off, respectively, with increased gait speed. Furthermore, a close relationship was found between the intra-stride change in standard deviation of foot velocity in the anterior-posterior direction and the intra-stride change of the initial perturbations. The present results indicate that local dynamical stability has gait phase-dependent changes that are not identified by conventional computation of a single λ.     

Between adaptive and innate immunity: TLR4-mediated perforin production by CD28<Superscript>null</Superscript>T-helper cells in ankylosing spondylitis

CD3⁺CD4⁺CD28^null and CD3⁺CD8⁺CD28^null T cells are enriched in patients with immune-mediated diseases compared with healthy controls. This study shows that CD4⁺CD28^null T cells express Toll-like receptors recognizing bacterial lipopolysaccharides in ankylosing spondylitis, psoriatic arthritis and rheumatoid arthritis. In ankylosing spondylitis, TLR4 (23.1 ± 21.9%) and, to a smaller extent, TLR2 (4.1 ± 5.8%) were expressed on CD4⁺CD28^null T cells, whereas expression was negligible on CD4⁺CD28⁺ and CD8⁺ T cells. CD4⁺CD28^null T cells produced perforin upon stimulation with lipopolysaccharide, and this effect was enhanced by autologous serum or recombinant soluble CD14. Perforin production could be prevented with blocking antibodies directed against CD14 or TLR4. Incubation of peripheral blood mononuclear cells with tumour necrosis factor alpha led to an upregulation of TLR4 and TLR2 on CD4⁺CD28^null T cells in vitro, and treatment of patients with antibodies specifically directed against tumour necrosis factor alpha resulted in decreased expression of TLR4 and TLR2 on CD4⁺CD28^null T cells in vivo. We describe here a new pathway for direct activation of cytotoxic CD4⁺ T cells by components of infectious pathogens. This finding supports the hypothesis that CD4⁺CD28^null T cells represent an immunological link between the innate immune system and the adaptive immune system.     

Interaction of the eukaryotic elongation factor 1A with newly synthesized polypeptides

eEF1A, the eukaryotic homologue of bacterial elongation factor Tu, is a well characterized translation elongation factor responsible for delivering aminoacyl-tRNAs to the A-site at the ribosome. Here we show for the first time that eEF1A also associates with the nascent chain distal to the peptidyltransferase center. This is demonstrated for a variety of nascent chains of different lengths and sequences. Interestingly, unlike other ribosome-associated factors, eEF1A also interacts with polypeptides after their release from the ribosome. We demonstrate that eEF1A does not bind to correctly folded full-length proteins but interacts specifically with proteins that are unable to fold correctly in a cytosolic environment. This association was demonstrated both by photo-cross-linking and by a functional refolding assay.     

Teneurin 2 is expressed by the neurons of the thalamofugal visual system in situ and promotes homophilic cell-cell adhesion in vitro

The transmembrane glycoprotein teneurin 2 is expressed by neurons in the developing avian thalamofugal visual system at periods that correspond with target recognition and synaptogenesis. Partial and full-length teneurin 2 constructs were expressed in cell lines in vitro. Expression of the cytoplasmic domain is required for the induction of filopodia, the transport of teneurin 2 into neurites and the co-localization of teneurin 2 with the cortical actin cytoskeleton. In addition, expression of the extracellular domain of teneurin 2 by HT1080 cells induced cell aggregation, and the extracellular domain of teneurin 2 became concentrated at sites of cell-cell contact in neuroblastoma cells. These observations indicate that the homophilic binding of teneurin 2 may play a role in the development of specific neuronal circuits in the developing visual system.     

Long-term maize-Desmodium intercropping shifts structure and composition of soil microbiome with stronger impact on fungal communities

Plant and Soil - Push–pull is an intercropping technology that is rapidly spreading among smallholder farmers in&nbsp;Sub-Saharan Africa. The technology intercrops cereals with Desmodium...     

Soil and bark biodiversity forms discrete islands between vineyards that are not affected by distance or management regime

Within geographic regions, the existing data suggest that physical habitat (bark, soil, etc.) is the strongest factor determining agroecosystem microbial community assemblage, followed by geographic location (site), and then management regime (organic, conventional, etc.). The data also suggest community similarities decay with increasing geographic distance. However, integrated hypotheses for these observations have not been developed. We formalized and tested such hypotheses by sequencing 3.8 million bacterial 16S, fungal ITS2 and non-fungal eukaryotic COI barcodes deriving from 108 samples across two habitats (soil and bark) from six vineyards sites under conventional or conservation management. We found both habitat and site significantly affected community assemblage, with habitat the stronger for bacteria only, but there was no effect of management. There was no evidence for community similarity distance–decay within sites within each habitat. While communities significantly differed between vineyard sites, there was no evidence for between site community similarity distance–decay apart from bark bacterial communities, and no correlations with soil and bark pH apart from soil bacterial communities. Thus, within habitats, vineyard sites represent discrete biodiversity islands, and while bacterial, fungal and non-fungal eukaryotic biodiversity mostly differs between sites, the distance by which they are separated does not define how different they are.     

Genetic diversity of the genus Cosavirus in the family Picornaviridae: a new species, recombination, and 26 new genotypes

The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses.     

Lipoic acid plays a role in scleroderma: insights obtained from scleroderma dermal fibroblasts

Introduction

Systemic sclerosis (SSc) is a connective tissue disease characterized by fibrosis of the skin and organs. Increase in oxidative stress and platelet-derived growth factor receptor (PDGFR) activation promote type I collagen (Col I) production, leading to fibrosis in SSc. Lipoic acid (LA) and its active metabolite dihydrolipoic acid (DHLA) are naturally occurring thiols that act as cofactors and antioxidants and are produced by lipoic acid synthetase (LIAS). Our goals in this study were to examine whether LA and LIAS were deficient in SSc patients and to determine the effect of DHLA on the phenotype of SSc dermal fibroblasts. N-acetylcysteine (NAC), a commonly used thiol antioxidant, was included as a comparison.

Methods

Dermal fibroblasts were isolated from healthy subjects and patients with diffuse cutaneous SSc. Matrix metalloproteinase (MMPs), tissue inhibitors of MMPs (TIMP), plasminogen activator inhibitor 1 (PAI-1) and LIAS were measured by enzyme-linked immunosorbent assay. The expression of Col I was measured by immunofluorescence, hydroxyproline assay and quantitative PCR. PDGFR phosphorylation and α-smooth muscle actin (αSMA) were measured by Western blotting. Student’s t-tests were performed for statistical analysis, and P-values less than 0.05 with two-tailed analysis were considered statistically significant.

Results

The expression of LA and LIAS in SSc dermal fibroblasts was lower than normal fibroblasts; however, LIAS was significantly higher in SSc plasma and appeared to be released from monocytes. DHLA lowered cellular oxidative stress and decreased PDGFR phosphorylation, Col I, PAI-1 and αSMA expression in SSc dermal fibroblasts. It also restored the activities of phosphatases that inactivated the PDGFR. SSc fibroblasts produced lower levels of MMP-1 and MMP-3, and DHLA increased them. In contrast, TIMP-1 levels were higher in SSc, but DHLA had a minimal effect. Both DHLA and NAC increased MMP-1 activity when SSc cells were stimulated with PDGF. In general, DHLA showed better efficacy than NAC in most cases.

Conclusions

DHLA acts not only as an antioxidant but also as an antifibrotic because it has the ability to reverse the profibrotic phenotype of SSc dermal fibroblasts. Our study suggests that thiol antioxidants, including NAC, LA, or DHLA, could be beneficial for patients with SSc.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-014-0411-6) contains supplementary material, which is available to authorized users.     

Quantifying the Association between Bovine and Human Trypanosomiasis in Newly Affected Sleeping Sickness Areas of Uganda

Background

Uganda has active foci of both chronic and acute HAT with the acute zoonotic form of disease classically considered to be restricted to southeast Uganda, while the focus of the chronic form of HAT was confined to the northwest of the country. Acute HAT has however been migrating from its traditional disease focus, spreading rapidly to new districts, a spread linked to movement of infected cattle following restocking. Cattle act as long-term reservoirs of human infective T. b. rhodesiense showing few signs of morbidity, yet posing a significant risk to human health. It is important to understand the relationship between infected cattle and infected individuals so that an appropriate response can be made to the risk posed to the community from animals infected with human pathogens in a village setting.

Methodology/Principal Findings

This paper examines the relationship between human T. b. rhodesiense infection and human infective and non-human T. brucei s.l. circulating in cattle at village level in Kaberamaido and Dokolo Districts, Uganda. The study was undertaken in villages that had reported a case of sleeping sickness in the six months prior to sample collection and those villages that had never reported a case of sleeping sickness.

Conclusions and Significance

The sleeping sickness status of the villages had a significant effect with higher odds of infection in cattle from case than from non-case villages for T. brucei s.l. (OR: 2.94, 95%CI: 1.38–6.24). Cattle age had a significant effect (p<0.001) on the likelihood of T. brucei s.l. infection within cattle: cattle between 18–36 months (OR: 3.51, 95%CI: 1.63–7.51) and cattle over 36 months (OR: 4.20, 95%CI: 2.08–8.67) had significantly higher odds of T. brucei s. l. infection than cattle under 18 months of age. Furthermore, village human sleeping sickness status had a significant effect (p<0.05) on the detection of T. b. rhodesiense in the village cattle herd, with significantly higher likelihood of T. b. rhodesiense in the village cattle of case villages (OR: 25, 95%CI: 1.2–520.71). Overall a higher than average T. brucei s.l. prevalence (>16.3%) in a village herd over was associated with significantly higher likelihood of T. b. rhodesiense being detected in a herd (OR: 25, 95%CI: 1.2–520.71).