Association analysis of tyrosine kinase FYN gene polymorphisms in asthmatic children

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures

Large amounts of data emerging from experiments in molecular medicine are leading to the identification of molecular signatures associated with disease subtypes. The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous types of data. In this review, we discuss knowledge representations that can be useful to explore the biological context of molecular signatures, in particular three main approaches, namely, pathway mapping approaches, molecular network centric approaches and approaches that represent biological statements as knowledge graphs. We discuss the utility of each of these paradigms, illustrate how they can be leveraged with selected practical examples and identify ongoing challenges for this field of research.

Role of the Fyn -93A>G polymorphism (rs706895) in acute rejection after liver transplantation

The tyrosine kinase Fyn phosphorylates tyrosine residues on key targets involved in early T-cell signal transduction. T-cell signal transduction is one essential step for acute transplant rejection. The aim of this study was to evaluate the association of Fyn -93A>G single nucleotide polymorphism (SNP) (rs706895) with the susceptibility to acute rejection episodes in liver transplantation. In total, 72 liver transplant recipients with one biopsy proven acute rejection (S-BPAR), 56 with multiple BPAR (M-BPAR), 105 without BPAR (No-BPAR), and 145 healthy controls were enrolled in this case-control study. The SNP was genotyped by polymerase chain reaction-allele specific restriction enzyme analysis (PCR-ASRA) and was analyzed for a recessive and a dominant model. The Fyn -93G allele exhibits in healthy controls a statistically significant lower frequency than in liver recipients (18% vs. 24%; p=0.046) or in liver recipients with BPAR (18% vs. 27%; p=0.017). However, the genotype and allele frequencies of the Fyn -93A>G SNP demonstrate no significant differences between recipients with acute rejection episodes (S-BPAR and M-BPAR) and No-BPAR recipients. Thus our results provide no evidence that the Fyn -93A>G SNP contributes to the susceptibility to acute liver transplant rejection in a Caucasian population.

Dysregulation of complement system and CD4+ T cell activation pathways implicated in allergic response

Allergy is a complex disease that is likely to involve dysregulated CD4+ T cell activation. Here we propose a novel methodology to gain insight into how coordinated behaviour emerges between disease-dysregulated pathways in response to pathophysiological stimuli. Using peripheral blood mononuclear cells of allergic rhinitis patients and controls cultured with and without pollen allergens, we integrate CD4+ T cell gene expression from microarray data and genetic markers of allergic sensitisation from GWAS data at the pathway level using enrichment analysis; implicating the complement system in both cellular and systemic response to pollen allergens. We delineate a novel disease network linking T cell activation to the complement system that is significantly enriched for genes exhibiting correlated gene expression and protein-protein interactions, suggesting a tight biological coordination that is dysregulated in the disease state in response to pollen allergen but not to diluent. This novel disease network has high predictive power for the gene and protein expression of the Th2 cytokine profile (IL-4, IL-5, IL-10, IL-13) and of the Th2 master regulator (GATA3), suggesting its involvement in the early stages of CD4+ T cell differentiation. Dissection of the complement system gene expression identifies 7 genes specifically associated with atopic response to pollen, including C1QR1, CFD, CFP, ITGB2, ITGAX and confirms the role of C3AR1 and C5AR1. Two of these genes (ITGB2 and C3AR1) are also implicated in the network linking complement system to T cell activation, which comprises 6 differentially expressed genes. C3AR1 is also significantly associated with allergic sensitisation in GWAS data.

Tau phosphorylation pathway genes and cerebrospinal fluid tau levels in Alzheimer's disease

Alzheimer's disease (AD) is characterized by the presence in the brain of amyloid plaques, consisting predominately of the amyloid β peptide (Aβ), and neurofibrillary tangles, consisting primarily of tau. Hyper-phosphorylated-tau (p-tau) contributes to neuronal damage, and both p-tau and total-tau (t-tau) levels are elevated in AD cerebrospinal fluid (CSF) compared to cognitively normal controls. Our hypothesis was that increased ratios of CSF phosphorylated-tau levels relative to total-tau levels correlate with regulatory region genetic variation of kinase or phosphatase genes biologically associated with the phosphorylation status of tau. Eighteen SNPs located within 5' and 3' regions of 5 kinase and 4 phosphatase genes, as well as two SNPs within regulatory regions of the MAPT gene were chosen for this analysis. The study sample consisted of 101 AD patients and 169 cognitively normal controls. Rs7768046 in the FYN kinase gene and rs913275 in the PPP2R4 phosphatase gene were both associated with CSF p-tau and t-tau levels in AD. These SNPs were also differentially associated with either CSF t-tau (rs7768046) or CSF p-tau (rs913275) relative to t-tau levels in AD compared to controls. These results suggest that rs7768046 and rs913275 both influence CSF tau levels in an AD-associated manner.

Identification of SRC as a potent drug target for asthma, using an integrative approach of protein interactome analysis and in silico drug discovery

Network-biology inspired modeling of interactome data and computational chemistry have the potential to revolutionize drug discovery by complementing conventional methods. We consider asthma, a complex disease characterized by intricate molecular mechanisms, for our study. We aim to integrate prediction of potent drug targets using graph-theoretical methods and subsequent identification of small molecules capable of modulating activity of the best target. In this work, we construct the protein interactome underlying this disease: Asthma Protein Interactome (API). Using a strategy based on network analysis of the interactome, we identify a set of potential drug targets for asthma. Topologically and dynamically, v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (SRC) emerges as the most central target in API. SRC is known to play an important role in promoting airway smooth muscle cell growth and facilitating migration in airway remodeling. From interactome analysis, and with the reported role in respiratory mechanisms, SRC emerges as a promising drug target for asthma. Further, we proceed to identify leads for SRC from a public database of small molecules. We predict two potential leads for SRC using ligand-based virtual screening methodology.

Multilocus analysis of candidate genes involved in neurogenic inflammation in pediatric asthma and related phenotypes: a case-control study

OBJECTIVES

Asthma is a heterogenous complex disorder caused by chronic inflammation of the airways. The key issue in genetic association studies of complex disorders is the identification of multiple low-risk genes that individually have little impact on the phenotype, but in combination account for the clinical manifestation of asthma. Since neurogenic inflammation is emerging as a candidate factor in the pathogenesis of asthma, the aim of the study was to investigate whether genetic variants of neurotrophin genes are associated with asthma disease severity or asthma-related phenotypes in a pediatric population.

METHODS

We genotyped 27 polymorphisms located in neurotrophin genes, using TaqMan SNP genotyping assays or Polymerase Chain Reaction - Restriction Fragments Lengths Polymorphism (PCR-RFLP) in 200 children diagnosed with asthma and 226 controls. Interactions between 27 polymorphic loci and asthma-related phenotypes were determined using the Multifactor Dimensionality Reduction (MDR) method.

RESULTS

In single marker analysis, we observed an association of MAP3K1 gene polymorphisms (rs702689 and rs889312) with asthma. We also observed that four Single Nucleotide Polymorphisms (SNPs) were associated with severe asthma. Analysis stratified by asthma-related phenotype revealed an association between atopy and NGFR (rs3785931), while BDNF (rs7124442), NTRK2 (rs1212171), NGFR (rs2072446), and FYN (rs3730353) variants were associated with increased exhaled nitric oxide (exNO). In addition, gene-gene interaction analysis revealed a significant epistatic interaction between MAPK (rs889312) and NGF (rs11102930) variants in asthma susceptibility.

CONCLUSIONS

Our results suggest that genetic variants of MAP3K1 and NGF genes involved in the regulation of neurogenic inflammation may contribute to asthma, possibly via enhanced NGF expression and MAPK signaling pathway activation.

Cytokine-induced arginase activity in pulmonary endothelial cells is dependent on Src family tyrosine kinase activity

We hypothesized that the Src family tyrosine kinases (STKs) are involved in the upregulation of arginase and inducible nitric oxide synthase (iNOS) expression in response to inflammatory stimuli in pulmonary endothelial cells. Treatment of bovine pulmonary arterial endothelial cells (bPAEC) with lipopolysaccharide and tumor necrosis factor-alpha (L/T) resulted in increased urea and nitric oxide (NO) production, and this increase in urea and NO production was inhibited by the STK inhibitor PP1 (10 microM). The STK inhibitors PP2 (10 microM) and herbimycin A (10 microM) also prevented the L/T-induced expression of both arginase II and iNOS mRNA in bPAEC. Together, the data demonstrate a central role of STK in the upregulation of both arginase II and iNOS in bPAEC in response to L/T treatment. To identify the specific kinase(s) required for the induction of urea and NO production, we studied human pulmonary microvascular endothelial cells (hPMVEC) so that short interfering RNA (siRNA) techniques could be employed. We found that hPMVEC express Fyn, Yes, c-Src, Lyn, and Blk and that the protein expression of Fyn, Yes, c-Src, and Lyn could be inhibited with specific siRNA. The siRNA targeting Fyn prevented the cytokine-induced increase in urea and NO production, whereas siRNAs specifically targeting Yes, c-Src, and Lyn had no appreciable effect on cytokine-induced urea and NO production. These findings support our hypothesis that inflammatory stimuli lead to increased urea and NO production through a STK-mediated pathway. Furthermore, these results indicate that the STK Fyn plays a critical role in this process.