Use of novel DNA methylation signatures to distinguish between human airway structural cell types

INTRODUCTION: Chronic inflammatory and fibrotic lung diseases like asthma, COPD and pulmonary fibrosis are characterised by modified phenotype of the airway structural cells. Airway walls are comprised of a robust epithelial layer that lines the lumen followed by the basement membrane, submucosa predominantly composed of fibroblasts and finally enveloped by a bulk of smooth muscle cells that determine the relaxation and constriction of the airways. The phenotype of airway structural cells is determined by epigenetic alterations such as DNA methylation, which alters the activation status of a range of important inflammatory and remodelling genes. Here we determined if airway structural cells (Epithelial cells, fibroblasts and smooth muscle cells) have different DNA methylome signatures that can be used to distinguish between them. This will offer a reference standard for identifying cell type specific DNA methylation changes induced by various inflammatory stimuli. EXPERIMENTAL METHODS: Illumina Human Methylation 450K Beadchip (HM450K) was used to perform genome-wide methylome screening on 17 bronchial fibroblast (BrF), 23 lung parenchymal fibroblast (LgF), 17 airway epithelial cell (Ep) and 6 airway smooth muscle cell (ASM) samples isolated from healthy individuals. The data was normalised using funtoonorm, a specialised algorithm in R developed for multiple tissue types. R packages minfi, limma and DMRcate was used for CpG site exclusion and identification of significant differentially methylated regions (DMR) specific to each of the four cell types. RESULTS AND DISCUSSION: Epithelial cells distinctly separated from other lung cells (791 DMR). LgF, BrF and ASM had 13, 10 and 1 signature DMR respectively. Despite close anatomical proximity, ASM and BrF displayed 2 DMR when compared to each other. Interestingly, fibroblasts obtained from airway showed 6 DMR in comparison to those obtained from lung parenchyma, suggesting that the same cell type obtained from different parts of the lung can have significantly different methylation patterns that might lead to phenotypic differences. CONCLUSION: We have identified cell and tissue specific methylation signatures which can be used to differentiate between different types of airway structural cells. The airway epithelial cells showed the greatest separation from other airway structural cells. The Bronchial fibroblasts varied minimally from airway smooth muscle cells despite its significant separation from airway epithelial cells and parenchymal fibroblasts

Lattice isomorphisms of bisimple monogenic orthodox semigroups

Using the classification and description of the structure of bisimple monogenic orthodox semigroups obtained in \cite{key10}, we prove that every bisimple orthodox semigroup generated by a pair of mutually inverse elements of infinite order is strongly determined by the lattice of its subsemigroups in the class of all semigroups. This theorem substantially extends an earlier result of \cite{key25} stating that the bicyclic semigroup is strongly lattice determined.Comment: Semigroup Forum (published online: 15 April 2011

Investigating genome wide DNA methylation in bronchial and lung fibroblasts from healthy individuals and individuals with COPD

Rationale: Lung fibroblasts are implicated in respiratory disease pathology including chronic obstructive pulmonary disease (COPD). Phenotypic differences between fibroblasts isolated from the bronchi versus the lung parenchyma have been described but no studies have compared the cell types on a genome wide scale. DNA methylation is a reversible modification of the DNA structure with the ability to affect cell function via the alteration of gene expression. Here we compared genome wide DNA methylation profiles from bronchial and lung fibroblasts and assessed modification to these profiles in cells isolated from individuals with COPD. Methods: DNA was isolated from lung (LgF) and bronchial fibroblasts (BrF) at passage 4 and bisulphite treated. Site specific, quantitative genome wide methylation was determined using the Illumina 450K Infinium Methylation BeadChip array. Linear modelling and DMRcate functions identified differentially methylated sites and regions respectively between BrF and LgF and from cells isolated from healthy individuals versus those with COPD. Results: 3980 CpG (methylation) sites significantly differed, following Bonferroni correction, between BrF and LgF isolated from healthy individuals. These sites had a broad distribution of effect size, with 240 CpG sites displaying a difference in methylation of >50%. 78 of these sites were validated in a second cohort of matched BrF and LgF isolated from the same individuals. There was genomic proximity to these sites and DMRcate was used to refine the individual CpG sites to 5 regions of interest associated with 5 genes; HLX, TWIST1, CREB5, SKAP2 and PRDM16. Differences in methylation were less pronounced when comparing cells isolated from healthy individuals to those with COPD. In BrF 47 DMRcate regions were identified with a maximum difference in methylation of at least 20%. In LgF 3 DMRcate regions were identified with a maximum difference in methylation of at least 20%. Conclusions: DNA methylation profiles are significantly different between BrF and LgF but only small modifications are associated with COPD. Future work will focus on validating a methylation based marker of lung versus bronchial fibroblasts to differentiate cell types by validating our differential DNA methylation observations with gene/protein expression

Investigating genome wide dna methylation in airway and parenchymal fibroblasts from healthy individuals and individuals with copd

Rationale: Lung fibroblasts are implicated in respiratory disease pathology including chronic obstructive pulmonary disease (COPD). Phenotypic differences between fibroblasts isolated from the airway versus the parenchyma have been described but no studies have compared the cell types on a genome wide scale. DNA methylation is a reversible modification of the DNA structure with the ability to affect cell function via the alteration of gene expression. Here we compared genome wide DNA methylation profiles from airway and parenchymal fibroblasts and assessed modification to these profiles in cells isolated from individuals with COPD. Methods: DNA was isolated from parenchymal and airway fibroblasts at passage 4, and bisulphite treated. Site specific, quantitative genome wide methylation was determined using the Illumina 450K Infinium Methylation BeadChip array. Linear modelling and DMRcate functions identified differentially methylated sites and regions respectively between airway and parenchymal fibroblasts isolated from individuals with normal lung function versus those with COPD. Results: 3980 CpG (methylation) sites significantly differed after Bonferroni correction between airway and parenchymal fibroblasts isolated from healthy individuals. These sites had a broad distribution of effect size, with 240 CpG sites displaying a difference in methylation of >50%. 78 of these sites validated in a second cohort of 7 sets of paired airway and parenchymal fibroblasts isolated from the same individual. There was genomic proximity to these sites and DMRcate was used to refine the individual CpG sites to 5 regions of interest associated with 5 genes; HLX, TWIST1, CREB5, SKAP2 and PRDM16. Differences in methylation were less pronounced when comparing cells isolated from healthy individuals to those with COPD. In airway fibroblasts 47 DMRcate regions were identified with a maximum difference in methylation of at least 20%. In parenchymal fibroblasts 3 DMRcate regions were identified with a maximum difference in methylation of at least 20%. Conclusions: DNA methylation profiles are significantly different between airway and parenchymal fibroblasts but only small modifications are associated with COPD. Future work will focus on validating a methylation based markers of parenchymal versus airway fibroblasts and associating our differential observations with gene/protein expression

Investigating genome wide dna methylation in airway smooth muscle cells from asthmatic and non-asthmatic donors

Rationale: Genetic mechanisms fail to fully explain asthma pathogenesis and environmental factors are considered to play an important role. Environmental factors may lead to permanent changes in epigenetic patterns and contribute to asthma. Epigenetics is the study of heritable changes in gene expression that are not due to changes in DNA sequence. DNA methylation is a reversible modification of DNA structure in which a methyl group is added to cytosine residues. Parental smoking affects the methylation of buccal cell DNA from children and children with early onset wheeze have an altered blood DNA methylation profile to healthy individuals. No studies have compared DNA methylation profiles in the disease relevant cell type of airway smooth muscle (ASM) cells. Methods: DNA was isolated from ASM cells at passage 5 and bisulphite treated to convert epigenetic information into sequence-based information. Site specific, quantitative genome wide methylation was determined using the Illumina 450K Infinium Methylation BeadChip array. Hits were validated by Pyrosequencing. RNA was extracted simultaneously for mRNA expression analysis by real time PCR. Results: There were no independent CpG sites associated with asthmatic status of ASM cells following multiple test correction. Without correction over 13000 CpG sites showed a significant difference in methylation (linear modelling, p value >0.05) between asthmatic and non-asthmatic cells, and a biologically relevant difference in methylation of greater that 10% (β value >0.1 ). 10 of these sites were selected as top hits. 7 sites positively validated by pyrosequencing. They were associated with 7 different genes; LGALS3BP, ATP11A, ZNF696, KLF6, TBX1, RUNX3, and SPINT2. Expression of these genes was measured in ASM cells isolated from asthmatic and non-asthmatic donors. LGALS3BP expression was undetectable while ATP11A and ZNF696 displayed no difference in expression between cells from asthmatic and non-asthmatic donors. KLF6 and SPINT2 showed a trend towards increased expression in cells from asthmatic donors while RUNX3 and TBX1 showed a trend towards decreased expression. Conclusions: Differences in CpG methylation exist between ASM isolated from asthmatic and non-asthmatic donors. Future work will focus on identifying differentially methylated regions of DNA and further defining the association to gene and protein expression

Development of a thermal ionizer as ion catcher

An effective ion catcher is an important part of a radioactive beam facility that is based on in-flight production. The catcher stops fast radioactive products and emits them as singly charged slow ions. Current ion catchers are based on stopping in He and H$_2$ gas. However, with increasing intensity of the secondary beam the amount of ion-electron pairs created eventually prevents the electromagnetic extraction of the radioactive ions from the gas cell. In contrast, such limitations are not present in thermal ionizers used with the ISOL production technique. Therefore, at least for alkaline and alkaline earth elements, a thermal ionizer should then be preferred. An important use of the TRI$\mu$P facility will be for precision measurements using atom traps. Atom trapping is particularly possible for alkaline and alkaline earth isotopes. The facility can produce up to 10$^9$ s$^{-1}$ of various Na isotopes with the in-flight method. Therefore, we have built and tested a thermal ionizer. An overview of the operation, design, construction, and commissioning of the thermal ionizer for TRI$\mu$P will be presented along with first results for $^{20}$Na and $^{21}$Na.Comment: 10 pages, 4 figures, XVth International Conference on Electromagnetic Isotope Separators and Techniques Related to their Applications (EMIS 2007

Mean-field analysis of the q-voter model on networks

We present a detailed investigation of the behavior of the nonlinear q-voter model for opinion dynamics. At the mean-field level we derive analytically, for any value of the number q of agents involved in the elementary update, the phase diagram, the exit probability and the consensus time at the transition point. The mean-field formalism is extended to the case that the interaction pattern is given by generic heterogeneous networks. We finally discuss the case of random regular networks and compare analytical results with simulations.Comment: 20 pages, 10 figure

A critical interpretive synthesis of evidence and values in recommendations to disinvest from population Screening

• the interplay between values and evidence in screening policy • methods of an ongoing systematic review • examples of disinvestment decision

Double agents: gendered organizational culture, control and resistance

Author's pre-publication draft. Final version of the article published in Sociology; available online on http://online.sagepub.com/This article presents ethnographic data showing how recruitment consultants negotiate managerial attempts to control workforce culture. I suggest the values which senior managers encourage consultants to embody prioritize so-called`masculine' attributes over `feminine' ones. I attempt to demonstrate the limits of cultural control by outlining three ways in which the consultants engage with this imposed culture: defiance, parody and ritual. These activities contain gendered assumptions similar to those embedded in corporate culture. I discuss the potential such practices have for resisting corporate culture and the gender within it, suggesting that one source of ambiguity within workplace `control' and `resistance' practices is that they employ overlapping cultural resources and assumptions

Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities

Frogs such as Rana temporaria and Litoria aurea secrete numerous closely related antimicrobial peptides (AMPs) as an effective chemical dermal defence. Damage or penetration of the bacterial plasma membrane is considered essential for AMP activity and such properties are commonly ascribed to their ability to form secondary amphipathic, α-helix conformations in membrane mimicking milieu. Nevertheless, despite the high similarity in physical properties and preference for adopting such conformations, the spectrum of activity and potency of AMPs often varies considerably. Hence distinguishing apparently similar AMPs according to their behaviour in, and effects on, model membranes will inform understanding of primary-sequence-specific antimicrobial mechanisms. Here we use a combination of molecular dynamics simulations, circular dichroism and patch-clamp to investigate the basis for differing anti-bacterial activities in representative AMPs from each species; temporin L and aurein 2.5. Despite adopting near identical, α-helix conformations in the steady-state in a variety of membrane models, these two AMPs can be distinguished both in vitro and in silico based on their dynamic interactions with model membranes, notably their differing conformational flexibility at the N-terminus, ability to form higher order aggregates and the characteristics of induced ion conductance. Taken together, these differences provide an explanation of the greater potency and broader antibacterial spectrum of activity of temporin L over aurein 2.5. Consequently, while the secondary amphipathic, α-helix conformation is a key determinant of the ability of a cationic AMP to penetrate and disrupt the bacterial plasma membrane, the exact mechanism, potency and spectrum of activity is determined by precise structural and dynamic contributions from specific residues in each AMP sequence