Institute for HeartLung Health

Vancouver, Canada

Institute for HeartLung Health

Vancouver, Canada
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Singh A.,University of British Columbia | Singh A.,Institute for HEARTLUNG Health | Cohen Freue G.V.,Institute for HEARTLUNG Health | Oosthuizen J.L.,University of British Columbia | And 14 more authors.
Proteomics - Clinical Applications | Year: 2012

Purpose: This proteomics study was designed to determine the utility of iTRAQ MALDI-TOF/TOF technology to compare plasma samples from carefully phenotyped mild, atopic asthma subjects undergoing allergen inhalation challenge. Experimental design: Eight adult subjects with mild, allergic asthma (four early responders (ERs) and four dual responders (DRs)) participated in the allergen inhalation challenge. Blood samples were collected prior to and 2 h after the inhalation challenge. Sixteen plasma samples (two per subject), technical replicates, and pooled controls were analyzed using iTRAQ. Technical validation was performed using LC-MRM/MS. Moderated robust regression was used to determine differentially expressed proteins. Results: Although this study did not show significant differences between pre- and post-challenge samples, discriminant analysis indicated that certain proteins responded differentially to allergen challenge with respect to responder type. At pre-challenge, fibronectin was significantly elevated in DRs compared to ERs and remained significant in the multiple reaction monitoring validation. Conclusions and clinical relevance: This proof of principle demonstration has shown that iTRAQ can uncover differences in the human plasma proteome between two endotypes of asthma and merits further application of iTRAQ to larger cohorts of asthma and other respiratory diseases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Yamamoto M.,University of British Columbia | Yamamoto M.,Institute for HEARTLUNG Health | Yamamoto M.,Vancouver Coastal Health Research Institute | Singh A.,University of British Columbia | And 12 more authors.
BMC Genomics | Year: 2012

Background: MicroRNAs are small non-coding RNAs that regulate gene expression at the post-transcriptional level. While they have been implicated in various diseases, the profile changes in allergen inhalation challenge are not clarified in human. We aimed to evaluate changes in the microRNA profiles in the peripheral blood of asthmatic subjects undergoing allergen inhalation challenge.Results: Seven mild asthmatic subjects participated in the allergen inhalation challenge. In addition, four healthy control subjects (HCs) were recruited. MicroRNA profiles in peripheral blood samples (pre-challenge and 2 hours post-challenge) were measured by the NanoString nCounter assay to determine changes in miRNA levels as these asthmatic subjects underwent an allergen inhalation challenge. One common miRNA, miR-192, was significantly expressed in both comparisons; HCs vs. pre-challenge and pre- vs. post-challenge, showing that miR-192 was significantly under-expressed in asthmatics compared to HCs and decreased in post-challenge at an FDR of 1%. Cell-specific statistical deconvolution attributed miR-192 expression in whole blood to PBMCs. MiR-192 was technically validated using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) showing that the level in asthmatics (pre-challenge) was significantly lower than HCs and that post-challenge was significantly lower than pre-challenge. The normalized relative miR-192 expression quantified using RT-qPCR specific to PBMCs was also validated. Ontology enrichment and canonical pathway analyses for target genes suggested several functions and pathways involved in immune response and cell cycle.Conclusions: The miRNA profile in peripheral blood was altered after allergen inhalation challenge. Change in miR-192 levels may be implicated in asthma mechanisms. These results suggest that allergen inhalation challenge is a suitable method to characterize peripheral miRNA profiles and potentially elucidate the mechanism of human asthma. © 2012 Yamamoto et al; licensee BioMed Central Ltd.

Singh A.,University of British Columbia | Singh A.,Institute for HEARTLUNG Health | Yamamoto M.,University of British Columbia | Yamamoto M.,Institute for HEARTLUNG Health | And 18 more authors.
PLoS ONE | Year: 2013

Some asthmatic individuals undergoing allergen inhalation challenge develop an isolated early response whereas others develop a dual response (early plus late response). In the present study we have used transcriptomics (microarrays) and metabolomics (mass spectrometry) of peripheral blood to identify molecular patterns that can discriminate allergen-induced isolated early from dual asthmatic responses. Peripheral blood was obtained prior to (pre-) and 2 hours post allergen inhalation challenge from 33 study participants. In an initial cohort of 14 participants, complete blood counts indicated significant differences in neutrophil and lymphocyte counts at pre-challenge between early and dual responders. At post-challenge, significant genes (ALOX15, FADS2 and LPCAT2) and metabolites (lysolipids) were enriched in lipid metabolism pathways. Enzymes encoding for these genes are involved in membrane biogenesis and metabolism of fatty acids into pro-inflammatory and anti-inflammatory mediators. Correlation analysis indicated a strong negative correlation between ALOX15, FADS2, and IL5RA expression with 2-arachidonoylglycerophosphocholine levels in dual responders. However, measuring arachidonic acid and docosahexaenoic acid levels in a validation cohort of 19 participants indicated that the free form of DHA (nmoles/μg of protein) was significantly (p = 0.03) different between early and dual responders after allergen challenge. Collectively these results may suggest an imbalance in lipid metabolism which dictates pro- (anti-) inflammatory and pro-resolving mechanisms. Future studies with larger sample sizes may reveal novel mechanisms and therapeutic targets of the late phase asthmatic response. © 2013 Singh et al.

Hollander Z.,University of British Columbia | Lin D.,University of British Columbia | Ng R.,University of British Columbia | Ignaszewski A.,University of British Columbia | And 8 more authors.
Transplantation | Year: 2010

Background. Acute rejection is still a significant barrier to long-term survival of the allograft. Current acute rejection diagnostic methods are not specific enough or are invasive. There have been a number of studies that have explored the blood or the biopsy to discover genomic biomarkers of acute rejection; however, none of the studies to date have used both. Methods. We analyzed endomyocardial biopsy tissue and whole blood-derived messenger RNA from 11 acute rejection and 20 nonrejection patients using Affymetrix Human Genome U133 Plus 2.0 chips. We used a novel approach and gained insight into the biology of rejection based on gene expression in the biopsy, and applied this knowledge to the blood analysis to identify novel blood biomarkers. Results. We identified probesets that are differentially expressed between acute rejection and nonrejection patients in the biopsy and blood, and developed three biomarker panels: (1) based on biopsy-only (area under the curve=0.85), (2) based on biopsy-targeted whole blood (area under the curve=0.83), and (3) based on whole blood-only (area under the curve=0.60) analyses. Conclusions. Most of the probesets replicated between biopsy and blood are regulated in opposite direction between the two sources of information. We also observed that the biopsy-targeted blood biomarker discovery approach can improve performance of the biomarker panel. The biomarker panel developed using this targeted approach is able to diagnose acute cardiac allograft rejection almost as well as the biopsy-only based biomarker panel. © 2010 by Lippincott Williams & Wilkins.

Freue G.C.,University of British Columbia | Balshaw R.F.,University of British Columbia | Balshaw R.F.,Simon Fraser University | Tebbutt S.J.,University of British Columbia | And 9 more authors.
BMC Bioinformatics | Year: 2012

Background: Biomarker panels derived separately from genomic and proteomic data and with a variety of computational methods have demonstrated promising classification performance in various diseases. An open question is how to create effective proteo-genomic panels. The framework of ensemble classifiers has been applied successfully in various analytical domains to combine classifiers so that the performance of the ensemble exceeds the performance of individual classifiers. Using blood-based diagnosis of acute renal allograft rejection as a case study, we address the following question in this paper: Can acute rejection classification performance be improved by combining individual genomic and proteomic classifiers in an ensemble?Results: The first part of the paper presents a computational biomarker development pipeline for genomic and proteomic data. The pipeline begins with data acquisition (e.g., from bio-samples to microarray data), quality control, statistical analysis and mining of the data, and finally various forms of validation. The pipeline ensures that the various classifiers to be combined later in an ensemble are diverse and adequate for clinical use. Five mRNA genomic and five proteomic classifiers were developed independently using single time-point blood samples from 11 acute-rejection and 22 non-rejection renal transplant patients. The second part of the paper examines five ensembles ranging in size from two to 10 individual classifiers. Performance of ensembles is characterized by area under the curve (AUC), sensitivity, and specificity, as derived from the probability of acute rejection for individual classifiers in the ensemble in combination with one of two aggregation methods: (1) Average Probability or (2) Vote Threshold. One ensemble demonstrated superior performance and was able to improve sensitivity and AUC beyond the best values observed for any of the individual classifiers in the ensemble, while staying within the range of observed specificity. The Vote Threshold aggregation method achieved improved sensitivity for all 5 ensembles, but typically at the cost of decreased specificity.Conclusion: Proteo-genomic biomarker ensemble classifiers show promise in the diagnosis of acute renal allograft rejection and can improve classification performance beyond that of individual genomic or proteomic classifiers alone. Validation of our results in an international multicenter study is currently underway. © 2012 Günther et al.; licensee BioMed Central Ltd.

Tebbutt S.J.,University of British Columbia | Tebbutt S.J.,Institute for HEARTLUNG Health | He J.-Q.,University of British Columbia | He J.-Q.,Institute for HEARTLUNG Health | And 9 more authors.
Genomics Insights | Year: 2012

Background: Methacholine challenge is commonly used within the asthma diagnostic algorithm. Methacholine challenge has recently been shown to induce airway remodelling in asthma via bronchoconstriction, without additional airway inflammation. We evaluated the effect of methacholine-induced bronchoconstriction on the peripheral whole-blood transcriptome. Methods: Fourteen males with adult-onset, occupational asthma, 26-77 years of age, underwent methacholine inhalation challenges. The concentration of methacholine eliciting a ≥20% fall in FEV 1 (PC 20) was determined. Blood was collected immediately prior to and two hours after challenge. Complete blood counts and leukocyte differentials were obtained. Transcriptome analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST arrays. Data were analyzed using robust LIMMA and SAM. The cell-specific Significance Analysis of Microarrays (csSAM) algorithm was used to deconvolute the gene expression data according to cell type. Results: Microarray pathway analysis indicated that inflammatory processes were differentially affected. CsSAM identified 1,559 transcripts differentially expressed (all down-regulated) between pre- and post-methacholine in eosinophils at a false discovery cutoff of 10%. Notable changes included the GOLGA5 and METTL2B genes and the protein ubiquitination and CCR3 pathways. Conclusions: We demonstrated significant changes in the peripheral blood eosinophil-specific transcriptome of asthmatics two hours after methacholine challenge. CCR3 and protein ubiquitination pathways are both significantly down-regulated. © The author(s), publisher and licensee Libertas Academica Ltd.

Kam S.H.Y.,University of British Columbia | Kam S.H.Y.,Institute for HEARTLUNG Health | Singh A.,University of British Columbia | Singh A.,Institute for HEARTLUNG Health | And 11 more authors.
Journal of Asthma | Year: 2012

Objectives. (1) To investigate the effects of globin mRNA depletion in detecting differential gene expression in peripheral blood and (2) to investigate changes in peripheral blood gene expression in atopic asthmatic individuals undergoing allergen inhalation challenge. Methods. Asthmatic subjects (2060 years of age, with stable, mild allergic asthma, n = 9) underwent allergen inhalation challenges. All had an early asthmatic response of ≥20% fall in forced expiratory volume in 1 second. Blood was collected immediately prior to and 2 hours after allergen challenge using PAXgene tubes (n = 4) and EDTA tubes (n = 5). Aliquots of the PAXgene blood samples were subjected to globin reduction (PAX-GR). Transcriptome analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST arrays. Data were preprocessed using factor analysis for robust microarray summarization and analyzed using linear models for microarrays. Pathway analyses were performed using Ingenuity Pathway Analysis. Results. Globin reduction uncovered probe sets of lower abundance. However, it significantly reduced the ability to detect differentially expressed genes (DEGs) when compared to non-globin-reduced PAXgene samples (PAX-NGR). Combined transcriptional analysis of four PAX-NGR and five EDTA sample pairs identified 1595 DEGs associated with allergen inhalation challenge (false discovery rate ≤ 5%), with the top-ranked network of perturbed biological functions consisting of inflammatory response, cellular movement, and immune cell trafficking. Conclusions. While we have demonstrated a diminished ability to detect DEGs after globin reduction, we have nevertheless identified significant changes in the peripheral blood transcriptome of people with mild asthma 2 hours after allergen inhalation challenge. © 2012 Informa Healthcare USA, Inc.

Abraham T.,Institute for HeartLung Health | Kayra D.,Institute for HeartLung Health | McManus B.,Institute for HeartLung Health | Scott A.,University of British Columbia
Journal of Structural Biology | Year: 2012

The structural remodeling of collagens is important in several biological processes including wound healing, tendon repair and adaptation, fibrosis and morphogenesis. Multiphoton microscopy is efficient in the induction of highly specific second harmonic generation (SHG) signal from non-centrosymmetric macromolecules such as fibrillar collagens. Although the detectors in the reflection geometry have been normally employed for capturing the backward scattered SHG considering the wide range of engineered thick tissue applications, there are still questions about the generated 3D collagen structures because of the directional pattern of SHG signals. The present study dealt with an in vitro collagen-fibroblast raft or bioartificial tendon model where the stimulation of fibroblast cells induced lateral orientation of collagen Type I fibers. The SHG signals originating from 3D collagen matrix were captured simultaneously in both forward and backward scattering directions. Our structural analysis indicates that collagen fibers formed in such in vitro model systems are predominantly of uniform sizes and are aligned preferentially in the lateral direction. The criss-cross arrangements of laterally oriented fibers are evident in the initial stages of contraction but eventually those laterally oriented collagen fibers are found to be aligned in parallel to each other as well as to the fibroblasts after an extended period of contraction. Our comprehensive quantitative assessment of simultaneously captured forward and backward 3D SHG image datasets, which includes the SHG signal decay, fiber diameter, cell dimensions, colocalization profiles, the 3D voxel volumes and Fourier analysis, indicates strong correlation of structural features identified in forward and backward directions. © 2012 Elsevier Inc.

Oosthuizen J.L.,Institute for HEARTLUNG Health | Gomez P.,Institute for HEARTLUNG Health | Ruan J.,Institute for HEARTLUNG Health | Hackett T.L.,Institute for HEARTLUNG Health | And 6 more authors.
PLoS ONE | Year: 2011

Background: Given the complex nature of the responses that can occur in host-pathogen interactions, dual transcriptomics offers a powerful method of elucidating these interactions during infection. The gene expression patterns of Aspergillus fumigatus conidia or host cells have been reported in a number of previous studies, but each focused on only one of the interacting organisms. In the present study, we profiled simultaneously the transcriptional response of both A. fumigatus and human airway epithelial cells (AECs). Methodology: 16HBE14o- transformed bronchial epithelial cells were incubated with A. fumigatus conidia at 37°C for 6 hours, followed by genome-wide transcriptome analysis using human and fungal microarrays. Differentially expressed gene lists were generated from the microarrays, from which biologically relevant themes were identified. Human and fungal candidate genes were selected for validation, using RT-qPCR, in both 16HBE14o- cells and primary AECs co-cultured with conidia. Principal Findings: We report that ontologies related to the innate immune response are activated by co-incubation with A. fumigatus condia, and interleukin-6 (IL-6) was confirmed to be up-regulated in primary AECs via RT-qPCR. Concomitantly, A. fumigatus was found to up-regulate fungal pathways involved in iron acquisition, vacuolar acidification, and formate dehydrogenase activity. Conclusion: To our knowledge, this is the first study to apply a dual organism transcriptomics approach to interactions of A. fumigatus conidia and human airway epithelial cells. The up-regulation of IL-6 by epithelia and simultaneous activation of several pathways by fungal conidia warrants further investigation as we seek to better understand this interaction in both health and disease. The cellular response of the airway epithelium to A. fumigatus is important to understand if we are to improve host-pathogen outcomes. © 2011 Oosthuizen et al.

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