Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma

Tessier, Laurence; Côté, Olivier; Clark, Mary E.; Viel, Laurent; Diaz-Méndez, Andrés; Anders, Simon; Bienzle, Dorothee

doi:10.1186/s12864-017-4107-6

“…The broad syndrome of asthma can therefore be divided into distinct disease entities, or subtypes, on the basis of 7 variables; these include clinical characteristics, biomarkers, lung physiology, genetics, histopathology, epidemiology, and response to treatment . Recently, several groups have used transcriptomic data derived from stimulated peripheral blood mononuclear cells (ex vivo) and bronchial epithelium (in vivo) to identify differentially expressed genes and pathways between RAO and non‐RAO horses. Stimulation with hay dust extract resulted in the greatest differential gene expression, the most dominant among the upregulated genes being those involved in immune cell trafficking, neutrophil chemotaxis, immune and inflammatory responses, and cell cycle regulation and apoptosis .…”

Section: Phenotype Versus Endotypementioning

confidence: 99%

“…Recently, several groups have used transcriptomic data derived from stimulated peripheral blood mononuclear cells (ex vivo) and bronchial epithelium (in vivo) to identify differentially expressed genes and pathways between RAO and non‐RAO horses. Stimulation with hay dust extract resulted in the greatest differential gene expression, the most dominant among the upregulated genes being those involved in immune cell trafficking, neutrophil chemotaxis, immune and inflammatory responses, and cell cycle regulation and apoptosis . The most upregulated hay dust extract‐induced chemokine was CXCL13, a B cell chemoattractant predominantly produced by Th17, but not Th1 or Th2, cells .…”

Section: Phenotype Versus Endotypementioning

confidence: 99%

“…Furthermore, treatment of a sensitized murine asthma model with an anti‐CXCL13 antibody reduces inflammatory cell recruitment, bronchial‐associated lymphoid tissue formation, and airway inflammation, potentially supporting CXCL13 as a novel treatment target . Another potential mechanistic pathway which could underpin the inflammatory cascade in RAO is the activation of neutrophils by the bronchial epithelium, leading to epithelial injury and impaired repair and differentiation . With the development of new biologic treatments in human asthma and the application of more targeted therapeutic approaches in the horse, it is appropriate to further investigate and clarify the clinical characteristics, biomarkers, lung physiology, genetics, histopathology, epidemiology, and response to treatment to better elucidate the pathophysiologic mechanisms in RAO, thus enabling the description of the allergic (Th‐2), non‐allergic (non‐Th‐2) and late‐onset endotypes of equine asthma.…”

Section: Phenotype Versus Endotypementioning

confidence: 99%

See 1 more Smart Citation

Equine asthma: Integrative biologic relevance of a recently proposed nomenclature

Bond

¹

,

Léguillette

²

,

Richard

³

et al. 2018

Veterinary Internal Medicne

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The term “equine asthma” has been proposed as a unifying descriptor of inflammatory airway disease (IAD), recurrent airway obstruction (RAO), and summer pasture‐associated obstructive airway disease. Whilst the term will increase comprehensibility for both the lay and scientific communities, its biologic relevance must be compared and contrasted to asthma in human medicine, recognizing the limited availability of peer‐reviewed equine‐derived data, which are largely restricted to clinical signs, measures of airway obstruction and inflammation and response to therapy. Such limitations constrain meaningful comparisons with human asthma phenotypes. Suggested minimum inclusion criteria supporting the term asthma, as well as similarities and differences between IAD, RAO, and multiple human asthma phenotypes are discussed. Furthermore, differences between phenotype and severity are described, and typical features for equine asthma subcategories are proposed. Based on shared features, we conclude that mild/moderate (IAD) and severe (RAO) equine asthma are biologically appropriate models for both allergic and non‐allergic human asthma, with RAO (severe equine asthma) also being an appropriate model for late‐onset asthma. With the development of new biologic treatments in humans and the application of more targeted therapeutic approaches in the horse, it would appear appropriate to further investigate the allergic (Th‐2) and non‐allergic (non‐Th‐2) phenotypes of equine asthma. Further research is required to more fully determine the potential clinical utility of phenotype classification.

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“…The mean of the total number of RNA-Seq reads for all samples was 36,252,701.08, and the mean of uniquely mapped number of reads was 33,127,466.35. The number of individual total reads, total mapped reads, uniquely mapped reads and multiple mapped reads is detailed elsewhere (39). The GATK workflow resulted in 2,823 and 1,788 sequence variants present specifically in the asthmatic group pre-and post-challenge, respectively (Suppl.…”

Section: Sequence Variant Calling and Filteringmentioning

confidence: 99%

Peer Review #1 of "Sequence variant analysis of RNA sequences in severe equine asthma (v0.2)"

2018

0

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Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants or potential relevance to the pathogenesis of asthma. Methods. RNA-Seq data were generated from endobronchial biopsies collected from 6 asthmatic and 7 non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant From Tolerant (SIFT) software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping (PolyPhen) 2 and Screening for Non-Acceptable Polymorphism (SNAP) 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson's Chi-squared test with Yates' continuity correction, and difference in genotype frequency was calculated using the Fisher's exact test for count data. Results. RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and

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“…Animal and sample procedures were previously described [39]. Briefly, six asthmatic and seven non-asthmatic horses without signs of asthma exacerbation belonging to the institutional research herd (mean ages of and 12 years, respectively, p =0.352, unpaired t test) were placed indoor in a dust-free environment.…”

Section: Animals and Proceduresmentioning

confidence: 99%

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Supplemental Information 1: Variants Detected in Asthmatic and Non-Asthmatic Horses With Genome Analysis Toolkit (GATK)

0

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Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants or potential relevance to the pathogenesis of asthma. Methods. RNA-Seq data were generated from endobronchial biopsies collected from 6 asthmatic and 7 non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant From Tolerant (SIFT) software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping (PolyPhen) 2 and Screening for Non-Acceptable Polymorphism (SNAP) 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson's Chi-squared test with Yates' continuity correction, and difference in genotype frequency was calculated using the Fisher's exact test for count data. Results. RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and

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Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma

Cited by 37 publications

References 111 publications

Equine asthma: Integrative biologic relevance of a recently proposed nomenclature

Equine asthma: Integrative biologic relevance of a recently proposed nomenclature

Peer Review #1 of "Sequence variant analysis of RNA sequences in severe equine asthma (v0.2)"

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