Digital Immune Gene Expression Profiling Discriminates Allergic Rhinitis Responders from Non-Responders to Probiotic Supplementation

Abstract

Probiotic supplementation for eight weeks with a multi-strain probiotic by individuals with allergic rhinitis (AR) reduced overall symptom severity, the frequency of medication use and improved quality of life. The purported mechanism of action is modulation of the immune system. This analysis examined changes in systemic and mucosal immune gene expression in a subgroup of individuals, classified as either responders or non-responders based on improvement of AR symptoms in response to the probiotic supplement. Based on established criteria of a beneficial change in the mini-rhinoconjunctivitis quality of life questionnaire (mRQLQ), individuals with AR were classified as either responders or non-responders. Systemic and mucosal immune gene expression was assessed using nCounter PanCancer Immune Profiling (Nanostring Technologies, Seattle, WA, USA) kit on blood samples and a nasal lysate. There were 414 immune genes in the blood and 312 immune genes in the mucosal samples expressed above the limit of detection. Unsupervised hierarchical clustering of immune genes separated responders from non-responders in blood and mucosal samples at baseline and after supplementation, with key T-cell immune genes differentially expressed between the groups. Striking differences in biological processes and pathways were evident in nasal mucosa but not blood in responders compared to non-responders. These findings support the use of network approaches to understand probiotic-induced changes to the immune system.

T and B Lymphocyte Transcriptional States Differentiate between Sensitized and Unsensitized Individuals in Alpha-Gal Syndrome

“…Nanostring technology is widely used to study cancers [ 25 , 26 ] and autoinflammatory and autoimmune diseases [ 27 , 28 , 29 , 30 ]. It has also been deployed to dissect transcription profiles in other allergic diseases, including asthma [ 31 , 32 ] and allergic rhinitis [ 33 , 34 ]. To our knowledge, this proof-of-concept study is the first application of this technology to alpha-gal mammalian meat allergy, and food allergy in general.…”

Evaluation of Intranasal TLR2/6 agonist INNA-051: Safety, Tolerability and Proof of Pharmacology

“…RNA extraction and concentration along with analysis with the NanoString nCounter Human PanCancer Immune Profiling Assay were completed as previously described (60)(61)(62). Individual viral load values were compared using a repeated measures model with treatment group and visit/time point as fixed effect, and the interaction between study visit/time point and treatment group using a compound symmetry covariance structure.…”

“…The parameter estimates (least square means, estimated differences between the least squares means and the associated confidence intervals and p-values) at each visit/time point were calculated using REML method and the Kenward-Roger's method was used to determine the degrees of freedom. To account for multiple comparisons, the For RNA analyses, quality control and normalisation was undertaken utilising nSolver 4.0 (NanoString Technologies, WA, USA) with gene expression analysis completed using a combination of limma for differential gene expression (63) in the R computing environment (64), and nSolver 4.0 for pathway scoring (65) and cell type profiling (60)(61)(62). Raw gene expression data was normalised against a set of 6 positive and 6 negative controls to account for background noise and platform-associated variation.…”