Comprehensive Gene Expression Signature Using RNA-Seq in Airways of Mouse Model of Severe Asthma with Fungal Sensitization

2021 ◽  
pp. 1-11
Author(s):  
Hideki Inoue ◽  
Kaho Akimoto ◽  
Hitoshi Ikeda ◽  
Hiroki Sato ◽  
Tomoki Uno ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Inflammatory Response ◽  
Airway Inflammation ◽  
Severe Asthma ◽  
Receptor Binding ◽  
Cell Activation ◽  
Airway Epithelial ◽  
Rna Seq ◽  
Go Analysis

<b><i>Introduction:</i></b> Inhalation of fungal allergens induces airway epithelial damage following airway inflammation and excessive mucus secretion, which can lead to severe asthma with fungal sensitization (SAFS). Comprehensive gene expression analysis in <i>Alternaria</i>-exposed mouse airways, a model of SAFS, has not been conducted. <b><i>Methods:</i></b> BALB/c mice received intranasal administration of <i>Alternaria</i> extract or phosphate-buffered saline twice a week for 6 weeks. Lung sections and bronchoalveolar lavage fluid were obtained to assess airway inflammation. RNA-Seq in the central airway was performed, and gene ontology (GO) analysis and gene set enrichment analysis (GSEA) were conducted for pathway analyses. An in vitro experiment using human airway epithelial cell 16HBE14o- was performed to validate the RNA-Seq findings. <b><i>Results:</i></b> Eosinophilic airway inflammation with mucus overproduction and airway remodeling was observed in mice exposed to <i>Alternaria</i>. RNA-Seq analysis revealed 403 upregulated and 108 downregulated genes in airways of <i>Alternaria-</i>exposed mice. In GO analysis, the functions of immunoglobulin (Ig) receptor binding, Ig production, inflammatory response, and T-cell activation were upregulated, while those of keratinization and defense response to other organisms were downregulated. GSEA revealed positive enrichment in T-cell receptor complex, immunological synapse, antigen binding, mast cell activation, and Ig receptor binding, and negative enrichment in keratinization and cornification in <i>Alternaria</i>-exposed mice relative to control. <i>Alternaria</i> exposure to 16HBE14o- cells validated the downregulation of epithelial keratinization-related genes, including <i>SPRR1A</i>, <i>SPRR1B</i>, and <i>KRT6B</i>. <b><i>Conclusion:</i></b> RNA-Seq analysis showed that <i>Alternaria</i> exposure induced inflammatory response and impaired defense mechanisms in mice airway epithelium, which might be therapeutic targets for SAFS.

scholarly journals RNA Sequencing to Explore Dominant Isoform Switch During CCR6+ Memory T Cell Activation

2021 ◽  
Author(s):  
Shanrong Zhao ◽  
Alexander Barron ◽  
Ken Dower
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Rna Sequencing ◽  
T Cell Activation ◽  
Cell Cycle Progression ◽  
Cell Activation ◽  
Cell Function ◽  
Control Cell ◽  
Biological Information ◽  
Rna Seq

Abstract Alternative splicing (AS) is an essential, but under-investigated component of T-cell function during immune responses. Recent developments in RNA sequencing (RNA-seq) technologies, combined with the advent of computational tools, have enabled transcriptome-wide studies of AS at an unprecedented scale and resolution. In this paper, we analysed AS in an RNA-seq dataset previously generated to investigate the expression changes during T-cell maturation and antigen stimulation. Eight genes were identified with their most dominant isoforms switched during T cell activation. Of those, seven genes either directly control cell cycle progression or are oncogenes. We selected CDKN2C, FBXO5, NT5E and NET1 for discussion of the functional importance of AS of these genes. Our case study demonstrates that combining AS and gene expression analyses derives greater biological information and deeper insights from RNA-seq datasets than gene expression analysis alone.

3073Leveraging transcriptome sequencing for detecting novel disease-related pathways using human cardiac sarcoidosis myocardium biopsies

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
S Yoshida ◽  
A Nomura ◽  
H Tada ◽  
K Sakata ◽  
C Nakanishi ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Pathway Analysis ◽  
T Cell Activation ◽  
Transcriptome Sequencing ◽  
Cell Activation ◽  
Cardiac Sarcoidosis ◽  
Rna Seq ◽  
Differential Gene ◽  
Myocardial Biopsies

Abstract Background/Introduction Cardiac sarcoidosis (CS) is one of the main causes of poor outcomes in patients with sarcoidosis, a systemic granulomatous disorder of complex etiology including a genetically susceptible host and specific exposure to disease-triggering antigens. Recently, transcriptome analysis using sarcoidosis peripheral monocytes was reported to be useful for exploring genetic susceptibility and novel disease-causing pathways. However, transcriptome sequencing has not been used to explore disease-related genes and pathways directly using human CS myocardial biopsies. Purpose This study aimed to identify transcriptome profiles and novel disease-related pathways of CS by comparing human CS myocardial biopsies with control samples using ribonucleic acid (RNA) sequencing (RNA-Seq). Methods We assessed 30 patients with suspected myocardial disorders who underwent transcatheter endomyocardial biopsies at our University Hospital, Japan. Of those, 7 were clinically diagnosed with CS, 9 with hypertrophic cardiomyopathy (HCM), and 14 with dilated cardiomyopathy (DCM). Messenger RNAs were extracted from cardiac muscle biopsies using the Ovation SoLo RNA-Seq System (NuGEN Technologies), according to the manufacturer's instructions. Sequencing was performed with coverage of approximately 20 million reads per sample using Illumina HiSeq 2000. Sequencing reads were mapped using the STAR 2-pass method with GRCh37 as the reference. The DESeq2 R package (version 3.8) was used for further analyses. Principal component analysis (PCA) on gene expression was conducted for detecting outliers such as non-muscular samples. Differential gene expression analysis was performed between the 7 patients with CS and 23 patients with cardiomyopathy (HCM and DCM, non-CS). Gene Ontology (GO) enrichment analysis was conducted to estimate possible disease-related pathways. Results We successfully sequenced 60 myocardial biopsy samples (original and biological duplicates) from 30 CS patients. Of these, 2 outlier samples shown by the PCA plot were removed, and 58 were used for further analyses. We found 243 genes that were differentially expressed between CS patients and non-CS patients. Top-rated genes were RP11–366M4.8, RELN, S100A6, WASF3and UCHL1. Pathway analysis using GO demonstrated enrichment oflymphocyte activation (P=4.8x10–16), organelle fission (P=6.1x10–14), the M phase of the mitotic cell cycle (P=2.2x10–13), nuclear division (P=2.4x10–13), mitosis (P=2.4x10–13) and T-cell activation pathways (P=1.2x10–12). Conclusions Our differential gene expression and pathway analysis results using human CS myocardial biopsies suggested that lymphocyte activation, specifically the T-cell activation pathway, is linked to CS pathogenesis. Further studies are needed to decipher the role of specific genes related to genetic susceptibility and/or pathways associated with CS occurrence.

Abstract MP05: The Mechanism Of The Pvat Pro-inflammatory Micro-environment Formation During The Development Of High Fat Diet-induced Hypertension

Hypertension ◽  
2021 ◽  
Vol 78 (Suppl_1) ◽  
Author(s):  
Yining Jin ◽  
Omar Kana ◽  
Ramya Kumar ◽  
Rance Nault ◽  
Hannah Garver ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
High Fat Diet ◽  
Cell Activation ◽  
Control Diet ◽  
Rna Seq ◽  
High Fat ◽  
Induced Hypertension ◽  
Th17 Differentiation

There is considerable evidence for a causative role for T cells in hypertension, including studies with immunosuppressive drugs and T cell-deficient models. Our previous studies showed that soluble mediators from mesenteric perivascular adipose tissue (mPVAT) modulate T cell function. Specifically, conditioned media from mPVAT (mPVAT-CM) from Dahl S rats on a high fat diet (HFD) promoted expression of the pro-inflammatory cytokines, IFNg, IL-17a and GM-CSF, by activated T cells. Furthermore, the Dahl S rats on HFD will later develop hypertension. Hypothesis: mPVAT is stimulated to produce immunomodulatory mediators that promotes Th1/17 differentiation preceding the development of HFD-induced hypertension. We conducted bulk RNA-seq on activated splenocytes cultured in mPVAT-CM from Dahl S rats on either control or HFD for 10 weeks. In accordance with our previous studies, PVAT-CM from HFD-fed rats significantly upregulated many genes associated with IFNg/IL-17 induction, including Mpeg1, Lyz2 and Tnfsf4 (5.0±1.78, 3.70±0.53 and 1.78±0.42 fold over Control diet, respectively). In contrast, Th2/Treg-associated genes, such as Ctla2a (-0.27±0.02) and Ccr4 (-0.41±0.03) were downregulated. We also performed single cell (sc) RNA-seq on the PVAT stromal vascular fraction (SVF) and found that acute inflammatory genes were enriched in the HFD group. Together with the bulk RNA-seq on mPVAT, these data strongly suggest that the pro-inflammatory mPVAT micro-environment may promote Th1/Th17 differentiation. To identify mediators in PVAT-CM that may induce Th1/Th17 differentiation, we compared the bulk RNA-seq on splenocytes cultured in PVAT-CM with bulk RNA-seq conducted on the whole mPVAT itself. We found that a T cell co-stimulatory receptor DPP4 (CD26), which is closely associated with T cell activation was significantly increased in mPVAT from HFD-fed rats (33.4±2.3 HFD vs. 15.3±1.8 Control diet). We also observed an increase in DPP4 global expression from mPVAT SVF in HFD-fed rats, as determined by scRNA-seq. Conclusion: The data suggest that HFD promotes the IFNg and IL-17a pathways in PVAT, which precedes hypertension in Dahl S rats and correlates with an increase in expression of DPP-4, a gene that promotes T cell activation. (NIH P01 HL070687).

T.69. T Cell Activation and Th2-related Gene Expression Correlate with Disease Activity in Glatiramer Acetate-treated Multiple Sclerosis

2009 ◽  
Vol 131 ◽  
pp. S70
Author(s):  
Finn Sellebjerg ◽  
Martin Krakauer ◽  
Dan Hesse ◽  
Henrik Lund ◽  
Signe Limborg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Sclerosis ◽  
T Cell ◽  
Disease Activity ◽  
Glatiramer Acetate ◽  
T Cell Activation ◽  
Cell Activation ◽  
Related Gene

scholarly journals Nanoconfinement of Microvilli Alters Gene Expression and Boosts T cell Activation

2021 ◽  
Author(s):  
Morteza Aramesh ◽  
Diana Stoycheva ◽  
Ioana Sandu ◽  
Stephan J. Ihle ◽  
Tamara Zund ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Cell Signaling ◽  
T Cell Activation ◽  
Cell Activation ◽  
Local Environment ◽  
T Cell Signaling ◽  
Sense And Respond ◽  
Altered Gene

T cells sense and respond to their local environment at the nanoscale by forming small actin-rich protrusions, called microvilli, which play critical roles in signaling and antigen recognition, particularly at the interface with the antigen presenting cells. However, the mechanisms by which microvilli contribute to cell signaling and activation is largely unknown. Here, we present a tunable engineered system that promotes microvilli formation and T cell signaling via physical stimuli. We discovered that nanoporous surfaces favored microvilli formation, and markedly altered gene expression in T cells and promoted their activation. Mechanistically, confinement of microvilli inside of nanopores leads to size-dependent sorting of membrane-anchored proteins, specifically segregating CD45 phosphatases and T cell receptors (TCR) from the tip of the protrusions when microvilli are confined in 200 nm pores, but not in 400 nm pores. Consequently, formation of TCR nanoclustered hotspots within 200 nm pores, allows sustained and augmented signaling that prompts T cell activation even in the absence of TCR agonists. The synergistic combination of mechanical and biochemical signals on porous surfaces presents a straightforward strategy to investigate the role of microvilli in T cell signaling as well as to boost T cell activation and expansion for application in the growing field of adoptive immunotherapy.

scholarly journals RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease

2017 ◽  
Vol 64 (4) ◽  
pp. 476-481 ◽  
Author(s):  
Jerome Bouquet ◽  
Jennifer L. Gardy ◽  
Scott Brown ◽  
Jacob Pfeil ◽  
Ruth R. Miller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Disease ◽  
T Cell ◽  
B Cell ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Rna Seq ◽  
Viral Pathogen ◽  
Complex Chronic Disease

scholarly journals The Role of Fucoidans Isolated from the Sporophylls of Undaria pinnatifida against Particulate-Matter-Induced Allergic Airway Inflammation: Evidence of the Attenuation of Oxidative Stress and Inflammatory Responses

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2869 ◽  
Author(s):  
Kalahe Hewage Iresha Nadeeka Madushani Herath ◽  
Hyo Jin Kim ◽  
Areum Kim ◽  
Chung Eui Sook ◽  
Boo-Yong Lee ◽  
...  
Keyword(s):  
Particulate Matter ◽  
Inflammatory Response ◽  
Airway Inflammation ◽  
Cell Activation ◽  
Inflammatory Responses ◽  
Undaria Pinnatifida ◽  
Mast Cell Activation ◽  
Cell Hyperplasia ◽  
Mucus Hypersecretion ◽  
Asthma Symptoms

Ambient particulate matter (PM) is a critical environment pollutant that promotes the onset and aggravation of respiratory diseases such as asthma through airway inflammation and hypersecretion of mucus. In this study, we aimed to identify the effects of fucoidans isolated from sporophylls of Undaria pinnatifida on asthma symptoms such as the inflammatory response and mucus secretion using a mouse model. Balb/c mice, intraperitoneally sensitized with ovalbumin (OVA, 10 μg) dissolved in 200 µL saline and 2 mg Al(OH)3, were exposed to PM (5 mg/m3) for 7 consecutive days. In parallel, along with PM exposure, we orally administrated fucoidans (100, 400 mg/Kg) or prednisone (5 mg/Kg), an anti-inflammatory drug. We found that oral administration of fucoidans significantly attenuated PM-induced lipid peroxidation and infiltration of inflammatory cells like F4/80+ macrophages, Gr-1+ granulocytes, and CD4+ T lymphocytes. Fucoidans also attenuated the level of PM-exacerbated IL-4, a primitive cytokine released in Th2 mediated eosinophilic asthma. This further suppressed mast cell activation, degranulation and IgE synthesis of PM exposed mice. Interestingly, fucoidans attenuated PM-exacerbated mucus hypersecretion and goblet cell hyperplasia. Therefore, our results suggest that fucoidans are effective at alleviating PM-exacerbated allergic asthma symptoms by attenuating the airway inflammatory response and mucus hypersecretion.

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