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Transcriptomic Analysis Reveals Different Sensitivities of Genes to EP <sub>4</sub> Receptor Agonist Stimulation in BEAS‐2B Human Bronchial Epithelial Cells

2020· article· en· W3018520815 on OpenAlexaff
Radhika Joshi, Omar Hamed, Mark A. Giembycz

Bibliographic record

VenueThe FASEB Journal · 2020
Typearticle
Languageen
FieldMedicine
TopicInflammatory mediators and NSAID effects
Canadian institutionsUniversity of Calgary
Fundersnot available
KeywordsAgonistTranscriptomeReceptorTransfectionReporter geneGene silencingStimulationGene expressionMolecular biologyChemistryPharmacologyGeneDownregulation and upregulationCell biologyBiologyEndocrinologyBiochemistry

Abstract

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Introduction Prostanoid EP 4 ‐receptors are highly expressed on human airway epithelial cells (AECs) and typically mediate canonical, Gs‐cAMP signaling. EP 4 ‐receptor agonists exhibit bronchodilator and anti‐inflammatory activity and could represent novel therapeutic candidates to treat obstructive lung diseases. We have reported previously that long‐acting β 2 ‐adrenoceptor agonists (LABAs) promote significant gene expression changes in human AECs, which could contribute to their clinical efficacy. In this study, we have determined the EP 4 ‐receptor‐regulated transcriptome in BEAS‐2B cells using the selective agonist, ONO‐AE1‐329, using the LABA, vilanterol, as a comparator. Methods BEAS‐2B cells were treated for 2h with vehicle, and two concentrations of ONO‐AE1‐329 (1nM, ONO 1 ; 1000nM, ONO 1000 ). A maximally effective concentration of vilanterol (100nM, Vil 100 ) was included to define maximum responses. Gene expression changes were determined by RNA sequencing. Simulated E /[A] curves were generated from ONO 1 and ONO 1000 data assuming a unity Hill coefficient for each gene expression change (≥3‐fold; FDR ≤5%). BEAS‐2B cells transfected with a cAMP response element (CRE) luciferase reporter were used to determine the affinity ( K A ) of ONO‐AE1‐329 for the EP 4 ‐receptor. This was estimated by operational model fitting of E /[A] curve data before and after fractional receptor depletion using siRNA mediated PTGER4 gene silencing. Occupancy‐response relationships for ONO‐AE1‐329‐induced genes were constructed using the simulated E /[A] curves and the K A value determined in CRE reporter cells. Results Transcriptomic changes produced by Vil 100 and ONO 1000 were highly correlated suggesting that the β 2 ‐adrenoceptor and the EP 4 ‐receptor shared a common mechanism of action. Vilanterol was a full agonist on all induced genes whereas ONO‐AE1‐329 was a partial agonist with intrinsic activity values that varied between genes. The K A of ONO‐AE1‐329 was found to be consistent with a previous radioligand binding study. ONO‐AE1‐329‐induced genes differed in sensitivity by ~18‐fold with NR4A3 and PDE4B representing transcripts at the extremes of this sensitivity spectrum. Accordingly, receptor occupancy‐response relationships varied from almost linear (where response is directly proportional to occupancy; e.g., NR4A3 ) to markedly hyperbolic (indicative of a significant receptor reserve; e.g., PDE4B ) (Fig. ). Conclusions Differences in the sensitivities of genes to ONO‐AE1‐329 indicate that the EP 4 ‐receptor interprets equivalent degrees of receptor occupancy differently. This may be explained by ‐ a) regulation by multiple cAMP‐induced transcription factors, and/or b) variability in promoter context and co‐factor binding which may differentially affect the ability of transcription factors to interact favorably with DNA. Support or Funding Information CIHR‐ PJT 152904 Receptor occupancyresponse relationships for ONO‐AE1‐329 induced genes Figure 1

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.002
Threshold uncertainty score0.007

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0010.000
Bibliometrics0.0010.001
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0020.001

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.016
GPT teacher head0.243
Teacher spread0.227 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

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Citations0
Published2020
Admission routes1
Has abstractyes

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