Virus Expression Database

GSE68479

Virograms for prediction of predisposition to asthma exacerbation

Submitted by Haiquan Li (University of Arizona, USA) on May 02 2015

Platform: microarray – [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]

Pubmed: None listed

Summary Background: Clinical transcriptomics of peripheral blood mononuclear cells (PBMC) are coming into focus as a surrogate approach for prognosis, diagnosis, biomarker discovery and examination disease mechanisms. However, bioassays paired with transcriptomic analytic tools are yet to be developed and made available at point of care. Harnessing personal dynamic genomic responses to tailor patient asthma treatment or prevent disease exacerbations remain unmet medical needs.
Method: We developed a rhinovirus-stimulated peripheral blood based-assay (virogram assay) coupled with single-subject analytics (N-of-1-patwhays) to capture dynamic genome-wide expression and dysregulated pathways to retrospectively predict childhood asthma exacerbation. We hypothesized that some genomic factors might predispose any given individual, healthy or asthmatic, to a set of similar transcriptional responses to rhinovirus stimulation. We first generated a classifier from paired sample microarrays, control and stimulated PBMC from healthy subjects and applied this classifier on the transcriptomic analysis of control and HRV-stimulated PBMC samples (virogram assay) from children with asthma.
Results: The analysis of the different genomic responses of single-subject paired PBMC samples (HRV-stimulated and control) derived from healthy individuals (external dataset) enabled the discovery of dysregulated pathways related to acquired immunity, epigenetics and morphogenesis. The classifier built on these results and applied on the transcriptional analysis derived from the virogram assay predicted that the risk of asthma exacerbation among asthmatic subjects with an accuracy of 70%.
Conclusion: We provide evidence that clinical prognosis can be predicted with a PBMC based-bioassay aligned with adequate single-subject analytics to assess dynamic transcriptomic response to specific disease-associated stimuli.

46 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM1673558 M3 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673559 M3 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673560 SUB09 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673561 SUB09 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673562 SUB12 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673563 SUB12 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673564 SUB15 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673565 SUB15 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673566 SUB20 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673567 SUB20 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673568 SUB22 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673569 SUB22 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673570 SUB23 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673571 SUB23 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673572 SUB25 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673573 SUB25 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673574 SUB29 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673575 SUB29 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673576 SUB30 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673577 SUB30 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673578 SUBM1 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673579 SUBM1 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673580 SUB04 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673581 SUB04 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673582 SUB05 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673583 SUB05 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673584 SUB10 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673585 SUB10 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673586 SUB13 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673587 SUB13 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673588 SUB14 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673589 SUB14 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673590 SUB16 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673591 SUB16 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673592 SUB17 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673593 SUB17 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673594 SUB2 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673595 SUB2 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673596 SUB21 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673597 SUB21 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673598 SUB26 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673599 SUB26 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673600 SUB7 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673601 SUB7 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A
GSM1673602 SUBM2 Patient, Control peripheral blood mononuclear cell  24 hrs control Uninfected
GSM1673603 SUBM2 Patient, Rhinovirus-exposed peripheral blood mononuclear cell  24 hrs HRV 16 Rhinovirus A