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Clinical

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen specific modulation of immune reactivity - GSE70050

Purpose

Timothy grass (TG) pollen is a common seasonal airborne allergen associated with symptoms ranging from mild rhinitis to severe asthma. The aim of this study was to characterize changes in TG-specific T cell responses as a function of seasonality. Peripheral blood mononuclear cells (PBMC) obtained either during the pollen season or out of season, from allergic individuals and non-allergic controls were stimulated either with TG extract or a pool of previously identified immunodominant antigenic regions. PBMC from in season allergic subjects exhibit higher IL-5 and IL-10 responses compared to out of season donors. In the case of non-allergic subjects, as expected we observed lower IL-5 responses and robust production of IFN? compared to allergic individuals. Strikingly, non-atopic donors exhibited an opposing pattern with decreased immune reactivity in-season. The broad downregulation in non-allergic donors indicates that healthy individuals are not oblivious to allergen exposure but rather react with an active modulation of the responses following the antigenic stimulus provided during the pollen season. Transcriptomic analysis of allergen-specific T cells defined genes modulated in concomitance with allergen exposure and inhibition of responses in non-allergic donors. Magnitude and functionality of T-helper cell responses differ substantially for in season versus out of season in allergic and non-allergic subjects. The results indicate specific and opposing modulation of immune responses following the antigenic stimulation during the pollen season. This seasonal modulation reflects the enactment of specific molecular programs associated with health and allergic disease.

Hypothesis

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Experimental Design

11 allergen-specific T cell RNA samples were analyzed: 5 isolated from PBMC of allergic individuals and 6 from non-allergic individuals (considered as the control group).

Experimental Variables

Allergy

Controls

6 non-allergic individuals.

Methods

Illumina filteringAlignment with TopHatDUST scores were calculated with PRINSEQ Lite (v 0.20.3)Low-complexity reads (DUST > 4) were removed from the BAM filesGeneration of SAM files with SAMtoolsObtention of read counts with htseq-count using "union" optionRemoving absent features (zero counts in all samples)Raw counts were imported to R/Bioconductor package DESeq2 to identify differentially expressed genes among samplesDESeq2 normalizes counts by dividing each column of the count table (samples) by the size factor of this column. The size factor is calculated by dividing the samples by geometric means of the genes.P-values for differential expression are calculated using binomial test for differences between the base means of two conditions.These p-values are then adjusted for multiple test correction using Benjamini Hochberg algorithm to control the false discovery rate.We considered genes differentially expressed between two groups of samples when the DESeq2 analysis resulted in an adjusted P-value of <0.05 and the fold-change in gene expression was 2-fold.Genome_build: UCSC hg19

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70050

Microarray
Ensembl Human v37
76 Samples Loaded: 76
Human (Homo sapiens)
PBMC , T cells
Allergy
4 million/ml PBMCs from 5 allergic and 6 non-allergic individuals were stimulated in vitro for 3 hours with 2.5 ?g/ml of a Tymothy Grass Allergen immunodominant peptides pool (see paper).
Cells were cultured for less than 18 hours in RPMI1640 supplemented with 5% human AB serum in 24 well plates at a density of 4x106/ml and incubated at 37?C
Sample Set Spreadsheet
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Samples Preview
Sample ID group disease Sample Names Type
sample1 Allergic-IFNG Allergic NextFXP12_1_RSS5_1_N701S502.1002.IFNG_TCM. IFNG
sample10 Allergic-IL5 Allergic NextFXP12_10_RSS5_10_N702S503.1002.IL5_TEM. IL5
sample11 Allergic-NEG Allergic NextFXP12_11_RSS5_11_N702S505.1002.NEG_TCM. NEG
sample12 Allergic-NEG Allergic NextFXP12_12_RSS5_12_N702S506.1002.NEG_TEM. NEG
sample13 Allergic-IFNG Allergic NextFXP12_13_RSS5_13_N702S507.1011.IFNG_TCM. IFNG
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File
GSE70050.csv
Sample Set Spreadsheet
GSE70050.csv
Sample Set Spreadsheet
sampleset4000102_sampleannotations.csv
Sample Set Spreadsheet
sampleset4000102_sampleannotations.csv
Sample Set Spreadsheet
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Sample ID Group Disease Sample Names Type
sample1
Allergic-IFNG
Allergic
NextFXP12_1_RSS5_1_N701S502.1002.IFNG_TCM.
IFNG
sample2
Allergic-IFNG
Allergic
NextFXP12_2_RSS5_2_N701S503.1002.IFNG_TEM.
IFNG
sample3
Allergic-IL5
Allergic
NextFXP12_3_RSS5_3_N701S505.1002.IL5_TCM.
IL5
sample4
Allergic-IL5
Allergic
NextFXP12_4_RSS5_4_N701S506.1002.IL5_TEM.
IL5
sample5
Allergic-NEG
Allergic
NextFXP12_5_RSS5_5_N701S507.1002.NEG_TCM.
NEG
sample6
Allergic-NEG
Allergic
NextFXP12_6_RSS5_6_N701S508.1002.NEG_TEM.
NEG
sample7
Allergic-IFNG
Allergic
NextFXP12_7_RSS5_7_N701S510.1002.IFNG_TCM.
IFNG
sample8
Allergic-IFNG
Allergic
NextFXP12_8_RSS5_8_N701S511.1002.IFNG_TEM.
IFNG
sample9
Allergic-IL5
Allergic
NextFXP12_9_RSS5_9_N702S502.1002.IL5_TCM.
IL5
sample10
Allergic-IL5
Allergic
NextFXP12_10_RSS5_10_N702S503.1002.IL5_TEM.
IL5
sample11
Allergic-NEG
Allergic
NextFXP12_11_RSS5_11_N702S505.1002.NEG_TCM.
NEG
sample12
Allergic-NEG
Allergic
NextFXP12_12_RSS5_12_N702S506.1002.NEG_TEM.
NEG
sample13
Allergic-IFNG
Allergic
NextFXP12_13_RSS5_13_N702S507.1011.IFNG_TCM.
IFNG
sample14
Allergic-IFNG
Allergic
NextFXP12_14_RSS5_14_N702S508.1011.IFNG_TEM.
IFNG
sample15
Allergic-IL5
Allergic
NextFXP12_15_RSS5_15_N702S510.1011.IL5_TCM.
IL5
sample16
Allergic-IL5
Allergic
NextFXP12_16_RSS5_16_N702S511.1011.IL5_TEM.
IL5
sample17
Allergic-IFNG
Allergic
NextFXP12_17_RSS5_17_N703S502.1011.IFNG_TCM.
IFNG
sample18
Allergic-IFNG
Allergic
NextFXP12_18_RSS5_18_N703S503.1011.IFNG_TEM.
IFNG
sample19
Allergic-IL5
Allergic
NextFXP12_19_RSS5_19_N703S505.1011.IL5_TCM.
IL5
sample20
Allergic-IL5
Allergic
NextFXP12_20_RSS5_20_N703S506.1011.IL5_TEM.
IL5
sample21
Allergic-IFNG
Allergic
NextFXP12_21_RSS5_21_N703S507.1574.IFNG_TCM.
IFNG
sample22
Allergic-IFNG
Allergic
NextFXP12_22_RSS5_22_N703S508.1574.IFNG_TEM.
IFNG
sample23
Allergic-IL5
Allergic
NextFXP12_23_RSS5_23_N703S510.1574.IL5_TCM.
IL5
sample24
Allergic-IL5
Allergic
NextFXP12_24_RSS5_24_N703S511.1574.IL5_TEM.
IL5
sample25
Allergic-IFNG
Allergic
NextFXP12_25_RSS5_25_N704S502.1574.IFNG_TCM.
IFNG
sample26
Allergic-IFNG
Allergic
NextFXP12_26_RSS5_26_N704S503.1574.IFNG_TEM.
IFNG
sample27
Allergic-IL5
Allergic
NextFXP12_27_RSS5_27_N704S505.1574.IL5_TCM.
IL5
sample28
Allergic-IL5
Allergic
NextFXP12_28_RSS5_28_N704S506.1574.IL5_TEM.
IL5
sample29
Allergic-IFNG
Allergic
NextFXP12_29_RSS5_29_N704S507.1579.IFNG_TCM.
IFNG
sample30
Allergic-IFNG
Allergic
NextFXP12_30_RSS5_30_N704S508.1579.IFNG_TEM.
IFNG
sample31
Allergic-IL5
Allergic
NextFXP12_31_RSS5_31_N704S510.1579.IL5_TCM.
IL5
sample32
Allergic-IL5
Allergic
NextFXP12_32_RSS5_32_N704S511.1579.IL5_TEM.
IL5
sample33
Allergic-IFNG
Allergic
NextFXP12_33_RSS5_33_N705S502.1579.IFNG_TCM.
IFNG
sample34
Allergic-IFNG
Allergic
NextFXP12_34_RSS5_34_N705S503.1579.IFNG_TEM.
IFNG
sample35
Allergic-IL5
Allergic
NextFXP12_35_RSS5_35_N705S505.1579.IL5_TCM.
IL5
sample36
Allergic-IL5
Allergic
NextFXP12_36_RSS5_36_N705S506.1579.IL5_TEM.
IL5
sample37
Allergic-IFNG
Allergic
NextFXP12_37_RSS5_37_N705S507.1593.IFNG_TCM.
IFNG
sample38
Allergic-IFNG
Allergic
NextFXP12_38_RSS5_38_N705S508.1593.IFNG_TEM.
IFNG
sample39
Allergic-IL5
Allergic
NextFXP12_39_RSS5_39_N705S510.1593.IL5_TCM.
IL5
sample40
Allergic-IL5
Allergic
NextFXP12_40_RSS5_40_N705S511.1593.IL5_TEM.
IL5
sample41
Allergic-IFNG
Allergic
NextFXP12_41_RSS5_41_N706S502.1593.IFNG_TCM.
IFNG
sample42
Allergic-IFNG
Allergic
NextFXP12_42_RSS5_42_N706S503.1593.IFNG_TEM.
IFNG
sample43
Allergic-IL5
Allergic
NextFXP12_43_RSS5_43_N706S505.1593.IL5_TCM.
IL5
sample44
Allergic-IL5
Allergic
NextFXP12_44_RSS5_44_N706S506.1593.IL5_TEM.
IL5
sample45
NonAllergic-IFNG
NonAllergic
DeHi_U52_IFNg_Tcm_W1.52.IFNG_TCM.
IFNG
sample46
NonAllergic-IFNG
NonAllergic
DeHi_U52_IFNg_Tem_W2.52.IFNG_TEM.
IFNG
sample47
NonAllergic-IL5
NonAllergic
DeHi_U52_Il5_Tcm_W3.52.IL5_TCM.
IL5
sample48
NonAllergic-IL5
NonAllergic
DeHi_U52_IL5_Tem_W4.52.IL5_TEM.
IL5
sample49
NonAllergic-NEG
NonAllergic
DeHi_U52_Neg_Tcm_W5.52.NEG_TCM.
NEG
sample50
NonAllergic-NEG
NonAllergic
DeHi_U52_Neg_Tem_W6.52.NEG_TEM.
NEG
sample51
NonAllergic-IFNG
NonAllergic
DeHi_U166_IFNg_Tcm_W7.166.IFNG_TCM.
IFNG
sample52
NonAllergic-IFNG
NonAllergic
DeHi_U166_IFNg_Tem_W8.166.IFNG_TEM.
IFNG
sample53
NonAllergic-IL5
NonAllergic
DeHi_U166_Il5_Tcm_W9.166.IL5_TCM.
IL5
sample54
NonAllergic-IL5
NonAllergic
DeHi_U166_IL5_Tem_W10.166.IL5_TEM.
IL5
sample55
NonAllergic-NEG
NonAllergic
DeHi_U166_Neg_Tcm_W11.166.NEG_TCM.
NEG
sample56
NonAllergic-NEG
NonAllergic
DeHi_U166_Neg_Tem_W12.166.NEG_TEM.
NEG
sample57
NonAllergic-IFNG
NonAllergic
DeHi_D167_Tcm_IFNg_RS04_1.167.IFNG_TCM.
IFNG
sample58
NonAllergic-IFNG
NonAllergic
DeHi_D167_Tem_IFNg_RS04_2.167.IFNG_TEM.
IFNG
sample59
NonAllergic-IL5
NonAllergic
DeHi_D167_Tcm_Il5_RS04_3.167.IL5_TCM.
IL5
sample60
NonAllergic-IL5
NonAllergic
DeHi_D167_Tem_Il5_RS04_4.167.IL5_TEM.
IL5
sample61
NonAllergic-IFNG
NonAllergic
DeHi_D192_Tcm_IFNg_RS04_5.192.IFNG_TCM.
IFNG
sample62
NonAllergic-IFNG
NonAllergic
DeHi_D192_Tem_IFNg_RS04_6.192.IFNG_TEM.
IFNG
sample63
NonAllergic-IL5
NonAllergic
DeHi_D192_Tcm_Il5_RS04_7.192.IL5_TCM.
IL5
sample64
NonAllergic-IL5
NonAllergic
DeHi_D192_Tem_Il5_RS04_8.192.IL5_TEM.
IL5
sample65
NonAllergic-IFNG
NonAllergic
DeHi_D190_Tcm_IFNg_RS04_9.190.IFNG_TCM.
IFNG
sample66
NonAllergic-IFNG
NonAllergic
DeHi_D190_Tem_IFNg_RS04_10.190.IFNG_TEM.
IFNG
sample67
NonAllergic-IL5
NonAllergic
DeHi_D190_Tcm_Il5_RS04_11.190.IL5_TCM.
IL5
sample68
NonAllergic-IL5
NonAllergic
DeHi_D190_Tem_Il5_RS04_12.190.IL5_TEM.
IL5
sample69
NonAllergic-NEG
NonAllergic
DeHi_D190_Tcm_Neg_RS04_13.190.NEG_TCM.
NEG
sample70
NonAllergic-NEG
NonAllergic
DeHi_D190_Tem_Neg_RS04_14.190.NEG_TEM.
NEG
sample71
NonAllergic-IFNG
NonAllergic
DeHi_D14_Tcm_IFNg_RS04_15.14.IFNG_TCM.
IFNG
sample72
NonAllergic-IFNG
NonAllergic
DeHi_D14_Tem_IFNg_RS04_16.14.IFNG_TEM.
IFNG
sample73
NonAllergic-IL5
NonAllergic
DeHi_D14_Tcm_Il5_RS04_17.14.IL5_TCM.
IL5
sample74
NonAllergic-IL5
NonAllergic
DeHi_D14_Tem_Il5_RS04_18.14.IL5_TEM.
IL5
sample75
NonAllergic-NEG
NonAllergic
DeHi_D14_Tcm_Neg_RS04_19.14.NEG_TCM.
NEG
sample76
NonAllergic-NEG
NonAllergic
DeHi_D14_Tem_Neg_RS04_20.14.NEG_TEM.
NEG

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