Sample Set Annotation Tool: Genome-wide profiling of whole blood from patients with defects in Toll-like receptors and IL-1Rs signaling-GSE25742

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

The objective of this study is to: 1) Characterize the innate immune responsiveness of patients with inborn errors in Toll-IL1 receptor signaling pathway (IRAK4, MyD88 deficiencies) compared to healthy subjects, through the analysis of blood leukocytes' transcriptional profiles after stimulation with ligands for the whole set of Toll-like receptors and IL-1Rs plus whole bacteria. 2) Understand the redundancies in TLR pathway in humans. 3) Explore the use of blood profiling approaches to assess the immune status of an individual by using Primary Immune Deficiencies as a proof of principle.

Hypothesis

Experimental Design

A total of 22 blood samples were collected from three groups of subjects: 4 patients with complete MYD88 deficiency, 4 patients with complete IRAK4 deficiency, and 14 healthy donors. Mutations from IRAK4 and MYD88 patients are loss-of-function. The subjects were recruited in two different batches: first set includes 4 healthy controls, MYD88 P1 and P2, IRAK4 P1 and P2 patients. Second set includes 10 different healthy controls, MYD88 P3 and P4 and IRAK4 P3 and P4. Healthy individuals are considered so based on past medical history (no recurrent infections). They were also healthy at the time of sampling. From each subject, peripheral blood was drawn into sodium heparin vacuum tubes on clinic site (Necker Hospital, Paris). Right away, 500µl whole blood was diluted with the same amount of RPMI before adding different stimulus. Diluted whole blood was activated with a wide range of ligands (16 conditions total, see below) in a volume of 50 µl, for 2 hours along with 10µg/ml of polymyxin B to clear LPS contamination in reagents. Whole blood was lysated with Tempus solution (from Tempus tubes, Applied Biosystems) to stabilize the RNA at 1:3 ratio after restimulation. The lysates were kept at -80ºC temperature until mRNA extraction. A total of 365 samples were analyzed. Choice of agonists: PAM3 (TLR1/2) and PAM2 (TLR2/6), 100 ng/ml final concentration, Invivogen®; poly(I:C) 25 µg/ml final concentration, Invivogen® (TLR3); LPS 100 ng/ml final concentration, Sigma® (TLR4); Flagellin 100 ng/ml final concentration, Invivogen® (TLR5); 3M13 (TLR7) and 3M2 (TLR8), 3µg/ml final concentration, 3M pharmaceuticals®; R848 3µg/ml final concentration, Invivogen® (TLR7/8); CpG-D19 and CPG C (TLR9), 3µg/ml final concentration, from collaborator. Agonists for IL-1R: IL-1b 20ng/ml final concentration, IL18 and IL33 50ng/ml final concentration, from RaD systems®; agonist for TNFa receptor, TNFa, 20ng/ml final concentration, from RaD systems®; PMA 25 ng/ml + Ionomycin 1µg/ml final concentration, Sigma®; heat killed whole bacteria: 3 pneumococcal strains (R6, 5.106 partical/ml final concentration; R8450 108 partical/ml final concentration; R11470, 5.106 partical/ml final concentration, heat killed at 65°C for 15 min) from collaborator, and Staphylococcus aureus (SAC), 107 partical/ml final concentration, from Invivogen®. No stimulation serves as negative control and PMA/ionomycin stimulation as positive control.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

68 Samples Loaded: 68

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Primary Immunodeficiency

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	Gender	Illness	!Sample_title	cell population	geographic
GSM632244	F	IRAK4 patient	IRAK4 P4_SAC	Whole blood	UK
GSM632248	F	IRAK4 patient	IRAK4 P4_PAM3	Whole blood	UK
GSM632249	M	IRAK4 patient	IRAK4 P3_LPS	Whole blood	Portugal
GSM632252	F	IRAK4 patient	IRAK4 P4_R848	Whole blood	UK
GSM632253	M	IRAK4 patient	IRAK4 P3_IL18	Whole blood	Portugal

Please log in in order to upload files.

File

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Gender	Illness	!Sample Title	Cell population	Geographic	In vitro stimulation blood volume per condition	Age at enrollment	In vitro stimulation condition	Race	In vitro stimulation incubation time
GSM632244	F	IRAK4 patient	IRAK4 P4_SAC	Whole blood	UK	1 ml	14	SAC	White	2h
GSM632248	F	IRAK4 patient	IRAK4 P4_PAM3	Whole blood	UK	1 ml	14	PAM3	White	2h
GSM632249	M	IRAK4 patient	IRAK4 P3_LPS	Whole blood	Portugal	1 ml	14	LPS	White	2h
GSM632252	F	IRAK4 patient	IRAK4 P4_R848	Whole blood	UK	1 ml	14	R848	White	2h
GSM632253	M	IRAK4 patient	IRAK4 P3_IL18	Whole blood	Portugal	1 ml	14	IL18	White	2h
GSM632254	F	IRAK4 patient	IRAK4 P4_IL33	Whole blood	UK	1 ml	14	IL33	White	2h
GSM632258	F	IRAK4 patient	IRAK4 P4_PMAIono	Whole blood	UK	1 ml	14	PMAIono	White	2h
GSM632259	F	IRAK4 patient	IRAK4 P4_TNFa	Whole blood	UK	1 ml	14	TNFa	White	2h
GSM632263	M	IRAK4 patient	IRAK4 P3_SAC	Whole blood	Portugal	1 ml	14	SAC	White	2h
GSM632264	M	IRAK4 patient	IRAK4 P3_CpG-D19	Whole blood	Portugal	1 ml	14	CpGD19	White	2h
GSM632265	F	IRAK4 patient	IRAK4 P4_R11470	Whole blood	UK	1 ml	14	R11470	White	2h
GSM632266	M	IRAK4 patient	IRAK4 P3_TNFa	Whole blood	Portugal	1 ml	14	TNFa	White	2h
GSM632267	M	IRAK4 patient	IRAK4 P3_PAM3	Whole blood	Portugal	1 ml	14	PAM3	White	2h
GSM632268	F	IRAK4 patient	IRAK4 P4_CpG-D19	Whole blood	UK	1 ml	14	CpGD19	White	2h
GSM632270	M	IRAK4 patient	IRAK4 P3_CpG C	Whole blood	Portugal	1 ml	14	CpG C	White	2h
GSM632272	M	IRAK4 patient	IRAK4 P3_PAM2	Whole blood	Portugal	1 ml	14	PAM2	White	2h
GSM632274	F	IRAK4 patient	IRAK4 P4__3M2	Whole blood	UK	1 ml	14	3M2	White	2h
GSM632278	M	IRAK4 patient	IRAK4 P3_IL33	Whole blood	Portugal	1 ml	14	IL33	White	2h
GSM632279	F	IRAK4 patient	IRAK4 P4_Flagellin	Whole blood	UK	1 ml	14	Flagellin	White	2h
GSM632282	F	IRAK4 patient	IRAK4 P4_R6	Whole blood	UK	1 ml	14	R6	White	2h
GSM632283	F	IRAK4 patient	IRAK4 P4_IL-1b	Whole blood	UK	1 ml	14	IL1b	White	2h
GSM632288	M	IRAK4 patient	IRAK4 P3_R848	Whole blood	Portugal	1 ml	14	R848	White	2h
GSM632292	F	IRAK4 patient	IRAK4 P4_polyIC	Whole blood	UK	1 ml	14	PolyIC	White	2h
GSM632295	M	IRAK4 patient	IRAK4 P3_R6	Whole blood	Portugal	1 ml	14	R6	White	2h
GSM632298	M	IRAK4 patient	IRAK4 P3_IL-1b	Whole blood	Portugal	1 ml	14	IL1b	White	2h
GSM632302	F	IRAK4 patient	IRAK4 P4_R8450	Whole blood	UK	1 ml	14	R8450	White	2h
GSM632314	F	IRAK4 patient	IRAK4 P4_3M13	Whole blood	UK	1 ml	14	3M13	White	2h
GSM632353	M	IRAK4 patient	IRAK4 P3_R11470	Whole blood	Portugal	1 ml	14	R11470	White	2h
GSM632354	M	IRAK4 patient	IRAK4 P3_Flagellin	Whole blood	Portugal	1 ml	14	Flagellin	White	2h
GSM632366	M	IRAK4 patient	IRAK4 P3_3M13	Whole blood	Portugal	1 ml	14	3M13	White	2h
GSM632368	M	IRAK4 patient	IRAK4 P3_No stimulation	Whole blood	Portugal	1 ml	14	No stimulation	White	2h
GSM632370	M	IRAK4 patient	IRAK4 P3_polyIC	Whole blood	Portugal	1 ml	14	PolyIC	White	2h
GSM632372	F	IRAK4 patient	IRAK4 P4_LPS	Whole blood	UK	1 ml	14	LPS	White	2h
GSM632374	F	IRAK4 patient	IRAK4 P4_IL18	Whole blood	UK	1 ml	14	IL18	White	2h
GSM632378	F	IRAK4 patient	IRAK4 P4_No stimulation	Whole blood	UK	1 ml	14	No stimulation	White	2h
GSM632393	M	IRAK4 patient	IRAK4 P3_R8450	Whole blood	Portugal	1 ml	14	R8450	White	2h
GSM632396	F	IRAK4 patient	IRAK4 P4_PAM2	Whole blood	UK	1 ml	14	PAM2	White	2h
GSM632491	M	IRAK4 patient	IRAK4 P1_polyIC	Whole blood	Hungary	1 ml	12	PolyIC	White	2h
GSM632495	M	IRAK4 patient	IRAK4 P2_Flagellin	Whole blood	Spain	1 ml	12	Flagellin	White	2h
GSM632501	M	IRAK4 patient	IRAK4 P2_TNFa	Whole blood	Spain	1 ml	12	TNFa	White	2h
GSM632502	M	IRAK4 patient	IRAK4 P2_IL33	Whole blood	Spain	1 ml	12	IL33	White	2h
GSM632506	M	IRAK4 patient	IRAK4 P1_TNFa	Whole blood	Hungary	1 ml	12	TNFa	White	2h
GSM632510	M	IRAK4 patient	IRAK4 P2_IL-1b	Whole blood	Spain	1 ml	12	IL1b	White	2h
GSM632517	M	IRAK4 patient	IRAK4 P1_IL-1b	Whole blood	Hungary	1 ml	12	IL1b	White	2h
GSM632519	M	IRAK4 patient	IRAK4 P1_PAM3	Whole blood	Hungary	1 ml	12	PAM3	White	2h
GSM632520	M	IRAK4 patient	IRAK4 P2__3M2	Whole blood	Spain	1 ml	12	3M2	White	2h
GSM632521	M	IRAK4 patient	IRAK4 P2_3M13	Whole blood	Spain	1 ml	12	3M13	White	2h
GSM632522	M	IRAK4 patient	IRAK4 P2_PAM2	Whole blood	Spain	1 ml	12	PAM2	White	2h
GSM632523	M	IRAK4 patient	IRAK4 P2_No stimulation	Whole blood	Spain	1 ml	12	No stimulation	White	2h
GSM632524	M	IRAK4 patient	IRAK4 P1_3M13	Whole blood	Hungary	1 ml	12	3M13	White	2h
GSM632537	M	IRAK4 patient	IRAK4 P1_CpG C	Whole blood	Hungary	1 ml	12	CpG C	White	2h
GSM632540	M	IRAK4 patient	IRAK4 P2_polyIC	Whole blood	Spain	1 ml	12	PolyIC	White	2h
GSM632542	M	IRAK4 patient	IRAK4 P2_IL18	Whole blood	Spain	1 ml	12	IL18	White	2h
GSM632543	M	IRAK4 patient	IRAK4 P1_IL18	Whole blood	Hungary	1 ml	12	IL18	White	2h
GSM632544	M	IRAK4 patient	IRAK4 P2_CpG-D19	Whole blood	Spain	1 ml	12	CpGD19	White	2h
GSM632546	M	IRAK4 patient	IRAK4 P2_PAM3	Whole blood	Spain	1 ml	12	PAM3	White	2h
GSM632547	M	IRAK4 patient	IRAK4 P2_LPS	Whole blood	Spain	1 ml	12	LPS	White	2h
GSM632548	M	IRAK4 patient	IRAK4 P2_CpG C	Whole blood	Spain	1 ml	12	CpG C	White	2h
GSM632550	M	IRAK4 patient	IRAK4 P1_PMAIono	Whole blood	Hungary	1 ml	12	PMAIono	White	2h
GSM632551	M	IRAK4 patient	IRAK4 P1_No stimulation	Whole blood	Hungary	1 ml	12	No stimulation	White	2h
GSM632554	M	IRAK4 patient	IRAK4 P1_LPS	Whole blood	Hungary	1 ml	12	LPS	White	2h
GSM632561	M	IRAK4 patient	IRAK4 P1_R848	Whole blood	Hungary	1 ml	12	R848	White	2h
GSM632562	M	IRAK4 patient	IRAK4 P1__3M2	Whole blood	Hungary	1 ml	12	3M2	White	2h
GSM632572	M	IRAK4 patient	IRAK4 P2_R848	Whole blood	Spain	1 ml	12	R848	White	2h
GSM632573	M	IRAK4 patient	IRAK4 P1_IL33	Whole blood	Hungary	1 ml	12	IL33	White	2h
GSM632575	M	IRAK4 patient	IRAK4 P1_CpG-D19	Whole blood	Hungary	1 ml	12	CpGD19	White	2h
GSM632593	M	IRAK4 patient	IRAK4 P1_PAM2	Whole blood	Hungary	1 ml	12	PAM2	White	2h
GSM632598	M	IRAK4 patient	IRAK4 P1_Flagellin	Whole blood	Hungary	1 ml	12	Flagellin	White	2h

Group Sets View in Gene Expression Browser

Name
All Samples		View
Culture conditions	Default	View
In order to make new Group Sets or change settings, please log in.

Module Analysis

Group Set
All Samples
Culture conditions

SIDRA