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Clinical

Blood Transcriptional Profiles of Active TB (Separated cells)-GSE19443

Purpose

We aimed to characterise the transcriptional response during TB and identify if cell subsets drove changes in whole blood cellular composition. The aim of the experiment was to define transcriptional signatures in neutrophils, monocytes, CD4+ and CD8+ cells from blood of active TB patients and healthy controls to distinguish the signature of active TB patients from each other and from healthy controls. This will help in the diagnosis of active tuberculosis, which normally relies on culture of the bacilli, which can take up to 6 weeks, sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL.

Hypothesis

This dataset aims to dissect the whole blood transcriptional signature by determining if elements of the whole blood signature are still present in purified cell subpopulations.

Experimental Design

Whole blood collected in EDTA tubes from patients with active TB disease and healthy controls. Blood was then processed or separated sequentially into neutrophil, monocyte, CD4+ or CD8+ populations and then processed. All patients were sampled prior to the initiation of any antimycobacterial therapy. Active pulmonary TB: PTB - all patients confirmed by isolation of Mycobacterium tuberculosis on culture of sputum or bronchoalvelolar lavage fluid. Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by IGRA (as described above). This dataset: PTB, n = 7 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+). BCG+, n = 4 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+). Experimental variables : Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+. Ethnicity - a range of ethnic groups is represented.

Experimental Variables

Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+. Ethnicity - a range of ethnic groups is represented.

Controls

Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<6mm unvaccinated); who were also negative by IGRA (as described above).

Methods

RNA was extracted from immune cells purified using Dynabeads (Invitrogen); cells selected were neutrophils, monocytes

Additional Information

Berry MP, Graham CM, McNab FW, Xu Z et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature2010 Aug 19;466(7309):973-7. PMID: 20725040

Microarray
Illumina HumanHT-12 v3
44 Samples Loaded: 44
Human (Homo sapiens)
CD8 T cells , CD4 T cells , Neutrophils , Monocytes
Tuberculosis
Sample Set Spreadsheet
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Samples Preview
Sample ID Age Bal Culture Bal Smear Ethnicity Exposure Latent
GSM484551 40 no_growth_6_weeks nil White n.a
GSM484552 40 no_growth_6_weeks nil White n.a
GSM484553 40 no_growth_6_weeks nil White n.a
GSM484554 40 no_growth_6_weeks nil White n.a
GSM484555 26 n.a n.a Asian other n.a
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Raw Signal
Raw Signal
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Samples Viewer / Editor

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Sample ID Age Bal Culture Bal Smear Ethnicity Exposure Latent Gender Illness Index Case Disease Site Isolate Sensitivity Sputum Culture Sputum Smear Tst !Sample Title Region of birth Geographical region Modal x-ray grade Bcg vaccinated Smear of index case
GSM484551
40
no_growth_6_weeks
nil
White
n.a
Male
PTB
True
Fully_sensitive
tuberculosis
nil
n.a
Neutrophil-Active TB
non_UK_Born
London
Minimal
Yes
True
GSM484552
40
no_growth_6_weeks
nil
White
n.a
Male
PTB
True
Fully_sensitive
tuberculosis
nil
n.a
Monocyte-Active TB
non_UK_Born
London
Minimal
Yes
True
GSM484553
40
no_growth_6_weeks
nil
White
n.a
Male
PTB
True
Fully_sensitive
tuberculosis
nil
n.a
CD4-Active TB
non_UK_Born
London
Minimal
Yes
True
GSM484554
40
no_growth_6_weeks
nil
White
n.a
Male
PTB
True
Fully_sensitive
tuberculosis
nil
n.a
CD8-Active TB
non_UK_Born
London
Minimal
Yes
True
GSM484555
26
n.a
n.a
Asian other
n.a
Male
PTB
n.a
Resistant Isoniazid + Ethambu
tuberculosis
+
n.a
Neutrophil-Active TB
non_UK_Born
London
Advanced
Not_Known
n.a
GSM484556
26
n.a
n.a
Asian other
n.a
Male
PTB
n.a
Resistant Isoniazid + Ethambu
tuberculosis
+
n.a
Monocyte-Active TB
non_UK_Born
London
Advanced
Not_Known
n.a
GSM484557
26
n.a
n.a
Asian other
n.a
Male
PTB
n.a
Resistant Isoniazid + Ethambu
tuberculosis
+
n.a
CD4-Active TB
non_UK_Born
London
Advanced
Not_Known
n.a
GSM484558
26
n.a
n.a
Asian other
n.a
Male
PTB
n.a
Resistant Isoniazid + Ethambu
tuberculosis
+
n.a
CD8-Active TB
non_UK_Born
London
Advanced
Not_Known
n.a
GSM484559
33
n.a
n.a
White
n.a
Male
PTB
n.a
Resistant Streptomycin, Ethio
tuberculosis
+++
21
Neutrophil-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484560
33
n.a
n.a
White
n.a
Male
PTB
n.a
Resistant Streptomycin, Ethio
tuberculosis
+++
21
Monocyte-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484561
33
n.a
n.a
White
n.a
Male
PTB
n.a
Resistant Streptomycin, Ethio
tuberculosis
+++
21
CD4-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484562
33
n.a
n.a
White
n.a
Male
PTB
n.a
Resistant Streptomycin, Ethio
tuberculosis
+++
21
CD8-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484563
18
tuberculosis
nil
South Asian
n.a
Female
PTB
unknown
Fully_sensitive
tuberculosis
nil
20
Neutrophil-Active TB
UK_Born
London
Advanced
Yes
n.a
GSM484564
18
tuberculosis
nil
South Asian
n.a
Female
PTB
unknown
Fully_sensitive
tuberculosis
nil
20
Monocyte-Active TB
UK_Born
London
Advanced
Yes
n.a
GSM484565
18
tuberculosis
nil
South Asian
n.a
Female
PTB
unknown
Fully_sensitive
tuberculosis
nil
20
CD4-Active TB
UK_Born
London
Advanced
Yes
n.a
GSM484566
18
tuberculosis
nil
South Asian
n.a
Female
PTB
unknown
Fully_sensitive
tuberculosis
nil
20
CD8-Active TB
UK_Born
London
Advanced
Yes
n.a
GSM484567
28
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
Neutrophil-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484568
28
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
Monocyte-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484569
28
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
CD4-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484570
28
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
CD8-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484571
22
n.a
n.a
South Asian
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
15
Neutrophil-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484572
22
n.a
n.a
South Asian
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
15
Monocyte-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484573
22
n.a
n.a
South Asian
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
15
CD4-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484574
22
n.a
n.a
South Asian
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
15
CD8-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484575
21
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
Neutrophil-Healthy
UK_Born
London
True
Yes
n.a
GSM484576
21
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
Monocyte-Healthy
UK_Born
London
True
Yes
n.a
GSM484577
21
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
CD4-Healthy
UK_Born
London
True
Yes
n.a
GSM484578
21
n.a
n.a
White
n.a
Male
Control (BCG+)
n.a
n.a
n.a
n.a
9
CD8-Healthy
UK_Born
London
True
Yes
n.a
GSM484579
32
tuberculosis
nil
Black
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
23
Neutrophil-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484580
32
tuberculosis
nil
Black
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
23
Monocyte-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484581
32
tuberculosis
nil
Black
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
23
CD4-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484582
32
tuberculosis
nil
Black
n.a
Male
PTB
n.a
Fully_sensitive
tuberculosis
nil
23
CD8-Active TB
non_UK_Born
London
Moderate
Yes
n.a
GSM484583
55
tuberculosis
nil
South Asian
n.a
Female
PTB
n.a
Fully_sensitive
n.a
n.a
n.a
Neutrophil-Active TB
non_UK_Born
London
Advanced
Yes
n.a
GSM484584
55
tuberculosis
nil
South Asian
n.a
Female
PTB
n.a
Fully_sensitive
n.a
n.a
n.a
Monocyte-Active TB
non_UK_Born
London
Advanced
Yes
n.a
GSM484585
55
tuberculosis
nil
South Asian
n.a
Female
PTB
n.a
Fully_sensitive
n.a
n.a
n.a
CD4-Active TB
non_UK_Born
London
Advanced
Yes
n.a
GSM484586
55
tuberculosis
nil
South Asian
n.a
Female
PTB
n.a
Fully_sensitive
n.a
n.a
n.a
CD8-Active TB
non_UK_Born
London
Advanced
Yes
n.a
GSM484587
49
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
0
Neutrophil-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484588
49
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
0
Monocyte-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484589
49
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
0
CD4-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484590
49
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
0
CD8-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484591
41
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
10
Neutrophil-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484592
41
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
10
Monocyte-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484593
41
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
10
CD4-Healthy
non_UK_Born
London
True
Yes
n.a
GSM484594
41
n.a
n.a
South Asian
n.a
Female
Control (BCG+)
n.a
n.a
n.a
n.a
10
CD8-Healthy
non_UK_Born
London
True
Yes
n.a

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