Sample Set Annotation Tool: Hosts responses in critical disease caused by pandemic H1N1. GSE21802

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Critical disease caused by the new 2009 pandemic influenza virus (nvH1N1) is a challenge for physicians and scientist. As evidenced in SARS and H5N1, the development of an effective immune response plays a key role to overcome viral diseases. We studied host`s gene expression signatures, cytokine and antibody responses along the first week of hospitalization in 19 critically ill patients with primary nvH1N1 pneumonia and two degrees of respiratory involvement. Presence of comorbidities and absence of immunosuppresory conditions were the common antecedents in both groups. The most severe patients (n=12) showed persistant respiratory viral secretion, increased levels of pro-inflammatory cytokines and chemokines in serum, and elevated systemic levels of two immunosuppresory cytokines (IL-10 and IL-1ra). Both groups were able to produce specific antibodies against the virus. The average day for antibody production was day 9 in the course of the disease, defining an early period of innate immunity and a late period of adaptive immunity. The most severe group evidenced a poor expression of a set of MHC class II and T cell receptor (TCR) related genes participating in antigen presentation and cell mediated immune responses in the late phase. 7 patients of this group finally died. This findings evidence that, as observed in sepsis, severe H1N1 disease course with immunoparalysis, which could explain the poor control of the virus along with the increased incidence of bacterial superinfection observed in these patients.

Hypothesis

Experimental Design

19 patients attending to the participants ICUs with primary viral pneumonia during the acute phase of influenza virus illness with acute respiratory distress and unequivocal alveolar opacification involving two or more lobes with negative respiratory and blood bacterial cultures at admission were recruited from November the 1st to December the 31st 2009. Serial blood samples for plasma, serum and RNA were collected by using Serum, EDTA and PaxGene (BD®) venous blood vacuum collection following manufacturer instructions at day 1, 3/5 and 7 according to an unified protocol for all the participant ICUs. A pharyngeal sample was collected in paralel. RNA from blood was processed for gene expression analysis by using Sentrix Human-6 v2 Expression BeadChips (Illumina, San Diego, CA). RNA from blood obtained from 4 healthy controls was used for comparison purposes. Samples were distributed in four groups depending on whether or not the patients nedeed of mechanical ventilation, and on the early/late phase of the disease (before or after day 9 respectively).

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

40 Samples Loaded: 40

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

H1N1

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	!Sample Title	tissue	group	patient	Disease phase
GSM542941	Healthy Control, biological rep1	Blood	Control	control	control
GSM542942	Healthy Control, biological rep2	Blood	Control	control	control
GSM542943	Healthy Control, biological rep3	Blood	Control	control	control
GSM542944	Healthy Control, biological rep4	Blood	Control	control	control
GSM542945	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep1	Blood	H1N1 NMV late period	1	late period

Please log in in order to upload files.

File
sampleset4000028_sampleannotations_Group.csv Sample Set Spreadsheet
sampleset4000028_sampleannotations_Group.csv Sample Set Spreadsheet
sampleset4000028_sampleannotations_Group.csv Sample Set Spreadsheet
sampleset4000028_sampleannotations_Group.csv Sample Set Spreadsheet

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	!Sample Title	Tissue	Group	Patient	Disease phase	Mechanical ventilation	Virus strain
GSM542941	Healthy Control, biological rep1	Blood	Control	control	control		none
GSM542942	Healthy Control, biological rep2	Blood	Control	control	control		none
GSM542943	Healthy Control, biological rep3	Blood	Control	control	control		none
GSM542944	Healthy Control, biological rep4	Blood	Control	control	control		none
GSM542945	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep1	Blood	H1N1 NMV late period	1	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542946	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep2	Blood	H1N1 NMV late period	1	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542947	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep3	Blood	H1N1 NMV late period	1	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542948	Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep1	Blood	H1N1 MV early period	2	early period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542949	Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep2	Blood	H1N1 MV early period	2	early period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542950	Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep1	Blood	H1N1 NMV early period	3	early period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542951	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep4	Blood	H1N1 NMV late period	4	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542952	Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep3	Blood	H1N1 MV early period	5	early period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542953	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep1	Blood	H1N1 MV late period	5	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542954	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep5	Blood	H1N1 NMV late period	6	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542955	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep2	Blood	H1N1 MV late period	7	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542956	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep3	Blood	H1N1 MV late period	8	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542957	Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep2	Blood	H1N1 NMV early period	4	early period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542958	Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep4	Blood	H1N1 MV early period	9	early period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542959	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep4	Blood	H1N1 MV late period	10	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542960	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep5	Blood	H1N1 MV late period	7	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542961	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep6	Blood	H1N1 NMV late period	4	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542962	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep6	Blood	H1N1 MV late period	10	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542963	Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep5	Blood	H1N1 MV early period	5	early period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542964	Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep3	Blood	H1N1 NMV early period	6	early period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542965	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep7	Blood	H1N1 MV late period	7	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542966	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep8	Blood	H1N1 MV late period	8	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542967	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep9	Blood	H1N1 MV late period	11	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542968	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep7	Blood	H1N1 NMV late period	4	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542969	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep10	Blood	H1N1 MV late period	12	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542970	Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep4	Blood	H1N1 NMV early period	13	early period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542971	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep8	Blood	H1N1 NMV late period	13	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542972	Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep5	Blood	H1N1 NMV early period	14	early period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542973	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep9	Blood	H1N1 NMV late period	14	late period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542974	Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep6	Blood	H1N1 MV early period	15	early period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542975	Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep6	Blood	H1N1 NMV early period	16	early period	no	Pandemic influenza (A/H1N1 new subtype)
GSM542976	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep11	Blood	H1N1 MV late period	17	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542977	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep12	Blood	H1N1 MV late period	17	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542978	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep13	Blood	H1N1 MV late period	18	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542979	Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep14	Blood	H1N1 MV late period	19	late period	yes	Pandemic influenza (A/H1N1 new subtype)
GSM542980	Pandemic H1N1 positive critical patient with no mechanical ventilation, late period,biological rep10	Blood	H1N1 NMV late period	16	late period	no	Pandemic influenza (A/H1N1 new subtype)

Group Sets View in Gene Expression Browser

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

Module Analysis

Group Set
All Samples

SIDRA