Sample Set Annotation Tool: Early and dynamic changes in gene expression in septic shock patients: a genome wide approach

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Background: As early and appropriate care of severe septic patients is associated with better outcome, understanding of very first events in the disease process is needed. Pan-genomic analyses offer an interesting opportunity to study global genomic response within the very first hours after sepsis. The objective of this study was to investigate the systemic genomic response in severe Intensive Care Unit (ICU) patients and determine whether patterns of gene expression could be associated with clinical severity evaluated by severity score. Methods: Twenty-eight ICU patients were enrolled at the onset of septic shock. Blood samples were collected within 30 minutes, 24 and 48 hours after shock and genomic response was evaluated using microarrays. The genome wide expression pattern of blood leukocytes was sequentially compared to healthy volunteers and after stratification based on SAPSII score to identify potential mechanisms of dysregulation. Results: Septic shock induces a global reprogramming of the whole leukocyte transcriptome affecting multiple functions and pathways (> 71% of the whole genome was modified). Most altered pathways were not significantly different between SAPSII-high and SAPSII-low groups of patients. However the magnitude and the duration of these alterations were different between these two groups. Importantly, we observed that the more severe patients did not exhibit the strongest modulation. This indicates that some regulation mechanisms leading to recovery seem to take place at early stage. Conclusion: In conclusion, both pro- and anti-inflammatory processes, measured at the transcriptomic level, are induced within the very first hours after septic shock. Interestingly, the more severe patients did not exhibit the strongest modulation. This highlights that, not only the responses mechanisms by themself but mainly their early and appropriate regulation, are crucial for patient recovery. This reinforces the idea that an immediate and tailored aggressive care of patients, aimed at restoring an appropriately regulated immune response, may have a beneficial impact on outcome.

Hypothesis

Experimental Design

Twenty-eight ICU patients were enrolled at the onset of septic shock. Blood samples were collected within 30 minutes, 24 and 48 hours after septic shock and compared to twenty-five healthy volunteers

Experimental Variables

Septic shock (2021 ICD-10-CM code* = R65.21)

Controls

Methods

The data were normalized using RMA methods.

Additional Information

https://icm-experimental.springeropen.com/articles/10.1186/s40635-014-0020-3

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57065

Expected Samples:

107 Samples Loaded: 107

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Septic Shock

Treatment Protocol

Growth Protocol

Extraction Protocol

Whole blood Paxgene tubes extraction

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Age	Gender	group	Grouping
GSM1373914	Blood_P001_H00	43	FEMALE	SAPSII-High	H0-High
GSM1373915	Blood_P001_H24	43	FEMALE	SAPSII-High	H24-High
GSM1373916	Blood_P001_H48	43	FEMALE	SAPSII-High	H48-High
GSM1373917	Blood_P002_H00	34	FEMALE	SAPSII-Low	H0-Low
GSM1373918	Blood_P002_H24	34	FEMALE	SAPSII-Low	H24-Low

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File
sampleset4000174_sampleannotations (1).csv Sample Set Spreadsheet
sampleset4000174_sampleannotations (1).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	Age	Gender	Group	Grouping	Sepsis	Sapsii	Collection time
GSM1373914	Blood_P001_H00	43	FEMALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373915	Blood_P001_H24	43	FEMALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373916	Blood_P001_H48	43	FEMALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373917	Blood_P002_H00	34	FEMALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373918	Blood_P002_H24	34	FEMALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373919	Blood_P002_H48	34	FEMALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373920	Blood_P003_H00	69	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373921	Blood_P003_H24	69	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373922	Blood_P003_H48	69	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373923	Blood_P004_H00	41	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373924	Blood_P004_H24	41	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373925	Blood_P004_H48	41	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373926	Blood_P005_H00	79	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373927	Blood_P005_H24	79	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373928	Blood_P005_H48	79	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373929	Blood_P006_H00	29	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373930	Blood_P006_H24	29	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373931	Blood_P006_H48	29	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373932	Blood_P007_H00	76	FEMALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373933	Blood_P007_H24	76	FEMALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373934	Blood_P007_H48	76	FEMALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373935	Blood_P008_H00	84	FEMALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373936	Blood_P008_H24	84	FEMALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373937	Blood_P008_H48	84	FEMALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373938	Blood_P009_H00	58	FEMALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373939	Blood_P009_H24	58	FEMALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373940	Blood_P009_H48	58	FEMALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373941	Blood_P010_H00	83	FEMALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373942	Blood_P010_H24	83	FEMALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373943	Blood_P010_H48	83	FEMALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373944	Blood_P011_H00	79	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373945	Blood_P011_H24	79	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373946	Blood_P011_H48	79	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373947	Blood_P013_H00	59	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373948	Blood_P013_H24	59	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373949	Blood_P013_H48	59	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373950	Blood_P014_H00	76	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373951	Blood_P014_H24	76	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373952	Blood_P014_H48	76	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373953	Blood_P015_H00	56	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373954	Blood_P015_H24	56	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373955	Blood_P015_H48	56	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373956	Blood_P017_H00	56	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373957	Blood_P017_H24	56	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373958	Blood_P017_H48	56	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373959	Blood_P018_H00	64	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373960	Blood_P018_H24	64	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373961	Blood_P018_H48	64	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373962	Blood_P019_H00	68	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373963	Blood_P019_H24	68	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373964	Blood_P019_H48	68	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373965	Blood_P020_H00	46	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373966	Blood_P020_H24	46	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373967	Blood_P021_H00	76	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373968	Blood_P021_H24	76	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373969	Blood_P021_H48	76	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373970	Blood_P101_H00	81	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373971	Blood_P101_H24	81	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373972	Blood_P101_H48	81	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373973	Blood_P102_H00	49	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373974	Blood_P102_H24	49	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373975	Blood_P102_H48	49	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373976	Blood_P104_H00	71	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373977	Blood_P104_H24	71	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373978	Blood_P104_H48	71	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373979	Blood_P105_H00	84	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373980	Blood_P105_H24	84	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373981	Blood_P106_H00	60	MALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373982	Blood_P106_H24	60	MALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373983	Blood_P106_H48	60	MALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373984	Blood_P107_H00	59	FEMALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373985	Blood_P107_H24	59	FEMALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373986	Blood_P107_H48	59	FEMALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373987	Blood_P108_H00	58	MALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373988	Blood_P108_H24	58	MALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373989	Blood_P108_H48	58	MALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373990	Blood_P109_H00	45	FEMALE	SAPSII-Low	H0-Low	Septic Shock I	SAPSII-Low	0 hr
GSM1373991	Blood_P109_H24	45	FEMALE	SAPSII-Low	H24-Low	Septic Shock I	SAPSII-Low	24 hr
GSM1373992	Blood_P109_H48	45	FEMALE	SAPSII-Low	H48-Low	Septic Shock I	SAPSII-Low	48 hr
GSM1373993	Blood_P111_H00	73	FEMALE	SAPSII-High	H0-High	Septic Shock I	SAPSII-High	0 hr
GSM1373994	Blood_P111_H24	73	FEMALE	SAPSII-High	H24-High	Septic Shock I	SAPSII-High	24 hr
GSM1373995	Blood_P111_H48	73	FEMALE	SAPSII-High	H48-High	Septic Shock I	SAPSII-High	48 hr
GSM1373996	Blood_HV01	20	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1373997	Blood_HV02	29	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1373998	Blood_HV03	52	MALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1373999	Blood_HV04	47	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374000	Blood_HV05	40	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374001	Blood_HV06	28	MALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374002	Blood_HV07	37	MALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374003	Blood_HV08	50	MALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374004	Blood_HV09	41	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374005	Blood_HV10	19	MALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374006	Blood_HV11	48	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374007	Blood_HV12	37	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374008	Blood_HV13	52	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374009	Blood_HV14	49	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374010	Blood_HV15	56	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374011	Blood_HV16	49	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374012	Blood_HV17	59	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374013	Blood_HV18	55	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374014	Blood_HV19	40	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374015	Blood_HV20	46	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374016	Blood_HV21	58	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374017	Blood_HV22	52	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374018	Blood_HV23	56	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374019	Blood_HV24	50	FEMALE	Healthy	Healthy	Healthy Volunteer	NA
GSM1374020	Blood_HV25	42	FEMALE	Healthy	Healthy	Healthy Volunteer	NA

Group Sets View in Gene Expression Browser

Name
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All timepoints combined	Default	View
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Module Analysis

Group Set
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All timepoints combined
SAPSII
Timepoints

SIDRA