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Clinical

Transcriptome analysis of blood monocytes from sepsis patients - GSE46955

Purpose

Blood monocytes serve as the first line of host defense and are equipped to recognize and respond to infection by triggering an immune-inflammatory response. While most information on these cells comes from in vitro studies in humans or in vivo studies in mice, little is known about monocytes under human disease conditions. We investigated the role of monocytes during sepsis and its resolution in humans. A transcriptomal and functional analysis of blood monocytes from patients during gram negative sepsis and at recovery was performed. Monocytes from sepsis patients showed upregulation of a large number of pro-inflammatory genes and cytokines/chemokines, consistent with an ongoing systemic inflammation. However, these cells showed impairment to ex vivo endotoxin (LPS) challenge, displaying a quantitative decrease in the number of LPS-inducible genes. Moreover, they downregulated the expression of several pro-inflammatory cytokine/chemokine genes, activation marker genes and transcription factors associated with monocyte/macrophage activation, upon ex vivo LPS stimulation. Functionally, they downregulated expression of inflammatory cytokines/chemokines and antigen presentation-related molecules and functions. In contrast, genes and functions related to phagocytosis, anti-microbial activity and tissue remodeling where remained unaffected or even enhanced . Collectively, our observations suggest a genetic and functional re-programming of these cells during human sepsis progression. Understanding the molecular mechanisms which regulate this re-programming will allow to devise strategies which could modulate the response of these cells and hence, disease progression.

Hypothesis

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Experimental Design

Blood monocytes from gram-negative sepsis patients during sepsis (Sepsis) and following their recovery (Recovery/Basal) as well as healthy donor (control) were isolated. Thereafter, these cells were treated ex vivo with or without LPS for 3h and analysed for transcriptomic study.

Experimental Variables

Lipopolysaccharide exposure (2021 ICD-10-CM code* = Not Applicable)

Controls

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Methods

Array data were extracted at the probe level with background correction using Illumina's BeadStudio software. These raw data were then quantile normalized in R v2.15.2

Additional Information

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Microarray
Illumina HumanRef-8 v2
44 Samples Loaded: 44
Human (Homo sapiens)
Monocytes
Lipopolysaccharide exposure
Monocytes cultured were untreated or treated ex vivo with LPS(100ng/ml) for 3h.
Monocytes cultured in complete DMEM media supplemented with antibiotics (100 IU/ml penicillin and 100 µg/ml streptomycin) , in a humidified incubator at 37 °C and 5% CO2.
RNA was extracted from monocytes using an RNAasy Mini Kit (Qiagen) as per manufacterers specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in microarray assay.
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample_title treatment cell Culture condition
GSM1141941 monocyte-recovery-basal-1 None monocyte Recovery_baseline
GSM1141942 monocyte-recovery-lps-1 LPS monocyte Recovery_LPS
GSM1141943 monocyte-healthy-basal-1 None monocyte Healthy_baseline
GSM1141944 monocyte-healthy-lps-1 LPS monocyte Healthy_LPS
GSM1141945 monocyte-sepsis-basal-1 None monocyte Sepsis_baseline
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File
sampleset4000098_sampleannotations.csv
Sample Set Spreadsheet
Log2 Transformed
Raw Signal
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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 Treatment Cell Culture condition
GSM1141941
monocyte-recovery-basal-1
None
monocyte
Recovery_baseline
GSM1141942
monocyte-recovery-lps-1
LPS
monocyte
Recovery_LPS
GSM1141943
monocyte-healthy-basal-1
None
monocyte
Healthy_baseline
GSM1141944
monocyte-healthy-lps-1
LPS
monocyte
Healthy_LPS
GSM1141945
monocyte-sepsis-basal-1
None
monocyte
Sepsis_baseline
GSM1141946
monocyte-sepsis-lps-1
LPS
monocyte
Sepsis_LPS
GSM1141947
monocyte-recovery-basal-2
None
monocyte
Recovery_baseline
GSM1141948
monocyte-recovery-lps-2
LPS
monocyte
Recovery_LPS
GSM1141949
monocyte-healthy-basal-2
None
monocyte
Healthy_baseline
GSM1141950
monocyte-healthy-lps-2
LPS
monocyte
Healthy_LPS
GSM1141951
monocyte-sepsis-basal-2
None
monocyte
Sepsis_baseline
GSM1141952
monocyte-sepsis-lps-2
LPS
monocyte
Sepsis_LPS
GSM1141953
monocyte-recovery-basal-3
None
monocyte
Recovery_baseline
GSM1141954
monocyte-recovery-lps-3
LPS
monocyte
Recovery_LPS
GSM1141955
monocyte-healthy-basal-3
None
monocyte
Healthy_baseline
GSM1141956
monocyte-healthy-lps-3
LPS
monocyte
Healthy_LPS
GSM1141957
monocyte-sepsis-basal-3
None
monocyte
Sepsis_baseline
GSM1141958
monocyte-sepsis-lps-3
LPS
monocyte
Sepsis_LPS
GSM1141959
monocyte-healthy-basal-4
None
monocyte
Healthy_baseline
GSM1141960
monocyte-healthy-lps-4
LPS
monocyte
Healthy_LPS
GSM1141961
monocyte-healthy-basal-5
None
monocyte
Healthy_baseline
GSM1141962
monocyte-healthy-lps-5
LPS
monocyte
Healthy_LPS
GSM1141963
monocyte-healthy-basal-6
None
monocyte
Healthy_baseline
GSM1141964
monocyte-healthy-lps-6
LPS
monocyte
Healthy_LPS
GSM1141965
monocyte-recovery-basal-4
None
monocyte
Recovery_baseline
GSM1141966
monocyte-recovery-lps-4
LPS
monocyte
Recovery_LPS
GSM1141967
monocyte-sepsis-basal-4
None
monocyte
Sepsis_baseline
GSM1141968
monocyte-sepsis-lps-4
LPS
monocyte
Sepsis_LPS
GSM1141969
monocyte-recovery-basal-5
None
monocyte
Recovery_baseline
GSM1141970
monocyte-recovery-lps-5
LPS
monocyte
Recovery_LPS
GSM1141971
monocyte-sepsis-basal-5
None
monocyte
Sepsis_baseline
GSM1141972
monocyte-sepsis-lps-5
LPS
monocyte
Sepsis_LPS
GSM1141973
monocyte-recovery-basal-6
None
monocyte
Recovery_baseline
GSM1141974
monocyte-recovery-lps-6
LPS
monocyte
Recovery_LPS
GSM1141975
monocyte-sepsis-basal-6
None
monocyte
Sepsis_baseline
GSM1141976
monocyte-sepsis-lps-6
LPS
monocyte
Sepsis_LPS
GSM1141977
monocyte-recovery-basal-7
None
monocyte
Recovery_baseline
GSM1141978
monocyte-recovery-lps-7
LPS
monocyte
Recovery_LPS
GSM1141979
monocyte-sepsis-basal-7
None
monocyte
Sepsis_baseline
GSM1141980
monocyte-sepsis-lps-7
LPS
monocyte
Sepsis_LPS
GSM1141981
monocyte-recovery-basal-8
None
monocyte
Recovery_baseline
GSM1141982
monocyte-recovery-lps-8
LPS
monocyte
Recovery_LPS
GSM1141983
monocyte-sepsis-basal-8
None
monocyte
Sepsis_baseline
GSM1141984
monocyte-sepsis-lps-8
LPS
monocyte
Sepsis_LPS

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