Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. GEO Dataset Exploration and Analyses
2.2. Literature Search and Synthesis
2.3. In Vitro Stimulation Assay
2.4. HL60 Culture, Differentiation, and In Vitro Stimulation
2.5. ERLIN1 Knock-Out in HL60 Cell Line
2.6. RNA Extraction and qPCR
2.7. Flow Cytometry
2.8. Intracellular Cholesterol Levels
2.9. Statistical Analyses
3. Results
3.1. Experimental Validations
3.2. Literature Evaluation between ERLIN1 and Sepsis
4. Discussions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
APOA1 | Apolipoprotein A1 |
ARV1 | Sterol homeostasis protein ARV1 |
CHOP | C/EBP homologous protein |
ERAD | Endoplasmic-reticulum-associated protein degradation |
ER | Endoplasmic reticulum |
ERLIN1 | ER lipid raft associated 1, human protein symbol |
ERLIN1 | ER lipid raft associated 1, human gene symbol |
GXB | Gene expression browser |
HDL | High-density lipoprotein |
Insig-1 | Insulin-induced gene 1 |
LPS | Lipopolysaccharide |
PGN | Peptidoglycan |
SCAP | SREBP cleavage-activating protein |
SREBP | Sterol regulatory element-binding protein |
SysInflam HuDB | Customized GXB platform, (http://sepsis.gxbsidra.org/dm3/landing.gsp, accessed on 30 July 2021) |
WB | Whole blood |
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Datasets | Title | Cell Types | No. of Sample | Conditions Compared | FC ** | p-Value * |
---|---|---|---|---|---|---|
In vivo | ||||||
GSE30119 | Genome-wide analysis of whole blood transcriptional response to community-acquired Staphylococcus aureus infection in vivo-GSE30119 | Whole Blood | 143 | Patients with S. aureus infection vs healthy controls | 1.34 | <0.001 |
GSE54514 | Whole blood transcriptome of survivors and nonsurvivors of sepsis-GSE54514 | Whole Blood | 163 | Patients admitted to the intensive care unit with sepsis (Non Survivor) vs healthy controls | 1.18 | 0.008 |
GSE25504 (GPL570) | Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis: GSE25504 (GPL570) | Whole Blood | 5 | Neonates with sepsis vs healthy controls | 6.12 | 0.04 |
GSE25504 (GPL13667) | Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis: GSE25504 (GPL1366) | Whole Blood | 20 | Neonates with sepsis vs healthy controls | 2.49 | <0.001 |
GSE25504 (GPL6947) | Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis - GSE25504 (GPL6947) | Whole Blood | 63 | Neonates with sepsis vs healthy controls | 1.35 | <0.001 |
GSE13015 | Genomic Transcriptional Profiling Identifies a Blood Biomarker Signature for the Diagnosis of Septicemic Melioidosis-GSE13015-Healthy-Melioidosis-Other Sepsis-T2D | Whole Blood | 39 | Patients with sepsis caused by B.pseudomallei vs sepsis caused by other pathogens | 7.1 | <0.001 |
GSE66890 | Expression of Neutrophil-related genes in patients with early sepsis-induced ARDS-GSE66890 | Whole Blood | 62 | Patients with sepsis + acute respiratory disease syndrom vs patients with sepsis alone | 1.22 | 0.18 |
Ex vivo | ||||||
GSE64457 | Marked alterations of neutrophil functions during sepsis-induced immunosuppression-GSE64457 | Neutrophils | 23 | Patients with sepsis vs healthy controls | 1.27 | 0.47 |
In vitro | ||||||
GSE11755 | Gene expression profiling in pediatric meningococcal sepsis reveals dynamic changes in NK-cell and cytotoxic molecules-GSE11755 | Lymphocytes, monocytes, Whole Blood | 41 | Monocytes from children with meningococcal sepsis vs monocytes from matched healthy controls (8 hrs) | 2.06 | 0.001 |
GSE49753 | A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients’ Plasma (DC)-GSE49753 | Dendritic Cells | 40 | Monocyte derived dendritic cells from healthy individuals exposed to plasma from patients with sepsis vs plasma from uninfected controls | 1.17 | 0.293 |
GSE49754 | A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients’ Plasma (PBMC)-GSE49754 | PBMC | 40 | PBMCs from healthy individuals exposed to plasma from patients with sepsis vs plasma from uninfected controls | 1 | 0.97 |
GSE49755 | A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients Plasma GSE49755 - Neutrophil | Neutrophils | 40 | Polymorphonuclear neutrophils from healthy individuals exposed to plasma from patients with sepsis vs plasma from uninfected controls | 5.29 | <0.001 |
GSE49756 | A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients’ Plasma (Expt. 2)- GSE49756 | Neutrophils | 49 | Polymorphonuclear neutrophils from healthy individuals exposed to plasma from patients with sepsis vs plasma from uninfected controls | 5.66 | 0.014 |
GSE49757 | A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients’ Plasma (Expt. 3)-GSE49757 | Neutrophils | 56 | Polymorphonuclear neutrophils from healthy individuals exposed to plasma from patients with sepsis vs plasma from uninfected controls | 4.43 | 0.004 |
GSE16837 | Gene expression data from S. aureus-exposed neutrophils-GSE16837 | Neutrophils | 113 | Polymorphonuclear neutrophils from healthy individuals exposed to S. aureus (strain 10254) vs unexposed (3 hrs) | 4.69 | <0.001 |
GSE40636 | PGN induced transcriptional changes in human neonatal neutrophils-GSE40636 | Neutrophils | 6 | cord blood purified neutrophils stimulated with peptidoglycan vs unstimulated | 3.82 | 0.024 |
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Huang, S.S.Y.; Toufiq, M.; Saraiva, L.R.; Van Panhuys, N.; Chaussabel, D.; Garand, M. Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis. Biology 2021, 10, 755. https://doi.org/10.3390/biology10080755
Huang SSY, Toufiq M, Saraiva LR, Van Panhuys N, Chaussabel D, Garand M. Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis. Biology. 2021; 10(8):755. https://doi.org/10.3390/biology10080755
Chicago/Turabian StyleHuang, Susie S. Y., Mohammed Toufiq, Luis R. Saraiva, Nicholas Van Panhuys, Damien Chaussabel, and Mathieu Garand. 2021. "Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis" Biology 10, no. 8: 755. https://doi.org/10.3390/biology10080755
APA StyleHuang, S. S. Y., Toufiq, M., Saraiva, L. R., Van Panhuys, N., Chaussabel, D., & Garand, M. (2021). Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis. Biology, 10(8), 755. https://doi.org/10.3390/biology10080755