Korean J Neurotrauma.  2019 Apr;15(1):2-10. 10.13004/kjnt.2019.15.e2.

Molecular Characterization of Primary Human Astrocytes Using Digital Gene Expression Analysis

• Kim JW
• Jeong JH

• KMID: 2444199
• DOI: http://doi.org/10.13004/kjnt.2019.15.e2

Abstract

OBJECTIVE
Astrocyte dysfunctions are related to several central nervous system (CNS) pathologies. Transcriptomic profiling of human mRNAs to investigate astrocyte functions may provide the basic molecular-biological data pertaining to the cellular activities of astrocytes.
METHODS
Human Primary astrocytes (HPAs) and human neural stem cell line (HB1.F3) were used for differential digital gene analysis. In this study, a massively parallel sequencing platform, next-generation sequencing (NGS), was used to obtain the digital gene expression (DGE) data from HPAs. A comparative analysis of the DGE from HPA and HB1.F3 cells was performed. Sequencing was performed using NGS platform, and subsequently, bioinformatic analyses were implemented to reveal the identity of the pathways, relatively up- or down-regulated in HPA cells.
RESULTS
The top, novel canonical pathways up-regulated in HPA cells than in the HB1.F3 cells were "Cyclins and cell cycle regulation,""Integrin signaling,""Regulation of eIF4 and p70S6K signaling,""Wnt/β-catenin signaling,""mTOR signaling,""Aryl hydrocarbon receptor signaling,""Hippo signaling,""RhoA signaling,""Signaling by Rho family GTPases," and "Glioma signaling" pathways. The down-regulated pathways were "Cell cycle: G1/S checkpoint regulation,""eIF2 signaling,""Cell cycle: G2/M DNA damage checkpoint regulation,""Telomerase signaling,""RhoGDI signaling,""NRF2-mediated oxidative stress response,""ERK/MAPK signaling,""ATM signaling,""Pancreatic adenocarcinoma signaling,""VEGF signaling," and "Role of CHK proteins in cell cycle checkpoint control" pathways.
CONCLUSION
This study would be a good reference to understand astrocyte functions at the molecular level, and to develop a diagnostic test, based on the DGE pattern of astrocytes, as a powerful, new clinical tool in many CNS diseases.

Keyword

Astrocytes; mRNA; Gene expression

MeSH Terms

Adenocarcinoma
Astrocytes*
Cell Cycle
Cell Cycle Checkpoints
Central Nervous System
Central Nervous System Diseases
Computational Biology
Diagnostic Tests, Routine
DNA Damage
Gene Expression*
High-Throughput Nucleotide Sequencing
Humans*
Neural Stem Cells
Oxidative Stress
Pathology
Ribosomal Protein S6 Kinases, 70-kDa
RNA, Messenger
RNA, Messenger
Ribosomal Protein S6 Kinases, 70-kDa

Figure

• 

  FIGURE 1 General work flow of differential digital gene expression analysis between HPA and HB1.F3.HPA: human primary astrocyte, HB1.F3: immortalized cell line of human neural stem cell.

• 

  FIGURE 2 The top canonical pathways which are analyzed with both up and down-regulated genes (p-value≤0.05) using Ingenuity pathway analysis (IPA®; Ingenuity Systems, Redwood City, USA) software. Blue bars mean up-regulated pathways in astrocytes (z-score≤−2.076); orange ones mean down-regulated pathways in astrocytes (z-score≥1.5553); the activity patterns are not confirmed in gray-colored pathways. Orange pints are the ratio of the number of genes that meet the cut off criteria/the number of genes that make up that pathway.

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