Study of Gene Expression Changes in Astrocytes Using Agilent Gene Expression Microarray at the Phalanx Biotech Service Lab.
We’re happy to report on a paper that takes a systems biology approach to understanding how astrocytes respond to amphetamines. This study is from the lab of Maria Cecilia Marcondes of the San Diego Biomedical Research Institute in San Diego, CA, and it includes Agilent gene expression microarray data generated by Phalanx Biotech. The article was published 9 Mar 2017 in the Journal of Neuroinflammation.
This study takes a systems biology approach to understanding how astrocytes respond to methamphetamine. The authors focused on astrocytes because studies of the brains of meth users found that astrogliosis was one of the hallmarks of meth exposure. Considering the many neurological conditions accompanied by meth abuse, the authors sought to identify the molecular and cellular pathways occurring within astrocytes that might contribute to the neuropathology of meth abuse.
The authors cultured primary rat astrocytes and exposed them to 3 different concentrations of meth. They looked at rates of apoptosis of treated astrocytes, and found that meth exposure did not alter the viability of the cells. The bulk of the study focused on microarray gene expression profiling, and validation of the microarray results using qPCR and protein-level techniques. Microarray gene expression profiling was carried out by Phalanx Biotech using the Agilent 4x44K whole genome microarray. You can read more about our Agilent microarray services here.
Hundreds of genes were up-regulated upon meth treatment, and 179 genes were consistently up-regulated greater than 4-fold in all meth treatments. Most of those 179 genes responded in a dose-dependent manner. Interesting, only 5 genes consistently appeared in the lists of the top 30 most up-regulated genes for each treatment. These genes were the mitogen-activated protein kinase kinase 5 (MAP2K5), the G protein coupled receptor 65 (GPR65), ectodysplasin A (ED1), the neuron navigator 3 (NAV3), and CXCL5. These genes were chosen as focal points for the deeper systems biology network analyses. MAP2K5, GPR65, and CXCL5 were also chosen for qPCR and protein-level validation. As expected, these 3 targets were found to be up-regulated using qPCR, western blotting, and immunocytochemistry.
The systems biology network analysis was carried out to identify genes with astrocytic meth-response behaviors consistent with MAP2K5, GPR65, ED1, NAV3, and CXCL5. In other words, these computational techniques are useful for predicting molecular networks by which astrocytes respond to acute drug abuse. The authors created gene networks based on pathway, physical, and genetic interactions, along with shared protein domains and coexpression. The highest scoring network contained 141 genes, all up-regulated following meth exposure, and included MAP2K5, GPR65, and ED1. The authors further dissected this network by focusing on only genes known to be physically associated and/or within the same pathways. The result of this analysis is included in the figure above. Genes in the center of the left group were the ones with the highest number of connections, which includes ErbB3, a known astrocyte marker. The authors also carried out a pathway enrichment analysis on the list of genes up-regulated during meth exposure. The enriched pathways are listed in the figure above.
In summary, the authors adopted systems biology approaches to characterize differentially expressed genes, networks, and pathways to understand gene expression changes underlying the astrocytic response to meth exposure. They note that further studies are needed to directly investigate the role of these gene networks in the neuropathology of meth abuse and their potential as biomarkers.
At Phalanx Biotech, we are your partners in driving discovery. Please contact us if you’re interested in our gene expression profiling services, similar to what was conducted in the paper described in this Research Highlight. We offer gene expression profiling services on both Agilent and our own OneArray platforms. If you already have microarray data, and you want to carry out systems biology network analyses and pathway enrichment analyses similar to those reported in this paper, our bioinformatics team can assist! Please visit our Bioinformatics webpage for more information.
Reference
Bortell N et al. Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro (2017). Journal of Neuroinflammation 14:49.