This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is a microarray?
Microarray is a new technology that can be used to study many different gene expressions at the same time. Microarray technology consists of thousands of gene sequences placed on a glass slip (known as a gene chip) in known locations. A DNA or RNA sample is then placed on the glass slip and complementary base pairing between the gene sequences and the DNA/RNA sample occurs to produce light. The lit areas (certain colors represent the amount of hybridization at each spot) are measured to identify genes that are expressed in the DNA/RNA sample [1]. Microarray technology gives insight in regards to the cell state during different conditions or genotypes.
Video 1. Youtube 3.6.2014. Using a DNA Microarray [HD Animation]. Retrieved from here.
Sema5A Microarray Data
The GEO Profiles database, which stores microarray results/profiles, was used to evaluate the SEMA5A gene. The profile is displayed as a chart that has the expression level of a single gene in all the samples. The bars on the bottom of the chart indicate the gene expression in different experimental conditions. A clear explanation of all the profile features can be found at About GEO Profiles.
A search for the SEMA5A gene alone gave hundreds of results, none of which related directly to Cri du Chat. However, since the focus of the project (found in the Specific Aims) is the SEMA5A gene and vascularization, a more selective search gave more applicable results. An interesting study stimulated vascular endothelial cell growth using Angiopoietin-1 in Homo sapiens (humans). The results indicated that Angiopoietin-1 varied SEMA5A gene expression levels. The 'confluent growth protocol' refers to the presence of cell-cell contacts, where as the 'sparse growth protocol' refers to the absence of cell-cell contacts [2].
A search for the SEMA5A gene alone gave hundreds of results, none of which related directly to Cri du Chat. However, since the focus of the project (found in the Specific Aims) is the SEMA5A gene and vascularization, a more selective search gave more applicable results. An interesting study stimulated vascular endothelial cell growth using Angiopoietin-1 in Homo sapiens (humans). The results indicated that Angiopoietin-1 varied SEMA5A gene expression levels. The 'confluent growth protocol' refers to the presence of cell-cell contacts, where as the 'sparse growth protocol' refers to the absence of cell-cell contacts [2].
(click GEO profiles to enlarge)
Figure 1. SEMA5A expression is increased in one of the confluent samples and both of the sparse samples.
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Figure 2. SEMA5A expression is increased in both of the confluent samples and decreased in both of the sparse samples.
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Figure 3. SEMA5A expression is slightly decreased in the confluent samples and one of the sparse samples, but increased in one of the sparse samples.
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Discussion
Since Cri du Chat syndrome is a homozygous chromosomal deletion disease, it is understandable that SEMA5A microarray profiles could not be directly relatable to the syndrome. Studies looking at transcriptome changes in various Cri du Chat phenotypes that do not include complete deletion of the SEMA5A gene could potentially benefit Cri du Chat patients.
The study that focused on stimulation of vascular endothelial growth using Angiopoietin-1 gave some interesting results for the SEMA5A gene. These results can potentially be applied to Cri du Chat patients who have organ defects due to improper vascularization patterning.
The study that focused on stimulation of vascular endothelial growth using Angiopoietin-1 gave some interesting results for the SEMA5A gene. These results can potentially be applied to Cri du Chat patients who have organ defects due to improper vascularization patterning.
References
Youtube video: https://youtu.be/_6ZMEZK-alM
[1] Microarray technology - Glossary Entry. (n.d.). Retrieved March 26, 2015, from http://ghr.nlm.nih.gov/glossary=microarraytechnology
[2] Fukuhara, S., Sako, K., Minami, T., Noda, K., Kim, H., Kodama, T., ... Mochizuki, N. (n.d.). Differential Function Of Tie2 At Cell–cell Contacts And Cell–substratum Contacts Regulated By Angiopoietin-1. Nature Cell Biology, 513-526.
[1] Microarray technology - Glossary Entry. (n.d.). Retrieved March 26, 2015, from http://ghr.nlm.nih.gov/glossary=microarraytechnology
[2] Fukuhara, S., Sako, K., Minami, T., Noda, K., Kim, H., Kodama, T., ... Mochizuki, N. (n.d.). Differential Function Of Tie2 At Cell–cell Contacts And Cell–substratum Contacts Regulated By Angiopoietin-1. Nature Cell Biology, 513-526.