Here, I utilize ClustalOmega to compare conserved amino acids in ALK across species that have lungs. Knock out identified conserved amino acids via CRISPR/Cas9 and find those that specifically cause NSCLC in mice. This is done as ALK is found in many different cancers and I want to determine knockouts that result specifically in lung cancers.
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I am interested in using the mutant mice from AIM 1 to perform RNA-seq. Then I would collect gene expression data on the mutant mice tumors compared to wild-type controls. Then examine genes involved in immune response. Since ALK has downstream effects on expression of various genes in immune privilege in the brain during development, I expect genes related to immune invasion will be unregulated.
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ALK NSCLC and wild-type lung tissue will be used in BioID followed by mass spectrometry to identify interacting proteins. These proteins will be compared to the changes in gene expression identified in Aim 2. Since ALK proteins are known to have an immune competent, I believe this assay will provide insight on how the immune response is altered.
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