Omics research has garnered popularity recently to integrate in-depth analysis of alterations at the molecular level to elucidate observable phenotypes resulting from knockdown/knockout models. Genomics, performed through RNA-seq, allows the user to evaluate alterations at the transcription level, oftentimes more sensitive than other types of analysis, especially when attempting to understand lack of observation of an expected phenotype. Proteomics facilitates an understanding of mechanisms being altered at the translational level allowing for an understanding of multiple layers of regulation occurring, elucidating discrepancies between what is seen at the RNA level compared to what is translated to a functional protein. Here we describe the methods currently being used to evaluate CCM-deficient strains in human brain microvascular endothelial cells (HBMVEC), zebrafish embryos as well as in vivo mouse model to evaluate impacts on various signaling cascades resulting from deficiencies in KRIT1 (CCM1), MGC4607 (CCM2), and PDCD10 (CCM3). The integration of data from genomics and proteomics analysis allows for the composition of interactomes, elucidating systems wide impacts resulting from disruption of the CCM signaling complex (CSC).
Keywords: CCM signaling complex (CSC); Cerebral cavernous malformations (CCM); ChIP-seq; Genomics; Interactome; LC-MS/MS; Proteomics; RNA-seq; Systems wide analysis.