Comprehensive Transcriptome Analysis of Cerebral Cavernous Malformation Across Multiple Species and Genotypes

Purpose: To determine important genes, functions, and networks contributing to the pathobiology of cerebral cavernous malformation (CCM) from transcriptomic analyses across 3 species and 2 disease genotypes. Methods: Sequencing of RNA from laser microdissected neurovascular units (NVUs) of 5 human surgically resected CCM lesions, mouse brain microvascular ECs (BMECs) and C. elegans with induced Ccm gene loss, and their respective controls, provided differentially expressed genes (DEGs). DEGs from mouse and C. elegans were annotated into human homologous genes. Cross-comparisons of DEGs between species and genotypes as well as network and Gene Ontology (GO) enrichment analyses were performed. Results: Among hundreds of DEGs identified in each model, common genes and one GO term (GO:0051656 establishment of organelle localization) were commonly identified across the different species and genotypes. In addition, 24 GO functions were present in 4 out of 5 models and were related to cell-cell adhesion, neutrophil mediated immunity, ion transmembrane transporter activity, and responses to oxidative stress. We provide a comprehensive transcriptome library of CCM disease across species, and for the first time in Ccm1/Krit1 versus Ccm3/Pdcd10 genotypes Conclusion: We provide examples of how results can be used in hypothesis generation or mechanistic confirmatory studies. Overall design: 32 total RNA samples, including 8 laser microdissected neurovascular units (NVUs) from 5 human cerebral cavernous malformations and 3 human brain autopsy contols, 12 mouse brain microvascular endothelium (3 Krit1 null, 3 Krit1 controls, 3 Pdcd10 null, 3 Pdcd10 controls), 12 C. elegans (3 Kri-1 null, 3 Kri-1 controls, 3 Pdcd10 null, 3 Pdcd10 controls)