Systems biology and proteomic analysis of cerebral cavernous malformation

Abstract

Cerebral cavernous malformations (CCM) are vascular anomalies caused by mutations in genes encoding KRIT1, OSM and PDCD10 proteins causing hemorrhagic stroke. We examine proteomic change of loss of CCM gene expression. Using human umbilical vein endothelial cells, label-free differential protein expression analysis with multidimensional liquid chromatography/tandem mass spectrometry was applied to three CCM protein knockdown cell lines and two control cell lines: ProteomeXchange identifier PXD000362. Principle component and cluster analyses were used to examine the differentially expressed proteins associated with CCM. The results from the five cell lines revealed 290 and 192 differentially expressed proteins (p < 0.005 and p < 0.001, respectively). Most commonly affected proteins were cytoskeleton-associated proteins, in particular myosin-9. Canonical genetic pathway analysis suggests that CCM may be a result of defective cell–cell interaction through dysregulation of cytoskeletal associated proteins. Conclusion: The work explores signaling pathways that may elucidate early detection and novel therapy for CCM.

Keywords::

• cerebral cavernous malformation
• cytoskeletal proteins
• mass spectrometry
• proteomics
• signaling
• systems biology

Acknowledgements

S Bencharit was supported by the National Heart, Lung and Blood Institute NHLBI, NIH Grant R21HL092338 and the University of North Carolina at Chapel Hill Junior Faculty Development Award. The authors thank GL Johnson and his laboratory for providing experimental assistance. The authors also thank K Knagge and the PRIDE team in the assistance for the data deposition [45].

Author contributions

S Schwartz-Baxter and S Bencharit designed the experiments. S Schwartz-Baxter, J Carlson performed mass spectrometry analysis. S Bencharit, S Schwartz-Baxter, AR Edelmann, J Carlson, WC Byrd, I Saldarriaga and CF Dibble analyzed data. CF Dibble performed cell biology experiments and knockdowns. S Bencharit, WC Byrd and AR Edelmann wrote the manuscript.

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.

Key issues

• Biology of cerebral cavernous malformations (CCM) lesion development is not clear.

• Proteomic global analysis of CCM gene knockdown has not been done.

• Application of label-free differential protein expression analysis to a CCM knockdown human cell line has not been reported.

• There is currently no systems biology analysis available for CCM.

• Elucidating the biology of CCM lesions may lead to a novel biomarker-based diagnosis.

• Early intervention of CCM lesions may prevent further lost of function.

• The proteins associated with specific CCM gene knockdown allow novel insight into CCM lesion development and therapy.

• Proteomic profiling and systems biology analysis may be an important tool to examine CCM in vitro and in humans.

Notes