A Multi-omics Study of Human Mitochondrial Proteins During Neurogenesis

Abstract

Mitochondria are double membrane organelles in eukaryotic cells, and play vital roles in neurogenesis. Disruptions of mitochondrial functions may lead to neurodegenerative disorders. Yet, the underlying mechanisms remain largely unknown. To elucidate the dynamic changes of transcriptomes during neurogenesis, the single cell RNA sequencing experiments were conducted on both cultured human embryonic carcinoma stem cells and and retinoic acid-induced differentiated neuron-like cells. The systematic analysis framework I have established revealed significant expression alternations between cell states, persistence of heterogeneity in differentiated neuron-like cells, and dynamic modeling during the differentiation, and also identified mitochondrial proteins as novel neuronal markers. To elucidate mitochondrial interactome in neurogenesis, biochemical fractionation coupled with in-depth mass spectrometry profiling experiments were performed in both cell states. The bioinformatics pipeline I have developed resulted in 6,442 high-quality protein-protein interactions among 600 mitochondrial proteins. Computational modeling further predicted that RAB5IF could play a role in the assembly of the respirasome (composed of complexes I, III and IV). Lastly, due to the complexity of BF-MS data and limitation of current software tool kits, I have developed an optimized approach, termed as Statistical Modeling Elution Data (SMED), to infer protein interactions from BF-MS. SMED took advantage of novel statistical modeling and machine learning strategies to achieve better prediction performances compared to previously published studies. Taken together, the multi-omics methods and computational strategies I have established in this study provided not only new insights of mitochondrial biology, but also a systems biology research focus to leverage the deluge of omics data. The findings from this study could accelerate our understanding of how mitochondrial proteins and their interactions play a role in neurobiology.