Cell-Type-Specific Proteogenomic Signal Diffusion for Integrating Multi-Omics Data Predicts Novel Schizophrenia Risk Genes

• Main Authors: Abolfazl Doostparast Torshizi, Jubao Duan, Kai Wang
• Format: Article
• Language: English
• Published: Elsevier 2020-09-01
• Series: Patterns
• Subjects: signal diffusion; protein-protein interaction; interaction networks; proteome; multi-omics; schizophrenia
• Online Access: http://www.sciencedirect.com/science/article/pii/S2666389920301197

Summary: Accumulation of diverse types of omics data on schizophrenia (SCZ) requires a systems approach to model the interplay between genome, transcriptome, and proteome. We introduce Markov affinity-based proteogenomic signal diffusion (MAPSD), a method to model intra-cellular protein trafficking paradigms and tissue-wise single-cell protein abundances. MAPSD integrates multi-omics data to amplify the signals at SCZ risk loci with small effect sizes, and reveal convergent disease-associated gene modules in the brain. We predicted a set of high-confidence SCZ risk loci followed by characterizing the subcellular localization of proteins encoded by candidate SCZ risk genes, and illustrated that most are enriched in neuronal cells in the cerebral cortex as well as Purkinje cells in the cerebellum. We demonstrated how the identified genes may be involved in neurodevelopment, how they may alter SCZ-related biological pathways, and how they facilitate drug repurposing. MAPSD is applicable in other polygenic diseases and can facilitate our understanding of disease mechanisms. The Bigger Picture: Proteins constitute the functional machinery in a cell. Genetic aberrations may cause disrupting the normal functionality of the proteins. On the other hand, biophysical and biochemical properties of proteins vary in distinct tissues mandating separate modeling of proteomic features given the tissue being studied, e.g. brain in case of schizophrenia. Using the concept of signal diffusion in graph theory, we proposed a model, termed MAPSD, which enables us to leverage proteomic properties of different tissues at single cell resolution along with genomic and epigenomic features of a disease in order to predict potential risk genes which cannot be annotated using common univariate approaches. Taking this approach helps create novel therapeutic hypotheses for precision medicine so that more effective treatments with less side effects on other organs can be developed. Application of MAPSD is not restricted to schizophrenia and most of complex diseases can benefit from the method.