Reconstruction of Cell and Tissue-specific Immune-protein Interactomes Using Single-cell RNA Sequencing Data

  • Atheer Althobaiti

Student thesis: Master's Thesis

Abstract

Protein molecules and their interactions via protein-protein interactions (PPIs) are at the core of cellular functions. While such global PPI networks have been useful for analyzing gene function and effects of genetic variants, they do not resolve tissue and cell-typespecific interactions. Here we leverage recent advances in single-cell RNA sequencing (scRNA-seq) to reconstruct cell-type-specific PPI networks across different tissues to enable a context-sensitive analysis of immune cells’ gene-protein pathways. Targeting B cells, T cells, and macrophage cells as a proof-of-principle, we used scRNA-seq data across different tissues from the Tabula Muris mouse consortium. We mapped the protein-coding DEGs to a protein-protein interaction network database (STRING v.11). Topological and global similarity analysis of the networks revealed distinct properties between tissues highlighting tissue-specific behaviors for each cell type. For example, we found that degree and clustering coefficients distributions were tissue-specific. Different cell types and tissues displayed specific characteristics, and in particular, the splenic PPI networks were different compared to other analyzed tissues for all the immune cell types examined. For example, the pairwise comparison of the Jaccard index for node similarity and the mantel test correlation analysis showed that the spleen’ node and PPI networks are more different than any other tissues for each cell type examined. The physiological and anatomical properties that distinguish the spleen from other examined tissues might explain why the splenic PPI networks tend to be less similar compared to other tissues. The cell-type-specific network analyses using the different distance measures between the adjacency matrices on the hub nodes such as Euclidean, Manhattan, Jaccard, and Hamming distances showed a macrophage-specific behavior not observed in B cells and T cells, confirming their lineage differences. Finally, we explored the rewiring of selected hub nodes and transcription factors in the PPI networks along with their biological enrichments to validate our observations. The suggested biological validity of our results confirms the relevance of data-driven reconstruction of these context-sensitive networks using more advanced network inference algorithms. In conclusion, scRNA-seq enables the reconstruction of global unspecific PPI networks into cell and tissue-specific networks, thereby providing an increased resolution of the biological context.
Date of AwardApr 2021
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Science and Engineering
SupervisorJesper Tegner (Supervisor)

Keywords

  • Protein-protein interaction
  • Network Analysis
  • scRNA-seq
  • Immune cells
  • Cell-specific interaction
  • Tissue-specific interaction

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