Integration of Transcriptomic and Proteomic Data during Nucleus Lobulation of Granulocytes

Nucleus is the origin of most phenotypic activities in a cell. Depending on the cell type, the nucleus can appear in different forms. Mature neutrophils are granulocytic white blood cells with lobulated nucleus that enables them to perform their specialized roles like cell migration in the immune system. Quantitative temporal profiles of human granulocytic cell ensembles of DNA transcripts and proteins, that were previously collected along the process of nuclear deformation, are examined in this thesis. The general aim is to screen the cellular changes during granulocytic differentiation accompanied by nuclear deformation and many other processes. As these transcriptomic and proteomic profiles are hard to interpret due to their large throughput with 10^4 and 10^3 orders of magnitude respectively, bioinformatic data processing including normalization, principal component analysis, differential expression analysis, functional enrichment analysis, and multi-omics integration across datasets, are performed. Granulocytic differentiation associated processes are identified in this study that validate the used experimental model and the data analysis pipeline. Moreover, the cellular functions that were found to be affected during the granulocytic differentiation process could be responsible for nuclear deformation, its downstream processes, or just independent processes occurring in parallel. As nuclear deformation is a relatively new field of research, it is not annotated in the available biological databases and as a result, the nuclear deformation category was not found by the functional enrichment analysis. However, some categories related to nuclear activities and a general accordance in RNA-protein regulation were found that represent interesting directions to be pursued in future studies after this first screening. Finally, this thesis leads the way towards discovering the mechanism of nuclear deformation in the process of differentiating the cells into neutrophils.