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Spatiotemporal characterization of the human proteome

Time: Fri 2019-10-25 09.00

Location: Atrium, Nobels väg 12B, Wargentinhuset, solna (English)

Doctoral student: Diana Mahdessian , Cellulär och klinisk proteomik

Opponent: Assoc. Prof. Arne Lindqvist, Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden

Supervisor: Universitetslektor Emma Lundberg, Skolan för kemi, bioteknologi och hälsa (CBH), Science for Life Laboratory, SciLifeLab, Albanova VinnExcellence Center for Protein Technology, ProNova

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Characterizing the molecular components of the basic unit of life; the cell, is crucial for a complete understanding of human biology. The cell is divided into compartments to create a suitable environment for the resident proteins to fulfill their functions. Therefore, spatial mapping of the human proteome is essential to understand protein function in health and disease.

Spatial proteomics is most commonly investigated using mass spectrometry or imaging, combined with machine learning for the data analysis. Until now, studies have been limited to high abundant proteins and relied on the purification of organelle fractions from a bulk of cells. Within the scope of this thesis, we were able to systematically localize proteins in their native cellular environment using antibody-based imaging techniques, and to investigate protein subcellular localization and dynamics on a single cell level, introducing a major advance within the field of spatial proteomics.

Paper I of this thesis presents a subcellular map of the human proteome, where the spatial distribution of 12,003 human proteins was mapped into 30 subcellular structures, half of which were not previously localized. Besides providing a valuable dataset for cell biology, this study is the first to reveal the spatial complexity of human cells with proteins localizing to multiple compartments and pronounced single cell variations. Paper II reports on the systematic temporal dissection of these single cell variations and the identification of cell cycle correlated variations. We identified 258 novel cell cycle regulated proteins and showed that several of these proteins may be connected to proliferative diseases. A key finding of Paper II is that proteins showing non-cell cycle dependent variations are significantly enriched in mitochondria, whereas cell cycle dependent proteins are enriched in nucleoli. In Paper III and IV, we spatiotemporally characterized the proteomes of these two organelles, mitochondria and nucleoli, in greater detail.

In Paper III, we expanded the mitochondrial proteome with 560 novel proteins. As many as 20% of the mitochondrial proteome showed variations in their expression pattern at the single cell level, most often independent of the cell cycle. Paper IV provides a complete characterization of the nucleolar proteome. Nucleoli are not only important for ribosome synthesis and assembly, but are also crucial for cell cycle regulation through the recruitment of its proteins to the chromosomal periphery during cell division. Here, we presented the first proteome-wide spatiotemporal analysis of the nucleolus with its sub-compartments, and identified 69 nucleolar proteins that relocated to the chromosomes periphery during mitosis.

In conclusion, this thesis unravels the spatiotemporal proteome organization of the human cell over the course of a cell cycle and offers a valuable starting point for a better understanding of human cell biology in health and disease.