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| 2. |
- Gnann, Christian, et al.
(författare)
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An image-based map of the mitochondrial proteome reveals widespread metabolic heterogeneity
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Mitochondria are involved in a wide range of cellular functions beyond their role in energy metabolism. Defining the human mitochondrial proteome is crucial to understand the mitochondria’s diverse functions and role in disease. Here, we present an image-based map of the human mitochondrial proteome containing 1,121 proteins with subcellular resolution. Our analysis shows that 48.3% (n=542) of the proteins localize to additional cellular compartments, further contributing to the diverse cellular functions of mitochondria and connectivity to other organelles. Furthermore, the mitochondrial proteome reveals tissue specific clustering, suggesting tissue specific functions and physiology. Strikingly, the single cell resolution of our dataset revealed extensive heterogeneity for as much as 33.5% (n=376) of the mitochondrial proteome which could not be explained by cell cycle progression. By performing a high throughput immunofluorescence screen, we conclude that heterogeneity in mitochondria protein expression can establish metabolic states in cell populations. This map of the mitochondrial proteome, part of the Human Protein Atlas database (www.proteinatlas.org), provides a valuable knowledge resource for studies of mitochondria function, dysfunction and disease.
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| 3. |
- Gnann, Christian, et al.
(författare)
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Widespread enzyme expression variations underlie diverse metabolic capacities within cell types
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Metabolic enzymes perform life-sustaining functions in various compartments of the cell. Recent studies have shown some enzymes to exhibit varied expression or localization between genetically identical cells and that this heterogeneity impacts drug resistance, metastasis, differentiation, and immune cell activation. However, no systematic analysis of metabolic cellular heterogeneity has been performed. Here, we leverage imaging-based single-cell spatial proteomic data to reveal the extent of non-genetic partitioning of the metabolic proteome. Over half of all enzymes localize to multiple cellular compartments, hinting at moonlighting potential. In addition, nearly two fifths of metabolic enzymes exhibit cell-to-cell variable expression. We demonstrate that individual cells reproduce these highly heterogeneous cell populations using clonal expansion, establishing that cells recapitulate myriad metabolic phenotypes over just a few cell divisions. To identify multifunctional moonlighting enzymes, we mine protein-protein interaction datasets to find interacting proteins with distinct functional roles, and using a timeresolved transcriptomic dataset, we find that metabolic heterogeneity arises largely independently of cell cycle progression and is established mostly post-transcriptionally or posttranslationally. Taken together, our data suggest that the heterogeneity of metabolic enzymes establish diverse cellular phenotypes, which are reflected in tissues, and which may ultimately allow targeted studies of their roles in health and disease.
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| 4. |
- Mahdessian, Diana, et al.
(författare)
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Profiling the human cytoplasmic proteome.
- 2016
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Ingår i: Molecular Biology of the Cell. - : AMER SOC CELL BIOLOGY. - 1059-1524 .- 1939-4586. ; 27
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Mahdessian, Diana, et al.
(författare)
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Spatiotemporal characterization of the human proteome.
- 2017
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Ingår i: Molecular Biology of the Cell. - : The American Society for Cell Biology - ASCB. - 1059-1524 .- 1939-4586. ; 28
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Mahdessian, Diana, et al.
(författare)
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Spatiotemporal dissection of the cell cycle regulated human proteome
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Here we present a spatiotemporal dissection of proteome single cell heterogeneity in human cells, performed with subcellular resolution over the course of a cell cycle. We identify 17% of the human proteome to display cell-to-cell variability, of which we could attribute 25% as correlated to cell cycle progression, and present the first evidence of cell cycle association for 258 proteins. A key finding is that the variance, of many of the cell cycle associated proteins, is only partially explained by the cell cycle, which hints at cross-talk between the cell cycle and other signaling pathways. We also demonstrate that several of the identified cell cycle regulated proteins may be clinically significant in proliferative disorders. This spatially resolved proteome map of the cell cycle, integrated into the Human Protein Atlas, serves as a valuable resource to accelerate the molecular knowledge of the cell cycle and opens up novel avenues for the understanding of cell proliferation.
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| 7. |
- Mahdessian, Diana, et al.
(författare)
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Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
- 2021
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 590:7847
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Tidskriftsartikel (refereegranskat)abstract
- Spatial and temporal variations among individual human cell proteomes are comprehensively mapped across the cell cycle using proteomic imaging and transcriptomics. The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer(1-3). The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.
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| 8. |
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| 9. |
- Skogs, Marie, et al.
(författare)
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Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins
- 2017
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 16:1, s. 147-155
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Tidskriftsartikel (refereegranskat)abstract
- Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence (IF) applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP-tagged target proteins at endogenous levels. Furthermore, we assessed batch-to-batch effects for 35 target proteins, showing that both the on- and off-target binding patterns vary significantly between antibody batches and that the proposed strategy serves as a reliable procedure for ensuring reproducibility upon production of new antibody batches. In summary, we present a systematic scheme for antibody validation in IF applications using endogenous expression of tagged proteins. This is an important step toward a reproducible approach for context- and application-specific antibody validation and improved reliability of antibody-based experiments and research data.
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| 10. |
- Stenström, Lovisa, et al.
(författare)
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Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder
- 2020
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Ingår i: Molecular Systems Biology. - : Wiley. - 1744-4292 .- 1744-4292. ; 16:8
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Tidskriftsartikel (refereegranskat)abstract
- The nucleolus is essential for ribosome biogenesis and is involved in many other cellular functions. We performed a systematic spatiotemporal dissection of the human nucleolar proteome using confocal microscopy. In total, 1,318 nucleolar proteins were identified; 287 were localized to fibrillar components, and 157 were enriched along the nucleoplasmic border, indicating a potential fourth nucleolar subcompartment: the nucleoli rim. We found 65 nucleolar proteins (36 uncharacterized) to relocate to the chromosomal periphery during mitosis. Interestingly, we observed temporal partitioning into two recruitment phenotypes: early (prometaphase) and late (after metaphase), suggesting phase-specific functions. We further show that the expression ofMKI67 is critical for this temporal partitioning. We provide the first proteome-wide analysis of intrinsic protein disorder for the human nucleolus and show that nucleolar proteins in general, and mitotic chromosome proteins in particular, have significantly higher intrinsic disorder level compared to cytosolic proteins. In summary, this study provides a comprehensive and essential resource of spatiotemporal expression data for the nucleolar proteome as part of the Human Protein Atlas.
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