| 1. |
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| 2. |
- Chang, Yun Chien, et al.
(författare)
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Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics
- 2024
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 43:6
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Tidskriftsartikel (refereegranskat)abstract
- Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma, but many aspects of their cellular mechanism of action (MoA) and substantial toxicity are not well understood. To shed more light on how KDACis elicit cellular responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, and protein expression in response to 21 clinical and pre-clinical KDACis. The resulting 862,000 dose-response curves revealed, for instance, limited cellular specificity of histone deacetylase (HDAC) 1, 2, 3, and 6 inhibitors; strong cross-talk between acetylation and phosphorylation pathways; localization of most drug-responsive acetylation sites to intrinsically disordered regions (IDRs); an underappreciated role of acetylation in protein structure; and a shift in EP300 protein abundance between the cytoplasm and the nucleus. This comprehensive dataset serves as a resource for the investigation of the molecular mechanisms underlying KDACi action in cells and can be interactively explored online in ProteomicsDB.
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| 3. |
- Dou, Diana R., et al.
(författare)
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Xist ribonucleoproteins promote female sex-biased autoimmunity
- 2024
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 187:3, s. 16-733
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Tidskriftsartikel (refereegranskat)abstract
- Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.
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| 4. |
- 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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| 5. |
- Johnson, Graham T., et al.
(författare)
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Building the next generation of virtual cells to understand cellular biology
- 2023
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 122:18, s. 3560-3569
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Tidskriftsartikel (refereegranskat)abstract
- Cell science has made significant progress by focusing on understanding individual cellular processes through reductionist approaches. However, the sheer volume of knowledge collected presents challenges in integrating this information across different scales of space and time to comprehend cellular behaviors, as well as making the data and methods more accessible for the community to tackle complex biological questions. This perspective proposes the creation of next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources, including simulations, biophysical models, image-based models, and evidence-based knowledge graphs. These virtual cells would provide statistically accurate and holistic views of real cells, bridging the gap between theoretical concepts and experimental data, and facilitating productive new collaborations among researchers across related fields.
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| 6. |
- King, Matthew R., et al.
(författare)
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Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient
- 2024
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 187:8, s. 24-1889
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Tidskriftsartikel (refereegranskat)abstract
- Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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| 7. |
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| 8. |
- Lázár, Enikő, et al.
(författare)
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Spatial Dynamics of the Developing Human Heart
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Heart development relies on a topologically defined interplay between a diverse array of cardiac cells. We finely curated spatial and single-cell measurements with subcellular imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. In summary, our study delineates the cellular and molecular landscape of the developing heart’s architecture, offering links to genetic causes of heart disease.
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| 9. |
- Lee, Hower, et al.
(författare)
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Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in-situ expression maps of hundreds of genes. We exploit direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high throughput, and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering, and annotation of cell types. By enabling easier access to high throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
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| 10. |
- Liu, Fei, et al.
(författare)
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Systems Proteomics View of the Endogenous Human Claudin Protein Family
- 2016
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 15:2, s. 339-359
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Forskningsöversikt (refereegranskat)abstract
- Claudius are the major transmembrane protein components of tight junctions in human endothelia and epithelia. Tissue-specific expression of claudin members suggests that this protein family is not only essential for sustaining the role of tight junctions in cell permeability control but also vital in organizing cell contact signaling by protein protein interactions. How this protein family is collectively processed and regulated is key to understanding the role of junctional proteins in preserving cell identity and tissue integrity. The focus of this review is to first provide a brief overview of the functional context, on the basis of the extensive body of claudin biology research that has been thoroughly reviewed, for endogenous human claudin members and then ascertain existing and future proteomics techniques that may be applicable to systematically characterizing the chemical forms and interacting protein partners of this protein family in human. The ability to elucidate claudin-based signaling networks may provide new insight into cell development and differentiation programs that are crucial to tissue stability and manipulation.
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| 11. |
- Omenn, Gilbert S., et al.
(författare)
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Metrics for the Human Proteome Project 2016 : Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications
- 2016
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 15:11, s. 3951-3960
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The HUPO Human Proteome Project (HP?) has two overall goals: (1) stepwise completion of the protein parts-list the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [www.thehpp.org/guidelines]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PEI under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 as in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven (B/D)-HPP has created comprehensive SRM resources, generated popular protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.
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| 12. |
- Quardokus, Ellen M., et al.
(författare)
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Organ Mapping Antibody Panels : a community resource for standardized multiplexed tissue imaging
- 2023
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Ingår i: Nature Methods. - : Springer Nature. - 1548-7091 .- 1548-7105. ; 20:8, s. 1174-1178
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Tidskriftsartikel (refereegranskat)abstract
- Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.
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| 13. |
- Sariyar, Sanem, et al.
(författare)
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High-parametric protein maps reveal the spatial organization in early-developing human lung
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The respiratory system, encompassing the lungs, trachea, and vasculature, is essential for terrestrial life. Although recent research has illuminated aspects of lung development, such as cell lineage origins and their molecular drivers, much of our knowledge is still based on animal models, or is deduced from transcriptome analyses. In this study, conducted within the Human Developmental Cell Atlas (HDCA) initiative, we describe the spatiotemporal organization of lung during the first trimester of human gestation in situ and at protein level. We used high-parametric tissue imaging on human lung samples, aged 6 to 13 post-conception weeks, using a 30-plex antibody panel. Our approach yielded over 2 million individual lung cells across five developmental timepoints, with an in-depth analysis of nearly 1 million cells. We present a spatially resolved cell type composition of the developing human lung, with a particular emphasis on their proliferative states, spatial arrangement traits, and their temporal evolution throughout lung development. We also offer new insights into the emerging patterns of immune cells during lung development. To the best of our knowledge, this study is the most extensive protein-level examination of the developing human lung. The generated dataset is a valuable resource for further research into the developmental roots of human respiratory health and disease.
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| 14. |
- Sariyar, Sanem
(författare)
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Spatiotemporal Profiling of Human Development Using Multiplexed Imaging
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human development is complex and intricate, where the positions of cells, expression of key markers, and cell-cell interactions contribute to the development of various organs from different germ layers and the establishment of the body axis. Therefore, understanding human development within spatial and temporal aspects is crucial. Spatial and temporal aspects can be studiedthrough multiplexed imaging, which enables the assessment of multiple markers on the same tissue, offering critical insights into protein expressions in the cells and tissues. Within the scope of this thesis, we focused on the spatial and single-cell profiling of cell types during the first trimester of human development, both at the systemic and organ levels, using multiplexed imaging. Paper I of this thesis presents a spatial and single-cell map of the developing human lung in the first trimester. We used multiplexed imaging on post-conception week 6 to 13 lungs employing a 30-plex antibody panel and, as a result, analyzed nearly 1 million cells. We provide a spatially resolved cell type composition of the developing human lung, focusing on spatiotemporal changes in the cell types, such as immune cells, endothelial cells, lymphatic cells, and proliferative cell states. Key findings of the first paper are that the proliferation patterns in the epithelium reveal differences in the elongation of smaller and larger distal and proximal airways and the presence of some immune cells around arteries, highlighting location-function relationships. Additionally, this paper represents the first application of multiplexed imaging on the developing human lung. Paper II aimed to systematically investigate human development in whole embryos by focusing on cell types such as immune and endothelial cells. We analyzed human whole embryo tissues from week 3 to 5 using a 28-plex multiplexed antibody panel. A key finding of the paper is the appearance of liver immune cells as early as week 4 and differences in their marker expression profiles compared to the other immune cells. In Paper III, we proposed a simple and flexible open-source method for visualizing in situ expressions of hundreds of genes, which can be combined with other methods, such as multiplexed imaging. In Paper IV, we explored the spatial dynamics of the developing human heart at the cellular and subcellular levels. In conclusion, this thesis elucidates the spatiotemporal changes during the first trimester of human development by presenting spatial maps of developing organs and whole embryos at various stages. The objective is to illustrate the characteristics of a healthy state, contributing to a better understanding of abnormalities associated with congenital diseases.
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| 15. |
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| 16. |
- Werne Solnestam, Beata, et al.
(författare)
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Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13:1, s. 574-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing. Results: For all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level. Conclusions: We conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.
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| 17. |
- Wiking, Mikaela, et al.
(författare)
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An image-based map of the human mitochondrial proteome
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- 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 1,070 proteins, of which 376 have previously not been reported to localize to the mitochondria. Our analysis shows that approximately 50% (n=493) of the proteins localize to additional cellular compartments, likely contributing to the diverse cellular functions of mitochondria. This map of the mitochondrial proteome, part of the Cell Atlas 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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