| 1. |
- 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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| 2. |
- 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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| 3. |
- lee, hower, et al.
(författare)
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Open-source, high-throughput targeted in-situ transcriptomics for developmental and tissue biology
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Tidskriftsartikel (refereegranskat)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 and tissue 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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| 4. |
- Lee, Hower, et al.
(författare)
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Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology
- 2024
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Ingår i: Development. - : COMPANY OF BIOLOGISTS LTD. - 0950-1991 .- 1477-9129. ; 151:16
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Tidskriftsartikel (refereegranskat)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 use 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 and tissue 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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| 5. |
- 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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| 6. |
- 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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| 7. |
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| 8. |
- 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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| 9. |
- Sountoulidis, Alexandros, et al.
(författare)
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A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
- 2023
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Ingår i: Nature Cell Biology. - : Springer Nature. - 1465-7392 .- 1476-4679.
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Tidskriftsartikel (refereegranskat)abstract
- Sountoulidis et al. provide a spatial gene expression atlas of human embryonic lung during the first trimester of gestation and identify 83 cell identities corresponding to stable cell types or transitional states. The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.
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