| 1. |
- 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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| 2. |
- Marco Salas, Sergio, 1996-, et al.
(författare)
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Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10X Genomics capable of mapping hundreds of genes in situ at a subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as the first independent analysis of the performance of Xenium, and provides best-practices and recommendations for analysis of such datasets.
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| 3. |
- Ruiz-Moreno, Cristian, et al.
(författare)
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Harmonized single-cell landscape, tumor architecture, and intercellular crosstalk ofIDH-wildtype glioblastoma
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Glioblastoma, isocitrate dehydrogenase (IDH)-wildtype (hereafter, GB), is an aggressivebrain malignancy associated with a dismal prognosis and poor quality of life. Single-cellRNA sequencing has aided in grasping the complexity of the cell states and dynamic changesin GB. Large-scale data integration can help to uncover unexplored tumor pathobiology.Here, we resolved the composition of the tumor milieu and created a cellular map of GB(‘GBmap’), a curated resource that harmonizes 26 datasets, gathering 240 patients andspanning over 1.1 million cells. We showcase the applications of our resource for referencemapping, transfer learning, and biological discoveries. Reconstructing the tumor architectureusing spatially resolved transcriptomics unveiled consistent niches across patients and theirorganizational gradient. Our findings shed light on specific crosstalk within GB niches,including the intricate proangiogenic signaling. The GBmap represents a framework thatallows the streamlined integration and interpretation of new data and provides a platform forexploratory analysis, hypothesis generation, and testing.
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| 4. |
- 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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| 5. |
- Bennett, Jack J., et al.
(författare)
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Towards a precision calculation of the effective number of neutrinos N-eff in the Standard Model. Part II. Neutrino decoupling in the presence of flavour oscillations and finite-temperature QED
- 2021
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; 2021:4
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Tidskriftsartikel (refereegranskat)abstract
- We present in this work a new calculation of the standard-model benchmark value for the effective number of neutrinos, N-eff(SM), that quantifies the cosmological neutrinoto-photon energy densities. The calculation takes into account neutrino flavour oscillations, finite-temperature effects in the quantum electrodynamics plasma to O(e(3)), where e is the elementary electric charge, and a full evaluation of the neutrino-neutrino collision integral. We provide furthermore a detailed assessment of the uncertainties in the benchmark N(eff)(SM )value, through testing the value's dependence on (i) optional approximate modelling of the weak collision integrals, (ii) measurement errors in the physical parameters of the weak sector, and (iii) numerical convergence, particularly in relation to momentum discretisation. Our new, recommended standard-model benchmark is N-eff(SM) 3.0440 +/- 0.0002, where the nominal uncertainty is attributed predominantly to errors incurred in the numerical solution procedure (vertical bar delta N-eff vertical bar similar to 10(-4)), augmented by measurement errors in the solar mixing angle sin(2) theta(12) (vertical bar delta N-eff vertical bar similar to 10(-4)).
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| 6. |
- Firsova, Alexandra, et al.
(författare)
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Topographic atlas of cell states identifies regional gene expression in the adult human lung
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Single cell mRNA sequencing of the whole organ has become a popular technique to reveal rare types and subtypes of previously characterized cells as well as to distinguish and characterize gene expression of previously unknown cell types. Unsupervised clustering can reveal tens or even hundreds of variable genes that characterize cell types. Variation in gene expression is often observed within one cell type, and sometimes cannot be biologically explained without mapping of mRNA on tissue. In this study we aim to (i) map the majority of cell types of human lung, (ii) describe variability in their gene expression and (iii) relate this gene expression to cellular location and neighborhoods. Using three different spatial transcriptomics approaches, we mapped epithelial cell states of airways and submucosal gland, and defined cell type-unrelated gene expression variability along proximo-distal axis, including potential regulators and co-regulators of such cell states in the mesenchymal and immune cell niches. In addition, we mapped rare cell types, such as subtypes of neuroendocrine cells, ionocytes and tuft (brush) cells, revealing tracheal preference for ionocytes, and distal airways for GHRL-positive neuroendocrine cells. Finally, we used the created map as a reference for the diseased tissue from patients with stage II COPD and revealed perturbed cell states and COPD-specific imbalance of cell types, affecting immune and AT0 clusters.
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| 7. |
- Gyllborg, Daniel, et al.
(författare)
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Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:19
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Tidskriftsartikel (refereegranskat)abstract
- Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.
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| 8. |
- Lee, Hower, et al.
(författare)
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Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.
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| 9. |
- Liu, Ilon, et al.
(författare)
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The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location
- 2022
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 54:12, s. 1881-1894
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Tidskriftsartikel (refereegranskat)abstract
- Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.
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| 10. |
- Magoulopoulou, Anastasia, 1986-, et al.
(författare)
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Padlock Probe-Based Targeted In Situ Sequencing : Overview of Methods and Applications
- 2023
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Ingår i: Annual review of genomics and human genetics (Print). - 1527-8204 .- 1545-293X. ; 24, s. 133-150
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Forskningsöversikt (refereegranskat)abstract
- Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.
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