| 1. |
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| 2. |
- Hildebrandt, Franziska, 1994-, et al.
(författare)
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Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Reconstruction of heterogeneity through single cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we apply Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology. Global transcriptional differences across lobular units in the liver remain unknown. Here the authors perform spatial transcriptomics of liver tissue to delineate transcriptional differences in physical space, confirm lobular zonation along transcriptional gradients and suggest the presence of previously uncharacterized structures within liver tissue.
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| 3. |
- Jemt, Anders, 1985-, et al.
(författare)
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An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.
- 2016
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Furthermore, an increased understanding of tissue heterogeneity has lead to the development of several unique sequencing protocols that aim to retain or infer spatial context. In this study, a protocol for retaining spatial information of transcripts has been adapted to run on a robotic workstation. The method spatial transcriptomics is evaluated in terms of robustness and variability through the preparation of reference RNA, as well as through preparation and sequencing of six replicate sections of a gingival tissue biopsy from a patient with periodontitis. The results are reduced technical variability between replicates and a higher throughput, processing four times more samples with less than a third of the hands on time, compared to the standard protocol.
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| 4. |
- Ji, Andrew L., et al.
(författare)
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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
- 2020
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Ingår i: Cell. - : Cell Press. - 0092-8674 .- 1097-4172. ; 182:2, s. 497-
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Tidskriftsartikel (refereegranskat)abstract
- To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.
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| 5. |
- Kaufmann, M., et al.
(författare)
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Identification of early neurodegenerative pathways in progressive multiple sclerosis
- 2022
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Ingår i: Nature Neuroscience. - : Springer Nature. - 1097-6256 .- 1546-1726. ; 25:7, s. 944-955
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Tidskriftsartikel (refereegranskat)abstract
- Progressive multiple sclerosis (MS) is characterized by unrelenting neurodegeneration, which causes cumulative disability and is refractory to current treatments. Drug development to prevent disease progression is an urgent clinical need yet is constrained by an incomplete understanding of its complex pathogenesis. Using spatial transcriptomics and proteomics on fresh-frozen human MS brain tissue, we identified multicellular mechanisms of progressive MS pathogenesis and traced their origin in relation to spatially distributed stages of neurodegeneration. By resolving ligand–receptor interactions in local microenvironments, we discovered defunct trophic and anti-inflammatory intercellular communications within areas of early neuronal decline. Proteins associated with neuronal damage in patient samples showed mechanistic concordance with published in vivo knockdown and central nervous system (CNS) disease models, supporting their causal role and value as potential therapeutic targets in progressive MS. Our findings provide a new framework for drug development strategies, rooted in an understanding of the complex cellular and signaling dynamics in human diseased tissue that facilitate this debilitating disease.
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| 6. |
- Kvastad, Linda, et al.
(författare)
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The spatial landscape of transcriptomes and genomes in pediatric brain tumors
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Treatment of pediatric brain tumors is continually being improved; still, there is a great need for new treatment options. Here we explore the spatial transcriptomic and genomic landscape in a cohort of pediatric brain tumors using a new generation of unbiased methodologies. We demonstrate the gene expression patterns of the essential cancer-related gene programs of epithelial-to-mesenchymal transition (EMT), the reverse process mesenchymal-to-epithelial transition (MET), and tumor microenvironment (TME) observations through microglia. Furthermore, we identify the gene expression of SPP1 by microglia in the TME as a potential prognostic mRNA marker - in pediatric brain tumor relapse patients.
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| 7. |
- Kvastad, Linda, et al.
(författare)
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The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
- 2021
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows. Kvastad et al. develop the spatial RNA Integrity Number (sRIN) assay that evaluates the RNA integrity at cellular resolution. This method improves the resolution of a similar method called the RNA Integrity Number (RIN), demonstrating spatial variation in the quality of RNA samples.
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| 8. |
- Lebrigand, Kevin, et al.
(författare)
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The spatial landscape of gene expression isoforms in tissue sections
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized with current methods. Here, we introduce Spatial Isoform Transcriptomics (SiT), an explorative method for characterizing spatial isoform and sequence heterogeneity in tissue sections, and show how it can be used to profile isoform expression and sequence heterogeneity in a tissue context
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| 9. |
- Lebrigand, Kevin, et al.
(författare)
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The spatial landscape of gene expression isoforms in tissue sections
- 2023
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 51:8
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Tidskriftsartikel (refereegranskat)abstract
- In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource, where isoform expression and RNA editing can be visualized in a spatial context.
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| 10. |
- Lundmark, A., et al.
(författare)
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Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Periodontitis is a highly prevalent chronic inflammatory disease of the periodontium, leading ultimately to tooth loss. In order to characterize the gene expression of periodontitis-affected gingival tissue, we have here simultaneously quantified and localized gene expression in periodontal tissue using spatial transcriptomics, combining RNA sequencing with histological analysis. Our analyses revealed distinct clusters of gene expression, which were identified to correspond to epithelium, inflamed areas of connective tissue, and non-inflamed areas of connective tissue. Moreover, 92 genes were identified as significantly up-regulated in inflamed areas of the gingival connective tissue compared to non-inflamed tissue. Among these, immunoglobulin lambda-like polypeptide 5 (IGLL5), signal sequence receptor subunit 4 (SSR4), marginal zone B and B1 cell specific protein (MZB1), and X-box binding protein 1 (XBP1) were the four most highly up-regulated genes. These genes were also verified as significantly higher expressed in gingival tissue of patients with periodontitis compared to healthy controls, using reverse transcription quantitative polymerase chain reaction. Moreover, the protein expressions of up-regulated genes were verified in gingival biopsies by immunohistochemistry. In summary, in this study, we report distinct gene expression signatures within periodontitis-affected gingival tissue, as well as specific genes that are up-regulated in inflamed areas compared to non-inflamed areas of gingival tissue. The results obtained from this study may add novel information on the genes and cell types contributing to pathogenesis of the chronic inflammatory disease periodontitis.
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| 11. |
- Maniatis, Silas, et al.
(författare)
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Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
- 2019
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Ingår i: Science. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075 .- 1095-9203. ; 364:6435, s. 89-
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Tidskriftsartikel (refereegranskat)abstract
- Paralysis occurring in amyotrophic lateral sclerosis (ALS) results from denervation of skeletal muscle as a consequence of motor neuron degeneration. Interactions between motor neurons and glia contribute to motor neuron loss, but the spatiotemporal ordering of molecular events that drive these processes in intact spinal tissue remains poorly understood. Here, we use spatial transcriptomics to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients, to characterize the underlying molecular mechanisms in ALS. We identify pathway dynamics, distinguish regional differences between microglia and astrocyte populations at early time points, and discern perturbations in several transcriptional pathways shared between murine models of ALS and human postmortem spinal cords.
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| 12. |
- Mollbrink, Annelie
(författare)
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Experimental and clinical studies on liver regeneration and hepatocellular carcinoma : roles of redox proteins, iron homeostasis and multikinase inhibition.
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Compensatory liver regeneration is triggered by chronic liver injury or surgery and is crucial to maintain tissue homeostasis. The underlying mechanisms which include a whole battery of complex signaling events have been thoroughly studied for decades. The majority of hepatocellular carcinomas develop in a highly proliferative environment caused by underlying chronic liver disease in which lost liver tissue must be restored to meet the needs of the organism. The chronic inflammatory condition with chronic liver repair enhances the presence of free radicals leading to an increased risk of cell alterations. This thesis includes four papers; the first three of which comprise studies regarding the importance of the regulation and endurance of cell proliferation, and also the sensitivity of the proliferating cells to compounds used in cancer prevention and treatment. In these studies we used a 2/3 partial hepatectomy (PH) rat model and also a chemically induced rat liver cancer model (The Solt and Farber Resistant hepatocyte model). The fourth paper is a human study in which we quantified immunohistochemical stainings for 6 different redox proteins in livers from patients resected for hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC) liver metastases. The specific aims were: (I) to characterize gene expression of the different pathways involved in hepcidin regulation after PH, until liver regeneration is complete; (II) to study the effects of sodium selenite on regenerative versus neoplastic liver cell proliferation in rat, and to investigate if TrxR1 is a constitutive tumour marker or an unspecific marker for cell growth in rat liver; (III) to study the effect of the anticancer agent sorafenib, a multikinase inhibitor, on normal liver regeneration after PH in rat; and (IV) to evaluate if redox protein (thioredoxins and glutaredoxins) expressions correlate to clinical features in human hepatocellular carcinoma and if they can be used as prognostic markers after liver surgery. Our results showed that high serum levels of IL6 induced the levels of STAT3 and the expression of hepcidin mRNA during the acute phase after PH. The gene expressions of the iron sensing proteins HFE, hemojuvelin (HJV) and transferrin receptor 2 (TfR2) were decreased during the whole regeneration, gradually decreasing hepcidin gene expression and thereby mobilizing iron to the growing liver. The expression of genes involved in iron uptake; transferrin receptor 1 (TfR1) and divalent metal transporter 1 (DMT1) were increased thereby facilitating iron uptake (paper I). After administration of sodium selenite in a tumour preventive, supranutritional dose followed by PH no effect on body weights or gain of liver mass was seen. In the hepatocarcinogenesis model the tumour volume was significantly decreased in animals supplied with selenium during the progression phase compared tumours in rats not treated with selenium. The expression of TrxR1 was exclusively seen in the neoplastic liver lesions but not in the remodelling preneoplastic lesions (paper II). Treatment with sorafenib transiently suppressed liver regeneration and the gain of relative liver mass, but was followed by a delayed compensatory increase of liver cell proliferation one week after resection with the result that after 14 days the treated animals reached the same relative liver weights as the controls did in five days (paper III). In the human study we saw an up-regulation of Trx1, Trx2 and Grx5 in HCC compared to its respective surrounding non-tumorous tissue. The same was observed in the CRC metastases where also the staining of Grx1 and Grx3 was significantly higher compared to non-tumorous tissue. Trx1 expression correlated well to cell proliferation but not to tumour differentiation, micro-vascular invasion or tumour recurrence. A relative down regulation of Trx1 was seen in tumours compared to the surrounding liver in males, smokers and in patients with high alcohol consumption. We concluded that the peak of hepcidin expression during the acute phase was eventually overruled by the downregulation of the iron sensing pathway in order to promote iron mobilization to the regenerating liver. We also concluded that selenium in a supranutritional dose impaired tumour growth without impairing the normal liver cell proliferation, and that the selenoprotein TrxR1 is a constituent of the neoplastic phenotype. Sorafenib prolonged liver regeneration in proportion to the length of treatment but the liver adapted to the early inhibitory effects of the drug. Thioredoxins and glutaredoxins were ubiquitously expressed in livers exposed to oxidative stress and various malignancies and can therefore not be used as diagnostic markers for HCC. Smoking and high alcohol consumption increased the Trx1 expression in tissue surrounding the HCCs, whereas expression of Trx1 in the HCCs correlated to cell proliferation. Redox protein expression in HCCs cannot be used as predictive markers for tumour recurrence after liver resection.
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| 13. |
- Newton, P. T., et al.
(författare)
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A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 567:7747
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Tidskriftsartikel (refereegranskat)abstract
- Longitudinal bone growth in children is sustained by growth plates, narrow discs of cartilage that provide a continuous supply of chondrocytes for endochondral ossification(1). However, it remains unknown how this supply is maintained throughout childhood growth. Chondroprogenitors in the resting zone are thought to be gradually consumed as they supply cells for longitudinal growth(1,2), but this model has never been proved. Here, using clonal genetic tracing with multicolour reporters and functional perturbations, we demonstrate that longitudinal growth during the fetal and neonatal periods involves depletion of chondroprogenitors, whereas later in life, coinciding with the formation of the secondary ossification centre, chondroprogenitors acquire the capacity for self-renewal, resulting in the formation of large, stable monoclonal columns of chondrocytes. Simultaneously, chondroprogenitors begin to express stem cell markers and undergo symmetric cell division. Regulation of the pool of self-renewing progenitors involves the hedgehog and mammalian target of rapamycin complex 1 (mTORC1) signalling pathways. Our findings indicate that a stem cell niche develops postnatally in the epiphyseal growth plate, which provides a continuous supply of chondrocytes over a prolonged period.
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| 14. |
- Rájová, Jana, et al.
(författare)
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Deconvolution of spatial sequencing provides accurate characterization of hESC-derived DA transplants in vivo
- 2023
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Ingår i: Molecular therapy. Methods & clinical development. - : Elsevier BV. - 2399-6951 .- 2329-0501. ; 29, s. 381-394
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Tidskriftsartikel (refereegranskat)abstract
- Cell therapy for Parkinson's disease has experienced substantial growth in the past decades with several ongoing clinical trials. Despite increasing refinement of differentiation protocols and standardization of the transplanted neural precursors, the transcriptomic analysis of cells in the transplant after its full maturation in vivo has not been thoroughly investigated. Here, we present spatial transcriptomics analysis of fully differentiated grafts in their host tissue. Unlike earlier transcriptomics analyses using single-cell technologies, we observe that cells derived from human embryonic stem cells (hESCs) in the grafts adopt mature dopaminergic signatures. We show that the presence of phenotypic dopaminergic genes, which were found to be differentially expressed in the transplants, is concentrated toward the edges of the grafts, in agreement with the immunohistochemical analyses. Deconvolution shows dopamine neurons being the dominating cell type in many features beneath the graft area. These findings further support the preferred environmental niche of TH-positive cells and confirm their dopaminergic phenotype through the presence of multiple dopaminergic markers.
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| 15. |
- Salmén, Fredrik, et al.
(författare)
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Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
- 2018
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Ingår i: Nature Protocols. - : Nature Publishing Group. - 1754-2189 .- 1750-2799. ; 13:11, s. 2501-2534
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Tidskriftsartikel (refereegranskat)abstract
- Spatial resolution of gene expression enables gene expression events to be pinpointed to a specific location in biological tissue. Spatially resolved gene expression in tissue sections is traditionally analyzed using immunohistochemistry (IHC) or in situ hybridization (ISH). These technologies are invaluable tools for pathologists and molecular biologists; however, their throughput is limited to the analysis of only a few genes at a time. Recent advances in RNA sequencing (RNA-seq) have made it possible to obtain unbiased high-throughput gene expression data in bulk. Spatial Transcriptomics combines the benefits of traditional spatially resolved technologies with the massive throughput of RNA-seq. Here, we present a protocol describing how to apply the Spatial Transcriptomics technology to mammalian tissue. This protocol combines histological staining and spatially resolved RNA-seq data from intact tissue sections. Once suitable tissue-specific conditions have been established, library construction and sequencing can be completed in similar to 5-6 d. Data processing takes a few hours, with the exact timing dependent on the sequencing depth. Our method requires no special instruments and can be performed in any laboratory with access to a cryostat, microscope and next-generation sequencing.
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| 16. |
- Sonavane, Sumalata, et al.
(författare)
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Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics
- 2024
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 10:33
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Tidskriftsartikel (refereegranskat)abstract
- Spiders produce nature’s toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders’ strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.
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| 17. |
- Ståhl, Patrik, Dr., et al.
(författare)
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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
- 2016
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Ingår i: Science. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075 .- 1095-9203. ; 353:6294, s. 78-82
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.
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| 18. |
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| 19. |
- Vickovic, Sanja, et al.
(författare)
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Massive and parallel expression profiling using microarrayed single-cell sequencing
- 2016
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.
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| 20. |
- Villacampa, Eva Gracia, et al.
(författare)
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Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here we present a procedure to perform genome-wide spatial analysis of mRNA in FFPE fixed tissue sections. The procedure takes advantage of well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3’ end of mRNA molecules in tissue sections. First, we conducted expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method’s capability to delineate anatomical regions from a molecular perspective. Second, we explored the spatial composition of transcriptomic signatures in ovarian carcinosarcoma samples using data-driven analysis methods, exemplifying the method’s potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize organoids and a human lung biopsy specimen infected with SARS-CoV-2.
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| 21. |
- Villacampa, Eva Gracia, et al.
(författare)
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Genome-wide spatial expression profiling in formalin-fixed tissues
- 2021
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 1:3
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Tidskriftsartikel (refereegranskat)abstract
- Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3′ end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.
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| 22. |
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