1
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van Leeuwen W, VanInsberghe M, Battich N, Salmén F, van Oudenaarden A, Rabouille C. Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo. Cell Rep Methods 2022; 2:100235. [PMID: 35784648 PMCID: PMC9243631 DOI: 10.1016/j.crmeth.2022.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 05/20/2022] [Indexed: 11/09/2022]
Abstract
Stress granules are phase-separated assemblies formed around RNAs. So far, the techniques available to identify these RNAs are not suitable for single cells and small tissues displaying cell heterogeneity. Here, we used TRIBE (target of RNA-binding proteins identified by editing) to profile stress granule RNAs. We used an RNA-binding protein (FMR1) fused to the catalytic domain of an RNA-editing enzyme (ADAR), which coalesces into stress granules upon oxidative stress. RNAs colocalized with this fusion are edited, producing mutations that are detectable by VASA sequencing. Using single-molecule FISH, we validated that this purification-free method can reliably identify stress granule RNAs in bulk and single S2 cells and in Drosophila neurons. Similar to mammalian cells, we find that stress granule mRNAs encode ATP binding, cell cycle, and transcription factors. This method opens the possibility to identify stress granule RNAs and other RNA-based assemblies in other single cells and tissues.
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Affiliation(s)
| | | | - Nico Battich
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
| | - Fredrik Salmén
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
| | | | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, Groningen, the Netherlands
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2
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Andersson A, Larsson L, Stenbeck L, Salmén F, Ehinger A, Wu SZ, Al-Eryani G, Roden D, Swarbrick A, Borg Å, Frisén J, Engblom C, Lundeberg J. Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. Nat Commun 2021; 12:6012. [PMID: 34650042 PMCID: PMC8516894 DOI: 10.1038/s41467-021-26271-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.
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Affiliation(s)
- Alma Andersson
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Linnea Stenbeck
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Salmén
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Anna Ehinger
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Sunny Z Wu
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Ghamdan Al-Eryani
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Daniel Roden
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Alex Swarbrick
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Åke Borg
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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3
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Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell 2020; 179:1647-1660.e19. [PMID: 31835037 DOI: 10.1016/j.cell.2019.11.025] [Citation(s) in RCA: 329] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/06/2019] [Accepted: 11/14/2019] [Indexed: 10/25/2022]
Abstract
The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
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Affiliation(s)
- Michaela Asp
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chenglin Wu
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel Fürth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoyan Qian
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Eva Wärdell
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Joaquin Custodio
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Salmén
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Cecilia Österholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Sundström
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Elisabet Åkesson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Olaf Bergmann
- Center for Regenerative Therapies Dresden, TU-Dresden, Dresden, Germany; Karolinska Institutet, Cell and Molecular Biology, Stockholm, Sweden
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christer Sylvén
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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4
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Yoosuf N, Navarro JF, Salmén F, Ståhl PL, Daub CO. Identification and transfer of spatial transcriptomics signatures for cancer diagnosis. Breast Cancer Res 2020; 22:6. [PMID: 31931856 PMCID: PMC6958738 DOI: 10.1186/s13058-019-1242-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/27/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Distinguishing ductal carcinoma in situ (DCIS) from invasive ductal carcinoma (IDC) regions in clinical biopsies constitutes a diagnostic challenge. Spatial transcriptomics (ST) is an in situ capturing method, which allows quantification and visualization of transcriptomes in individual tissue sections. In the past, studies have shown that breast cancer samples can be used to study their transcriptomes with spatial resolution in individual tissue sections. Previously, supervised machine learning methods were used in clinical studies to predict the clinical outcomes for cancer types. METHODS We used four publicly available ST breast cancer datasets from breast tissue sections annotated by pathologists as non-malignant, DCIS, or IDC. We trained and tested a machine learning method (support vector machine) based on the expert annotation as well as based on automatic selection of cell types by their transcriptome profiles. RESULTS We identified expression signatures for expert annotated regions (non-malignant, DCIS, and IDC) and build machine learning models. Classification results for 798 expression signature transcripts showed high coincidence with the expert pathologist annotation for DCIS (100%) and IDC (96%). Extending our analysis to include all 25,179 expressed transcripts resulted in an accuracy of 99% for DCIS and 98% for IDC. Further, classification based on an automatically identified expression signature covering all ST spots of tissue sections resulted in prediction accuracy of 95% for DCIS and 91% for IDC. CONCLUSIONS This concept study suggest that the ST signatures learned from expert selected breast cancer tissue sections can be used to identify breast cancer regions in whole tissue sections including regions not trained on. Furthermore, the identified expression signatures can classify cancer regions in tissue sections not used for training with high accuracy. Expert-generated but even automatically generated cancer signatures from ST data might be able to classify breast cancer regions and provide clinical decision support for pathologists in the future.
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Affiliation(s)
- Niyaz Yoosuf
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden. .,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - José Fernández Navarro
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Salmén
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
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5
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Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL. High-definition spatial transcriptomics for in situ tissue profiling. Nat Methods 2019; 16:987-990. [PMID: 31501547 PMCID: PMC6765407 DOI: 10.1038/s41592-019-0548-y] [Citation(s) in RCA: 527] [Impact Index Per Article: 105.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/02/2019] [Indexed: 12/21/2022]
Abstract
Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-μm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.
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Affiliation(s)
- Sanja Vickovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Gökcen Eraslan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fredrik Salmén
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Linnea Stenbeck
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Denis Schapiro
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ludvig Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - José Fernandéz Navarro
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel K Griffin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden. .,Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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6
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Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections. Nat Protoc 2019; 13:2501-2534. [PMID: 30353172 DOI: 10.1038/s41596-018-0045-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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 ~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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Affiliation(s)
- Fredrik Salmén
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Annelie Mollbrink
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - José Fernández Navarro
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Sanja Vickovic
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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7
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Navarro JF, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL. ST Pipeline: an automated pipeline for spatial mapping of unique transcripts. Bioinformatics 2018; 33:2591-2593. [PMID: 28398467 DOI: 10.1093/bioinformatics/btx211] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 01/01/2023] Open
Abstract
Motivation In recent years we have witnessed an increase in novel RNA-seq based techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based technique that allows spatial mapping of transcripts in tissue sections. The spatial resolution adds an extra level of complexity, which requires the development of new tools and algorithms for efficient and accurate data processing. Results Here we present a pipeline to automatically and efficiently process RNA-seq data obtained from spatial transcriptomics experiments to generate datasets for downstream analysis. Availability and implementation The ST Pipeline is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_pipeline. Contact jose.fernandez.navarro@scilifelab.se. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- José Fernández Navarro
- Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden
| | - Joel Sjöstrand
- Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden
| | - Fredrik Salmén
- Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden
| | - Joakim Lundeberg
- Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden
| | - Patrik L Ståhl
- Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.,Department of Cell and Molecular Biology, SE-171 77 Karolinska Institutet, Stockholm, Sweden
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8
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Asp M, Salmén F, Ståhl PL, Vickovic S, Felldin U, Löfling M, Fernandez Navarro J, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J. Spatial detection of fetal marker genes expressed at low level in adult human heart tissue. Sci Rep 2017; 7:12941. [PMID: 29021611 PMCID: PMC5636908 DOI: 10.1038/s41598-017-13462-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 09/25/2017] [Indexed: 11/09/2022] Open
Abstract
Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.
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Affiliation(s)
- Michaela Asp
- Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Fredrik Salmén
- Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Patrik L Ståhl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sanja Vickovic
- Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ulrika Felldin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Marie Löfling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Jonas Maaskola
- Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maria J Eriksson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Bengt Persson
- Department of Molecular Biology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Matthias Corbascio
- Department of Cardiothoracic Surgery and Anesthesiology, Karolinska University Hospital, Solna, Sweden
| | - Hans Persson
- Department of Cardiology, Danderyd Hospital, Stockholm, Sweden.,Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Linde
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Cardiology, Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Lundeberg
- Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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9
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Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J. Spatially resolved transcriptome profiling in model plant species. Nat Plants 2017; 3:17061. [PMID: 28481330 DOI: 10.1038/nplants.2017.61] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/31/2017] [Indexed: 05/08/2023]
Abstract
Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.
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Affiliation(s)
- Stefania Giacomello
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17165 Solna, Sweden
| | - Fredrik Salmén
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
| | - Barbara K Terebieniec
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Sanja Vickovic
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
| | | | - Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17165 Solna, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, 17121 Solna, Sweden
| | - Johan Reimegård
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75237 Uppsala, Sweden
| | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 11421 Stockholm, Sweden
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 11421 Stockholm, Sweden
- ARC Centre of Excellence in Plant and Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Adelaide, South Australia 5064, Australia
| | - Patrik L Ståhl
- Department of Cell and Molecular Biology, Karolinska Institute, 17165 Solna, Sweden
| | - Jens F Sundström
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Joakim Lundeberg
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
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Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 2016; 353:78-82. [DOI: 10.1126/science.aaf2403] [Citation(s) in RCA: 1166] [Impact Index Per Article: 145.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/31/2016] [Indexed: 12/27/2022]
Abstract
Analysis of the pattern of proteins or messengerRNAs (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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