1
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Grujčić V, Saarenpää S, Sundh J, Sennblad B, Norgren B, Latz M, Giacomello S, Foster RA, Andersson AF. Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. PLoS One 2024; 19:e0296672. [PMID: 38241213 PMCID: PMC10798536 DOI: 10.1371/journal.pone.0296672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/13/2023] [Indexed: 01/21/2024] Open
Abstract
Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.
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Affiliation(s)
- Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Sami Saarenpää
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, Sweden
| | - Bengt Sennblad
- Science for Life Laboratory, Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Benjamin Norgren
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Meike Latz
- 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
| | - Rachel A. Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Anders F. Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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2
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Engblom C, Thrane K, Lin Q, Andersson A, Toosi H, Chen X, Steiner E, Lu C, Mantovani G, Hagemann-Jensen M, Saarenpää S, Jangard M, Saez-Rodriguez J, Michaëlsson J, Hartman J, Lagergren J, Mold JE, Lundeberg J, Frisén J. Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics. Science 2023; 382:eadf8486. [PMID: 38060664 DOI: 10.1126/science.adf8486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/23/2023] [Indexed: 12/18/2023]
Abstract
The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.
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Affiliation(s)
- Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kim Thrane
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Qirong Lin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alma Andersson
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hosein Toosi
- SciLifeLab, Computational Science and Technology department, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xinsong Chen
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Embla Steiner
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Chang Lu
- Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Giulia Mantovani
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Sami Saarenpää
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mattias Jangard
- ENT Unit, Sophiahemmet University Research Laboratory and Sophiahemmet Hospital, Stockholm, Sweden
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Jens Lagergren
- SciLifeLab, Computational Science and Technology department, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Lundeberg
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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3
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Saarenpää S, Shalev O, Ashkenazy H, Carlos V, Lundberg DS, Weigel D, Giacomello S. Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. Nat Biotechnol 2023:10.1038/s41587-023-01979-2. [PMID: 37985875 DOI: 10.1038/s41587-023-01979-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/06/2023] [Indexed: 11/22/2023]
Abstract
The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks and spatial patterns. Existing technology does not allow the simultaneous investigation of spatial interactions between a host and the multitude of its colonizing microorganisms, which limits our understanding of host-microorganism interactions within a plant or animal tissue. Here we present spatial metatranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and find tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intrakingdom spatial interactions among microorganisms, as well as the host response to microbial hotspots. SmT provides an approach for answering fundamental questions on host-microbiome interplay.
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Affiliation(s)
- Sami Saarenpää
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Or Shalev
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Systems Biology of Microbial Communities, University of Tübingen, Tübingen, Germany
| | - Haim Ashkenazy
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Vanessa Carlos
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Derek Severi Lundberg
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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4
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Sounart H, Voronin D, Masarapu Y, Chung M, Saarenpää S, Ghedin E, Giacomello S. Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale. Nat Commun 2023; 14:6500. [PMID: 37838705 PMCID: PMC10576761 DOI: 10.1038/s41467-023-42237-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 10/03/2023] [Indexed: 10/16/2023] Open
Abstract
Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization; to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia. However, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we spatially explored how Wolbachia interacts with the worm's reproductive system by performing a spatial characterization using Spatial Transcriptomics (ST) across a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method's ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions, also under antibiotic treatment. We envision our approach will open up new avenues for the study of infectious diseases caused by micro-scale parasitic worms.
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Affiliation(s)
- Hailey Sounart
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Denis Voronin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yuvarani Masarapu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sami Saarenpää
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Stefania Giacomello
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.
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5
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Hildebrandt F, Andersson A, Saarenpää S, Larsson L, Van Hul N, Kanatani S, Masek J, Ellis E, Barragan A, Mollbrink A, Andersson ER, Lundeberg J, Ankarklev J. Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver. Nat Commun 2021; 12:7046. [PMID: 34857782 PMCID: PMC8640072 DOI: 10.1038/s41467-021-27354-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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: 01/10/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022] Open
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.
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Affiliation(s)
- Franziska Hildebrandt
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden.
| | - Alma Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Sami Saarenpää
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Noémi Van Hul
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, SE-171 77, Solna, Sweden
| | - Sachie Kanatani
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden
| | - Jan Masek
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, SE-171 77, Solna, Sweden
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Ewa Ellis
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 141-86, Stockholm, Sweden
| | - Antonio Barragan
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden
| | - Annelie Mollbrink
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, SE-171 77, Solna, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Johan Ankarklev
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden.
- Microbial Single Cell Genomics facility, SciLifeLab, Biomedical Center (BMC) Uppsala University, SE-751 23, Uppsala, Sweden.
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6
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Berglund E, Saarenpää S, Jemt A, Gruselius J, Larsson L, Bergenstråhle L, Lundeberg J, Giacomello S. Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues. BMC Genomics 2020; 21:298. [PMID: 32293264 PMCID: PMC7158132 DOI: 10.1186/s12864-020-6631-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 09/20/2019] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and co-expression of cells in tissues. Unfortunately, manual preparation of high-quality sequencing libraries is time-consuming and subject to technical variability due to human error during manual pipetting, which results in sample swapping and the accidental introduction of batch effects. All these factors complicate the production and interpretation of biological datasets. RESULTS We have integrated an Agilent Bravo Automated Liquid Handling Platform into the Spatial Transcriptomics workflow. Compared to the previously reported Magnatrix 8000+ automated protocol, this approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples. The new approach is also shown to be highly accurate and almost completely free from technical variability between prepared samples. CONCLUSIONS The new automated Spatial Transcriptomics protocol using the Agilent Bravo Automated Liquid Handling Platform rapidly generates high-quality Spatial Transcriptomics libraries. Given the wide use of the Agilent Bravo Automated Liquid Handling Platform in research laboratories and facilities, this will allow many researchers to quickly create robust Spatial Transcriptomics libraries.
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Affiliation(s)
- Emelie Berglund
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Sami Saarenpää
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Anders Jemt
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joel Gruselius
- Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Ludvig Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
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7
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Viljakainen L, Borshagovski AM, Saarenpää S, Kaitala A, Jurvansuu J. Identification and characterisation of common glow-worm RNA viruses. Virus Genes 2020; 56:236-248. [PMID: 31900852 PMCID: PMC7093385 DOI: 10.1007/s11262-019-01724-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 01/04/2023]
Abstract
The common glow-worms (Lampyris noctiluca) are best known for emission of green light by their larvae and sexually active adult females. However, both their DNA and RNA viruses remain unknown. Glow-worms are virologically interesting, as they are non-social and do not feed as adults, and hence their viral transmission may be limited. We identified viral sequences from 11 different virus taxa by the RNA-sequencing of two Finnish populations of adult glow-worms. The viruses represent nine different virus families and have negative, positive, or double-stranded RNA genomes. We also found a complete retroviral genome. Similar viral sequences were found from the sequencing data of common eastern firefly of North America, a species belonging to the same family (Lampyridae) as that of the common glow-worm. On average, an individual glow-worm had seven different RNA virus types and most of them appeared to establish a stable infection since they were found from glow-worms during two consecutive years. Here we present the characterization of load, prevalence, and interactions for each virus. Most of the glow-worm RNA viruses seem to be transmitted vertically, which may reflect the biology of glow-worms as non-social capital breeders, i.e., they invest stored resources in reproduction.
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Affiliation(s)
- Lumi Viljakainen
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Anna-Maria Borshagovski
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Sami Saarenpää
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Arja Kaitala
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Jaana Jurvansuu
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland.
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8
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Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivová Ž, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science 2019; 364:89-93. [PMID: 30948552 DOI: 10.1126/science.aav9776] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/01/2019] [Indexed: 12/12/2022]
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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Affiliation(s)
- Silas Maniatis
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Sanja Vickovic
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Catherine Braine
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kristy Kang
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Annelie Mollbrink
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Delphine Fagegaltier
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Žaneta Andrusivová
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Sami Saarenpää
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Gonzalo Saiz-Castro
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Miguel Cuevas
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Aaron Watters
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - 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
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA. .,Center for Data Science, New York University, New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA. .,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
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