Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease.
Wei Ting Chen,Wei Ting Chen,Ashley Lu,Ashley Lu,Katleen Craessaerts,Katleen Craessaerts,Benjamin Pavie,Carlo Sala Frigerio,Carlo Sala Frigerio,Carlo Sala Frigerio,Nikky Corthout,Xiaoyan Qian,Jana Lalakova,Malte Kühnemund,Iryna Voytyuk,Iryna Voytyuk,Leen Wolfs,Leen Wolfs,Renzo Mancuso,Renzo Mancuso,Evgenia Salta,Evgenia Salta,Sriram Balusu,Sriram Balusu,An Snellinx,An Snellinx,Sebastian Munck,Aleksandra Jurek,José Fernández Navarro,Takaomi C. Saido,Inge Huitinga,Inge Huitinga,Joakim Lundeberg,Mark Fiers,Mark Fiers,Mark Fiers,Bart De Strooper,Bart De Strooper,Bart De Strooper +38 more
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TLDR
Genome-wide spatial transcriptomics analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.About:
This article is published in Cell.The article was published on 2020-07-22 and is currently open access. It has received 417 citations till now. The article focuses on the topics: Alzheimer's disease & Gene expression profiling.read more
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Journal ArticleDOI
Reactive astrocyte nomenclature, definitions, and future directions
Carole Escartin,Elena Galea,Andras Lakatos,James P. O'Callaghan,Gabor C. Petzold,Gabor C. Petzold,Alberto Serrano-Pozo,Christian Steinhäuser,Andrea Volterra,Giorgio Carmignoto,Giorgio Carmignoto,Amit Agarwal,Nicola J. Allen,Alfonso Araque,Luis Barbeito,Ari Barzilai,Dwight E. Bergles,Gilles Bonvento,Arthur M. Butt,Wei Ting Chen,Martine Cohen-Salmon,Colm Cunningham,Benjamin Deneen,Bart De Strooper,Bart De Strooper,Blanca Diaz-Castro,Cinthia Farina,Marc R. Freeman,Vittorio Gallo,James E. Goldman,Steven A. Goldman,Steven A. Goldman,Magdalena Götz,Antonia Gutierrez,Philip G. Haydon,Dieter Henrik Heiland,Elly M. Hol,Matthew Holt,Masamitsu Iino,Ksenia V. Kastanenka,Helmut Kettenmann,Baljit S. Khakh,Schuichi Koizumi,C. Justin Lee,Shane A. Liddelow,Brian A. MacVicar,Pierre J. Magistretti,Pierre J. Magistretti,Albee Messing,Anusha Mishra,Anna V. Molofsky,Keith K. Murai,Christopher M. Norris,Seiji Okada,Stéphane H. R. Oliet,João Filipe Oliveira,João Filipe Oliveira,Aude Panatier,Vladimir Parpura,Marcela Pekna,Milos Pekny,Luc Pellerin,Gertrudis Perea,Beatriz G. Pérez-Nievas,Frank W. Pfrieger,Kira E. Poskanzer,Francisco J. Quintana,Richard M. Ransohoff,Miriam Riquelme-Perez,Stefanie Robel,Christine R. Rose,Jeffrey D. Rothstein,Nathalie Rouach,David H. Rowitch,Alexey Semyanov,Alexey Semyanov,Swetlana Sirko,Harald Sontheimer,Raymond A. Swanson,Javier Vitorica,Ina B. Wanner,Levi B. Wood,Jia Qian Wu,Binhai Zheng,Eduardo R. Zimmer,Robert Zorec,Michael V. Sofroniew,Alexei Verkhratsky,Alexei Verkhratsky +88 more
TL;DR: In this article, the authors point out the shortcomings of binary divisions of reactive astrocytes into good-vs-bad, neurotoxic vs-neuroprotective or A1-vs.A2.
Journal ArticleDOI
Exploring tissue architecture using spatial transcriptomics.
TL;DR: Spatial transcriptomics can also be used for hypothesis testing using experimental designs that compare time points or conditions, including genetic or environmental perturbations as mentioned in this paper, and is naturally amenable to integration with other data modalities, providing an expandable framework for insight into tissue organization.
Journal ArticleDOI
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
TL;DR: In this paper, a suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue.
Posted ContentDOI
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network.
Jian Hu,Xiangjie Li,Kyle Coleman,Amelia Schroeder,Nan Ma,David J. Irwin,Edward B. Lee,Russell T. Shinohara,Mingyao Li +8 more
TL;DR: Analyzing five spatially resolved transcriptomics datasets using SpaGCN, it is shown it can detect genes with much more enriched spatial expression patterns than existing methods and are transferrable and can be utilized to study spatial variation of gene expression in other datasets.
Journal ArticleDOI
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Kun Leng,Emmy Li,Rana Eser,Antonia M. H. Piergies,Rene Sit,Michelle Tan,Norma Neff,Song Hua Li,Roberta Diehl Rodriguez,Claudia K. Suemoto,Renata Elaine Paraizo Leite,Alexander J. Ehrenberg,Carlos Augusto Pasqualucci,William W. Seeley,Salvatore Spina,Helmut Heinsen,Helmut Heinsen,Lea T. Grinberg,Lea T. Grinberg,Martin Kampmann +19 more
TL;DR: This article identified RORB as a marker of selectively vulnerable excitatory neurons in the entorhinal cortex and subsequently validated their depletion and selective susceptibility to neurofibrillary inclusions during disease progression using quantitative neuropathological methods.
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TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.
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A General Framework for Weighted Gene Co-Expression Network Analysis
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