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Literature DB >> 33434721

Spatially resolved transcriptomics and its applications in cancer.

Silas Maniatis¹, Joana Petrescu², Hemali Phatnani³.

Abstract

Spatially resolved transcriptomics (SRT) offers the promise of understanding cells and their modes of dysfunction in the context of intact tissues. Technologies for SRT have advanced rapidly with a large number being published in recent years. Diverse methods for SRT produce data at widely varying depth, throughput, accessibility and cost. Many published SRT methods have been demonstrated only in their labs of origin, while others have matured to the point of commercialization and widespread availability. Here we review technologies for SRT, and their application in studies of tumor heterogeneity.

Entities: Chemical

Mesh：

Year: 2021 PMID： 33434721 PMCID： PMC7969406 DOI： 10.1016/j.gde.2020.12.002

Source DB: PubMed Journal: Curr Opin Genet Dev ISSN： 0959-437X Impact factor: 5.578

50 in total

1. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.

Authors: Samuel G Rodriques; Robert R Stickels; Aleksandrina Goeva; Carly A Martin; Evan Murray; Charles R Vanderburg; Joshua Welch; Linlin M Chen; Fei Chen; Evan Z Macosko
Journal: Science Date: 2019-03-28 Impact factor: 47.728

2. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Authors: Patrik L Ståhl; Fredrik Salmén; Sanja Vickovic; Anna Lundmark; José Fernández Navarro; Jens Magnusson; Stefania Giacomello; Michaela Asp; Jakub O Westholm; Mikael Huss; Annelie Mollbrink; Sten Linnarsson; Simone Codeluppi; Åke Borg; Fredrik Pontén; Paul Igor Costea; Pelin Sahlén; Jan Mulder; Olaf Bergmann; Joakim Lundeberg; Jonas Frisén
Journal: Science Date: 2016-07-01 Impact factor: 47.728

3. Biomarkers Associated with Beneficial PD-1 Checkpoint Blockade in Non-Small Cell Lung Cancer (NSCLC) Identified Using High-Plex Digital Spatial Profiling.

Authors: Jon Zugazagoitia; Swati Gupta; Yuting Liu; Kit Fuhrman; Scott Gettinger; Roy S Herbst; Kurt A Schalper; David L Rimm
Journal: Clin Cancer Res Date: 2020-04-06 Impact factor: 12.531

4. Multiplex digital spatial profiling of proteins and RNA in fixed tissue.

Authors: Christopher R Merritt; Giang T Ong; Sarah E Church; Kristi Barker; Patrick Danaher; Gary Geiss; Margaret Hoang; Jaemyeong Jung; Yan Liang; Jill McKay-Fleisch; Karen Nguyen; Zach Norgaard; Kristina Sorg; Isaac Sprague; Charles Warren; Sarah Warren; Philippa J Webster; Zoey Zhou; Daniel R Zollinger; Dwayne L Dunaway; Gordon B Mills; Joseph M Beechem
Journal: Nat Biotechnol Date: 2020-05-11 Impact factor: 54.908

5. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Authors: Michaela Asp; Stefania Giacomello; Ludvig Larsson; Chenglin Wu; Daniel Fürth; Xiaoyan Qian; Eva Wärdell; Joaquin Custodio; Johan Reimegård; Fredrik Salmén; Cecilia Österholm; Patrik L Ståhl; Erik Sundström; Elisabet Åkesson; Olaf Bergmann; Magda Bienko; Agneta Månsson-Broberg; Mats Nilsson; Christer Sylvén; Joakim Lundeberg
Journal: Cell Date: 2019-12-12 Impact factor: 41.582

6. The single-cell pathology landscape of breast cancer.

Authors: Hartland W Jackson; Jana R Fischer; Vito R T Zanotelli; H Raza Ali; Robert Mechera; Savas D Soysal; Holger Moch; Simone Muenst; Zsuzsanna Varga; Walter P Weber; Bernd Bodenmiller
Journal: Nature Date: 2020-01-20 Impact factor: 49.962

7. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.

Authors: Jia-Ren Lin; Benjamin Izar; Shu Wang; Clarence Yapp; Shaolin Mei; Parin M Shah; Sandro Santagata; Peter K Sorger
Journal: Elife Date: 2018-07-11 Impact factor: 8.140

Spatially resolved transcriptomics and its applications in cancer.

1. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.

2. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

3. Biomarkers Associated with Beneficial PD-1 Checkpoint Blockade in Non-Small Cell Lung Cancer (NSCLC) Identified Using High-Plex Digital Spatial Profiling.

4. Multiplex digital spatial profiling of proteins and RNA in fixed tissue.

5. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

6. The single-cell pathology landscape of breast cancer.

7. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.

8. Simultaneous epitope and transcriptome measurement in single cells.

9. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.

10. Fusion transcript detection using spatial transcriptomics.

Review 1. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.

Review 2. Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment.

3. Nuclei Detection for 3D Microscopy With a Fully Convolutional Regression Network.

4. Clinical challenges of tissue preparation for spatial transcriptome.

5. An Interactive Pipeline for Quantitative Histopathological Analysis of Spatially Defined Drug Effects in Tumors.

Review 6. Single-Cell Approaches to Deconvolute the Development of HSCs.

Review 7. From bench to bedside: Single-cell analysis for cancer immunotherapy.

8. Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE.

Review 9. Modeling colorectal cancer evolution.

Review 10. Statistical and machine learning methods for spatially resolved transcriptomics data analysis.