Literature DB >> 33826920

Applicability of spatial transcriptional profiling to cancer research.

Rania Bassiouni1, Lee D Gibbs1, David W Craig1, John D Carpten1, Troy A McEachron2.   

Abstract

Spatial transcriptional profiling provides gene expression information within the important anatomical context of tissue architecture. This approach is well suited to characterizing solid tumors, which develop within a complex landscape of malignant cells, immune cells, and stroma. In a single assay, spatial transcriptional profiling can interrogate the role of spatial relationships among these cell populations as well as reveal spatial patterns of relevant oncogenic genetic events. The broad utility of this approach is reflected in the array of strategies that have been developed for its implementation as well as in the recent commercial development of several profiling platforms. The flexibility to apply these technologies to both hypothesis-driven and discovery-driven studies allows widespread applicability in research settings. This review discusses available technologies for spatial transcriptional profiling and several applications for their use in cancer research. Published by Elsevier Inc.

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Year:  2021        PMID： 33826920      PMCID： PMC8052283          DOI： 10.1016/j.molcel.2021.03.016

Source DB:  PubMed          Journal:  Mol Cell        ISSN： 1097-2765            Impact factor:   17.970


  59 in total

1.  DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence.

Authors:  Qianqian Song; Jing Su
Journal:  Brief Bioinform       Date:  2021-01-22       Impact factor: 11.622

Review 2.  The role of cytogenetics and molecular diagnostics in the diagnosis of soft-tissue tumors.

Authors:  Julia A Bridge
Journal:  Mod Pathol       Date:  2014-01       Impact factor: 7.842

3.  Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.

Authors:  Kim Thrane; Hanna Eriksson; Jonas Maaskola; Johan Hansson; Joakim Lundeberg
Journal:  Cancer Res       Date:  2018-08-28       Impact factor: 12.701

4.  SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.

Authors:  Marc Elosua-Bayes; Paula Nieto; Elisabetta Mereu; Ivo Gut; Holger Heyn
Journal:  Nucleic Acids Res       Date:  2021-05-21       Impact factor: 16.971

5.  Multiplexed ion beam imaging of human breast tumors.

Authors:  Michael Angelo; Sean C Bendall; Rachel Finck; Matthew B Hale; Chuck Hitzman; Alexander D Borowsky; Richard M Levenson; John B Lowe; Scot D Liu; Shuchun Zhao; Yasodha Natkunam; Garry P Nolan
Journal:  Nat Med       Date:  2014-03-02       Impact factor: 53.440

6.  mRNA transcript quantification in archival samples using multiplexed, color-coded probes.

Authors:  Patricia P Reis; Levi Waldron; Rashmi S Goswami; Wei Xu; Yali Xuan; Bayardo Perez-Ordonez; Patrick Gullane; Jonathan Irish; Igor Jurisica; Suzanne Kamel-Reid
Journal:  BMC Biotechnol       Date:  2011-05-09       Impact factor: 2.563

7.  High dose-rate brachytherapy of localized prostate cancer converts tumors from cold to hot.

Authors:  Simon P Keam; Heloise Halse; Thu Nguyen; Minyu Wang; Nicolas Van Kooten Losio; Catherine Mitchell; Franco Caramia; David J Byrne; Sue Haupt; Georgina Ryland; Phillip K Darcy; Shahneen Sandhu; Piers Blombery; Ygal Haupt; Scott G Williams; Paul J Neeson
Journal:  J Immunother Cancer       Date:  2020-06       Impact factor: 13.751

8.  Determining cell type abundance and expression from bulk tissues with digital cytometry.

Authors:  Aaron M Newman; Chloé B Steen; Chih Long Liu; Andrew J Gentles; Aadel A Chaudhuri; Florian Scherer; Michael S Khodadoust; Mohammad S Esfahani; Bogdan A Luca; David Steiner; Maximilian Diehn; Ash A Alizadeh
Journal:  Nat Biotechnol       Date:  2019-05-06       Impact factor: 54.908

9.  Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography.

Authors:  Alma Andersson; Joseph Bergenstråhle; Michaela Asp; Ludvig Bergenstråhle; Aleksandra Jurek; José Fernández Navarro; Joakim Lundeberg
Journal:  Commun Biol       Date:  2020-10-09

10.  Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

Authors:  Xiao Wang; William E Allen; Matthew A Wright; Emily L Sylwestrak; Nikolay Samusik; Sam Vesuna; Kathryn Evans; Cindy Liu; Charu Ramakrishnan; Jia Liu; Garry P Nolan; Felice-Alessio Bava; Karl Deisseroth
Journal:  Science       Date:  2018-06-21       Impact factor: 47.728
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  6 in total

Review 1.  Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment.

Authors:  Kate Bridges; Kathryn Miller-Jensen
Journal:  Front Immunol       Date:  2022-04-28       Impact factor: 8.786

2.  Identifying tumor cells at the single-cell level using machine learning.

Authors:  Jan Dohmen; Artem Baranovskii; Jonathan Ronen; Bora Uyar; Vedran Franke; Altuna Akalin
Journal:  Genome Biol       Date:  2022-05-30       Impact factor: 17.906

Review 3.  High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy.

Authors:  Camelia Quek; Xinyu Bai; Georgina V Long; Richard A Scolyer; James S Wilmott
Journal:  Genes (Basel)       Date:  2021-10-16       Impact factor: 4.096

Review 4.  Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology.

Authors:  Tushar Garg; Clifford R Weiss; Rahul A Sheth
Journal:  Cancers (Basel)       Date:  2022-07-26       Impact factor: 6.575

5.  Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning.

Authors:  Yuzhou Chang; Fei He; Juexin Wang; Shuo Chen; Jingyi Li; Jixin Liu; Yang Yu; Li Su; Anjun Ma; Carter Allen; Yu Lin; Shaoli Sun; Bingqiang Liu; José Javier Otero; Dongjun Chung; Hongjun Fu; Zihai Li; Dong Xu; Qin Ma
Journal:  Comput Struct Biotechnol J       Date:  2022-08-24       Impact factor: 6.155

Review 6.  Statistical and machine learning methods for spatially resolved transcriptomics data analysis.

Authors:  Zexian Zeng; Yawei Li; Yiming Li; Yuan Luo
Journal:  Genome Biol       Date:  2022-03-25       Impact factor: 13.583
  6 in total

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