Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease

Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorp...

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Detalles Bibliográficos
Autores principales: Kuswanto, Wilson, Nolan, Garry, Lu, Guolan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2022
Materias:
Review
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9684921/
https://www.ncbi.nlm.nih.gov/pubmed/36414691
http://dx.doi.org/10.1007/s00281-022-00974-0
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author Kuswanto, Wilson
Nolan, Garry
Lu, Guolan
author_facet Kuswanto, Wilson
Nolan, Garry
Lu, Guolan
author_sort Kuswanto, Wilson
collection PubMed
description Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling.
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spelling pubmed-96849212022-11-28 Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease Kuswanto, Wilson Nolan, Garry Lu, Guolan Semin Immunopathol Review Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling. Springer Berlin Heidelberg 2022-11-21 2023 /pmc/articles/PMC9684921/ /pubmed/36414691 http://dx.doi.org/10.1007/s00281-022-00974-0 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Review
Kuswanto, Wilson
Nolan, Garry
Lu, Guolan
Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
title Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
title_full Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
title_fullStr Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
title_full_unstemmed Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
title_short Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease
title_sort highly multiplexed spatial profiling with codex: bioinformatic analysis and application in human disease
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9684921/
https://www.ncbi.nlm.nih.gov/pubmed/36414691
http://dx.doi.org/10.1007/s00281-022-00974-0
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