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Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics

Increasing evidence strongly supports the key role of the tumour microenvironment in response to systemic therapy, particularly immune checkpoint inhibitors (ICIs). The tumour microenvironment is a complex tapestry of immune cells, some of which can suppress T-cell immunity to negatively impact ICI...

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Autores principales: Shek, Dmitrii, Gloss, Brian, Lai, Joey, Ma, Li, Zhang, Hui E., Carlino, Matteo S., Mahajan, Hema, Nagrial, Adnan, Gao, Bo, Read, Scott A., Ahlenstiel, Golo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10146955/
https://www.ncbi.nlm.nih.gov/pubmed/37104017
http://dx.doi.org/10.3390/mps6020035
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author Shek, Dmitrii
Gloss, Brian
Lai, Joey
Ma, Li
Zhang, Hui E.
Carlino, Matteo S.
Mahajan, Hema
Nagrial, Adnan
Gao, Bo
Read, Scott A.
Ahlenstiel, Golo
author_facet Shek, Dmitrii
Gloss, Brian
Lai, Joey
Ma, Li
Zhang, Hui E.
Carlino, Matteo S.
Mahajan, Hema
Nagrial, Adnan
Gao, Bo
Read, Scott A.
Ahlenstiel, Golo
author_sort Shek, Dmitrii
collection PubMed
description Increasing evidence strongly supports the key role of the tumour microenvironment in response to systemic therapy, particularly immune checkpoint inhibitors (ICIs). The tumour microenvironment is a complex tapestry of immune cells, some of which can suppress T-cell immunity to negatively impact ICI therapy. The immune component of the tumour microenvironment, although poorly understood, has the potential to reveal novel insights that can impact the efficacy and safety of ICI therapy. Successful identification and validation of these factors using cutting-edge spatial and single-cell technologies may enable the development of broad acting adjunct therapies as well as personalised cancer immunotherapies in the near future. In this paper we describe a protocol built upon Visium (10x Genomics) spatial transcriptomics to map and characterise the tumour-infiltrating immune microenvironment in malignant pleural mesothelioma. Using ImSig tumour-specific immune cell gene signatures and BayesSpace Bayesian statistical methodology, we were able to significantly improve immune cell identification and spatial resolution, respectively, improving our ability to analyse immune cell interactions within the tumour microenvironment.
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spelling pubmed-101469552023-04-29 Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics Shek, Dmitrii Gloss, Brian Lai, Joey Ma, Li Zhang, Hui E. Carlino, Matteo S. Mahajan, Hema Nagrial, Adnan Gao, Bo Read, Scott A. Ahlenstiel, Golo Methods Protoc Protocol Increasing evidence strongly supports the key role of the tumour microenvironment in response to systemic therapy, particularly immune checkpoint inhibitors (ICIs). The tumour microenvironment is a complex tapestry of immune cells, some of which can suppress T-cell immunity to negatively impact ICI therapy. The immune component of the tumour microenvironment, although poorly understood, has the potential to reveal novel insights that can impact the efficacy and safety of ICI therapy. Successful identification and validation of these factors using cutting-edge spatial and single-cell technologies may enable the development of broad acting adjunct therapies as well as personalised cancer immunotherapies in the near future. In this paper we describe a protocol built upon Visium (10x Genomics) spatial transcriptomics to map and characterise the tumour-infiltrating immune microenvironment in malignant pleural mesothelioma. Using ImSig tumour-specific immune cell gene signatures and BayesSpace Bayesian statistical methodology, we were able to significantly improve immune cell identification and spatial resolution, respectively, improving our ability to analyse immune cell interactions within the tumour microenvironment. MDPI 2023-03-28 /pmc/articles/PMC10146955/ /pubmed/37104017 http://dx.doi.org/10.3390/mps6020035 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocol
Shek, Dmitrii
Gloss, Brian
Lai, Joey
Ma, Li
Zhang, Hui E.
Carlino, Matteo S.
Mahajan, Hema
Nagrial, Adnan
Gao, Bo
Read, Scott A.
Ahlenstiel, Golo
Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics
title Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics
title_full Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics
title_fullStr Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics
title_full_unstemmed Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics
title_short Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics
title_sort identification and characterisation of infiltrating immune cells in malignant pleural mesothelioma using spatial transcriptomics
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10146955/
https://www.ncbi.nlm.nih.gov/pubmed/37104017
http://dx.doi.org/10.3390/mps6020035
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