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Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis

A subset of patients with mycosis fungoides (MF) progress to the tumor stage, which correlates with a worse clinical outcome. The molecular events driving this progression are not well-understood. To identify the key molecular drivers, we performed gene expression profiling (GEP) using NanoString. T...

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Autores principales: Lai, Justine, Li, Jing, Gniadecki, Robert, Lai, Raymond
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8621072/
https://www.ncbi.nlm.nih.gov/pubmed/34831413
http://dx.doi.org/10.3390/cells10113190
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author Lai, Justine
Li, Jing
Gniadecki, Robert
Lai, Raymond
author_facet Lai, Justine
Li, Jing
Gniadecki, Robert
Lai, Raymond
author_sort Lai, Justine
collection PubMed
description A subset of patients with mycosis fungoides (MF) progress to the tumor stage, which correlates with a worse clinical outcome. The molecular events driving this progression are not well-understood. To identify the key molecular drivers, we performed gene expression profiling (GEP) using NanoString. Ten formalin-fixed/paraffin-embedded skin biopsies from six patients (six non-tumor and four tumor MF) were included; non-tumor and tumor samples were available in three patients. Laser capture/single cell microdissection of epidermotropic MF cells was used for non-tumor cases. We found that the RNA extracted from 700–800 single cells was consistently sufficient for GEP, provided that multiplexed target enrichment amplification was used. An un-supervised/hierarchical analysis revealed clustering of non-tumor and tumor cases. Many of the most upregulated or downregulated genes are implicated in the PI3K, RAS, cell cycle/apoptosis and MAPK pathways. Two of the targets, HMGA1 and PTPN11 (encodes SHP2), were validated using immunohistochemistry. HMGA1 was positive in six out of six non-tumor MF samples and negative in five out of five tumor MF samples. An opposite pattern was seen with SHP2. Our study has provided a proof-of-concept that single-cell microdissection/GEP can be applied to archival tissues. Some of our identified gene targets might be key drivers of the disease progression of MF.
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spelling pubmed-86210722021-11-27 Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis Lai, Justine Li, Jing Gniadecki, Robert Lai, Raymond Cells Article A subset of patients with mycosis fungoides (MF) progress to the tumor stage, which correlates with a worse clinical outcome. The molecular events driving this progression are not well-understood. To identify the key molecular drivers, we performed gene expression profiling (GEP) using NanoString. Ten formalin-fixed/paraffin-embedded skin biopsies from six patients (six non-tumor and four tumor MF) were included; non-tumor and tumor samples were available in three patients. Laser capture/single cell microdissection of epidermotropic MF cells was used for non-tumor cases. We found that the RNA extracted from 700–800 single cells was consistently sufficient for GEP, provided that multiplexed target enrichment amplification was used. An un-supervised/hierarchical analysis revealed clustering of non-tumor and tumor cases. Many of the most upregulated or downregulated genes are implicated in the PI3K, RAS, cell cycle/apoptosis and MAPK pathways. Two of the targets, HMGA1 and PTPN11 (encodes SHP2), were validated using immunohistochemistry. HMGA1 was positive in six out of six non-tumor MF samples and negative in five out of five tumor MF samples. An opposite pattern was seen with SHP2. Our study has provided a proof-of-concept that single-cell microdissection/GEP can be applied to archival tissues. Some of our identified gene targets might be key drivers of the disease progression of MF. MDPI 2021-11-16 /pmc/articles/PMC8621072/ /pubmed/34831413 http://dx.doi.org/10.3390/cells10113190 Text en © 2021 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 Article
Lai, Justine
Li, Jing
Gniadecki, Robert
Lai, Raymond
Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis
title Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis
title_full Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis
title_fullStr Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis
title_full_unstemmed Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis
title_short Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage—A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis
title_sort gene expression profiling of mycosis fungoides in early and tumor stage—a proof-of-concept study using laser capture/single cell microdissection and nanostring analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8621072/
https://www.ncbi.nlm.nih.gov/pubmed/34831413
http://dx.doi.org/10.3390/cells10113190
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