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Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus

In this study we analyzed gene co-expression networks of three immune-related skin diseases: cutaneous sarcoidosis (CS), discoid lupus erythematosus (DLE), and psoriasis. We propose that investigation of gene co-expression networks may provide insights into underlying disease mechanisms. Microarray...

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Autores principales: Nickles, Melissa A., Huang, Kai, Chang, Yi-Shin, Tsoukas, Maria M., Sweiss, Nadera J., Perkins, David L., Finn, Patricia W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724034/
https://www.ncbi.nlm.nih.gov/pubmed/33324666
http://dx.doi.org/10.3389/fmed.2020.606461
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author Nickles, Melissa A.
Huang, Kai
Chang, Yi-Shin
Tsoukas, Maria M.
Sweiss, Nadera J.
Perkins, David L.
Finn, Patricia W.
author_facet Nickles, Melissa A.
Huang, Kai
Chang, Yi-Shin
Tsoukas, Maria M.
Sweiss, Nadera J.
Perkins, David L.
Finn, Patricia W.
author_sort Nickles, Melissa A.
collection PubMed
description In this study we analyzed gene co-expression networks of three immune-related skin diseases: cutaneous sarcoidosis (CS), discoid lupus erythematosus (DLE), and psoriasis. We propose that investigation of gene co-expression networks may provide insights into underlying disease mechanisms. Microarray expression data from two cohorts of patients with CS, DLE, or psoriasis skin lesions were analyzed. We applied weighted gene correlation network analysis (WGCNA) to construct gene-gene similarity networks and cluster genes into modules based on similar expression profiles. A module of interest that was preserved between datasets and corresponded with case/control status was identified. This module was related to immune activation, specifically leukocyte activation, and was significantly increased in both CS lesions and DLE lesions compared to their respective controls. Protein-protein interaction (PPI) networks constructed for this module revealed seven common hub genes between CS lesions and DLE lesions: TLR1, ITGAL, TNFRSF1B, CD86, SPI1, BTK, and IL10RA. Common hub genes were highly upregulated in CS lesions and DLE lesions compared to their respective controls in a differential expression analysis. Our results indicate common gene expression patterns in the immune processes of CS and DLE, which may have indications for future therapeutic targets and serve as Th1-mediated disease biomarkers. Additionally, we identified hub genes unique to CS and DLE, which can help differentiate these diseases from one another and may serve as unique therapeutic targets and biomarkers. Notably, we find common gene expression patterns in the immune processes of CS and DLE through utilization of WGCNA.
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spelling pubmed-77240342020-12-14 Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus Nickles, Melissa A. Huang, Kai Chang, Yi-Shin Tsoukas, Maria M. Sweiss, Nadera J. Perkins, David L. Finn, Patricia W. Front Med (Lausanne) Medicine In this study we analyzed gene co-expression networks of three immune-related skin diseases: cutaneous sarcoidosis (CS), discoid lupus erythematosus (DLE), and psoriasis. We propose that investigation of gene co-expression networks may provide insights into underlying disease mechanisms. Microarray expression data from two cohorts of patients with CS, DLE, or psoriasis skin lesions were analyzed. We applied weighted gene correlation network analysis (WGCNA) to construct gene-gene similarity networks and cluster genes into modules based on similar expression profiles. A module of interest that was preserved between datasets and corresponded with case/control status was identified. This module was related to immune activation, specifically leukocyte activation, and was significantly increased in both CS lesions and DLE lesions compared to their respective controls. Protein-protein interaction (PPI) networks constructed for this module revealed seven common hub genes between CS lesions and DLE lesions: TLR1, ITGAL, TNFRSF1B, CD86, SPI1, BTK, and IL10RA. Common hub genes were highly upregulated in CS lesions and DLE lesions compared to their respective controls in a differential expression analysis. Our results indicate common gene expression patterns in the immune processes of CS and DLE, which may have indications for future therapeutic targets and serve as Th1-mediated disease biomarkers. Additionally, we identified hub genes unique to CS and DLE, which can help differentiate these diseases from one another and may serve as unique therapeutic targets and biomarkers. Notably, we find common gene expression patterns in the immune processes of CS and DLE through utilization of WGCNA. Frontiers Media S.A. 2020-11-25 /pmc/articles/PMC7724034/ /pubmed/33324666 http://dx.doi.org/10.3389/fmed.2020.606461 Text en Copyright © 2020 Nickles, Huang, Chang, Tsoukas, Sweiss, Perkins and Finn. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Medicine
Nickles, Melissa A.
Huang, Kai
Chang, Yi-Shin
Tsoukas, Maria M.
Sweiss, Nadera J.
Perkins, David L.
Finn, Patricia W.
Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
title Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
title_full Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
title_fullStr Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
title_full_unstemmed Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
title_short Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
title_sort gene co-expression networks identifies common hub genes between cutaneous sarcoidosis and discoid lupus erythematosus
topic Medicine
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724034/
https://www.ncbi.nlm.nih.gov/pubmed/33324666
http://dx.doi.org/10.3389/fmed.2020.606461
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