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Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
BACKGROUND: Hematoporphyrin derivative (HPD) has a sensibilization effect in lung adenocarcinoma. This study was conducted to identify the target genes of HPD in lung adenocarcinoma. METHODS: RNA sequencing was performed using the lung adenocarcinoma cell line A549 after no treatment or treatment wi...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360726/ https://www.ncbi.nlm.nih.gov/pubmed/30717818 http://dx.doi.org/10.1186/s40659-019-0213-z |
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author | Yin, Hongtao Yu, Yan |
author_facet | Yin, Hongtao Yu, Yan |
author_sort | Yin, Hongtao |
collection | PubMed |
description | BACKGROUND: Hematoporphyrin derivative (HPD) has a sensibilization effect in lung adenocarcinoma. This study was conducted to identify the target genes of HPD in lung adenocarcinoma. METHODS: RNA sequencing was performed using the lung adenocarcinoma cell line A549 after no treatment or treatment with X-ray or X-ray + HPD. The differentially expressed genes (DEGs) were screened using Mfuzz package by noise-robust soft clustering analysis. Enrichment analysis was carried out using “BioCloud” online tool. Protein–protein interaction (PPI) network and module analyses were performed using Cytoscape software. Using WebGestalt tool and integrated transcription factor platform (ITFP), microRNA target and transcription factor (TF) target pairs were separately predicted. An integrated regulatory network was visualized with Cytoscape software. RESULTS: A total of 815 DEGs in the gene set G1 (continuously dysregulated genes along with changes in processing conditions [untreated—treated with X-ray—X-ray + treated with HPD]) and 464 DEGs in the gene set G2 (significantly dysregulated between X-ray + HPD-treated group and untreated/X-ray-treated group) were screened. The significant module identified from the PPI network for gene set G1 showed that ribosomal protein L3 (RPL3) gene could interact with heat shock protein 90 kDa alpha, class A member 1 (HSP90AA1). TFs AAA domain containing 2 (ATAD2) and protein inhibitor of activated STAT 1 (PIAS1) were separately predicted for the genes in gene set G1 and G2, respectively. In the integrated network for gene set G2, ubiquitin-specific peptidase 25 (USP25) was targeted by miR-200b, miR-200c, and miR-429. CONCLUSION: RPL3, HSP90AA1, ATAD2, and PIAS1 as well as USP25, which is targeted by miR-200b, miR-200c, and miR-429, may be the potential targets of HPD in lung adenocarcinoma. |
format | Online Article Text |
id | pubmed-6360726 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63607262019-02-08 Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis Yin, Hongtao Yu, Yan Biol Res Research Article BACKGROUND: Hematoporphyrin derivative (HPD) has a sensibilization effect in lung adenocarcinoma. This study was conducted to identify the target genes of HPD in lung adenocarcinoma. METHODS: RNA sequencing was performed using the lung adenocarcinoma cell line A549 after no treatment or treatment with X-ray or X-ray + HPD. The differentially expressed genes (DEGs) were screened using Mfuzz package by noise-robust soft clustering analysis. Enrichment analysis was carried out using “BioCloud” online tool. Protein–protein interaction (PPI) network and module analyses were performed using Cytoscape software. Using WebGestalt tool and integrated transcription factor platform (ITFP), microRNA target and transcription factor (TF) target pairs were separately predicted. An integrated regulatory network was visualized with Cytoscape software. RESULTS: A total of 815 DEGs in the gene set G1 (continuously dysregulated genes along with changes in processing conditions [untreated—treated with X-ray—X-ray + treated with HPD]) and 464 DEGs in the gene set G2 (significantly dysregulated between X-ray + HPD-treated group and untreated/X-ray-treated group) were screened. The significant module identified from the PPI network for gene set G1 showed that ribosomal protein L3 (RPL3) gene could interact with heat shock protein 90 kDa alpha, class A member 1 (HSP90AA1). TFs AAA domain containing 2 (ATAD2) and protein inhibitor of activated STAT 1 (PIAS1) were separately predicted for the genes in gene set G1 and G2, respectively. In the integrated network for gene set G2, ubiquitin-specific peptidase 25 (USP25) was targeted by miR-200b, miR-200c, and miR-429. CONCLUSION: RPL3, HSP90AA1, ATAD2, and PIAS1 as well as USP25, which is targeted by miR-200b, miR-200c, and miR-429, may be the potential targets of HPD in lung adenocarcinoma. BioMed Central 2019-02-04 /pmc/articles/PMC6360726/ /pubmed/30717818 http://dx.doi.org/10.1186/s40659-019-0213-z Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Yin, Hongtao Yu, Yan Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
title | Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
title_full | Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
title_fullStr | Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
title_full_unstemmed | Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
title_short | Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
title_sort | identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360726/ https://www.ncbi.nlm.nih.gov/pubmed/30717818 http://dx.doi.org/10.1186/s40659-019-0213-z |
work_keys_str_mv | AT yinhongtao identificationofthetargetsofhematoporphyrinderivativeinlungadenocarcinomausingintegratednetworkanalysis AT yuyan identificationofthetargetsofhematoporphyrinderivativeinlungadenocarcinomausingintegratednetworkanalysis |