Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis

Abstract 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 t...

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Autores principales:	Yin,Hongtao, Yu,Yan
Lenguaje:	English
Publicado:	Sociedad de Biología de Chile 2019
Materias:	Lung adenocarcinoma Hematoporphyrin derivative X-ray Protein–protein interaction network Integrated network
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602019000100203
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spelling	oai:scielo:S0716-976020190001002032019-10-10Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysisYin,HongtaoYu,Yan Lung adenocarcinoma Hematoporphyrin derivative X-ray Protein–protein interaction network Integrated network Abstract 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.info:eu-repo/semantics/openAccessSociedad de Biología de ChileBiological Research v.52 20192019-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602019000100203en10.1186/s40659-019-0213-z
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Lung adenocarcinoma Hematoporphyrin derivative X-ray Protein–protein interaction network Integrated network
spellingShingle	Lung adenocarcinoma Hematoporphyrin derivative X-ray Protein–protein interaction network Integrated network Yin,Hongtao Yu,Yan Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
description	Abstract 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.
author	Yin,Hongtao Yu,Yan
author_facet	Yin,Hongtao Yu,Yan
author_sort	Yin,Hongtao
title	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_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_sort	identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
publisher	Sociedad de Biología de Chile
publishDate	2019
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602019000100203
work_keys_str_mv	AT yinhongtao identificationofthetargetsofhematoporphyrinderivativeinlungadenocarcinomausingintegratednetworkanalysis AT yuyan identificationofthetargetsofhematoporphyrinderivativeinlungadenocarcinomausingintegratednetworkanalysis
_version_	1718441584186359808

Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis

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