Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible lung disorder of unknown cause. This disease is characterized by profibrotic activation of resident pulmonary fibroblasts resulting in aberrant deposition of extracellular matrix (ECM) proteins. However, although much is kno...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/9/5032 |
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| author | Juan Manuel Velázquez-Enríquez Alma Aurora Ramírez-Hernández Luis Manuel Sánchez Navarro Itayetzi Reyes-Avendaño Karina González-García Cristian Jiménez-Martínez Luis Castro-Sánchez Xariss Miryam Sánchez-Chino Verónica Rocío Vásquez-Garzón Rafael Baltiérrez-Hoyos |
| author_facet | Juan Manuel Velázquez-Enríquez Alma Aurora Ramírez-Hernández Luis Manuel Sánchez Navarro Itayetzi Reyes-Avendaño Karina González-García Cristian Jiménez-Martínez Luis Castro-Sánchez Xariss Miryam Sánchez-Chino Verónica Rocío Vásquez-Garzón Rafael Baltiérrez-Hoyos |
| author_sort | Juan Manuel Velázquez-Enríquez |
| collection | DOAJ |
| description | Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible lung disorder of unknown cause. This disease is characterized by profibrotic activation of resident pulmonary fibroblasts resulting in aberrant deposition of extracellular matrix (ECM) proteins. However, although much is known about the pathophysiology of IPF, the cellular and molecular processes that occur and allow aberrant fibroblast activation remain an unmet need. To explore the differentially expressed proteins (DEPs) associated with aberrant activation of these fibroblasts, we used the IPF lung fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2), compared to the normal lung fibroblast cell line CCD19Lu (NL-1). Protein samples were quantified and identified using a label-free quantitative proteomic analysis approach by liquid chromatography-tandem mass spectrometry (LC-MS/MS). DEPs were identified after pairwise comparison, including all experimental groups. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein–Protein Interaction (PPI) network construction were used to interpret the proteomic data. Eighty proteins expressed exclusively in the IPF-1 and IPF-2 clusters were identified. In addition, 19 proteins were identified up-regulated in IPF-1 and 10 in IPF-2; 10 proteins were down-regulated in IPF-1 and 2 in IPF-2 when compared to the NL-1 proteome. Using the search tool for retrieval of interacting genes/proteins (STRING) software, a PPI network was constructed between the DEPs and the 80 proteins expressed exclusively in the IPF-2 and IPF-1 clusters, containing 115 nodes and 136 edges. The 10 hub proteins present in the IPP network were identified using the CytoHubba plugin of the Cytoscape software. GO and KEGG pathway analyses showed that the hub proteins were mainly related to cell adhesion, integrin binding, and hematopoietic cell lineage. Our results provide relevant information on DEPs present in IPF lung fibroblast cell lines when compared to the normal lung fibroblast cell line that could play a key role during IPF pathogenesis. |
| first_indexed | 2024-03-10T04:04:19Z |
| format | Article |
| id | doaj.art-68861dc5404249308d3a26ea34474fde |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T04:04:19Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-68861dc5404249308d3a26ea34474fde2023-11-23T08:26:01ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-05-01239503210.3390/ijms23095032Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell LinesJuan Manuel Velázquez-Enríquez0Alma Aurora Ramírez-Hernández1Luis Manuel Sánchez Navarro2Itayetzi Reyes-Avendaño3Karina González-García4Cristian Jiménez-Martínez5Luis Castro-Sánchez6Xariss Miryam Sánchez-Chino7Verónica Rocío Vásquez-Garzón8Rafael Baltiérrez-Hoyos9Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, MexicoLaboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, MexicoFacultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68020, MexicoLaboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, MexicoLaboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, MexicoDepartamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Zacatenco, Av. Wilfrido Massieu Esq. Cda. Miguel Stampa S/N, Alcaldía Gustavo A. Madero, Mexico City 07738, MexicoConacyt-Centro Universitario de Investigaciones Biomédicas “CUIB”, Universidad de Colima, Colima 28045, MexicoCatedra-Conacyt, Departamento de Salud El Colegio de La Frontera Sur, Unidad Villahermosa, Tabasco 86280, MexicoConacyt-Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, MexicoConacyt-Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, MexicoIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible lung disorder of unknown cause. This disease is characterized by profibrotic activation of resident pulmonary fibroblasts resulting in aberrant deposition of extracellular matrix (ECM) proteins. However, although much is known about the pathophysiology of IPF, the cellular and molecular processes that occur and allow aberrant fibroblast activation remain an unmet need. To explore the differentially expressed proteins (DEPs) associated with aberrant activation of these fibroblasts, we used the IPF lung fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2), compared to the normal lung fibroblast cell line CCD19Lu (NL-1). Protein samples were quantified and identified using a label-free quantitative proteomic analysis approach by liquid chromatography-tandem mass spectrometry (LC-MS/MS). DEPs were identified after pairwise comparison, including all experimental groups. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein–Protein Interaction (PPI) network construction were used to interpret the proteomic data. Eighty proteins expressed exclusively in the IPF-1 and IPF-2 clusters were identified. In addition, 19 proteins were identified up-regulated in IPF-1 and 10 in IPF-2; 10 proteins were down-regulated in IPF-1 and 2 in IPF-2 when compared to the NL-1 proteome. Using the search tool for retrieval of interacting genes/proteins (STRING) software, a PPI network was constructed between the DEPs and the 80 proteins expressed exclusively in the IPF-2 and IPF-1 clusters, containing 115 nodes and 136 edges. The 10 hub proteins present in the IPP network were identified using the CytoHubba plugin of the Cytoscape software. GO and KEGG pathway analyses showed that the hub proteins were mainly related to cell adhesion, integrin binding, and hematopoietic cell lineage. Our results provide relevant information on DEPs present in IPF lung fibroblast cell lines when compared to the normal lung fibroblast cell line that could play a key role during IPF pathogenesis.https://www.mdpi.com/1422-0067/23/9/5032idiopathic pulmonary fibrosisfibroblastsproteomic analysismass spectrometryproteomicsdifferentially expressed proteins |
| spellingShingle | Juan Manuel Velázquez-Enríquez Alma Aurora Ramírez-Hernández Luis Manuel Sánchez Navarro Itayetzi Reyes-Avendaño Karina González-García Cristian Jiménez-Martínez Luis Castro-Sánchez Xariss Miryam Sánchez-Chino Verónica Rocío Vásquez-Garzón Rafael Baltiérrez-Hoyos Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines International Journal of Molecular Sciences idiopathic pulmonary fibrosis fibroblasts proteomic analysis mass spectrometry proteomics differentially expressed proteins |
| title | Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines |
| title_full | Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines |
| title_fullStr | Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines |
| title_full_unstemmed | Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines |
| title_short | Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines |
| title_sort | proteomic analysis reveals differential expression profiles in idiopathic pulmonary fibrosis cell lines |
| topic | idiopathic pulmonary fibrosis fibroblasts proteomic analysis mass spectrometry proteomics differentially expressed proteins |
| url | https://www.mdpi.com/1422-0067/23/9/5032 |
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