Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer
Microtubule-associated proteins (MAPs) play essential roles in cancer development. This study aimed to identify transcriptomic biomarkers among MAP genes for the diagnosis and prognosis of lung cancer by analyzing differential gene expressions and correlations with tumor progression. Gene expression...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/23/14724 |
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| author | Natsaranyatron Singharajkomron Varalee Yodsurang Suthasinee Seephan Sakkarin Kungsukool Supinda Petchjorm Nara Maneeganjanasing Warunyu Promboon Wadsana Dangwilailuck Varisa Pongrakhananon |
| author_facet | Natsaranyatron Singharajkomron Varalee Yodsurang Suthasinee Seephan Sakkarin Kungsukool Supinda Petchjorm Nara Maneeganjanasing Warunyu Promboon Wadsana Dangwilailuck Varisa Pongrakhananon |
| author_sort | Natsaranyatron Singharajkomron |
| collection | DOAJ |
| description | Microtubule-associated proteins (MAPs) play essential roles in cancer development. This study aimed to identify transcriptomic biomarkers among MAP genes for the diagnosis and prognosis of lung cancer by analyzing differential gene expressions and correlations with tumor progression. Gene expression data of patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) from the Cancer Genome Atlas (TCGA) database were used to identify differentially expressed MAP genes (DEMGs). Their prognostic value was evaluated by Kaplan–Meier and Cox regression analysis. Moreover, the relationships between alterations in lung cancer hallmark genes and the expression levels of DEMGs were investigated. The candidate biomarker genes were validated using three independent datasets from the Gene Expression Omnibus (GEO) database and by quantitative reverse transcription polymerase chain reaction (qRT-PCR) on clinical samples. A total of 88 DEMGs were identified from TCGA data. The 20 that showed the highest differential expression were subjected to association analysis with hallmark genes. Genetic alterations in <i>TP53, EGFR, PTEN, NTRK1,</i> and <i>PIK3CA</i> correlated with the expression of most of these DEMGs. Of these, six candidates—<i>NUF2, KIF4A, KIF18B, DLGAP5, NEK2,</i> and <i>LRRK2</i>—were significantly differentially expressed and correlated with the overall survival (OS) of the patients. The mRNA expression profiles of these candidates were consistently verified using three GEO datasets and qRT-PCR on patient lung tissues. The expression levels of <i>NUF2, KIF4A, KIF18B, DLGAP5, NEK2,</i> and <i>LRRK2</i> can serve as diagnostic biomarkers for LUAD and LUSC. Moreover, the first five can serve as prognostic biomarkers for LUAD, while <i>LRRK2</i> can be a prognostic biomarker for LUSC. Our research describes the novel role and potential application of MAP-encoding genes in clinical practice. |
| first_indexed | 2024-03-09T17:46:44Z |
| format | Article |
| id | doaj.art-abbf8d572adf4c2999b1947dd26df855 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T17:46:44Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-abbf8d572adf4c2999b1947dd26df8552023-11-24T11:06:49ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123231472410.3390/ijms232314724Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung CancerNatsaranyatron Singharajkomron0Varalee Yodsurang1Suthasinee Seephan2Sakkarin Kungsukool3Supinda Petchjorm4Nara Maneeganjanasing5Warunyu Promboon6Wadsana Dangwilailuck7Varisa Pongrakhananon8Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandDepartment of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandPharmaceutical Sciences and Technology Graduate Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandRespiratory Medicine Department, Central Chest Institute of Thailand, Muang District, Nonthaburi 11000, ThailandDivision of Anatomical Pathology, Central Chest Institute of Thailand, Muang District, Nonthaburi 11000, ThailandDepartment of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandDepartment of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandDepartment of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandDepartment of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, ThailandMicrotubule-associated proteins (MAPs) play essential roles in cancer development. This study aimed to identify transcriptomic biomarkers among MAP genes for the diagnosis and prognosis of lung cancer by analyzing differential gene expressions and correlations with tumor progression. Gene expression data of patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) from the Cancer Genome Atlas (TCGA) database were used to identify differentially expressed MAP genes (DEMGs). Their prognostic value was evaluated by Kaplan–Meier and Cox regression analysis. Moreover, the relationships between alterations in lung cancer hallmark genes and the expression levels of DEMGs were investigated. The candidate biomarker genes were validated using three independent datasets from the Gene Expression Omnibus (GEO) database and by quantitative reverse transcription polymerase chain reaction (qRT-PCR) on clinical samples. A total of 88 DEMGs were identified from TCGA data. The 20 that showed the highest differential expression were subjected to association analysis with hallmark genes. Genetic alterations in <i>TP53, EGFR, PTEN, NTRK1,</i> and <i>PIK3CA</i> correlated with the expression of most of these DEMGs. Of these, six candidates—<i>NUF2, KIF4A, KIF18B, DLGAP5, NEK2,</i> and <i>LRRK2</i>—were significantly differentially expressed and correlated with the overall survival (OS) of the patients. The mRNA expression profiles of these candidates were consistently verified using three GEO datasets and qRT-PCR on patient lung tissues. The expression levels of <i>NUF2, KIF4A, KIF18B, DLGAP5, NEK2,</i> and <i>LRRK2</i> can serve as diagnostic biomarkers for LUAD and LUSC. Moreover, the first five can serve as prognostic biomarkers for LUAD, while <i>LRRK2</i> can be a prognostic biomarker for LUSC. Our research describes the novel role and potential application of MAP-encoding genes in clinical practice.https://www.mdpi.com/1422-0067/23/23/14724diagnosisgene expressionlung cancermicrotubule-associated proteinsprognosis |
| spellingShingle | Natsaranyatron Singharajkomron Varalee Yodsurang Suthasinee Seephan Sakkarin Kungsukool Supinda Petchjorm Nara Maneeganjanasing Warunyu Promboon Wadsana Dangwilailuck Varisa Pongrakhananon Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer International Journal of Molecular Sciences diagnosis gene expression lung cancer microtubule-associated proteins prognosis |
| title | Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer |
| title_full | Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer |
| title_fullStr | Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer |
| title_full_unstemmed | Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer |
| title_short | Evaluating the Expression and Prognostic Value of Genes Encoding Microtubule-Associated Proteins in Lung Cancer |
| title_sort | evaluating the expression and prognostic value of genes encoding microtubule associated proteins in lung cancer |
| topic | diagnosis gene expression lung cancer microtubule-associated proteins prognosis |
| url | https://www.mdpi.com/1422-0067/23/23/14724 |
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