Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells
Apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) is involved in the DNA damage repair pathways and associates with the metastasis of several human cancers. However, the signaling pathway of APEX1 in cholangiocarcinoma (CCA) has never been reported. In this study, to predict the signaling pathwa...
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MDPI AG
2021-04-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/9/2587 |
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| author | Doungdean Tummanatsakun Tanakorn Proungvitaya Sittiruk Roytrakul Siriporn Proungvitaya |
| author_facet | Doungdean Tummanatsakun Tanakorn Proungvitaya Sittiruk Roytrakul Siriporn Proungvitaya |
| author_sort | Doungdean Tummanatsakun |
| collection | DOAJ |
| description | Apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) is involved in the DNA damage repair pathways and associates with the metastasis of several human cancers. However, the signaling pathway of APEX1 in cholangiocarcinoma (CCA) has never been reported. In this study, to predict the signaling pathways of APEX1 and related proteins and their functions, the effects of APEX1 gene silencing on APEX1 and related protein expression in CCA cell lines were investigated using mass spectrometry and bioinformatics tools. Bioinformatic analyses predicted that APEX1 might interact with cell division cycle 42 (CDC42) and son of sevenless homolog 1 (SOS1), which are involved in tumor metastasis. RNA and protein expression levels of APEX1 and its related proteins, retrieved from the Gene Expression Profiling Interactive Analysis (GEPIA) and the Human Protein Atlas databases, revealed that their expressions were higher in CCA than in the normal group. Moreover, higher levels of APEX1 expression and its related proteins were correlated with shorter survival time. In conclusion, the signaling pathway of APEX1 in metastasis might be mediated via CDC42 and SOS1. Furthermore, expression of APEX1 and related proteins is able to predict poor survival of CCA patients. |
| first_indexed | 2024-03-10T11:51:15Z |
| format | Article |
| id | doaj.art-8538f258621c41f883798f38c1c9b00f |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T11:51:15Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-8538f258621c41f883798f38c1c9b00f2023-11-21T17:41:47ZengMDPI AGMolecules1420-30492021-04-01269258710.3390/molecules26092587Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma CellsDoungdean Tummanatsakun0Tanakorn Proungvitaya1Sittiruk Roytrakul2Siriporn Proungvitaya3Centre of Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, KhonKaen University, KhonKaen 40002, ThailandCentre of Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, KhonKaen University, KhonKaen 40002, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), Functional Ingredients and Food Innovation Research Group, National Science and Technology Development Agency (NSTDA), Pathumthani 12120, ThailandCentre of Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, KhonKaen University, KhonKaen 40002, ThailandApurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) is involved in the DNA damage repair pathways and associates with the metastasis of several human cancers. However, the signaling pathway of APEX1 in cholangiocarcinoma (CCA) has never been reported. In this study, to predict the signaling pathways of APEX1 and related proteins and their functions, the effects of APEX1 gene silencing on APEX1 and related protein expression in CCA cell lines were investigated using mass spectrometry and bioinformatics tools. Bioinformatic analyses predicted that APEX1 might interact with cell division cycle 42 (CDC42) and son of sevenless homolog 1 (SOS1), which are involved in tumor metastasis. RNA and protein expression levels of APEX1 and its related proteins, retrieved from the Gene Expression Profiling Interactive Analysis (GEPIA) and the Human Protein Atlas databases, revealed that their expressions were higher in CCA than in the normal group. Moreover, higher levels of APEX1 expression and its related proteins were correlated with shorter survival time. In conclusion, the signaling pathway of APEX1 in metastasis might be mediated via CDC42 and SOS1. Furthermore, expression of APEX1 and related proteins is able to predict poor survival of CCA patients.https://www.mdpi.com/1420-3049/26/9/2587APEX1CCAsignaling pathwaymass spectrometrybioinformatics |
| spellingShingle | Doungdean Tummanatsakun Tanakorn Proungvitaya Sittiruk Roytrakul Siriporn Proungvitaya Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells Molecules APEX1 CCA signaling pathway mass spectrometry bioinformatics |
| title | Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells |
| title_full | Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells |
| title_fullStr | Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells |
| title_full_unstemmed | Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells |
| title_short | Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells |
| title_sort | bioinformatic prediction of signaling pathways for apurinic apyrimidinic endodeoxyribonuclease 1 apex1 and its role in cholangiocarcinoma cells |
| topic | APEX1 CCA signaling pathway mass spectrometry bioinformatics |
| url | https://www.mdpi.com/1420-3049/26/9/2587 |
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