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Caglar HO, Aytatli A, Barlak N, Aydin Karatas E, Tatar A, Sahin A, Karatas OF. Bioinformatics approach combined with experimental verification reveals OAS3 gene implicated in paclitaxel resistance in head and neck cancer. Head Neck 2024; 46:2178-2196. [PMID: 38752376 DOI: 10.1002/hed.27803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/18/2024] [Accepted: 05/05/2024] [Indexed: 08/09/2024] Open
Abstract
BACKGROUND This study aimed to identify a candidate gene associated with paclitaxel (PTX) resistance and to evaluate functionally its biological role in the PTX-resistant head and neck squamous cell carcinoma (HNSCC) cell lines and clinical specimens. METHODS Microarray data series containing samples of different types of cancers resistant to PTX were analyzed and then a candidate gene associated with PTX resistance was identified using various bioinformatics tools. After the suppression of the target gene expression, changes in cell viability and colony-forming ability were evaluated in PTX-resistant FaDu and SCC-9 cell lines. RESULTS Bioinformatics analyses of upregulated genes in PTX-resistant cancer cells indicated that OAS3 was associated with PTX resistance. The downregulation of OAS3 expression significantly reduced the viability and colony-forming capacity of PTX-resistant SCC-9 cells by inducing apoptosis and cell cycle arrest at G0/G1 phase. CONCLUSIONS The therapeutic targeting of OAS3 may resensitize PTX-resistant HNSCC cells with high OAS3 expression to PTX treatment.
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Affiliation(s)
- Hasan Onur Caglar
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Abdulmelik Aytatli
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Neslisah Barlak
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Elanur Aydin Karatas
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Arzu Tatar
- Department of Otorhinolaryngology Diseases, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Abdulkadir Sahin
- Department of Otorhinolaryngology Diseases, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Omer Faruk Karatas
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
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Bhattacharjya A, Islam MM, Uddin MA, Talukder MA, Azad AKM, Aryal S, Paul BK, Tasnim W, Almoyad MAA, Moni MA. Exploring gene regulatory interaction networks and predicting therapeutic molecules for hypopharyngeal cancer and EGFR-mutated lung adenocarcinoma. FEBS Open Bio 2024; 14:1166-1191. [PMID: 38783639 PMCID: PMC11216941 DOI: 10.1002/2211-5463.13807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Hypopharyngeal cancer is a disease that is associated with EGFR-mutated lung adenocarcinoma. Here we utilized a bioinformatics approach to identify genetic commonalities between these two diseases. To this end, we examined microarray datasets from GEO (Gene Expression Omnibus) to identify differentially expressed genes, common genes, and hub genes between the selected two diseases. Our analyses identified potential therapeutic molecules for the selected diseases based on 10 hub genes with the highest interactions according to the degree topology method and the maximum clique centrality (MCC). These therapeutic molecules may have the potential for simultaneous treatment of these diseases.
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Affiliation(s)
- Abanti Bhattacharjya
- Department of Computer Science and EngineeringJagannath UniversityDhakaBangladesh
| | - Md Manowarul Islam
- Department of Computer Science and EngineeringJagannath UniversityDhakaBangladesh
| | - Md Ashraf Uddin
- School of Information TechnologyDeakin UniversityGeelongAustralia
| | - Md Alamin Talukder
- Department of Computer Science and EngineeringInternational University of Business Agriculture and TechnologyDhakaBangladesh
| | - AKM Azad
- Department of Mathematics and Statistics, Faculty of ScienceImam Mohammad Ibn Saud Islamic University (IMSIU)RiyadhSaudi Arabia
| | - Sunil Aryal
- School of Information TechnologyDeakin UniversityGeelongAustralia
| | - Bikash Kumar Paul
- Department of Information and Communication TechnologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
- Department of Software EngineeringDaffodil International UniversityDhakaBangladesh
| | - Wahia Tasnim
- Department of Information and Communication TechnologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | | | - Mohammad Ali Moni
- Artificial Intelligence & Data Science, Faculty of Health and Behavioural SciencesThe University of QueenslandBrisbaneAustralia
- AI & Digital Health Technology, Artificial Intelligence and Cyber Futures InstituteCharles Sturt UniversityBathurstAustralia
- Rural Health Research InstituteCharles Sturt UniversityOrangeAustralia
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Wu G, Wang D, Xiong F, Wang Q, Liu W, Chen J, Chen Y. The emerging roles of CEACAM6 in human cancer (Review). Int J Oncol 2024; 64:27. [PMID: 38240103 PMCID: PMC10836497 DOI: 10.3892/ijo.2024.5615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Carcinoembryonic antigen (CEA)‑related cell adhesion molecule 6 (CEACAM6) is a cell adhesion protein of the CEA family of glycosyl phosphatidyl inositol anchored cell surface glycoproteins. A wealth of research has demonstrated that CEACAM6 is generally upregulated in pancreatic adenocarcinoma, breast cancer, non‑small cell lung cancer, gastric cancer, colon cancer and other cancers and promotes tumor progression, invasion and metastasis. The transcriptional expression of CEACAM6 is regulated by various factors, including the CD151/TGF‑β1/Smad3 axis, microRNA (miR)‑146, miR‑26a, miR‑29a/b/c, miR‑128, miR‑1256 and DNA methylation. In addition, the N‑glycosylation of CEACAM6 protein at Asn256 is mediated by α‑1,6‑mannosylglycoptotein 6‑β‑N‑acetylglucosaminyltransferase. In terms of downstream signaling pathways, CEACAM6 promotes tumor proliferation by increasing levels of cyclin D1 and cyclin‑dependent kinase 4 proteins. CEACAM6 can activate the ERK1/2/MAPK or SRC/focal adhesion kinase/PI3K/AKT pathways directly or through EGFR, leading to stimulation of tumor proliferation, invasion, migration, resistance to anoikis and chemotherapy, as well as angiogenesis. This article provides a review of the expression pattern, biological function and relationship with prognosis of CEACAM6 in cancer. In summary, CEACAM6 may be a valuable diagnostic biomarker and potential therapeutic target for human cancers exhibiting overexpression of CEACAM6.
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Affiliation(s)
- Guanhua Wu
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Da Wang
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Fei Xiong
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Qi Wang
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Wenzheng Liu
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Junsheng Chen
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yongjun Chen
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
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Arfin S, Kumar D, Lomagno A, Mauri PL, Di Silvestre D. Differentially Expressed Genes, miRNAs and Network Models: A Strategy to Shed Light on Molecular Interactions Driving HNSCC Tumorigenesis. Cancers (Basel) 2023; 15:4420. [PMID: 37686696 PMCID: PMC10563081 DOI: 10.3390/cancers15174420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is among the most common cancer worldwide, accounting for hundreds thousands deaths annually. Unfortunately, most patients are diagnosed in an advanced stage and only a percentage respond favorably to therapies. To help fill this gap, we hereby propose a retrospective in silico study to shed light on gene-miRNA interactions driving the development of HNSCC. Moreover, to identify topological biomarkers as a source for designing new drugs. To achieve this, gene and miRNA profiles from patients and controls are holistically reevaluated using protein-protein interaction (PPI) and bipartite miRNA-target networks. Cytoskeletal remodeling, extracellular matrix (ECM), immune system, proteolysis, and energy metabolism have emerged as major functional modules involved in the pathogenesis of HNSCC. Of note, the landscape of our findings depicts a concerted molecular action in activating genes promoting cell cycle and proliferation, and inactivating those suppressive. In this scenario, genes, including VEGFA, EMP1, PPL, KRAS, MET, TP53, MMPs and HOXs, and miRNAs, including mir-6728 and mir-99a, emerge as key players in the molecular interactions driving HNSCC tumorigenesis. Despite the heterogeneity characterizing these HNSCC subtypes, and the limitations of a study pointing to relationships that could be context dependent, the overlap with previously published studies is encouraging. Hence, it supports further investigation for key molecules, both those already and not correlated to HNSCC.
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Affiliation(s)
- Saniya Arfin
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, Uttrakhand, India; (S.A.); (D.K.)
| | - Dhruv Kumar
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, Uttrakhand, India; (S.A.); (D.K.)
| | - Andrea Lomagno
- Institute for Biomedical Technologies, National Research Council, F.lli Cervi 93, Segrate, 20054 Milan, Italy; (A.L.); (P.L.M.)
- IRCCS Foundation, Istituto Nazionale dei Tumori, Via Venezian, 1, 20133 Milan, Italy
| | - Pietro Luigi Mauri
- Institute for Biomedical Technologies, National Research Council, F.lli Cervi 93, Segrate, 20054 Milan, Italy; (A.L.); (P.L.M.)
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council, F.lli Cervi 93, Segrate, 20054 Milan, Italy; (A.L.); (P.L.M.)
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