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He J, Zhu X, Xu K, Li Y, Zhou J. Network toxicological and molecular docking to investigate the mechanisms of toxicity of agricultural chemical Thiabendazole. CHEMOSPHERE 2024; 363:142711. [PMID: 38964723 DOI: 10.1016/j.chemosphere.2024.142711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Food safety is closely linked to human health. Thiabendazole is widely used as a fungicide and deodorant on agricultural products like vegetables and fruits to prevent fungal infections during transport and storage. This study aims to investigate the toxicity and potential mechanisms of Thiabendazole using novel network toxicology and molecular docking techniques. First, the ADMETlab2.0 and ADMETsar databases, along with literature, predicted Thiabendazole's potential to induce cancer and liver damage. Disease target libraries were constructed using GeneCards and TCMIP databases, while Thiabendazole target libraries were constructed using Swiss Target Prediction and TCMIP databases. The Venn database identified potential targets associated with Thiabendazole-induced cancer and liver injury. Protein-protein interaction (PPI) networks were derived from the STRING database, and gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways were obtained from the DAVID database. Molecular docking assessed the binding affinity between Thiabendazole and core targets. The study revealed 29 potential targets for Thiabendazole-induced cancer and 30 potential targets for liver injury. PPI identified 5 core targets for Thiabendazole-induced cancers and 4 core targets for induced liver injury. KEGG analysis indicated that Thiabendazole might induce gastric and prostate cancer via cyclin-dependent kinase 2 (CDK2) and epidermal growth factor receptor (EGFR) targets, and liver injury through the same targets, with the p53 signaling pathway being central. GO analysis indicated that Thiabendazole-induced cancers and liver injuries were related to mitotic cell cycle G2/M transition and DNA replication. Molecular docking showed stable binding of Thiabendazole with core targets including CDK1, CDK2, EGFR, and checkpoint kinase 1 (CHEK1). These findings suggest Thiabendazole may affect the G2/M transition of the mitotic cell cycle through the p53 signaling pathway, potentially inducing cancer and liver injury. This study provides a theoretical basis for understanding the potential molecular mechanisms underlying Thiabendazole toxicity, aiding in the prevention and treatment of related diseases. Additionally, the network toxicology approach accelerates the elucidation of toxic pathways for uncharacterized agricultural chemicals.
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Affiliation(s)
- Junhui He
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products/Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530006, China; Department of Pharmacology, Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Naning, 530022, China.
| | - Xiufang Zhu
- School of Material Science and Engineering, Hubei University of Automotive Technology, Shiyan, 442000, China
| | - Kaimeng Xu
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming, 650224, China
| | - Ye Li
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Juying Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products/Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530006, China.
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Kaur E, Agrawal R, Arun R, Madhavan V, Srivastava V, Kumar D, Rath PP, Kumar N, Vedagopuram S, Pandey N, Priya S, Legembre P, Gourinath S, Bajaj A, Sengupta S. Small molecules that disrupt RAD54-BLM interaction hamper tumor proliferation in colon cancer chemoresistance models. J Clin Invest 2024; 134:e161941. [PMID: 38421735 PMCID: PMC11014671 DOI: 10.1172/jci161941] [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: 08/04/2022] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
RAD54 and BLM helicase play pivotal roles during homologous recombination repair (HRR) to ensure genome maintenance. BLM amino acids (aa 181-212) interact with RAD54 and enhance its chromatin remodeling activity. Functionally, this interaction heightens HRR, leading to a decrease in residual DNA damage in colon cancer cells. This contributes to chemoresistance in colon cancer cells against cisplatin, camptothecin, and oxaliplatin, eventually promoting tumorigenesis in preclinical colon cancer mouse models. ChIP-Seq analysis and validation revealed increased BLM and RAD54 corecruitment on the MRP2 promoter in camptothecin-resistant colon cancer cells, leading to BLM-dependent enhancement of RAD54-mediated chromatin remodeling. We screened the Prestwick small-molecule library, with the intent to revert camptothecin- and oxaliplatin-induced chemoresistance by disrupting the RAD54-BLM interaction. Three FDA/European Medicines Agency-approved candidates were identified that could disrupt this interaction. These drugs bound to RAD54, altered its conformation, and abrogated RAD54-BLM-dependent chromatin remodeling on G5E4 and MRP2 arrays. Notably, the small molecules also reduced HRR efficiency in resistant lines, diminished anchorage-independent growth, and hampered the proliferation of tumors generated using camptothecin- and oxaliplatin-resistant colon cancer cells in both xenograft and syngeneic mouse models in BLM-dependent manner. Therefore, the 3 identified small molecules can serve as possible viable candidates for adjunct therapy in colon cancer treatment.
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Affiliation(s)
- Ekjot Kaur
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Ritu Agrawal
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Rimpy Arun
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Vinoth Madhavan
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Vivek Srivastava
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Dilip Kumar
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Nitin Kumar
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Sreekanth Vedagopuram
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Nishant Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Swati Priya
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Patrick Legembre
- UMR CNRS 7276, INSERM U1262, CRIBL, Université Limoges, Limoges, France
| | | | - Avinash Bajaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sagar Sengupta
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
- Biotechnology Research Innovation Council—National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, India
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Petkovic M, Yalçin M, Heese O, Relógio A. Differential expression of the circadian clock network correlates with tumour progression in gliomas. BMC Med Genomics 2023; 16:154. [PMID: 37400829 DOI: 10.1186/s12920-023-01585-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Gliomas are tumours arising mostly from astrocytic or oligodendrocytic precursor cells. These tumours are classified according to the updated WHO classification from 2021 in 4 grades depending on molecular and histopathological criteria. Despite novel multimodal therapeutic approaches, the vast majority of gliomas (WHO grade III and IV) are not curable. The circadian clock is an important regulator of numerous cellular processes and its dysregulation had been found during the progression of many cancers, including gliomas. RESULTS In this study, we explore expression patterns of clock-controlled genes in low-grade glioma (LGG) and glioblastoma multiforme (GBM) and show that a set of 45 clock-controlled genes can be used to distinguish GBM from normal tissue. Subsequent analysis identified 17 clock-controlled genes with a significant association with survival. The results point to a loss of correlation strength within elements of the circadian clock network in GBM compared to LGG. We further explored the progression patterns of mutations in LGG and GBM, and showed that tumour suppressor APC is lost late both in LGG and GBM. Moreover, HIF1A, involved in cellular response to hypoxia, exhibits subclonal losses in LGG, and TERT, involved in the formation of telomerase, is lost late in the GBM progression. By examining multi-sample LGG data, we find that the clock-controlled driver genes APC, HIF1A, TERT and TP53 experience frequent subclonal gains and losses. CONCLUSIONS Our results show a higher level of disrgulation at the gene expression level in GBM compared to LGG, and indicate an association between the differentially expressed clock-regulated genes and patient survival in both LGG and GBM. By reconstructing the patterns of progression in LGG and GBM, our data reveals the relatively late gains and losses of clock-regulated glioma drivers. Our analysis emphasizes the role of clock-regulated genes in glioma development and progression. Yet, further research is needed to asses their value in the development of new treatments.
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Affiliation(s)
- Marina Petkovic
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
| | - Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, 20457, Hamburg, Germany
| | - Oliver Heese
- Department of Neurosurgery and Spinal Surgery, HELIOS Medical Center Schwerin, University Campus of MSH Medical School Hamburg, 20457, Hamburg, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany.
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany.
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, 20457, Hamburg, Germany.
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Xu Z, Zhou T, Wang Y, Zhu L, Tu J, Xu Z, Li L, Li Y. Integrated PPI- and WGCNA-retrieval of hub gene signatures for soft substrates inhibition of human fibroblasts proliferation and differentiation. Aging (Albany NY) 2022; 14:6957-6974. [PMID: 36057261 PMCID: PMC9512501 DOI: 10.18632/aging.204258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022]
Abstract
Fibroblasts (FBs) are the most important functional cells in the process of wound repair, and their functions can be activated by different signals at the pathological site. Although wound repair is associated with microenvironmental stiffness, the effect of matrix stiffness on FBs remains elusive. In this study, TGF-β1 was used to mimic the fibrotic environment under pathological conditions. We found that the soft substrates made FBs slender compared with tissue culture plastic, and the main altered biological function was the inhibition of proliferation and differentiation ability. Through PPI and WGCNA analysis, 63 hub genes were found, including GADD45A, CDKN3, HIST2H3PS2, ACTB, etc., which may be the main targets of soft substrates affecting the proliferation and differentiation of FBs. Our findings not only provide a more detailed report on the effect of matrix stiffness on the function of human skin FBs, but also may provide new intervention ideas for improving scars and other diseases caused by excessive cell proliferation, with potential clinical application prospects.
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Affiliation(s)
- Ziran Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Tian Zhou
- The First Norman Bethune Clinical Medical College, Jilin University, Changchun 130021, China
| | - Yin Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Leijie Zhu
- The Third Norman Bethune Clinical Medical College, Jilin University, Changchun 130021, China
| | - Jihao Tu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Zhixiang Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Yulin Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
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MiR-139-3p Targets CHEK1 Modulating DNA Repair and Cell Viability in Lung Squamous Carcinoma Cells. Mol Biotechnol 2022; 64:832-840. [PMID: 35150405 DOI: 10.1007/s12033-022-00462-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/06/2022] [Indexed: 12/24/2022]
Abstract
Non-small-cell lung carcinoma (NSCLC) can be classified into several subtypes, where lung squamous carcinoma (LUSC) is one common subtype. Though miR-139-3p has been reported to be implicated in the development of various cancers, its mechanisms and functions remain unclear in LUSC. In this study, miR-139-3p was screened as one of the significantly down-regulated miRNAs in LUSC by an "edgeR" differential analysis based on TCGA database, which was verified by qRT-PCR in LUSC cell lines as well. The viability and cell cycle of the LUSC cells were examined by CCK-8 and flow cytometry, respectively, exhibiting that upregulating miR-139-3p restrained cell viability and thus accelerating the cell cycle. To explain this phenomenon, we further explored the downstream target gene through miRTarBase and starBase databases, where CHEK1 was predicted as one candidate. The targeting relationship was verified by a dual luciferase assay, identifying that CHEK1 could be targeted by miR-139-3p. Then, qRT-PCR and western blot analyses were performed to detect the expression of CHEK1 mRNA and proteins under the alteration of miR-139-3p expression. Rescue experiments were conducted to confirm the impacts of miR-139-3p/CHEK1 axis on the cell viability and cell cycle of LUSC. The results indicated that the effects of miR-139-3p on the LUSC cell phenotypes could be blocked by overexpressing CHEK1. In conclusion, our study provides a novel insight into the regulatory role of miR-139-3p in the development of LUSC.
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In silico modeling and molecular docking insights of kaempferitrin for colon cancer-related molecular targets. JOURNAL OF SAUDI CHEMICAL SOCIETY 2021. [DOI: 10.1016/j.jscs.2021.101319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Johnson RM, Phillips HS, Bais C, Brennan CW, Cloughesy TF, Daemen A, Herrlinger U, Jenkins RB, Lai A, Mancao C, Weller M, Wick W, Bourgon R, Garcia J. Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma. Neuro Oncol 2020; 22:1742-1756. [PMID: 32897363 PMCID: PMC7746941 DOI: 10.1093/neuonc/noaa157] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. METHODS Samples were collected from newly diagnosed patients with IDH wild-type glioblastoma in the ARTE, TAMIGA, EORTC 26101 (referred to as "ATE"), AVAglio, and GLARIUS trials, or treated at UCLA. Transcriptional profiling was achieved with the NanoString gene expression platform. To identify genes prognostic for overall survival (OS), we built an elastic net penalized Cox proportional hazards regression model using the discovery ATE dataset. For validation in independent datasets (AVAglio, GLARIUS, UCLA), we combined elastic net-selected genes into a robust z-score signature (ATE score) to overcome gene expression platform differences between discovery and validation cohorts. RESULTS NanoString data were available from 512 patients in the ATE dataset. Elastic net identified a prognostic signature of 9 genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to the ATE score conserved the prognostic value of the genes. The ATE score was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.02; UCLA, P = 0.004). The ATE score remained prognostic following adjustment for O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status and corticosteroid use at baseline. A positive correlation between ATE score and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status. CONCLUSIONS The ATE score showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.
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Affiliation(s)
- Radia M Johnson
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, USA
| | - Heidi S Phillips
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, USA
| | - Carlos Bais
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, USA
| | - Cameron W Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Timothy F Cloughesy
- Department of Neurology, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Anneleen Daemen
- Department of Translational Medicine, ORIC Pharmaceuticals Inc, South San Francisco, California, USA
| | - Ulrich Herrlinger
- Division of Clinical Neurooncology, Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Albert Lai
- Department of Neurology, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Christoph Mancao
- Oncology Biomarker Development, Genentech Inc., Basel, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Wolfgang Wick
- Department of Neurology, Ruprecht-Karls University Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Richard Bourgon
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, USA
| | - Josep Garcia
- Global Clinical Development, F. Hoffmann-La Roche Ltd, Basel, Switzerland
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Yang CY, Liu CR, Chang IYF, OuYang CN, Hsieh CH, Huang YL, Wang CI, Jan FW, Wang WL, Tsai TL, Liu H, Tseng CP, Chang YS, Wu CC, Chang KP. Cotargeting CHK1 and PI3K Synergistically Suppresses Tumor Growth of Oral Cavity Squamous Cell Carcinoma in Patient-Derived Xenografts. Cancers (Basel) 2020; 12:cancers12071726. [PMID: 32610557 PMCID: PMC7408003 DOI: 10.3390/cancers12071726] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 01/27/2023] Open
Abstract
Oral cavity squamous cell carcinomas (OSCCs) are aggressive tumors, and their recurrence leads to poor prognosis and reduced survival rates. This study aimed to identify therapeutic targets and to evaluate the efficacy of targeted inhibitors in OSCC patient-derived xenograft (PDX) models. Herein, we reported that OSCC PDXs recapitulated the genomic signatures of their paired primary tumors and the expression of CHEK1, PIK3CA, and PIK3CD was significantly upregulated in OSCC. The antitumor efficacy of CHK1 inhibitors (PF477736, AZD7762, LY2606368) and PI3K inhibitors (BYL719, GDC0941, GSK1059615) was investigated in OSCC cell lines and PDX models. Targeting either CHK1 or PI3K effectively inhibited cell proliferation and colony formation by inducing cell cycle arrest and apoptosis in in vitro cell-based assays. Cisplatin-based chemotherapy combined with CHK1 inhibitor treatment synergistically inhibited cell proliferation by suppressing CHK1 phosphorylation and inducing PARP cleavage. Furthermore, compared with monotherapy, cotreatment with CHK1 and PI3K inhibitors exerted synergistic anticancer effects by suppressing CHK1, AKT, and 4E-BP1 phosphorylation. In summary, our study identified CHK1 and PI3K as promising targets, especially in a dual treatment strategy combining a CHK1 inhibitor with cisplatin or a PI3K inhibitor as a novel therapeutic approach for OSCC patients with aberrant cell cycle regulation and PI3K signaling activation.
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Affiliation(s)
- Chia-Yu Yang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.Y.); (C.-R.L.); (F.-W.J.); (W.-L.W.); (T.-L.T.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (H.L.); (Y.-S.C.)
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
| | - Chiao-Rou Liu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.Y.); (C.-R.L.); (F.-W.J.); (W.-L.W.); (T.-L.T.)
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
| | - Chun-Nan OuYang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
| | - Chia-Hsun Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yen-Lin Huang
- Department of Pathology, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
| | - Chun-I Wang
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
| | - Fei-Wen Jan
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.Y.); (C.-R.L.); (F.-W.J.); (W.-L.W.); (T.-L.T.)
| | - Wan-Ling Wang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.Y.); (C.-R.L.); (F.-W.J.); (W.-L.W.); (T.-L.T.)
| | - Ting-Lin Tsai
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-Y.Y.); (C.-R.L.); (F.-W.J.); (W.-L.W.); (T.-L.T.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (H.L.); (Y.-S.C.)
| | - Hsuan Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (H.L.); (Y.-S.C.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
| | - Ching-Ping Tseng
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (H.L.); (Y.-S.C.)
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
| | - Chih-Ching Wu
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
- Correspondence: (C.-C.W.); or (K.-P.C.)
| | - Kai-Ping Chang
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; (I.Y.-F.C.); (C.-N.O.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Correspondence: (C.-C.W.); or (K.-P.C.)
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Comprehensive analysis of competitive endogenous RNAs network reveals potential prognostic lncRNAs in gastric cancer. Heliyon 2020; 6:e03978. [PMID: 32455175 PMCID: PMC7235626 DOI: 10.1016/j.heliyon.2020.e03978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/13/2020] [Accepted: 05/11/2020] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of a range of human diseases, including various cancers, with multiple previous studies having explored lncRNA dysregulation in the context of gastric cancer (GC). The present study sought to expand upon these previous results by downloading lncRNA, mRNA, and microRNA (miRNA) expression profiles derived from 180 GC tissues and 24 normal control tissues within the Cancer Genome Atlas (TCGA) database. These datasets were then interrogated to identify GC-related differentially expressed (DE) RNAs (|fold change| ≥ 2, FDR< 0.01), leading to the identification of 1946 DE lncRNAs, 123 DE miRNAs, and 3159 DE mRNAs. These results were then used to generate a putative GC-related competitive endogenous RNA (ceRNA) network composed of 131 lncRNAs, 9 miRNAs, and 78 mRNAs. Subsequent survival analyses based upon this network revealed 17 of these lncRNAs to be significantly associated with GC patient survival (P < 0.05). Further multivariable Cox regression and lasso analyses allowed for the construction of an 8-lncRNA risk score that was able to effectively predict GC patient survival with good discriminative ability. The Kaplan-Meier Plotter database further confirmed that network hub genes that were related to these 8 lncRNAs were associated with GC patient prognosis (P < 0.05). As the ceRNA network in the present study was constructed with a focus on both disease stage and differential gene expression, it represents a key resource that will offer valuable insights into the mechanistic roles of ceRNA pathways in GC development and progression.
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Liao Y, Wang Y, Cheng M, Huang C, Fan X. Weighted Gene Coexpression Network Analysis of Features That Control Cancer Stem Cells Reveals Prognostic Biomarkers in Lung Adenocarcinoma. Front Genet 2020; 11:311. [PMID: 32391047 PMCID: PMC7192063 DOI: 10.3389/fgene.2020.00311] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/16/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose We aimed to identify new prognostic biomarkers of lung adenocarcinoma (LUAD) based on cancer stem cell theory. Materials and Methods: RNA-seq and microarray data were obtained with clinical information downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Weighted gene coexpression network analysis (WGCNA) was applied to identify significant module and hub genes. The hub genes were validated via microarray data from GEO, and a prognostic signature with prognostic hub genes was constructed. Results LUAD patients enrolled from TCGA had a higher mRNA expression-based stemness index (mRNAsi) in tumor tissue than in adjacent normal tissue. Some clinical features and prognoses were found to be highly correlated with mRNAsi. WGCNA found that the green module and blue module were the most significant modules related to mRNAsi; 50 key genes were identified in the green module and were enriched mostly in the cell cycle, chromosome segregation, chromosomal region and microtubule binding. Six hub genes were revealed through the protein-protein interaction (PPI) network and Molecular Complex Detection (MCODE) plugin of Cytoscape software. Based on external verification with the GEO database, these six genes are not only expressed at different levels in LUAD and normal tissues but also associated with different clinical features. In addition, the construction of a prognostic signature with three hub genes showed high predictive value. Conclusion mRNAsi-related biomarkers may suggest a new potential treatment strategy for LUAD.
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Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yulei Wang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Mengqing Cheng
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chengliang Huang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xianming Fan
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Gong D, Feng PC, Ke XF, Kuang HL, Pan LL, Ye Q, Wu JB. Silencing Long Non-coding RNA LINC01224 Inhibits Hepatocellular Carcinoma Progression via MicroRNA-330-5p-Induced Inhibition of CHEK1. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:482-497. [PMID: 31902747 PMCID: PMC6948252 DOI: 10.1016/j.omtn.2019.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) accounts for approximately 85%–90% of primary liver cancers. Based on in silico analysis, differentially expressed long non-coding RNA (lncRNA) LINC01224 in HCC, the downstream microRNA (miRNA) miR-330-5p, and its target gene checkpoint kinase 1 (CHEK1) were selected as research subjects. Herein, this study was designed to evaluate their interaction effects on the malignant phenotypes of HCC cells. LINC01224 and CHEK1 were upregulated and miR-330-5p was downregulated in HCC cells. miR-330-5p shared negative correlations with LINC01224 and CHEK1, and LINC01224 shared a positive correlation with CHEK1. Notably, LINC01224 could specifically bind to miR-330-5p, and CHEK1 was identified as a target gene of miR-330-5p. When LINC01224 was silenced or miR-330-5p was elevated, the sphere and colony formation abilities and proliferative, migrative, and invasive potentials of HCC cells were diminished, while cell cycle arrest and apoptosis were enhanced. Moreover, LINC01224 induced HCC progression in vitro and accelerated tumor formation in nude mice by increasing CHEK1 expression. The key findings of the present study demonstrated that silencing LINC01224 could downregulate the expression of CHEK1 by competitively binding to miR-330-5p, thus inhibiting HCC progression. This result highlights the LINC01224/miR-330-5p/CHEK1 axis as a novel molecular mechanism involved in the pathology of HCC.
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Affiliation(s)
- Dan Gong
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China
| | - Peng-Cheng Feng
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China
| | - Xing-Fei Ke
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China
| | - Hui-Lan Kuang
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China
| | - Li-Li Pan
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China
| | - Qiang Ye
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China
| | - Jian-Bing Wu
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China; Jiangxi Key Laboratory of Cinical and Translational Cancer Research, Nanchang 330006, P.R. China.
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