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Ahmad SU, Ali Y, Jan Z, Rasheed S, Nazir NUA, Khan A, Rukh Abbas S, Wadood A, Rehman AU. Computational screening and analysis of deleterious nsSNPs in human p14ARF ( CDKN2A gene) protein using molecular dynamic simulation approach. J Biomol Struct Dyn 2023; 41:3964-3975. [PMID: 35446184 DOI: 10.1080/07391102.2022.2059570] [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: 12/29/2021] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
Cyclin-dependent kinase inhibitor 2 A (CDKN2A) gene belongs to the cyclin-dependent kinase family that code for two transcripts (p16INK4A and p14ARF), both work as tumor suppressors proteins. The mutation that occurs in the p14ARF protein can lead to different types of cancers. Single nucleotide polymorphisms (SNPs) are an important type of genetic alteration that can lead to different types of diseases. In this study, we applied the computational strategy on human p14ARF protein to identify the potential deleterious nsSNPs and check their impact on the structure, function, and protein stability. We applied more than ten prediction tools to screen the retrieved 288 nsSNPs, consequently extracting four deleterious nsSNPs i.e., rs139725688 (R10G), rs139725688 (R21W), rs374360796 (F23L) and rs747717236 (L124R). Homology modeling, conservation and conformational analysis of mutant models were performed to examine the divergence of these variants from the native p14ARF structure. All-atom molecular dynamics simulation revealed a significant impact of these mutations on protein stability, compactness, globularity, solvent accessibility and secondary structure elements. Protein-protein interactions indicated that p14ARF operates as a hub linking clusters of different proteins and that changes in p14ARF may result in the disassociation of numerous signal cascades. Our current study is the first survey of computational analysis on p14ARF protein that determines the association of these nsSNPs with the altered function of p14ARF protein and leads to the development of various types of cancers. This research proposes the described functional SNPs as possible targets for proteomic investigations, diagnostic procedures, and treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i- Azam University, Islamabad, Pakistan
| | - Zainab Jan
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-i- Azam University, Islamabad, Pakistan
| | - Noor Ul Ain Nazir
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Asif Khan
- Department of Botany, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Shah Rukh Abbas
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
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Linc00312 Single Nucleotide Polymorphism as Biomarker for Chemoradiotherapy Induced Hematotoxicity in Nasopharyngeal Carcinoma Patients. DISEASE MARKERS 2022; 2022:6707821. [PMID: 35990252 PMCID: PMC9381851 DOI: 10.1155/2022/6707821] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 12/08/2022]
Abstract
Background. Linc00312 is downregulated in nasopharyngeal carcinoma (NPC) and associates with poor treatment efficacy. Genetic variations are the main cause of individual differences in treatment response. The objective of this study is to explore the relationship between genetic variations of linc00312 and the risk of chemoradiotherapy induced toxic reactions in NPC patients. Methods. We used a bioinformatics approach to select 3 single nucleotide polymorphisms (SNPs) with regulatory feature in linc00312 (rs12497104, rs15734, and rs164966). 505 NPC patients receiving chemoradiotherapy with complete follow-up data were recruited. Genotyping was carried out by MassARRAY iPLEX platform. Univariate logistic and multivariate logistic regression were used to analyze the risk factors responsible for toxic reactions of NPC patients. Results. Our result demonstrated that linc00312 rs15734 (
) was significantly associated with severe leukopenia in NPC patients underwent chemoradiotherapy (AA vs. GG,
,
). In addition, the risk of severe leukopenia was remarkably increased to 5.635 times (
) in female with rs15734 AA genotype compared to male with rs15734 GG genotype. Moreover, patients with rs12497104 (
) AA genotype showed a 67.5% lower risk of thrombocytopenia than those with GG genotype (
). Remarkably, the younger patients (
) with rs12497104 AA genotype displayed a 90% decreased risk of thrombocytopenia compared with older patients (
) carrying rs12497104 GG genotype (
). Conclusions. Genetic variations of linc00312 affect the risk of chemoradiotherapy induced hematotoxicity in nasopharyngeal carcinoma patients and may serve as biomarkers for personalized medicine.
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Li X, Duan S, Zheng Y, Yang Y, Wang L, Li X, Zhang Q, Thorne RF, Li W, Yang D. Hyperthermia inhibits growth of nasopharyngeal carcinoma through degradation of c-Myc. Int J Hyperthermia 2022; 39:358-371. [PMID: 35184661 DOI: 10.1080/02656736.2022.2038282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Xiaole Li
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Radiotherapy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shichao Duan
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingjuan Zheng
- Department of Radiotherapy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongqiang Yang
- Department of Radiotherapy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Wang
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinqiang Li
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qing Zhang
- Translational Research Institute, Henan Provincial People’s Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Rick F. Thorne
- Translational Research Institute, Henan Provincial People’s Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wencai Li
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Daoke Yang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Radiotherapy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Kozin MS, Kiselev IS, Baulina NM, Pavlova GV, Boyko AN, Kulakova OG, Favorova OO. Risk of Multiple Sclerosis: Analysis of Interactions between Variants of Nuclear and Mitochondrial Genomes. Mol Biol 2021. [DOI: 10.1134/s0026893321050071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Guo Z, Bao MH, Fan YX, Zhang Y, Liu HY, Zhou XL, Wu B, Lu QQ, He BS, Nan XY, Lu JY. Genetic Polymorphisms of Long Non-coding RNA Linc00312 Are Associated With Susceptibility and Predict Poor Survival of Nasopharyngeal Carcinoma. Front Cell Dev Biol 2021; 9:698558. [PMID: 34336850 PMCID: PMC8322760 DOI: 10.3389/fcell.2021.698558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background Linc00312 is dysregulated in nasopharyngeal carcinoma (NPC) and participates in the initiation and progression of NPC. Our previous studies suggested that linc00312 was able to enhance the sensitivity of NPC cells to irradiation and NPC patients with higher expression of linc00312 was associated with better short-term curative effect and overall survival. The single nucleotide polymorphisms (SNPs) of lncRNAs may influence the disease course and outcome by affecting the expression, secondary structure or function of lncRNAs. However, the role of SNPs in linc00312 on the occurrence and survival of NPC remains unknown. Methods We recruited 684 NPC patients and 823 healthy controls to evaluate the association between linc00312 SNPs and NPC susceptibility by using multivariate logistic regression analysis. Kaplan-Meier analysis and Cox proportional hazards regression were applied to assess the effect of linc00312 SNPs on the survival of NPC patients. The relative expression of linc00312 in NPC tissues was determined by real-time PCR. The interaction between linc00312 and mir-411-3p was explored by luciferase reporter assay. In silico prediction of the changes on linc00312 folding structure was conducted by RNAfold WebServer. Result We demonstrated that rs12497104 (G > A) GA genotype carriers had a higher risk than others for suffering from NPC (GA vs GG, OR = 1.437, P = 0.003). Besides, patients with rs12497104 AA genotype showed a poorer overall survival in contrast to GG genotype (AA vs GG, HR = 2.117, P = 0.011). In addition, the heterozygous carriers of rs15734 (G > A) and rs164966 (A > G) were correlated with decreased risk of NPC (GA vs GG, OR = 0.778, P = 0.031; GA vs AA, OR = 0.781, P = 0.033, respectively). We found that the three SNPs might influence the expression of linc00312 in a genotype specific feature. The local centroid secondary structure as well as the minimum free energy of linc00312 were changed following the candidate SNPs alterations. Besides, we revealed that the G to A alteration at rs12497104 disrupted the binding between mir-411-3p and linc00312. Conclusion Our results indicated genetic polymorphisms of linc00312 might serve as potential biomarkers for NPC carcinogenesis and prognosis.
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Affiliation(s)
- Zhen Guo
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Mei-Hua Bao
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Yun-Xia Fan
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Yan Zhang
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Hai-Yan Liu
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Xiao-Long Zhou
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Ben Wu
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | | | - Bin-Sheng He
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Xu-Ying Nan
- Academician Workstation, Changsha Medical University, Changsha, China.,School of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, China
| | - Jiao-Yang Lu
- Academician Workstation, Changsha Medical University, Changsha, China.,Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
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Amjadi-Moheb F, Paniri A, Akhavan-Niaki H. Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer Therapy. Cancer Res 2021; 81:1925-1936. [PMID: 33472888 DOI: 10.1158/0008-5472.can-20-3613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
MYC is embedded in the transcriptional oasis of the 8q24 gene desert. A plethora of genomic elements has roles in MYC aberrant expression in cancer development by interacting with transcription factors and epigenetics regulators as well as altering the structure of chromatin at the MYC locus and tissue-specific long-range enhancer-promoter contacts. Furthermore, MYC is a master regulator of several human cancers by modulating the transcription of numerous cancer-related genes through epigenetic mechanisms. This review provides a comprehensive overview of the three-dimensional genomic organization around MYC and the role of epigenetic machinery in transcription and function of MYC as well as discusses various epigenetic-targeted therapeutic strategies in MYC-driven cancers.
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Affiliation(s)
- Fatemeh Amjadi-Moheb
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Alireza Paniri
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Haleh Akhavan-Niaki
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
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Pan J, Zhu J, Wang M, Yang T, Hu C, Yang J, Zhang J, Cheng J, Zhou H, Xia H, He J, Zou Y. Association of MYC gene polymorphisms with neuroblastoma risk in Chinese children: A four-center case-control study. J Gene Med 2020; 22:e3190. [PMID: 32222109 DOI: 10.1002/jgm.3190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/04/2020] [Accepted: 03/15/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Neuroblastoma is one of the most common malignant tumors in childhood. Polymorphisms in proto-oncogene MYC are implicated in many cancers, although their role in neuroblastoma remains unclear. In the present study, we attempted to investigate the association between MYC gene polymorphisms and neuroblastoma susceptibility in Chinese children. METHODS We included two MYC polymorphisms (rs4645943 and rs2070583) and assessed their effects on neuroblastoma risk in 505 cases and 1070 controls via the Taqman method. RESULTS In single and combined locus analysis, no significant association was found between the two selected polymorphisms and neuroblastoma susceptibility. In stratification analysis, the rs4645943 CT/TT genotypes were significantly associated with a decreased neuroblastoma risk in subjects with tumors originating from other sites [adjusted odds ratio (OR) = 0.42, 95% confidence interval (CI) = 0.21-0.84, p = 0.013]. Meanwhile, the presence of one or two protective genotypes was significantly associated with a decreased neuroblastoma risk in subjects with tumors arising from other sites (adjusted OR = 0.50, 95% CI = 0.26-0.96, p = 0.036). CONCLUSIONS The present study indicates that MYC gene polymorphisms may have a weak effect on the neuroblastoma risk, which neeeds to be verified further.
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Affiliation(s)
- Jing Pan
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jinhong Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Mi Wang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tianyou Yang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chao Hu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiliang Yang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiao Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yan Zou
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Yasri S, Wiwanitkit V. Regenerating gene 1A single-nucleotide polymorphisms and nasopharyngeal carcinoma susceptibility. Eur Arch Otorhinolaryngol 2019; 276:3519. [PMID: 31595315 DOI: 10.1007/s00405-019-05675-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Sora Yasri
- KMT Primary Care Center, Bangkok, Thailand.
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Liu J, Hua RX, Fu W, Zhu J, Jia W, Zhang J, Zhou H, Cheng J, Xia H, Liu G, He J. MYC gene associated polymorphisms and Wilms tumor risk in Chinese children: a four-center case-control study. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:475. [PMID: 31700911 PMCID: PMC6803173 DOI: 10.21037/atm.2019.08.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Wilms tumor (WT) is a common embryonal malignancy in the kidney, ranking fourth in childhood cancer worldwide. MYC, a critical proto-oncogene, plays an important role in tumorigenesis. Single nucleotide polymorphisms in the MYC gene may lead to the deregulation of MYC proto-oncogene protein and thereby promote the initiation and development of tumors. METHODS Here, we assessed the association between MYC gene associated polymorphisms and WT susceptibility by performing a case-control study with 355 cases and 1070 controls. Two MYC gene associated polymorphisms (rs4645943 C > T, rs2070583 A > G) were genotyped by TaqMan technique. Odds ratios (ORs) and 95% confidence intervals (CIs) were used for evaluating the association between these two polymorphisms and WT susceptibility. RESULTS No significant association was detected between the selected polymorphisms and WT risk in the overall analysis as well as stratification analysis. CONCLUSIONS These results indicate that neither of two selected MYC gene associated polymorphisms might affect WT susceptibility in the Chinese population. Large well-designed studies with diverse ethnicities are warranted to verify these results.
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Affiliation(s)
- Jiabin Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Rui-Xi Hua
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Wen Fu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jinhong Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Department of Clinical Laboratory, Molecular Epidemiology Laboratory, Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Wei Jia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Guochang Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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Wei GG, Gao L, Tang ZY, Lin P, Liang LB, Zeng JJ, Chen G, Zhang LC. Drug repositioning in head and neck squamous cell carcinoma: An integrated pathway analysis based on connectivity map and differential gene expression. Pathol Res Pract 2019; 215:152378. [PMID: 30871913 DOI: 10.1016/j.prp.2019.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/07/2019] [Accepted: 03/02/2019] [Indexed: 02/07/2023]
Abstract
The severe damage to health and social burden caused by head and neck squamous cell carcinoma (HNSCC) generated an urgent need to develop novel anti-cancer therapy. Currently, drug repositioning has risen in responses to the proper time as an efficient approach to invention of new anti-cancer therapies. In the present study, we aimed to screen candidate drugs for HNSCC by integrating HNSCC-related pathways from differentially expressed genes (DEGs) and drug-affected pathways from connectivity map (CMAP). We also endeavored to unveil the molecular mechanism of HNSCC through creating drug-target network and protein-to-protein (PPI) network of component DEGs in key overlapping pathways. As a result, a total of 401 DEGs were obtained from TCGA and GTEx mRNA-seq data. Taking the intersection part of 27 HNSCC-related Kyoto Encyclopedia of Genes and Genomes pathways and 33 drug-affected pathways, we retained 22 candidate drugs corresponding to two key pathways (cell cycle and p53 signaling pathways) of the five overlapping pathways. Two of the hub genes (PCNA and CCND1) identified from the PPI network of component DEGs in cell cycle and p53 signaling pathways were defined as the critical targets of candidate drugs with increased protein expression in HNSCC tissues, which was reported by the human protein atlas (HPA) database and cBioPortal. Finally, we validated via molecular docking analysis that two drugs with unknown effects in HNSCC: MG-262 and bepridil might perturb the development of HNSCC through targeting PCNA. These candidate drugs possessed broad application prospect as medication for HNSCC.
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Affiliation(s)
- Gan-Guan Wei
- Department of Otolaryngology Head and Neck Surgery, NO.303 Hospital of PLA, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Li Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Zheng-Yi Tang
- Department of Otolaryngology Head and Neck Surgery, NO.303 Hospital of PLA, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Peng Lin
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Li-Bin Liang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jing-Jing Zeng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China.
| | - Long-Cheng Zhang
- Department of Otolaryngology Head and Neck Surgery, NO.303 Hospital of PLA, Nanning, Guangxi Zhuang Autonomous Region, China.
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