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Lin X, Ma Q, Chen L, Guo W, Huang Z, Huang T, Cai YD. Identifying genes associated with resistance to KRAS G12C inhibitors via machine learning methods. Biochim Biophys Acta Gen Subj 2023; 1867:130484. [PMID: 37805078 DOI: 10.1016/j.bbagen.2023.130484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Targeted therapy has revolutionized cancer treatment, greatly improving patient outcomes and quality of life. Lung cancer, specifically non-small cell lung cancer, is frequently driven by the G12C mutation at the KRAS locus. The development of KRAS inhibitors has been a breakthrough in the field of cancer research, given the crucial role of KRAS mutations in driving tumor growth and progression. However, over half of patients with cancer bypass inhibition show limited response to treatment. The mechanisms underlying tumor cell resistance to this treatment remain poorly understood. METHODS To address above gap in knowledge, we conducted a study aimed to elucidate the differences between tumor cells that respond positively to KRAS (G12C) inhibitor therapy and those that do not. Specifically, we analyzed single-cell gene expression profiles from KRAS G12C-mutant tumor cell models (H358, H2122, and SW1573) treated with KRAS G12C (ARS-1620) inhibitor, which contained 4297 cells that continued to proliferate under treatment and 3315 cells that became quiescent. Each cell was represented by the expression levels on 8687 genes. We then designed an innovative machine learning based framework, incorporating seven feature ranking algorithms and four classification algorithms to identify essential genes and establish quantitative rules. RESULTS Our analysis identified some top-ranked genes, including H2AFZ, CKS1B, TUBA1B, RRM2, and BIRC5, that are known to be associated with the progression of multiple cancers. CONCLUSION Above genes were relevant to tumor cell resistance to targeted therapy. This study provides important insights into the molecular mechanisms underlying tumor cell resistance to KRAS inhibitor treatment.
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Affiliation(s)
- Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Clinical Oncology School of Fujian Medical University and Fujian Cancer Hospital, Fuzhou 350014, China.
| | - QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Zhiyi Huang
- College of Chemistry, Fuzhou University, Fuzhou 350000, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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Mohamed AA, Yassin AS, Gomaa BS, Darwish H, Mohamed RS, Makled S, Ramdan A, Abd-Elsalam S, Raafat MM. Association of Polymorphism in Survivin Gene and the Risk of Liver Cancer Resulting from Hepatitis C Virus Among Egyptian Patients. Curr Cancer Drug Targets 2021; 21:536-543. [PMID: 33653251 DOI: 10.2174/1568009621666210302090917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 12/06/2020] [Accepted: 12/26/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND This study aims to investigate the relation between Survivin gene polymorphisms and the risk of Hepatocellular carcinoma (HCC) resulting from hepatitis C infection among the Egyptian population. METHODS This prospective study was conducted on 164 patients, 57 patients were diagnosed with hepatitis C, where 57 were diagnosed with HCC in addition to 50 healthy volunteers as controls. Genotyping for Survivin rs1042489 and rs8073069 single nucleotide polymorphisms was carried out by the allelic discrimination Real-Time Polymerase Chain Reaction Single Nucleotide Polymorphisms genotyping technology. RESULTS The results of Survivin rs1042489 polymorphism revealed that the TC and CC genotypes were significantly different between hepatocellular carcinoma patients (OR=15.5, 95%CI: 3.299-72.825,P<0.001), and controls (OR=44, 95%CI: 8.025-241.254, P<0.001). Furthermore, CC genotype was significantly different between cirrhotic and hepatocellular carcinoma patients (OR=19.2, 95%CI: 3.097-119.049, P=0.002). Moreover, the TC genotype shows a significant difference between controls and cirrhotic patients (OR=5.5, 95%CI: 2.111-14.328, P<0.001). However, when comparing TT genotypes, CC+TC genotypes results showed a significant association with increasing the risk of cirrhosis and hepatocellular carcinoma (OR=4.812, 95%CI: 1.893-12.233, P=0.001), (OR=21.607, 95%CI: 4.738-98.532, P<0.01), respectively. On the other hand, there was no significant difference among all studied groups for all genotypes regarding Survivin rs8073069. Also, the CC+GC genotype showed no significant association with increased risk of hepatocellular carcinoma (P=0.999) compared with the GG genotypes. CONCLUSION The study indicates that functional Survivin rs1042489 polymorphism may contribute to the risk of hepatocellular carcinoma while Survivin rs8073069 polymorphism has no significant association with increased risk of hepatocellular carcinoma among the studied groups.
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Affiliation(s)
- Amal A Mohamed
- Biochemistry Department, National Hepatology and Tropical Medicine Research Institution, Cairo, Egypt
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Basma S Gomaa
- Microbiology and Immunology Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Future University in Egypt, Cairo, Egypt
| | - Hossam Darwish
- Oncology Department, Ismailia Teaching Hospital, Ismailia, Egypt
| | - Rasha S Mohamed
- Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Sahar Makled
- Tropical Department, National Hepatology and Tropical Medicine Research Institute Cairo, Egypt
| | - Ahmed Ramdan
- Department of Tropical, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Sherief Abd-Elsalam
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Marwa M Raafat
- Microbiology and Immunology Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Future University in Egypt, Cairo, Egypt
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Liao S, He J, Liu C, Zhang Z, Liao H, Liao Z, Yu C, Guan J, Mo H, Yuan Z, Liang T, Lu Z, Xu G, Wang Z, Chen J, Jiang J, Zhan X. Construction of autophagy prognostic signature and analysis of prospective molecular mechanisms in skin cutaneous melanoma patients. Medicine (Baltimore) 2021; 100:e26219. [PMID: 34087900 PMCID: PMC8183723 DOI: 10.1097/md.0000000000026219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Autophagy is closely related to skin cutaneous melanoma (SKCM), but the mechanism involved is unclear. Therefore, exploration of the role of autophagy-related genes (ARGs) in SKCM is necessary. MATERIALS AND METHODS Differential expression autophagy-related genes (DEARGs) were first analysed. Univariate and multivariate Cox regression analyses were used to evaluate the expression of DEARGs and prognosis of SKCM. Further, the expression levels of prognosis-related DEARGs were verified by immunohistochemical (IHC) staining. Finally, gene set enrichment analysis (GSEA) was used to explore the underlying molecular mechanisms of SKCM. RESULTS Five ARGs (APOL1, BIRC5, EGFR, TP63, and SPNS1) were positively correlated with the prognosis of SKCM. IHC verified the results of the differential expression of these 5 ARGs in the bioinformatics analysis. According to the receiver operating characteristic curve, the signature had a good performance at predicting overall survival in SKCM. The signature could classify SKCM patients into high-risk or low-risk groups according to distinct overall survival. The nomogram confirmed that the risk score has a particularly large impact on the prognosis of SKCM. Calibration plot displayed excellent agreement between nomogram predictions and actual observations. Principal component analysis indicated that patients in the high-risk group could be distinguished from those in low-risk group. Results of GSEA indicated that the low-risk group is enriched with aggressiveness-related pathways such as phosphatidylinositol-3-kinase/protein kinase B and mitogen-activated protein kinase signalling pathways. CONCLUSION Our study identified a 5-gene signature. It revealed the mechanisms of autophagy that lead to the progression of SKCM and established a prognostic nomogram that can predict overall survival of patients with SKCM. The findings of this study provide novel insights into the relationship between ARGs and prognosis of SKCM.
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Affiliation(s)
- Shian Liao
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi
| | - Juliang He
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital
| | - Chong Liu
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi
| | - Zide Zhang
- Guangxi Medical University, Nanning, Guangxi
| | - Hongyu Liao
- Southern Medical University, Guangzhou, Guangdong
| | - Zuowei Liao
- Department of General Surgery, The Ninth Affiliated Hospital of Guangxi Medical University, Beihai, Guangxi, China
| | - Chaojie Yu
- Guangxi Medical University, Nanning, Guangxi
| | - Jian Guan
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital
| | - Hao Mo
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital
| | - Zhenchao Yuan
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital
| | - Tuo Liang
- Guangxi Medical University, Nanning, Guangxi
| | - Zhaojun Lu
- Guangxi Medical University, Nanning, Guangxi
| | - Guoyong Xu
- Guangxi Medical University, Nanning, Guangxi
| | - Zequn Wang
- Guangxi Medical University, Nanning, Guangxi
| | - Jiarui Chen
- Guangxi Medical University, Nanning, Guangxi
| | - Jie Jiang
- Guangxi Medical University, Nanning, Guangxi
| | - Xinli Zhan
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi
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Han F, Yang S, Wang W, Huang X, Huang D, Chen S. Silencing of lncRNA LINC00857 Enhances BIRC5-Dependent Radio-Sensitivity of Lung Adenocarcinoma Cells by Recruiting NF-κB1. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:981-993. [PMID: 33251047 PMCID: PMC7679245 DOI: 10.1016/j.omtn.2020.09.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/17/2020] [Indexed: 01/08/2023]
Abstract
Lung adenocarcinoma (LUAD) is a predominant type of lung cancer in never-smoker patients. In this study, we identified a long noncoding RNA (lncRNA) LINC00857 that might regulate radio-sensitivity of LUAD cells. Expression of LINC00857 and baculoviral IAP repeat containing 5 (BIRC5) was determined to be upregulated in LUAD cells and tissues using qRT-PCR and western blot analysis. The correlation between LINC00857 and nuclear factor kappa B subunit 1 (NF-κB1) was verified using RNA immunoprecipitation and chromatin immunoprecipitation assays, while the binding relationship between NF-κB1 and BIRC5 was determined by dual-luciferase reporter assay. It was suggested that LINC00857 could recruit NF-κB1 in BIRC5 promoter region. BIRC5 promoter activity was repressed in response to small interfering-LINC00857 (si-LINC00857) in LUAD cells. Silencing LINC00857 or BIRC5 reduced proliferation and colony formation but enhanced apoptosis and radio-sensitivity of LUAD cells. The experiment in vivo verified the function of silencing LINC00857 on enhancing radio-sensitivity of LUAD cells. Our results reveal a functional regulatory LINC00857-NF-κB1-BIRC5 triplet in LUAD cells, suggesting LINC00857 as a potential target for LUAD treatment.
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Affiliation(s)
- Fushi Han
- Department of Nuclear Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Shusong Yang
- Department of Radiotherapy, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Wei Wang
- Department of Internal Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Xinghong Huang
- Department of Radiology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Dongdong Huang
- Department of Emergency Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Shuzhen Chen
- Department of Nuclear Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
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Casalou C, Ferreira A, Barral DC. The Role of ARF Family Proteins and Their Regulators and Effectors in Cancer Progression: A Therapeutic Perspective. Front Cell Dev Biol 2020; 8:217. [PMID: 32426352 PMCID: PMC7212444 DOI: 10.3389/fcell.2020.00217] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
The Adenosine diphosphate-Ribosylation Factor (ARF) family belongs to the RAS superfamily of small GTPases and is involved in a wide variety of physiological processes, such as cell proliferation, motility and differentiation by regulating membrane traffic and associating with the cytoskeleton. Like other members of the RAS superfamily, ARF family proteins are activated by Guanine nucleotide Exchange Factors (GEFs) and inactivated by GTPase-Activating Proteins (GAPs). When active, they bind effectors, which mediate downstream functions. Several studies have reported that cancer cells are able to subvert membrane traffic regulators to enhance migration and invasion. Indeed, members of the ARF family, including ARF-Like (ARL) proteins have been implicated in tumorigenesis and progression of several types of cancer. Here, we review the role of ARF family members, their GEFs/GAPs and effectors in tumorigenesis and cancer progression, highlighting the ones that can have a pro-oncogenic behavior or function as tumor suppressors. Moreover, we propose possible mechanisms and approaches to target these proteins, toward the development of novel therapeutic strategies to impair tumor progression.
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Affiliation(s)
- Cristina Casalou
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Andreia Ferreira
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Duarte C Barral
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
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Man J, Zhang X, Dong H, Li S, Yu X, Meng L, Gu X, Yan H, Cui J, Lai Y. Screening and identification of key biomarkers in lung squamous cell carcinoma by bioinformatics analysis. Oncol Lett 2019; 18:5185-5196. [PMID: 31612029 PMCID: PMC6781567 DOI: 10.3892/ol.2019.10873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/22/2019] [Indexed: 12/21/2022] Open
Abstract
The high mortality rate of lung squamous cell carcinoma (LUSC) is in part due to the lack of early detection of its biomarkers. The identification of key molecules involved in LUSC is therefore required to improve clinical diagnosis and treatment outcomes. The present study used the microarray datasets GSE31552, GSE6044 and GSE12428 from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were conducted to construct the protein-protein interaction network of DEGs and hub genes module using STRING and Cytoscape. The 67 DEGs identified consisted of 42 upregulated genes and 25 downregulated genes. The pathways predicted by KEGG and GO enrichment analyses of DEGs mainly included cell cycle, cell proliferation, glycolysis or gluconeogenesis, and tetrahydrofolate metabolic process. Further analysis of the University of California Santa Cruz and ONCOMINE databases identified 17 hub genes. Overall, the present study demonstrated hub genes that were closely associated with clinical tissue samples of LUSC, and identified TYMS, CCNB2 and RFC4 as potential novel biomarkers of LUSC. The findings of the present study contribute to an improved understanding of the molecular mechanisms of carcinogenesis and progression of LUSC, and assist with the identification of potential diagnostic and therapeutic targets of LUSC.
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Affiliation(s)
- Jun Man
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xiaomei Zhang
- Department of Respiratory Medicine, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing 100078, P.R. China
| | - Huan Dong
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Simin Li
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xiaolin Yu
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Lihong Meng
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xiaofeng Gu
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Hong Yan
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Jinwei Cui
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Yuxin Lai
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
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Gong S, Chen Y, Meng F, Zhang Y, Wu H, Li C, Zhang G. RCC2, a regulator of the RalA signaling pathway, is identified as a novel therapeutic target in cisplatin-resistant ovarian cancer. FASEB J 2019; 33:5350-5365. [PMID: 30768358 DOI: 10.1096/fj.201801529rr] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Currently, cisplatin (DDP) is the first-line chemotherapeutic agent used for treatment of ovarian cancer, but gradually acquired drug resistance minimizes its therapeutic outcomes. We aimed to identify crucial genes associated with DDP resistance in ovarian cancer and uncover potential mechanisms. Two sets of gene expression data were downloaded from Gene Expression Omnibus, and bioinformatics analysis was conducted. In our study, the differentially expressed genes between DDP-sensitive and DDP-resistant ovarian cancer were screened in GSE15709 and GSE51373 database, and chromosome condensation 2 regulator (RCC2) and nucleoporin 160 were identified as 2 genes that significantly up-regulated in DDP-resistant ovarian cancer cell lines compared with DDP-sensitive cell lines. Moreover, RCC2, Ral small GTPase (RalA), and Ral binding protein-1 (RalBP1) expression was found to be significantly higher in DDP-resistant ovarian cancer tissues than in DDP-sensitive tissues. RCC2 plays a positive role in cell proliferation, apoptosis, and migration in DDP-resistant ovarian cancer cell lines in vitro and in vivo. Furthermore, RCC2 could interact with RalA, thus promoting its downstream effector RalBP1. RalA knockdown could reverse the effects of RCC2 overexpression on DDP-resistant ovarian cancer cell proliferation, apoptosis, and migration. Similarly, RalA overexpression could alleviate the effects of RCC2 knockdown in DDP-resistant ovarian cancer cells. Taken together, RCC2 may function as an oncogene, regulating the RalA signaling pathway, and intervention of RCC2 expression might be a promising therapeutic strategy for DDP-resistant ovarian cancer.-Gong, S., Chen, Y., Meng, F., Zhang, Y., Wu, H., Li, C., Zhang, G. RCC2, a regulator of the RalA signaling pathway, is identified as a novel therapeutic target in cisplatin-resistant ovarian cancer.
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Affiliation(s)
- Shipeng Gong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongning Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fanliang Meng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yadi Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Huan Wu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China; and
| | - Chanyuan Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guangping Zhang
- Department of Gynecology, People's Hospital of Huadu District, Guangzhou, China
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Chen J, Peng H, Han G, Cai H, Cai J. HOGMMNC: a higher order graph matching with multiple network constraints model for gene–drug regulatory modules identification. Bioinformatics 2018; 35:602-610. [DOI: 10.1093/bioinformatics/bty662] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/18/2018] [Accepted: 07/23/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jiazhou Chen
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Lab of Computational Intelligence and Cyberspace Information, South China University of Technology, Guangzhou, China
| | - Hong Peng
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Guoqiang Han
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongmin Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Lab of Computational Intelligence and Cyberspace Information, South China University of Technology, Guangzhou, China
| | - Jiulun Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
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Wnt Signaling in Cell Motility and Invasion: Drawing Parallels between Development and Cancer. Cancers (Basel) 2016; 8:cancers8090080. [PMID: 27589803 PMCID: PMC5040982 DOI: 10.3390/cancers8090080] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 12/12/2022] Open
Abstract
The importance of canonical and non-canonical Wnt signal transduction cascades in embryonic development and tissue homeostasis is well recognized. The aberrant activation of these pathways in the adult leads to abnormal cellular behaviors, and tumor progression is frequently a consequence. Here we discuss recent findings and analogies between Wnt signaling in developmental processes and tumor progression, with a particular focus on cell motility and matrix invasion and highlight the roles of the ARF (ADP-Ribosylation Factor) and Rho-family small GTP-binding proteins. Wnt-regulated signal transduction from cell surface receptors, signaling endosomes and/or extracellular vesicles has the potential to profoundly influence cell movement, matrix degradation and paracrine signaling in both development and disease.
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Hongu T, Yamauchi Y, Funakoshi Y, Katagiri N, Ohbayashi N, Kanaho Y. Pathological functions of the small GTPase Arf6 in cancer progression: Tumor angiogenesis and metastasis. Small GTPases 2016; 7:47-53. [PMID: 26909552 PMCID: PMC4905277 DOI: 10.1080/21541248.2016.1154640] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although several lines of evidence have shown that the small GTPase ADP-ribosylation factor 6 (Arf6) plays pivotal roles in cancer progression of several types of cancers, little is known about the functions of Arf6 in tumor microenvironment. We demonstrated that Arf6 in vascular endothelial cells (VECs) plays a crucial role in tumor angiogenesis and growth using endothelial cell-specific Arf6 conditional knockout mice into which B16 melanoma and Lewis lung carcinoma cells were implanted. It was also found that Arf6 in VECs positively regulates hepatocyte growth factor (HGF)-induced β1 integrin recycling, which is a critical event for tumor angiogenesis by promoting cell migration. Importantly, pharmacological inhibition of HGF-induced Arf6 activation significantly suppresses tumor angiogenesis and growth in mice, suggesting that Arf6 signaling would be a potential target for anti-angiogenic therapy. In this manuscript, we summarize the multiple roles of Arf6 in cancer progression, particularly in cancer cell invasion/metastasis and our recent findings on tumor angiogenesis, and discuss a possible approach to develop innovative anti-cancer drugs.
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Affiliation(s)
- Tsunaki Hongu
- a Department of Physiological Chemistry , Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba , Japan
| | - Yohei Yamauchi
- a Department of Physiological Chemistry , Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba , Japan
| | - Yuji Funakoshi
- a Department of Physiological Chemistry , Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba , Japan
| | - Naohiro Katagiri
- a Department of Physiological Chemistry , Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba , Japan
| | - Norihiko Ohbayashi
- a Department of Physiological Chemistry , Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba , Japan
| | - Yasunori Kanaho
- a Department of Physiological Chemistry , Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba , Japan
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Pu F, Shao Z, Yang S, Liu J, Lin S, Ma X, Yang H. Association between functional variants in BIRC5/survivin gene 3' untranslated region and mRNA expression in lymphoblastoid cell lines. Oncol Lett 2015; 10:2319-2322. [PMID: 26622842 DOI: 10.3892/ol.2015.3507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/25/2015] [Indexed: 11/06/2022] Open
Abstract
Baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5)/survivin genetic microRNA (miRNA) binding site variants in the 3' untranslated region (3'UTR) are known to be significantly associated with cancer risk. However, the roles of genetic variants in BIRC5/survivin gene 3'UTRs and post-transcriptional regulation have not been elucidated. In the present study, we revealed that rs1042489, rs1042542, rs17882360, rs2239680, rs2661694 and rs4789560 in the BIRC5/survivin 3'UTR have potential miRNA binding sites using bioinformatics analysis. However, only rs1042489 was significantly associated with BIRC5/survivin mRNA expression in lymphoblastoid cell lines (P=0.030); rs1042489 may be a putative variant mediating the post-transcriptional regulation of the target BIRC5/survivin gene. An in-depth understanding of how 3'UTR variants regulate BIRC5/survivin activity is expected to pave the way to targeting the BIRC5/survivin pathway in cancer therapy.
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Affiliation(s)
- Feifei Pu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zengwu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Shuhua Yang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jianxiang Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Song Lin
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiucai Ma
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Haofei Yang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Huang CH, Wu MY, Chang PMH, Huang CY, Ng KL. In silico identification of potential targets and drugs for non-small cell lung cancer. IET Syst Biol 2014; 8:56-66. [PMID: 25014226 PMCID: PMC8687210 DOI: 10.1049/iet-syb.2013.0035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/03/2013] [Accepted: 12/23/2013] [Indexed: 12/28/2022] Open
Abstract
Lung cancer is one of the leading causes of death in both the USA and Taiwan, and it is thought that the cause of cancer could be because of the gain of function of an oncoprotein or the loss of function of a tumour suppressor protein. Consequently, these proteins are potential targets for drugs. In this study, differentially expressed genes are identified, via an expression dataset generated from lung adenocarcinoma tumour and adjacent non-tumour tissues. This study has integrated many complementary resources, that is, microarray, protein-protein interaction and protein complex. After constructing the lung cancer protein-protein interaction network (PPIN), the authors performed graph theory analysis of PPIN. Highly dense modules are identified, which are potential cancer-associated protein complexes. Up- and down-regulated communities were used as queries to perform functional enrichment analysis. Enriched biological processes and pathways are determined. These sets of up- and down-regulated genes were submitted to the Connectivity Map web resource to identify potential drugs. The authors' findings suggested that eight drugs from DrugBank and three drugs from NCBI can potentially reverse certain up- and down-regulated genes' expression. In conclusion, this study provides a systematic strategy to discover potential drugs and target genes for lung cancer.
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Affiliation(s)
- Chien-Hung Huang
- Department of Computer Science and Information Engineering, National Formosa University, 64, Wen-Hwa Road, Hu-wei 632, Yun-Lin, Taiwan
| | - Min-You Wu
- Department of Computer Science and Information Engineering, National Formosa University, 64, Wen-Hwa Road, Hu-wei 632, Yun-Lin, Taiwan
| | - Peter Mu-Hsin Chang
- Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Faculty of Medicine, National Yang Ming University, Taipei 112, Taiwan
| | - Chi-Ying Huang
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, 155, Sec. 2, Linong Street, Taipei 112, Taiwan
| | - Ka-Lok Ng
- School of Pharmacy, China Medical University, Taichung 40402, Taiwan.
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Onodera Y, Nam JM, Sabe H. Intracellular trafficking of integrins in cancer cells. Pharmacol Ther 2013; 140:1-9. [PMID: 23711790 DOI: 10.1016/j.pharmthera.2013.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 02/01/2023]
Abstract
Integrins are heterodimeric cell surface receptors, which principally mediate the interaction between cells and their extracellular microenvironments. Because of their pivotal roles in cancer proliferation, survival, invasion and metastasis, integrins have been recognized as promising targets for cancer treatment. As is the case with other receptors, the localization of integrins on the cell surface has provided opportunities to block their functions by various inhibitory monoclonal antibodies. A number of small molecule agents blocking integrin-ligand binding have also been established, and some such agents are currently on the market or in clinical trials for some diseases including cancer. This review exclusively focuses on another strategy for cancer therapy, which comes from the obligate localization of integrins on the cell surface; targeting the intracellular trafficking of integrins. A number of studies have shown the essential roles of integrin trafficking in hallmarks of cancer, such as activation of oncogenic signaling pathways as well as acquisition of invasiveness. Recent findings have shown that increased integrin recycling activity is associated with some types of gain-of-function mutations of p53, a common feature of diverse types of cancers, which also indicates that targeting integrin recycling could be widely applicable and effective against many cancers. We also discuss possible therapeutic contexts where integrin trafficking can be effectively targeted, and what molecular interfaces may hopefully be druggable.
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Affiliation(s)
- Yasuhito Onodera
- Department of Molecular Biology Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
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Abstract
Small GTP-binding proteins of the ADP-ribosylation factor (Arf) family control various cell functional responses including protein transport and recycling between different cellular compartments, phagocytosis, proliferation, cytoskeletal remodelling, and migration. The activity of Arfs is tightly regulated. GTPase-activating proteins (GAPs) inactivate Arfs by stimulating GTP hydrolysis, and guanine nucleotide exchange factors (GEFs) stimulate the conversion of inactive GDP-bound Arf to the active GTP-bound conformation. There is increasing evidence that Arf small GTPases contribute to cancer growth and invasion. Increased expression of Arf6 and of Arf-GEPs, or deregulation Arf-GAP functions have been correlated with enhanced invasive capacity of tumor cells and metastasis. The spatiotemporal specificity of Arf activation is dictated by their GEFs that integrate various signals in stimulated cells. Brefeldin A (BFA), which inactivates a subset of Arf-GEFs, has been very useful for assessing the function of Golgi-localized Arfs. However, specific inhibitors to investigate the individual function of BFA-sensitive and insensitive Arf-GEFs are lacking. In recent years, specific screens have been developed, and new inhibitors with improved selectivity and potency to study cell functional responses regulated by BFA-sensitive and BFA-insensitive Arf pathways have been identified. These inhibitors have been instrumental for our understanding of the spatiotemporal activation of Arf proteins in cells and demonstrate the feasibility of developing small molecules interfering with Arf activation to prevent tumor invasion and metastasis.
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Male H, Patel V, Jacob MA, Borrego-Diaz E, Wang K, Young DA, Wise AL, Huang C, Van Veldhuizen P, O'Brien-Ladner A, Williamson SK, Taylor SA, Tawfik O, Esfandyari T, Farassati F. Inhibition of RalA signaling pathway in treatment of non-small cell lung cancer. Lung Cancer 2012; 77:252-9. [PMID: 22498113 DOI: 10.1016/j.lungcan.2012.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 03/07/2012] [Accepted: 03/14/2012] [Indexed: 12/11/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and relatively resistant to chemotherapy. The most prevalent molecular abnormality in NSCLC is the overactivation of K-Ras proto-oncogene; therefore, elucidating down-stream Ras signaling in NSCLC is significantly important in developing novel therapies against this malignancy. Our work indicates that RalA, an important effector of Ras, is activated in NSCLC cell lines. While RalA was also overactivated in fetal human broncho-epithelial cells, RalBP1 (Ral binding protein-1), an important down-stream effector of RalA, was expressed at higher levels in cancer cell lines. Aurora kinase-A (AKA), an upstream activator of RalA, was also found to be active only in malignant cells. The outcome of inhibition of RalA (by gene specific silencing using a lentivirus) on the malignant phenotype of A549 cells was also studied. While proliferation and invasiveness of A549 cells were reduced upon silencing RalA, apoptosis and necrosis were elevated in such conditions. Additionally, the in vivo tumorigenesis of A549 cells was reduced upon partial inhibition of RalA and AKA using pharmacological inhibitors. Finally, we were interested in evaluating the level of active RalA in the fraction of NSCLC cells expressing cancer stem cell markers. For this purpose cells with increased expression of CD44 were separated from A549 cells and compared with cells with low level of expression of this marker and an unsorted population. A significant enhancement of RalA activation in high CD44+ cells was found as potential evidence for involvement of RalA signaling in initiation of the neoplastic procedure and an important contributor for tumor maintenance in NSCLC. Further studies can reveal therapeutic, preventive and diagnostic value of RalA pathway in this deadly disease.
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Affiliation(s)
- Heather Male
- The University of Kansas Medical Center, Department of Medicine - Divisions of Hematology/Oncology & Gastroenterology, Molecular Medicine Laboratory, Kansas City, KS, USA
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