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Integrating Pharmacogenomics Data-Driven Computational Drug Prediction with Single-Cell RNAseq to Demonstrate the Efficacy of a NAMPT Inhibitor against Aggressive, Taxane-Resistant, and Stem-like Cells in Lethal Prostate Cancer. Cancers (Basel) 2022; 14:cancers14236009. [PMID: 36497496 PMCID: PMC9738762 DOI: 10.3390/cancers14236009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Metastatic prostate cancer/PCa is the second leading cause of cancer deaths in US men. Most early-stage PCa are dependent on overexpression of the androgen receptor (AR) and, therefore, androgen deprivation therapies/ADT-sensitive. However, eventual resistance to standard medical castration (AR-inhibitors) and secondary chemotherapies (taxanes) is nearly universal. Further, the presence of cancer stem-like cells (EMT/epithelial-to-mesenchymal transdifferentiation) and neuroendocrine PCa (NEPC) subtypes significantly contribute to aggressive/lethal/advanced variants of PCa (AVPC). In this study, we introduced a pharmacogenomics data-driven optimization-regularization-based computational prediction algorithm ("secDrugs") to predict novel drugs against lethal PCa. Integrating secDrug with single-cell RNA-sequencing/scRNAseq as a 'Double-Hit' drug screening tool, we demonstrated that single-cells representing drug-resistant and stem-cell-like cells showed high expression of the NAMPT pathway genes, indicating potential efficacy of the secDrug FK866 which targets NAMPT. Next, using several cell-based assays, we showed substantial impact of FK866 on clinically advanced PCa as a single agent and in combination with taxanes or AR-inhibitors. Bulk-RNAseq and scRNAseq revealed that, in addition to NAMPT inhibition, FK866 regulates tumor metastasis, cell migration, invasion, DNA repair machinery, redox homeostasis, autophagy, as well as cancer stemness-related genes, HES1 and CD44. Further, we combined a microfluidic chip-based cell migration assay with a traditional cell migration/'scratch' assay and demonstrated that FK866 reduces cancer cell invasion and motility, indicating abrogation of metastasis. Finally, using PCa patient datasets, we showed that FK866 is potentially capable of reversing the expression of several genes associated with biochemical recurrence, including IFITM3 and LTB4R. Thus, using FK866 as a proof-of-concept candidate for drug repurposing, we introduced a novel, universally applicable preclinical drug development pipeline to circumvent subclonal aggressiveness, drug resistance, and stemness in lethal PCa.
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The Comprehensive Analysis of Hub Gene ARRB2 in Prostate Cancer. DISEASE MARKERS 2022; 2022:8518378. [PMID: 36284990 PMCID: PMC9588343 DOI: 10.1155/2022/8518378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 12/01/2022]
Abstract
Methods The differential expressed genes (DEGs) were screened from the gene expression profile GSE30994 related to PRAD and then analyzed by protein-protein interaction (PPI) to screen the hub gene. Subsequently, the relation between hub gene and pan cancers, PRAD prognosis, and immunotherapy was analyzed. Besides, the effects of hub gene on the growth and metastasis of PRAD cell lines and inflammatory factors (IFs) were detected by functional experiments. Results 276 upregulated and 1,861 downregulated DEGs were analyzed from GSE30994 gene expression profiles. Through enrichment analysis, it was found that upregulated DEGs were significantly enriched in nitric oxide-mediated signal transduction, insulin signaling pathway, etc. Through PPI networks, ARRB2 was determined as the hub gene that was highly expressed in pan cancers, including PRAD, and contributed to poor prognosis of PRAD patients. Immunoassay showed that ARRB2 was associated with B cells, NK cells, endothelial cells, etc. and also connected with tumor-infiltrating lymphocytes (TILs). Next, the signature model analysis revealed that ARRB2 had a clinical value in predicting PRAD prognosis. In functional experiments, ARRB2 was highly expressed in PRAD cell lines, promoted PRAD cell growth and metastasis, and positively associated with IFs. Conclusion ARRB2 has a good prognostic ability in PRAD, and it could be a potential target of PRAD immunotherapy, which offers new directions for PRAD research.
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Li W, Xu W, Sun K, Wang F, Wong TW, Kong AN. Identification of novel biomarkers in prostate cancer diagnosis and prognosis. J Biochem Mol Toxicol 2022; 36:e23137. [PMID: 35686336 DOI: 10.1002/jbt.23137] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/23/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is a common urinary malignancy. The lack of specific and sensitive biomarkers for the early diagnosis and prognosis of PCa makes it important to seek alternatives. R software was used to analyze the PCa expression profile from data sets in Gene Expression Omnibus. Core differential genes were identified by String and Cytoscape and further validated by Gene Expression Profiling Interactive Analysis (GEPIA) and The Human Protein Atlas (HPA). Gene Ontology analysis was done in the DIVID database and visualization analysis was conducted by Hiplot. Pathway enrichment was analyzed by IPA. To identify potential competitive endogenous RNAs (ceRNA) networks, the experimentally validated microRNA-target interactions database (miRTarBase), The Encyclopedia of RNA Interactomes (StarBase), lncBase, and GEPIA were used. The lncLocator was utilized to perform subcellular localization of long noncoding RNAs (lncRNAs). Both miRTarBase and StarBase were used to find the binding site of mRNAs-miRNAs and miRNAs-lncRNAs. Visualization of the ceRNA network was performed with Cytoscape. Nine genes closely related to the diagnosis and prognosis of PCa were obtained, including four identified biomarkers by HPA, CENPF, TPX2, TK1, and CCNB1, and five novel PCa biomarkers, RRM2, UBE2C, TOP2A, BIRC5, and ZWINT. Pathway analysis indicated that PCa carcinogenesis was highly correlated with liver fibrosis pathways, ILK signaling, and NRF2-mediated oxidative stress response. Two sets of ceRNA networks, BIRC5/hsa-miR-218-5p/NEAT1 and UBE2C/hsa-miR-483-3p/NEAT1 were found to be novel biomarkers for the identification of PCa. The quantitative real-time polymerase chain reaction results verified that UBE2C, BIRC5, and NEAT1 were upregulated and hsa-miR-218-5p and hsa-miR-483-3p were downregulated in human PCa cells compared with normal prostate epithelial cells. The novel identified biomarkers in this study would be valuable for the diagnosis and prognosis of PCa.
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Affiliation(s)
- Wenji Li
- Department of TCM, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Sino-Malaysia Molecular Oncology and Traditional Chinese Medicine Delivery Joint Research Centre, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Wei Xu
- Department of TCM, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Sino-Malaysia Molecular Oncology and Traditional Chinese Medicine Delivery Joint Research Centre, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Kai Sun
- Department of TCM, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Sino-Malaysia Molecular Oncology and Traditional Chinese Medicine Delivery Joint Research Centre, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Fujun Wang
- Department of TCM, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Sino-Malaysia Molecular Oncology and Traditional Chinese Medicine Delivery Joint Research Centre, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Tin Wui Wong
- Sino-Malaysia Molecular Oncology and Traditional Chinese Medicine Delivery Joint Research Centre, Medical College, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Non-Destructive Biomedical and Pharmaceutical Research Centre, Smart Manufacturing Research Institute, Universiti Teknologi MARA, Puncak Alam, Selangor, Malaysia
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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Downregulation of MicroRNA-1 and Its Potential Molecular Mechanism in Nasopharyngeal Cancer: An Investigation Combined with In Silico and In-House Immunohistochemistry Validation. DISEASE MARKERS 2022; 2022:7962220. [PMID: 35251377 PMCID: PMC8896954 DOI: 10.1155/2022/7962220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/31/2021] [Accepted: 01/29/2022] [Indexed: 11/18/2022]
Abstract
Background This study was aimed at elucidating the molecular biological mechanisms of microRNA-1 (miR-1) in nasopharyngeal carcinoma (NPC). Method In this study, we performed a pooled analysis of miR-1 expression data derived from public databases, such as GEO, ArrayExpress, TCGA, and GTEx. The miRWalk 2.0 database, combined with the mRNA microarray datasets, was used to screen the target genes, and the genes were then subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis using the DAVID 6.8 database. We then used the STRING 11.0 database and Cytoscape 3.80 software to construct a protein-protein interaction (PPI) network for screening hub genes. Immunohistochemistry (IHC) was further used to validate the expression of hub genes. Finally, potential therapeutic agents for NPC were screened by the Connectivity Map (cMap) database. Results Pooled analysis showed that miR-1 expression was significantly decreased in NPC (SMD = −0.57; P < 0.05). The summary receiver operating characteristic curve suggested that miR-1 had a good ability to distinguish cancerous tissues from noncancerous tissues (AUC = 0.78). The results of GO analysis focused on mitotic nuclear division, DNA replication, cell division, cell adhesion, extracellular space, kinesin complex, and extracellular matrix (ECM) structural constituent. The KEGG analysis suggested that the target genes played a role in key signaling pathways, such as cell cycle, focal adhesion, cytokine-cytokine receptor interaction, ECM-receptor interaction, and PI3K/Akt signaling pathway. The PPI network suggested that cyclin-dependent kinase 1 (CDK1) was the hub gene, and the CDK1 protein was subsequently confirmed to be significantly upregulated in NPC tissues by IHC. Finally, potential therapeutic drugs, such as masitinib, were obtained by the cMap database. Conclusion miR-1 may play a vital part in NPC tumorigenesis and progression by regulating focal adhesion kinase to participate in cell mitosis, regulating ECM degradation, and affecting the PI3K/Akt signaling pathway. miR-1 has the potential to be a therapeutic target for NPC.
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The Role of Androgen Receptor and microRNA Interactions in Androgen-Dependent Diseases. Int J Mol Sci 2022; 23:ijms23031553. [PMID: 35163477 PMCID: PMC8835816 DOI: 10.3390/ijms23031553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022] Open
Abstract
The androgen receptor (AR) is a member of the steroid hormone receptor family of nuclear transcription factors. It is present in the primary/secondary sexual organs, kidneys, skeletal muscles, adrenal glands, skin, nervous system, and breast. Abnormal AR functioning has been identified in numerous diseases, specifically in prostate cancer (PCa). Interestingly, recent studies have indicated a relationship between the AR and microRNA (miRNA) crosstalk and cancer progression. MiRNAs are small, endogenous, non-coding molecules that are involved in crucial cellular processes, such as proliferation, apoptosis, or differentiation. On the one hand, AR may be responsible for the downregulation or upregulation of specific miRNA, while on the other hand, AR is often a target of miRNAs due to their regulatory function on AR gene expression. A deeper understanding of the AR–miRNA interactions may contribute to the development of better diagnostic tools as well as to providing new therapeutic approaches. While most studies usually focus on the role of miRNAs and AR in PCa, in this review, we go beyond PCa and provide insight into the most recent discoveries about the interplay between AR and miRNAs, as well as about other AR-associated and AR-independent diseases.
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Liu LJ, Liao JM, Zhu F. Proliferating cell nuclear antigen clamp associated factor, a potential proto-oncogene with increased expression in malignant gastrointestinal tumors. World J Gastrointest Oncol 2021; 13:1425-1439. [PMID: 34721775 PMCID: PMC8529917 DOI: 10.4251/wjgo.v13.i10.1425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancers, including malignancies in the gastrointestinal tract and accessory organs of digestion, represent the leading cause of death worldwide due to the poor prognosis of most GI cancers. An investigation into the potential molecular targets of prediction, diagnosis, prognosis, and therapy in GI cancers is urgently required. Proliferating cell nuclear antigen (PCNA) clamp associated factor (PCLAF), which plays an essential role in cell proliferation, apoptosis, and cell cycle regulation by binding to PCNA, is a potential molecular target of GI cancers as it contributes to a series of malignant properties, including tumorigenesis, epithelial-mesenchymal transition, migration, and invasion. Furthermore, PCLAF is an underlying plasma prediction target in colorectal cancer and liver cancer. In addition to GI cancers, PCLAF is also involved in other types of cancers and autoimmune diseases. Several pivotal pathways, including the Rb/E2F pathway, NF-κB pathway, and p53-p21 cascade, are implicated in PCLAF-mediated diseases. PCLAF also contributes to some diseases through dysregulation of the p53 pathway, WNT signal pathway, MEK/ERK pathway, and PI3K/AKT/mTOR signal cascade. This review mainly describes in detail the role of PCLAF in physiological status and GI cancers. The signaling pathways involved in PCLAF are also summarized. Suppression of the interaction of PCLAF/PCNA or the expression of PCLAF might be potential biological therapeutic strategies for GI cancers.
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Affiliation(s)
- Li-Juan Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Jian-Ming Liao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan 430071, Hubei Province, China
- Department of Neurosurgery, Renmin Hospital, Wuhan University, Wuhan 430060, Hubei Province, China
| | - Fan Zhu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan 430071, Hubei Province, China
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Capik O, Sanli F, Kurt A, Ceylan O, Suer I, Kaya M, Ittmann M, Karatas OF. CASC11 promotes aggressiveness of prostate cancer cells through miR-145/IGF1R axis. Prostate Cancer Prostatic Dis 2021; 24:891-902. [PMID: 33753875 DOI: 10.1038/s41391-021-00353-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/24/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is the most common malignancy diagnosed among men after lung cancer in developed countries. Investigation of the underlying molecular mechanisms of PCa is urgently needed in order to develop better therapeutic strategies and to reveal more effective therapeutic targets. In this study, we aimed at exploring the potential functions of CASC11 in association with miR-145 and IGF1R during the malignant progression of PCa cells. METHODS We initially investigated the oncogenic potential of noncoding members of CASC gene family and analyzed the effects of CASC11 overexpression on proliferation, migration, and colony formation ability of DU145, LNCaP, and PC3 PCa cells. We, then, exprlored the association of CASC11, miR-145, and IGF1R expression and their impacts on PI3K/AKT/mTOR signaling pathway in in vitro models. RESULTS In silico analysis revealed that of the CASC family only CASC11 showed consistent results considering its differential expression as well as its association with the overall survival of patients. We demonstrated that ectopic overexpression of CASC11 significantly increased the proliferation, colony formation, and migration capacity in all three cell lines. CASC11 overexpression caused suppression of miR-145 and overexpression of IGF1R, leading to activation of PI3K/AKT/mTOR signaling pathway. CONCLUSION In summary, we found that CASC11 is upregulated in PCa cells and clinical tumor samples in comparison to corresponding controls and revealed that ectopic CASC11 overexpression promotes cellular phenotypes associated with PCa progression through CASC11/miR-145/IGF1R axis.
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Affiliation(s)
- Ozel Capik
- Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey.,Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Fatma Sanli
- Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey.,Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Ali Kurt
- Department of Pathology, Erzurum Faculty of Medicine, Health Sciences University, Erzurum, Turkey
| | - Onur Ceylan
- Department of Pathology, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Ilknur Suer
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Murat Kaya
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Michael Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.,Michael E. DeBakey VAMC, Houston, TX, USA
| | - Omer Faruk Karatas
- Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey. .,Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey.
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Lin Y, Miao Z, Zhang X, Wei X, Hou J, Huang Y, Shen B. Identification of Key MicroRNAs and Mechanisms in Prostate Cancer Evolution Based on Biomarker Prioritization Model and Carcinogenic Survey. Front Genet 2021; 11:596826. [PMID: 33519899 PMCID: PMC7844321 DOI: 10.3389/fgene.2020.596826] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/21/2020] [Indexed: 02/05/2023] Open
Abstract
Background: Prostate cancer (PCa) is occurred with increasing incidence and heterogeneous pathogenesis. Although clinical strategies are accumulated for PCa prevention, there is still a lack of sensitive biomarkers for the holistic management in PCa occurrence and progression. Based on systems biology and artificial intelligence, translational informatics provides new perspectives for PCa biomarker prioritization and carcinogenic survey. Methods: In this study, gene expression and miRNA-mRNA association data were integrated to construct conditional networks specific to PCa occurrence and progression, respectively. Based on network modeling, hub miRNAs with significantly strong single-line regulatory power were topologically identified and those shared by the condition-specific network systems were chosen as candidate biomarkers for computational validation and functional enrichment analysis. Results: Nine miRNAs, i.e., hsa-miR-1-3p, hsa-miR-125b-5p, hsa-miR-145-5p, hsa-miR-182-5p, hsa-miR-198, hsa-miR-22-3p, hsa-miR-24-3p, hsa-miR-34a-5p, and hsa-miR-499a-5p, were prioritized as key players for PCa management. Most of these miRNAs achieved high AUC values (AUC > 0.70) in differentiating different prostate samples. Among them, seven of the miRNAs have been previously reported as PCa biomarkers, which indicated the performance of the proposed model. The remaining hsa-miR-22-3p and hsa-miR-499a-5p could serve as novel candidates for PCa predicting and monitoring. In particular, key miRNA-mRNA regulations were extracted for pathogenetic understanding. Here hsa-miR-145-5p was selected as the case and hsa-miR-145-5p/NDRG2/AR and hsa-miR-145-5p/KLF5/AR axis were found to be putative mechanisms during PCa evolution. In addition, Wnt signaling, prostate cancer, microRNAs in cancer etc. were significantly enriched by the identified miRNAs-mRNAs, demonstrating the functional role of the identified miRNAs in PCa genesis. Conclusion: Biomarker miRNAs together with the associated miRNA-mRNA relations were computationally identified and analyzed for PCa management and carcinogenic deciphering. Further experimental and clinical validations using low-throughput techniques and human samples are expected for future translational studies.
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Affiliation(s)
- Yuxin Lin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhijun Miao
- Department of Urology, Suzhou Dushuhu Public Hospital, Suzhou, China
| | - Xuefeng Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xuedong Wei
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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Liu J, Li W, Zhang J, Ma Z, Wu X, Tang L. Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma. PeerJ 2019; 7:e8021. [PMID: 31695969 PMCID: PMC6827457 DOI: 10.7717/peerj.8021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although multiple efforts have been made to understand the development of HCC, morbidity, and mortality rates remain high. In this study, we aimed to discover the mRNAs and long non-coding RNAs (lncRNAs) that contribute to the progression of HCC. We constructed a lncRNA-related competitive endogenous RNA (ceRNA) network to elucidate the molecular regulatory mechanism underlying HCC. Methods A microarray dataset (GSE54238) containing information about both mRNAs and lncRNAs was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) in tumor tissues and non-cancerous tissues were identified using the limma package of the R software. The miRNAs that are targeted by DElncRNAs were predicted using miRcode, while the target mRNAs of miRNAs were retrieved from miRDB, miRTarBas, and TargetScan. Functional annotation and pathway enrichment of DEGs were performed using the EnrichNet website. We constructed a protein–protein interaction (PPI) network of DEGs using STRING, and identified the hub genes using Cytoscape. Survival analysis of the hub genes and DElncRNAs was performed using the gene expression profiling interactive analysis database. The expression of molecules with prognostic values was validated on the UALCAN database. The hepatic expression of hub genes was examined using the Human Protein Atlas. The hub genes and DElncRNAs with prognostic values as well as the predictive miRNAs were selected to construct the ceRNA networks. Results We found that 10 hub genes (KPNA2, MCM7, CKS2, KIF23, HMGB2, ZWINT, E2F1, MCM4, H2AFX, and EZH2) and four lncRNAs (FAM182B, SNHG6, SNHG1, and SNHG3) with prognostic values were overexpressed in the hepatic tumor samples. We also constructed a network containing 10 lncRNA–miRNA–mRNA pathways, which might be responsible for regulating the biological mechanisms underlying HCC. Conclusion We found that the 10 significantly overexpressed hub genes and four lncRNAs were negatively correlated with the prognosis of HCC. Further, we suggest that lncRNA SNHG1 and the SNHG3-related ceRNAs can be potential research targets for exploring the molecular mechanisms of HCC.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shaoguan, Guangdong, China.,Morning Star Academic Cooperation, Shanghai, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Jian Zhang
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Zhanzhong Ma
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Xiaoyan Wu
- Community Healthcare Center, Shanghai, Shanghai, China
| | - Lirui Tang
- Morning Star Academic Cooperation, Shanghai, China.,Shanghai JiaoTong University School of Medicine, Shanghai Ninth People's Hospital, Shanghai, China
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