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Oketch DJA, Giulietti M, Piva F. A Comparison of Tools That Identify Tumor Cells by Inferring Copy Number Variations from Single-Cell Experiments in Pancreatic Ductal Adenocarcinoma. Biomedicines 2024; 12:1759. [PMID: 39200223 PMCID: PMC11351975 DOI: 10.3390/biomedicines12081759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technique has enabled detailed analysis of gene expression at the single cell level, enhancing the understanding of subtle mechanisms that underly pathologies and drug resistance. To derive such biological meaning from sequencing data in oncology, some critical processing must be performed, including identification of the tumor cells by markers and algorithms that infer copy number variations (CNVs). We compared the performance of sciCNV, InferCNV, CopyKAT and SCEVAN tools that identify tumor cells by inferring CNVs from scRNA-seq data. Sequencing data from Pancreatic Ductal Adenocarcinoma (PDAC) patients, adjacent and healthy tissues were analyzed, and the predicted tumor cells were compared to those identified by well-assessed PDAC markers. Results from InferCNV, CopyKAT and SCEVAN overlapped by less than 30% with InferCNV showing the highest sensitivity (0.72) and SCEVAN the highest specificity (0.75). We show that the predictions are highly dependent on the sample and the software used, and that they return so many false positives hence are of little use in verifying or filtering predictions made via tumor biomarkers. We highlight how critical this processing can be, warn against the blind use of these software and point out the great need for more reliable algorithms.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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Yang Y, Gong Y, Ding Y, Sun S, Bai R, Zhuo S, Zhang Z. LINC01133 promotes pancreatic ductal adenocarcinoma epithelial-mesenchymal transition mediated by SPP1 through binding to Arp3. Cell Death Dis 2024; 15:492. [PMID: 38987572 PMCID: PMC11237081 DOI: 10.1038/s41419-024-06876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment methods. Long non-coding RNAs (lncRNAs) have been found involved in tumorigenic and progression. The present study revealed that LINC01133, a fewly reported lncRNA, was one of 16 hub genes that could predict PDAC patients' prognosis. LINC01133 was over-expressed in PDAC tumors compared to adjacent pancreas and could promote PDAC proliferation and metastasis in vitro and in vivo, as well as inhibit PDAC apoptosis. LINC01133 expression positively correlated to secreted phosphoprotein 1 (SPP1) expression, leading to an enhanced epithelial-mesenchymal transition (EMT) process. LINC01133 bound with actin-related protein 3 (Arp3), the complex reduced SPP1 mRNA degradation which increased SPP1 mRNA level, ultimately leading to PDAC proliferation. This research revealed a novel mechanism of PDAC development and provided a potential prognosis indicator that may benefit PDAC patients.
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Affiliation(s)
- Yefan Yang
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Yuxi Gong
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Ying Ding
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Shuning Sun
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Rumeng Bai
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Shuaishuai Zhuo
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Zhihong Zhang
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, 210029, China.
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Huang Y, Zhang R, Lyu H, Xiao S, Guo D, Chen XZ, Zhou C, Tang J. LncRNAs as nodes for the cross-talk between autophagy and Wnt signaling in pancreatic cancer drug resistance. Int J Biol Sci 2024; 20:2698-2726. [PMID: 38725864 PMCID: PMC11077374 DOI: 10.7150/ijbs.91832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/06/2024] [Indexed: 05/12/2024] Open
Abstract
Pancreatic cancer is a malignancy with high mortality. In addition to the few symptoms until the disease reaches an advanced stage, the high fatality rate is attributed to its rapid development, drug resistance and lack of appropriate treatment. In the selection and research of therapeutic drugs, gemcitabine is the first-line drug for pancreatic cancer. Solving the problem of gemcitabine resistance in pancreatic cancer will contribute to the progress of pancreatic cancer treatment. Long non coding RNAs (lncRNAs), which are RNA transcripts longer than 200 nucleotides, play vital roles in cellular physiological metabolic activities. Currently, our group and others have found that some lncRNAs are aberrantly expressed in pancreatic cancer cells, which can regulate the process of cancer through autophagy and Wnt/β-catenin pathways simultaneously and affect the sensitivity of cancer cells to therapeutic drugs. This review presents an overview of the recent evidence concerning the node of lncRNA for the cross-talk between autophagy and Wnt/β-catenin signaling in pancreatic cancer, together with the practicability of lncRNAs and the core regulatory factors as targets in therapeutic resistance.
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Affiliation(s)
- Yuhan Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada, T6G2R3
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
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Dai YW, Pan YT, Lin DF, Chen XH, Zhou X, Wang WM. Bulk anda single-cell transcriptome profiling reveals the molecular characteristics of T cell-mediated tumor killing in pancreatic cancer. Heliyon 2024; 10:e27216. [PMID: 38449660 PMCID: PMC10915414 DOI: 10.1016/j.heliyon.2024.e27216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
Background Despite the potential of immune checkpoint blockade (ICB) as a promising treatment for Pancreatic adenocarcinoma (PAAD), there is still a need to identify specific subgroups of PAAD patients who may benefit more from ICB. T cell-mediated tumor killing (TTK) is the primary concept behind ICB. We explored subtypes according to genes correlated with the sensitivity to TKK and unraveled their underlying associations for PAAD immunotherapies. Methods Genes that control the responsiveness of T cell-induced tumor destruction (GSTTK) were examined in PAAD, focusing on their varying expression levels and association with survival results. Moreover, samples with PAAD were separated into two subsets using unsupervised clustering based on GSTTK. Variability was evident in the tumor immune microenvironment, genetic mutation, and response to immunotherapy among different groups. In the end, we developed TRGscore, an innovative scoring system, and investigated its clinical and predictive significance in determining sensitivity to immunotherapy. Results Patients with PAAD were categorized into 2 clusters based on the expression of 52 GSTTKs, which showed varying levels and prognostic relevance, revealing unique TTK patterns. Survival outcome, immune cell infiltration, immunotherapy responses, and functional enrichment are also distinguished among the two clusters. Moreover, we found the CATSPER1 gene promotes the progression of PAAD through experiments. In addition, the TRGscore effectively predicted the responses to chemotherapeutics or immunotherapy in patients with PAAD and overall survival. Conclusions TTK exerted a vital influence on the tumor immune environment in PAAD. A greater understanding of TIME characteristics was gained through the evaluation of the variations in TTK modes across different tumor types. It highlights variations in the performance of T cells in PAAD and provides direction for improved treatment approaches.
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Affiliation(s)
- Yin-wei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ya-ting Pan
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan-feng Lin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao-hu Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiang Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei-ming Wang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Guo Z, Ashrafizadeh M, Zhang W, Zou R, Sethi G, Zhang X. Molecular profile of metastasis, cell plasticity and EMT in pancreatic cancer: a pre-clinical connection to aggressiveness and drug resistance. Cancer Metastasis Rev 2024; 43:29-53. [PMID: 37453022 DOI: 10.1007/s10555-023-10125-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The metastasis is a multistep process in which a small proportion of cancer cells are detached from the colony to enter into blood cells for obtaining a new place for metastasis and proliferation. The metastasis and cell plasticity are considered major causes of cancer-related deaths since they improve the malignancy of cancer cells and provide poor prognosis for patients. Furthermore, enhancement in the aggressiveness of cancer cells has been related to the development of drug resistance. Metastasis of pancreatic cancer (PC) cells has been considered one of the major causes of death in patients and their undesirable prognosis. PC is among the most malignant tumors of the gastrointestinal tract and in addition to lifestyle, smoking, and other factors, genomic changes play a key role in its progression. The stimulation of EMT in PC cells occurs as a result of changes in molecular interaction, and in addition to increasing metastasis, EMT participates in the development of chemoresistance. The epithelial, mesenchymal, and acinar cell plasticity can occur and determines the progression of PC. The major molecular pathways including STAT3, PTEN, PI3K/Akt, and Wnt participate in regulating the metastasis of PC cells. The communication in tumor microenvironment can provide by exosomes in determining PC metastasis. The components of tumor microenvironment including macrophages, neutrophils, and cancer-associated fibroblasts can modulate PC progression and the response of cancer cells to chemotherapy.
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Affiliation(s)
- Zhenli Guo
- Department of Oncology, First Affiliated Hospital, Gannan Medical University, 128 Jinling Road, Ganzhou City, Jiangxi Province, 341000, China
| | - Milad Ashrafizadeh
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China.
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Wei Zhang
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Gautam Sethi
- Department of Pharmacology, National University of Singapore, 16 Medical Drive, Singapore, 117600, Singapore.
| | - Xianbin Zhang
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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Gao Y, Ren J, Chen K, Guan G. Construction and validation of a prognostic signature for mucinous colonic adenocarcinoma based on N7-methylguanosine-related long non-coding RNAs. J Gastrointest Oncol 2024; 15:203-219. [PMID: 38482248 PMCID: PMC10932661 DOI: 10.21037/jgo-23-980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/21/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND Mucinous colonic adenocarcinoma remains a challenging disease due to its high propensity for metastasis and recurrence. N7-methylguanosine (m7G) and long non-coding RNA (lncRNA) are closely associated with the occurrence and progression of tumors. However, research on m7G-related lncRNA in mucinous colonic adenocarcinoma is lacking. Therefore, we sought to explore the prognostic impact of m7G-related lncRNAs in mucinous adenocarcinoma (MC) patients. METHODS In this study, Pearson analysis was used to identify m7G-related lncRNAs from transcriptome data in The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression were used to further screen m7G-related lncRNAs and incorporate them into a prognostic signature. Based on the risk model, patients were divided into low- and high-risk groups and randomly assigned to the training set and test sets in a 6:4 ratio. Kaplan-Meier, receiver operating characteristic (ROC) curve, multivariate regression, and nomogram analyses were used to confirm the accuracy of the signature. The CIBERSORT algorithm was used to calculate the degree of immune cell infiltration (ICI). Finally, the correlation of the prognostic signature with tumor mutational burden (TMB) and immunophenotype score (IPS) was evaluated. RESULTS A total of 432 m7G-related lncRNAs were identified by Pearson analysis. Univariate Cox regression, LASSO regression and survival analysis were performed to further select six m7G-related lncRNAs (P<0.05): AC254629.1, LINC01133, LINC01134, MHENCR, SMIM2-AS1, and XACT. Based on the risk model, heat maps, Kaplan-Meier curves, and ROC curves were constructed, and the results showed that there were significant differences in expression levels and survival status between the two risk groups. The area under the ROC curve (AUC) values for 3-, 5-, and 10-year survival in the training set were 0.944, 0.957, and 1.000, respectively. And in the test set were 0.964, 1.000, and 1.000, respectively. Subsequently, univariate and multivariate regression analyses of clinical characteristics and risk score were performed. The results of risk score were [hazard ratio (HR): 6.458, 95% confidence interval (CI): 2.708-15.403, P<0.001; HR: 7.280, 95% CI: 2.500-21.203, P<0.001], respectively. Using the risk score as an independent prognostic factor, the AUC of it over 3, 5, and 10 years was 0.911, 0.955, and 0.961, respectively. Calibration plots for the nomogram show that the model calibration line is very close to the ideal calibration line, indicating good calibration. The level of ICI was significantly different in the different risk groups. Survival analysis showed that, regardless of TMB risk, patients with MC and a high-risk score consistently had a poor overall survival (OS). CONCLUSIONS The m7G-related lncRNA prognostic signature has potential value for the prognosis of mucinous colonic adenocarcinoma.
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Affiliation(s)
- Yuan Gao
- Department of Colorectal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Colorectal Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jinjin Ren
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Guoxian Guan
- Department of Colorectal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Colorectal Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Abdominal Surgery Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Chen SJ, Ren LK, Fei XB, Liu P, Wang X, Zhu CH, Pan YZ. A study on the role of Taxifolin in inducing apoptosis of pancreatic cancer cells: screening results using weighted gene co-expression network analysis. Aging (Albany NY) 2024; 16:2617-2637. [PMID: 38305809 PMCID: PMC10911370 DOI: 10.18632/aging.205500] [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: 09/06/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024]
Abstract
Pancreatic adenocarcinoma (PAAD) is a frequent malignant tumor in the pancreas. The incomplete understanding of cancer etiology and pathogenesis, as well as the limitations in early detection and diagnostic methods, have created an urgent need for the discovery of new therapeutic targets and drugs to control this disease. As a result, the current therapeutic options are limited. In this study, the weighted gene co-expression network analysis (WGCNA) method was employed to identify key genes associated with the progression and prognosis of pancreatic adenocarcinoma (PAAD) patients in the Gene Expression Profiling Interactive Analysis (GEPIA) database. To identify small molecule drugs with potential in the treatment of pancreatic adenocarcinoma (PAAD), we compared key genes to the reference dataset in the CMAP database. First, we analyzed the antitumor properties of small molecule drugs using cell counting kit-8 (CCK-8), AO/EB and Transwell assays. Subsequently, we integrated network pharmacology with molecular docking to explore the potential mechanisms of the identified molecules' anti-tumor effects. Our findings indicated that the progression and prognosis of PAAD patients in pancreatic cancer were associated with 11 genes, namely, DKK1, S100A2, CDA, KRT6A, ITGA3, GPR87, IL20RB, ZBED2, PMEPA1, CST6, and MUC16. These genes were filtered based on their therapeutic potential through comparing them with the reference dataset in the CMAP database. Taxifolin, a natural small molecule drug with the potential for treating PAAD, was screened by comparing it with the reference dataset in the CMAP database. Cell-based experiments have validated the potential of Taxifolin to facilitate apoptosis in pancreatic cancer cells while restraining their invasion and metastasis. This outcome is believed to be achieved via the HIF-1 signaling pathway. In conclusion, this study provided a theoretical basis for screening genes related to the progression of pancreatic cancer and discovered potentially active small molecule drugs. The experimental results confirm that Taxifolin has the ability to promote apoptosis in pancreatic cancer cells.
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Affiliation(s)
- Shao-Jie Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Li-Kun Ren
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Xiao-Bin Fei
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Peng Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xing Wang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Chang-Hao Zhu
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Yao-Zhen Pan
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
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Wang S, Chen J, Li P, Chen Y. LINC01133 can induce acquired ferroptosis resistance by enhancing the FSP1 mRNA stability through forming the LINC01133-FUS-FSP1 complex. Cell Death Dis 2023; 14:767. [PMID: 38007473 PMCID: PMC10676390 DOI: 10.1038/s41419-023-06311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/27/2023]
Abstract
Due to a lack of research on the critical non-coding RNAs in regulating ferroptosis, our study aimed to uncover the crucial ones involved in the process. We found that LINC01133 could make pancreatic cancer cells more resistant to ferroptosis. A higher expression of LINC01133 was associated with a higher IC50 of sorafenib in clinical samples. Furthermore, we discovered that LINC01133 induced this process through enhancing the mRNA stability of FSP1. CEBPB was the transcription factor to increase the expression of LINC01133. A higher CEBPB could also indicate a higher IC50 of sorafenib in patients with cancer. Moreover, we confirmed that LINC01133 could form a triple complex with FUS and FSP1 to increase the mRNA stability of FSP1.
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Affiliation(s)
- Shaowen Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
- Neuromedicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, 518053, China
| | - Jionghuang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Pengping Li
- Department of Thyroid & Breast Surgery, The First People's Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang, China
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518087, China.
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Zhang Y, Wang Y, He X, Yao R, Fan L, Zhao L, Lu B, Pang Z. Genome instability-related LINC02577, LINC01133 and AC107464.2 are lncRNA prognostic markers correlated with immune microenvironment in pancreatic adenocarcinoma. BMC Cancer 2023; 23:430. [PMID: 37173624 PMCID: PMC10176692 DOI: 10.1186/s12885-023-10831-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 04/09/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma (PAAD) is a leading cause of malignancy-related deaths worldwide, and the efficacy of immunotherapy on PAAD is limited. Studies report that long non-coding RNAs (lncRNAs) play an important role in modulating genomic instability and immunotherapy. However, the identification of genome instability-related lncRNAs and their clinical significance has not been investigated in PAAD. METHODS The current study developed a computational framework for mutation hypothesis based on lncRNA expression profile and somatic mutation spectrum in pancreatic adenocarcinoma genome. We explored the potential of GInLncRNAs(genome instability-related lncRNAs) through co-expression analysis and function enrichment analysis. We further analyzed GInLncRNAs by Cox regression and used the results to construct a prognostic lncRNA signature. Finally, we analyzed the relationship between GILncSig (genomic instability derived 3-lncRNA signature) and immunotherapy. RESULTS A GILncSig was developed using bioinformatics analyses. It could divide patients into high-risk and low-risk groups, and there was a significant difference in OS between the two groups. In addition, GILncSig was associated with genome mutation rate in pancreatic adenocarcinoma, indicating its potential value as a marker for genomic instability. The GILncSig accurately grouped wild type patients of KRAS into two risk groups. The prognosis of the low-risk group was significantly improved. GILncSig was significantly correlated with the level of immune cell infiltration and immune checkpoint. CONCLUSIONS In summary, the current study provides a basis for further studies on the role of lncRNA in genomic instability and immunotherapy. The study provides a novel method for identification of cancer biomarkers related to genomic instability and immunotherapy.
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Affiliation(s)
- Yinjiang Zhang
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Yao Wang
- Department of Radiation Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xu He
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Rongfei Yao
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Lu Fan
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Linyi Zhao
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China
| | - Binan Lu
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China.
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China.
| | - Zongran Pang
- School of Pharmacy, Minzu University of China, No. 27, Zhongguancunnan Street, Haidian District, Beijing, 100081, People's Republic of China.
- Key Laboratory of Ethnomedicine, Ministry of Education, Minzu University of China), Beijing, People's Republic of China.
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Al-Noshokaty TM, Mansour A, Abdelhamid R, Abdellatif N, Alaaeldien A, Reda T, Abdelmaksoud NM, Doghish AS, Abulsoud AI, Elshaer SS. Role of long non-coding RNAs in pancreatic cancer pathogenesis and treatment resistance- A review. Pathol Res Pract 2023; 245:154438. [PMID: 37043965 DOI: 10.1016/j.prp.2023.154438] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023]
Abstract
Pancreatic cancer (PC) is one of the deadliest cancers associated with poor prognosis. The lack of reliable means of early cancer detection contributes to this disease's dismal prognosis. Long non-coding RNAs (LncRNAs) are protein-free RNAs produced by genome transcription; they play critical roles in gene expression regulation, epigenetic modification, cell proliferation, differentiation, and reproduction. Recent research has shown that lncRNAs play important regulatory roles in PC behaviors, in addition to their recently found functions. Several in-depth investigations have shown that lncRNAs are strongly linked to PC development and progression. Here, we discuss how lncRNAs, which are often overlooked, play many roles as regulators in the molecular mechanism underlying PC. This review also discusses the involved LncRNAs in PC pathogenesis and treatment resistance.
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Affiliation(s)
- Tohada M Al-Noshokaty
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Abdallah Mansour
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Rehab Abdelhamid
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Nourhan Abdellatif
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Ayat Alaaeldien
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Tasnim Reda
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Nourhan M Abdelmaksoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr, Cairo 11231, Egypt.
| | - Ahmed I Abulsoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr, Cairo 11231, Egypt.
| | - Shereen Saeid Elshaer
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr, Cairo, Egypt
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11
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Li J, Li W, Wang H, Ni B, Liu Y. Development and validation of a novel ferroptosis‑related lncRNA prognostic signature for pancreatic adenocarcinoma. Mol Med Rep 2023; 27:56. [PMID: 36660936 PMCID: PMC9879080 DOI: 10.3892/mmr.2023.12943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/29/2022] [Indexed: 01/19/2023] Open
Abstract
Long non‑coding RNAs (lncRNAs) serve a pivotal role in the regulation of cancer cell ferroptosis. However, the prognostic value of ferroptosis‑related lncRNAs in pancreatic adenocarcinoma (PAAD) largely remains unclear. We aimed at constructing a lncRNA‑based signature to improve the prognosis prediction of PAAD. In the present study, the transcriptome profiling data and clinical information of patients with PAAD were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Gene Consortium (ICGC) databases. Univariate Cox regression analysis of the TCGA cohort demonstrated that 26 ferroptosis‑related lncRNAs had significant prognostic value for PAAD (all P<0.01). Least absolute shrinkage and selection operator regression and multivariate Cox proportional hazards regression analyses were performed to construct a prognostic ferroptosis‑related lncRNA signature (FRLS) comprising nine ferroptosis‑related lncRNAs. The efficacy of this FRLS was verified in the training (TCGA) and validation (ICGC) cohorts. Based on the risk model, high risk scores were significantly correlated with poor overall survival (OS) (hazard ratio, 1.314; 95% confidence interval, 1.218‑1.418; P<0.001). The receiver operating characteristic curves and principal component analysis further demonstrated the robust prognostic ability of the FRLS. Furthermore, a nomogram with favorable predictive efficacy for the prediction of OS was constructed based on the FRLS and clinical features. Gene set enrichment analysis demonstrated that the genes in the FRLS participated in a number of cancer‑associated immunoregulatory pathways. Importantly, it was demonstrated that immune infiltration and response to cancer immunotherapy differed significantly between the high and low‑risk groups according to the FRLS. In conclusion, the risk signature based on the FRLS has potential for the clinical prediction of prognosis and immunotherapy response in patients with PAAD.
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Affiliation(s)
- Jian Li
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China,Department of General Surgery, Air Force Hospital of Western Theater Command, Chengdu, Sichuan 610065, P.R. China,Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Wenhua Li
- Department of Cadre Ward, Air Force Hospital of Western Theater Command, Chengdu, Sichuan 610065, P.R. China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China,Correspondence to: Professor Bing Ni, Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, 30 Gaotanyan Main Street, Shapingba, Chongqing 400038, P.R. China, E-mail:
| | - Yongkang Liu
- Department of General Surgery, Air Force Hospital of Western Theater Command, Chengdu, Sichuan 610065, P.R. China,Dr Yongkang Liu, Department of General Surgery, Air Force Hospital of Western Theater Command, 18 Shunjiang Street, Jinjiang, Chengdu, Sichuan 610065, P.R. China, E-mail:
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12
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Weng Y, Qian H, Hong L, Zhao S, Deng X, Shen B. Identification of EMT-related alternative splicing event of TMC7 to promote invasion and migration of pancreatic cancer. Front Immunol 2023; 13:1089008. [PMID: 36713450 PMCID: PMC9878378 DOI: 10.3389/fimmu.2022.1089008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Objective Epithelial-to-mesenchymal transition (EMT) is tightly associated with the invasion and metastasis of pancreatic cancer with rapid progression and poor prognosis. Notably, gene alternative splicing (AS) event plays a critical role in regulating the progression of pancreatic cancer. Therefore, this study aims to identify the EMT-related AS event in pancreatic cancer. Methods The EMT-related gene sets, transcriptomes, and matched clinical data were obtained from the MSigDB, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. Key gene AS events associated with liver metastasis were identified by prognostic analysis, gene set variation analysis (GSVA), and correlation analysis in pancreatic cancer. The cell line and organoid model was constructed to evaluate these key gene AS events in regulating pancreatic cancer in vitro. Furthermore, we established an EMT-related gene set consisting of 13 genes by prognostic analysis, the role of which was validated in two other databases. Finally, the human pancreatic cancer tissue and organoid model was used to evaluate the correlation between the enrichment of this gene set and liver metastasis. Results Prognostic analysis and correlation analysis revealed that eight AS events were closely associated with the prognosis of pancreatic cancer. Furthermore, the expression of TMC7 and CHECK1 AS events was increased in the metastatic lesions of the human tissue and organoid model. Additionally, the knockdown of exon 17 of TMC7 significantly inhibited the proliferation, invasion, and migration of pancreatic cancer cells in 2D and 3D cell experiments. Finally, the expression of exon 17 of TMC17 exhibited a significant correlation with the poor prognosis in pancreatic ductal adenocarcinoma (PDAC). Conclusion The AS events of TMC7 and CHECK1 were associated with liver metastasis in pancreatic cancer. Moreover, exon 17 of TMC7 could be a potential therapeutic target in pancreatic cancer.
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Affiliation(s)
- Yuanchi Weng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Qian
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liwen Hong
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Xiaxing Deng, ; Baiyong Shen,
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Xiaxing Deng, ; Baiyong Shen,
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13
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Prediction of Survival and Tumor Microenvironment Infiltration Based on Pyroptosis-Related lncRNAs in Pancreatic Cancer. DISEASE MARKERS 2022; 2022:5634887. [PMID: 36618967 PMCID: PMC9822759 DOI: 10.1155/2022/5634887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 01/01/2023]
Abstract
Pancreatic cancer (PC) is a fatal tumor with high mortality. Pyroptosis plays a tumor suppressor role as a novel cell death. However, the influences of the pyroptosis-related lncRNAs (PRlncRNAs) on the prognosis and tumor microenvironment (TME) infiltration have not been fully studied in PC. Using coexpression analysis and univariate Cox regression analysis, we identified seventeen prognostic PRlncRNAs from The Cancer Genome Atlas (TCGA) dataset, which were all expressed differently in normal and tumor samples. A seven-PRlncRNA risk signature was constructed and validated using the least absolute shrinkage and selection operator (LASSO) regression. Furthermore, we verified its independence and created a nomogram to validate the clinical viability of the risk signature. We then identified its relationship with clinical factors and evaluated its values in TME infiltration, functional enrichment, tumor mutation, and therapeutic responses in PC. Lower ImmuneScore, ESTIMATEScore, and advanced tumor stage were connected with high-risk score. The low-risk group was characterized by better OS, elevated immune activation, and higher susceptibility of pazopanib and sunitinib. The high-risk group possessed a worse immune infiltration and poor survival, with higher tumor mutations and lapatinib and paclitaxel that may be better choices in this group. In conclusion, we developed an original seven-PRlncRNA risk signature to predict prognosis, TME infiltration, tumor mutation, and therapeutic options for PC patients.
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14
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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15
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Mokhtari M. A review on the role of LINC01133 in cancers. Cancer Cell Int 2022; 22:270. [PMID: 36042493 PMCID: PMC9429693 DOI: 10.1186/s12935-022-02690-z] [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: 01/04/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Long Intergenic Non-Protein Coding RNA 1133 (LINC01133) is a long non-coding RNA (lncRNA) which interacts with miR-106a-3p, miR-576-5p, miR-495-3p, miR-205, miR-199a-5p, miR-4784, miR-30a-5p, miR-199a, miR-30b-5p, miR-216a -5p and miR-422a, thus increasing expression of mRNA targets of these miRNAs. LINC01133 can affect cancer metastasis through regulation of epithelial-mesenchymal transition program. Dysregulation of this lncRNA has been repeatedly detected in the process of tumorigenesis. In this review, we summarize the results of various studies that reported dysregulation of LINC01133 in different samples and described the role of this lncRNA as a marker for these disorders.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany. .,Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Majid Mokhtari
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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16
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Ashrafizadeh M, Rabiee N, Kumar AP, Sethi G, Zarrabi A, Wang Y. Long noncoding RNAs (lncRNAs) in pancreatic cancer progression. Drug Discov Today 2022; 27:2181-2198. [PMID: 35589014 DOI: 10.1016/j.drudis.2022.05.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/18/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules involved in gene regulation at transcriptional, post-transcriptional, and epigenetic levels. LncRNAs participate in regulating apoptosis and autophagy in pancreatic cancer (PCa) and can promote and/or decrease the proliferation rate of tumor cells. The metastasis of PCa cells is tightly regulated by lncRNAs and they can affect the mechanism of epithelial-mesenchymal transition (EMT) to modulate metastasis. The drug resistance of PCa cells, especially to gemcitabine, can be affected by lncRNAs. In addition, lncRNAs enriched in exosomes can be transferred among tumor cells to regulate their proliferation and metastasis. Antitumor compounds, such as curcumin and ginsenosides, can regulate lncRNA expression in PCa therapy. As we discuss here, the expression level of lncRNAs can be considered as both a diagnostic and prognostic tool in patients with PCa.
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Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey.
| | - Navid Rabiee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea; School of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Sariyer 34396, Istanbul, Turkey.
| | - Yuzhuo Wang
- Department of Urological Sciences, Vancouver, BC V6H3Z6, Canada; Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada.
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Jiang S, Zhang Q, Li J, Raziq K, Kang X, Liang S, Sun C, Liang X, Zhao D, Fu S, Cai M. New Sights Into Long Non-Coding RNA LINC01133 in Cancer. Front Oncol 2022; 12:908162. [PMID: 35747817 PMCID: PMC9209730 DOI: 10.3389/fonc.2022.908162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
LINC01133 is a long intergenic non-coding RNA that regulates malignancy in several cancers, including those of the digestive, female reproductive, respiratory, and urinary system. LINC01133 is an extensively studied lncRNA that is highly conserved, and its relatively stable expression is essential for its robust biological function. Its expression is highly tissue-specific with a distinct subcellular localization. It functions as an oncogene or a tumor suppressor gene in different cancers via multiple mechanisms, such as those that involve competing with endogenous RNA and binding to RNA-binding proteins or DNA. Moreover, the secretion and transportation of LINC01133 by extracellular vesicles in the tumor micro-environment is regulated by other cells in the tumor micro-environment. To date, two mechanisms, an increase in copy number and regulation of transcription elements, have been found to regulate LINC01133 expression. Clinically, LINC01133 is an ideal marker for cancer prognosis and a potential therapeutic target in cancer treatment regimes. In this review, we aimed to summarize the aforementioned information as well as posit future directions for LINC01133 research.
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Affiliation(s)
- Shengnan Jiang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Qian Zhang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jiaqi Li
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Khadija Raziq
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xinyu Kang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Shiyin Liang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chaoyue Sun
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xiao Liang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Di Zhao
- Department of Genecology and Obstetrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Songbin Fu
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Mengdi Cai
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- *Correspondence: Mengdi Cai,
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da Paixão VF, Sosa OJ, da Silva Pellegrina DV, Dazzani B, Corrêa TB, Risério Bertoldi E, da Cruz E Alves-de-Moraes LB, de Oliveira Pessoa D, de Paiva Oliveira V, Alberto Chiong Zevallos R, Russo LC, Forti FL, Eduardo Ferreira J, Carioca Freitas H, Jukemura J, Machado MCC, Dirlei Begnami M, Setubal JC, Bassères DS, Moraes Reis E. Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma. Cell Oncol (Dordr) 2022; 45:479-504. [PMID: 35567709 DOI: 10.1007/s13402-022-00678-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Transcriptome analysis of pancreatic ductal adenocarcinoma (PDAC) has been useful to identify gene expression changes that sustain malignant phenotypes. Yet, most studies examined only tumor tissues and focused on protein-coding genes, leaving long non-coding RNAs (lncRNAs) largely underexplored. METHODS We generated total RNA-Seq data from patient-matched tumor and nonmalignant pancreatic tissues and implemented a computational pipeline to survey known and novel lncRNAs. siRNA-mediated knockdown in tumor cell lines was performed to assess the contribution of PDAC-associated lncRNAs to malignant phenotypes. Gene co-expression network and functional enrichment analyses were used to assign deregulated lncRNAs to biological processes and molecular pathways. RESULTS We detected 9,032 GENCODE lncRNAs as well as 523 unannotated lncRNAs, including transcripts significantly associated with patient outcome. Aberrant expression of a subset of novel and known lncRNAs was confirmed in patient samples and cell lines. siRNA-mediated knockdown of a subset of these lncRNAs (LINC01559, LINC01133, CCAT1, LINC00920 and UCA1) reduced cell proliferation, migration and invasion. Gene co-expression network analysis associated PDAC-deregulated lncRNAs with diverse biological processes, such as cell adhesion, protein glycosylation and DNA repair. Furthermore, UCA1 knockdown was shown to specifically deregulate co-expressed genes involved in DNA repair and to negatively impact DNA repair following damage induced by ionizing radiation. CONCLUSIONS Our study expands the repertoire of lncRNAs deregulated in PDAC, thereby revealing novel candidate biomarkers for patient risk stratification. It also provides a roadmap for functional assays aimed to characterize novel mechanisms of action of lncRNAs in pancreatic cancer, which could be explored for therapeutic development.
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Affiliation(s)
- Vinicius Ferreira da Paixão
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Omar Julio Sosa
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Bianca Dazzani
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Thalita Bueno Corrêa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Ester Risério Bertoldi
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luís Bruno da Cruz E Alves-de-Moraes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Diogo de Oliveira Pessoa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Victoria de Paiva Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Ricardo Alberto Chiong Zevallos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Lilian Cristina Russo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Fabio Luis Forti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - João Eduardo Ferreira
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - José Jukemura
- Departamento de Gastroenterologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Maria Dirlei Begnami
- Departamento de Anatomia Patológica - AC Camargo Cancer Center, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Daniela Sanchez Bassères
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil.
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19
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Jiang H, Zhang Z, Yu Y, Chu HY, Yu S, Yao S, Zhang G, Zhang BT. Drug Discovery of DKK1 Inhibitors. Front Pharmacol 2022; 13:847387. [PMID: 35355709 PMCID: PMC8959454 DOI: 10.3389/fphar.2022.847387] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/21/2022] [Indexed: 12/24/2022] Open
Abstract
Dickkopf-1 (DKK1) is a well-characterized Wnt inhibitor and component of the Wnt/β-catenin signaling pathway, whose dysregulation is associated with multiple abnormal pathologies including osteoporosis, Alzheimer's disease, diabetes, and various cancers. The Wnt signaling pathway has fundamental roles in cell fate determination, cell proliferation, and survival; thus, its mis-regulation can lead to disease. Although DKK1 is involved in other signaling pathways, including the β-catenin-independent Wnt pathway and the DKK1/CKAP4 pathway, the inhibition of DKK1 to propagate Wnt/β-catenin signals has been validated as an effective way to treat related diseases. In fact, strategies for developing DKK1 inhibitors have produced encouraging clinical results in different pathological models, and many publications provide detailed information about these inhibitors, which include small molecules, antibodies, and nucleic acids, and may function at the protein or mRNA level. However, no systematic review has yet provided an overview of the various aspects of their development and prospects. Therefore, we review the DKK1 inhibitors currently available or under study and provide an outlook on future studies involving DKK1 and drug discovery.
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Affiliation(s)
- Hewen Jiang
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Zongkang Zhang
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Yuanyuan Yu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China.,Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Hang Yin Chu
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Sifan Yu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China.,Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Shanshan Yao
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Ge Zhang
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China.,Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
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20
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Sharma U, Barwal TS, Murmu M, Acharya V, Pant N, Dey D, Vivek, Gautam A, Bazala S, Singh I, Azzouz F, Bishayee A, Jain A. Clinical potential of long non-coding RNA LINC01133 as a promising biomarker and therapeutic target in cancers. Biomark Med 2022; 16:349-369. [PMID: 35195032 DOI: 10.2217/bmm-2021-0682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recently, long intergenic non-protein coding RNA 01133 (LINC01133) was identified as a novel transcript in cancers. It modulates various hallmarks of cancers and acts as oncogenic in some cancers while tumor-suppressive in others. Furthermore, the expression of LINC01133 correlates with tumor size, advanced tumor node metastasis stage and lymphatic node metastasis, Ki-67 levels and overall survival of patients. Herein, the authors provide an in-depth analysis describing how LINC01133 modulates the multiple cancer-associated signaling pathways and the pathogenesis of various malignancies and treatment regimens. Based on the role played by LINC01133, the authors propose LINC01133 as both a potential biomarker and a therapeutic target in cancer.
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Affiliation(s)
- Uttam Sharma
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Tushar Singh Barwal
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Masang Murmu
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Varnali Acharya
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Neha Pant
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Damayanti Dey
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Vivek
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Ashima Gautam
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Sonali Bazala
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Ipsa Singh
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
| | - Farah Azzouz
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Ghudda, 151 401, Punjab, India
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21
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Zhai X, Wu Y, Wang Z, Zhao D, Li H, Chong T, Zhao J. Long Noncoding RNA LINC01133 Promotes the Malignant Behaviors of Renal Cell Carcinoma by Regulating the miR-30b-5p/Rab3D Axis. Cell Transplant 2021; 29:963689720964413. [PMID: 33054325 PMCID: PMC7784578 DOI: 10.1177/0963689720964413] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinoma (RCC) is the most common type of kidney cancer with rising incidence. Long noncoding RNA (lncRNA) LINC01133 is a novel lncRNA that is involved in the development of several types of cancers. However, the role of LINC01133 in RCC has not been reported. Thus, in this study, we investigated the functions of LINC01133 in RCC. The qualitative real-time polymerase chain reaction analysis was performed to examine the levels of LINC01133 in RCC tissues and adjacent tissues, as well as RCC cell lines. The results showed that LINC01133 was highly expressed in RCC tissue specimens and cell lines. Downregulation of LINC01133 significantly inhibited the proliferation, migration, and invasion of RCC cells. Further mechanistic investigations proved that LINC01133 directly interacted with microRNA (miR)-30b-5p and regulated the miR-30b-5p expression in RCC cell lines. Moreover, miR-30b-5p exhibited tumor-suppressive activity in RCC cell lines, which was mediated by targeting Ras-related protein Rab-3D (Rab3D). In vivo study showed that LINC01133 knockdown suppressed tumor growth in the nude mice. Taken together, these findings indicated that LINC01133 might be an oncogene in RCC through regulation of the miR-30b-5p/Rab3D axis. Thus, LINC01133 might serve as a potential therapeutic target for the treatment of RCC.
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Affiliation(s)
- Xiaoqiang Zhai
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Wu
- Department of Obstetrics and Gynecology, Xijing Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Zhenlong Wang
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Dawei Zhao
- Department of Urology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi, China
| | - Hecheng Li
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jun Zhao
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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22
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Farooqi AA, Nayyab S, Martinelli C, Berardi R, Katifelis H, Gazouli M, Cho WC. Regulation of Hippo, TGFβ/SMAD, Wnt/ β-Catenin, JAK/STAT, and NOTCH by Long Non-Coding RNAs in Pancreatic Cancer. Front Oncol 2021; 11:657965. [PMID: 34178644 PMCID: PMC8220219 DOI: 10.3389/fonc.2021.657965] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Rapidly evolving and ever-increasing knowledge of the molecular pathophysiology of pancreatic cancer has leveraged our understanding altogether to a next level. Compared to the exciting ground-breaking discoveries related to underlying mechanisms of pancreatic cancer onset and progression, however, there had been relatively few advances in the therapeutic options available for the treatment. Since the discovery of the DNA structure as a helix which replicates semi-conservatively to pass the genetic material to the progeny, there has been conceptual refinement and continuous addition of missing pieces to complete the landscape of central dogma. Starting from transcription to translation, modern era has witnessed non-coding RNA discovery and central role of these versatile regulators in onset and progression of pancreatic cancer. Long non-coding RNAs (lncRNAs) have been shown to act as competitive endogenous RNAs through sequestration and competitive binding to myriad of microRNAs in different cancers. In this article, we set spotlight on emerging evidence of regulation of different signaling pathways (Hippo, TGFβ/SMAD, Wnt/β-Catenin, JAK/STAT and NOTCH) by lncRNAs. Conceptual refinements have enabled us to understand how lncRNAs play central role in post-translational modifications of various proteins and how lncRNAs work with epigenetic-associated machinery to transcriptionally regulate gene network in pancreatic cancer.
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Affiliation(s)
| | - Sawera Nayyab
- Department of Biotechnology, Faculty of Science, University of Sialkot, Sialkot, Pakistan
| | | | - Rossana Berardi
- Università Politecnica delle Marche-Ospedali Riuniti Ancona, Ancona, Italy
| | - Hector Katifelis
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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23
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Dipeptidyl peptidase like 6 promoter methylation is a potential prognostic biomarker for pancreatic ductal adenocarcinoma. Biosci Rep 2021; 40:225864. [PMID: 32701143 PMCID: PMC7396423 DOI: 10.1042/bsr20200214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/07/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Hypermethylation of gene promoters plays an important role in tumorigenesis. The present study aimed to identify and validate promoter methylation-driven genes (PMDGs) for pancreatic ductal adenocarcinoma (PDAC). Methods: Based on GSE49149 and the PDAC cohort of The Cancer Genome Atlas (TCGA), differential analyses of promoter methylation, correlation analysis, and Cox regression analysis were performed to identify PMDGs. The promoter methylation level was assessed by bisulfite sequencing polymerase chain reaction (BSP) in paired tumor and normal tissues of 72 PDAC patients. Kaplan−Meier survival analyses were performed to evaluate the clinical value of PMDGs. Results: In GSE49149, the β-value of the dipeptidyl peptidase like 6 (DPP6) promoter was significantly higher in tumor compared with normal samples (0.50 vs. 0.24, P<0.001). In the PDAC cohort of TCGA, the methylation level of the DPP6 promoter was negatively correlated with mRNA expression (r = −0.54, P<0.001). In a multivariate Cox regression analysis, hypermethylation of the DPP6 promoter was an independent risk factor for PDAC (hazard ratio (HR) = 543.91, P=0.002). The results of BSP revealed that the number of methylated CG sites in the DPP6 promoter was greater in tumor samples than in normal samples (7.43 vs. 2.78, P<0.001). The methylation level of the DPP6 promoter was moderately effective at distinguishing tumor from normal samples (area under ROC curve (AUC) = 0.74, P<0.001). Hypermethylation of the DPP6 promoter was associated with poor overall (HR = 3.61, P<0.001) and disease-free (HR = 2.01, P=0.016) survivals for PDAC patients. Conclusion: These results indicate that DPP6 promoter methylation is a potential prognostic biomarker for PDAC.
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24
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Zhu G, Song J, Chen W, Yuan D, Wang W, Chen X, Liu H, Su H, Zhu J. Expression and Role of Dickkopf-1 (Dkk1) in Tumors: From the Cells to the Patients. Cancer Manag Res 2021; 13:659-675. [PMID: 33536782 PMCID: PMC7847771 DOI: 10.2147/cmar.s275172] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022] Open
Abstract
Dickkopf-1 (Dkk1) is a secretory antagonist of the classical Wnt signaling pathway. Many studies have reported that Dkk1 is abnormally expressed in tumor cells, and abnormal expression of Dkk1 can inhibit cell proliferation or induce apoptosis through pro-apoptotic factors, However, due to the differences in tumor environment and the complex regulatory mechanisms in different tumors, Dkk1 has different effects on the progression of different tumors. In many tumors, high expression of Dkk1 may promote tumor metastasis. However, Dkk1, which is highly expressed in other tumors, can inhibit tumor invasion and metastasis. More and more evidence shows that Dkk1 plays a complex and different role in tumor occurrence, development and metastasis in different tumor environments and through a variety of complex regulatory mechanisms. Therefore, Dkk1 may not only be a useful biomarker of metastasis, but also a target for studying the metabolic mechanism of tumor cells and treating tumors in many tumor types. Therefore, this article reviews the research progress on the expression, mechanism and function of Dkk1 in different tumors, and at the same time, based on the public database data, we made a further analysis of the expression of Dkk1 in different tumors.
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Affiliation(s)
- Guohua Zhu
- Guizhou Medical University, Guiyang, Guizhou Province 550002, People's Republic of China.,Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China
| | - Jukun Song
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China.,Guizhou University School of Medicine, Guiyang, Guizhou Province 550025, People's Republic of China
| | - Weimin Chen
- Guizhou University School of Medicine, Guiyang, Guizhou Province 550025, People's Republic of China
| | - Dongbo Yuan
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China.,Guizhou University School of Medicine, Guiyang, Guizhou Province 550025, People's Republic of China
| | - Wei Wang
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China
| | - Xiaoyue Chen
- Guizhou University School of Medicine, Guiyang, Guizhou Province 550025, People's Republic of China
| | - Hen Liu
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China.,Zunyi Medical University, Zunyi, Guizhou Province 563000, People's Republic of China
| | - Hao Su
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China.,Zunyi Medical University, Zunyi, Guizhou Province 563000, People's Republic of China
| | - Jianguo Zhu
- Guizhou Medical University, Guiyang, Guizhou Province 550002, People's Republic of China.,Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province 550002, People's Republic of China.,Guizhou University School of Medicine, Guiyang, Guizhou Province 550025, People's Republic of China.,Zunyi Medical University, Zunyi, Guizhou Province 563000, People's Republic of China
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25
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Aftabi Y, Ansarin K, Shanehbandi D, Khalili M, Seyedrezazadeh E, Rahbarnia L, Asadi M, Amiri-Sadeghan A, Zafari V, Eyvazi S, Bakhtiyari N, Zarredar H. Long non-coding RNAs as potential biomarkers in the prognosis and diagnosis of lung cancer: A review and target analysis. IUBMB Life 2020; 73:307-327. [PMID: 33369006 DOI: 10.1002/iub.2430] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022]
Abstract
Long non-coding RNAs (lncRNA) have been emerged as a novel class of molecular regulators in cancer. They are dysregulated in many types of cancer; however, there is not enough knowledge available on their expression and functional profiles. Lung cancer is the leading cause of the cancer deaths worldwide. Generally, lncRNAs may be associated with lung tumor pathogenesis and they may act as biomarkers for the cancer prognosis and diagnosis. Compared to other invasive prognostic and diagnostic methods, detection of lncRNAs might be a user-friendly and noninvasive method. In this review article, we selected 27 tumor-associated lncRNAs by literature reviewing to further discussing in detail for using as diagnostic and prognostic biomarkers in lung cancer. Also, in an in silico target analysis, the "Experimentally supported functional regulation" approach of the LncTarD web tool was used to identifying the target genes and regulatory mechanisms of the selected lncRNAs. The reports on diagnostic and prognostic potential of all selected lncRNAs were discussed. However, the target genes and regulatory mechanisms of the 22 lncRNAs were identified by in silico analysis and we found the pathways that are controlled by each target group of lncRNAs. They use epigenetic mechanisms, ceRNA mechanisms, protein interaction and sponge mechanism. Also, 10, 23, 5, and 28 target genes for each of these mechanisms were identified, respectively. Finally, each group of target genes controls 50, 12, 7, and 2 molecular pathways, respectively. In conclusion, LncRNAs could be used as biomarkers in lung cancer due to their roles in control of several signaling pathways related to lung tumors. Also, it seems that lncRNAs, which use epigenetic mechanisms for modulating a large number of pathways, could be considered as important subjects for lung cancer-related diagnostic and prognostic biomarkers.
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Affiliation(s)
- Younes Aftabi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Khalil Ansarin
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Dariush Shanehbandi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Khalili
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran.,Rahat Breathe and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Asadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Amiri-Sadeghan
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Venus Zafari
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Shirin Eyvazi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Nasim Bakhtiyari
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Science, Tabriz, Iran
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26
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Li Z, Xu D, Chen X, Li S, Chan MTV, Wu WKK. LINC01133: an emerging tumor-associated long non-coding RNA in tumor and osteosarcoma. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:32467-32473. [PMID: 32556990 DOI: 10.1007/s11356-020-09631-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Emerging evidence suggested that long non-coding RNAs (lncRNAs) play pivotal roles in tumorigenesis. LINC01133 is a newly identified lncRNA first discovered as an oncogene in lung squamous cell carcinoma. Subsequent studies further demonstrated this lncRNA was deregulated in a wide spectrum of tumors, including colorectal, gastric, lung, and pancreatic ductal adenocarcinoma as well as osteosarcoma and hepatocellular carcinoma. Intriguingly, this lncRNA exerted oncogenic or tumor-suppressive action in a tissue-dependent manner. This review sought to summarize our current understanding concerning the deregulation of LINC01133 in human tumors in relation to its molecular mechanisms and cellular functions. The clinical utilization of LINC01133 as a potential prognostic biomarker and a treatment target is also discussed.
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Affiliation(s)
- Zheng Li
- Department of Orthopaedic, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Derong Xu
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Xin Chen
- Department of Orthopaedic, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugang Li
- Department of Orthopaedic, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - William K K Wu
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The University of Hong Kong, Pok Fu Lam, Hong Kong
- State Laboratory of Digestive Diseases, Centre for Gut Microbiota Research, Institute of Digestive Diseases and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
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27
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DKK1 is epigenetically downregulated by promoter methylation and inhibits bile acid-induced gastric intestinal metaplasia. Biochem Biophys Res Commun 2020; 523:780-786. [PMID: 31952791 DOI: 10.1016/j.bbrc.2019.12.109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023]
Abstract
Dickkopf-related protein 1 (DKK1) is essential to gastric cancer as an inhibitor of Wnt signaling. Gastric intestinal metaplasia (GIM) is an important precancerous lesion of gastric cancer that can be activated by bile acid reflux and chronic inflammation. However, the exact mechanism of DKK1 in bile acid-induced GIM has not been completely elucidated. We aimed to explore the epigenetic alterations and biological functions of DKK1 in the development of GIM. In the present study, bile acid was found to induce the expression of intestinal markers in gastric epithelial cells, whereas DKK1 was downregulated in response to bile acid stimulation. The mRNA and protein expression levels of DKK1 were decreased in GIM tissues as evidenced by qRT-PCR and immunohistochemical staining. Surprisingly, the methylation of the DKK1 promoter increased in GIM tissues, and we discovered 28 differential methylation sites of the DKK1 promoter in GIM tissues. Bile acid was able to induce the partial methylation of the DKK1 promoter, while 5-aza could increase DKK1 expression as well as decrease intestinal markers expression in gastric epithelial cells. In conclusion, the promoter methylation and downregulation of DKK1 might play important roles in the development of GIM, especially bile acid-induced GIM.
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28
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Ram Makena M, Gatla H, Verlekar D, Sukhavasi S, K Pandey M, C Pramanik K. Wnt/β-Catenin Signaling: The Culprit in Pancreatic Carcinogenesis and Therapeutic Resistance. Int J Mol Sci 2019; 20:E4242. [PMID: 31480221 PMCID: PMC6747343 DOI: 10.3390/ijms20174242] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 12/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is responsible for 7.3% of all cancer deaths. Even though there is a steady increase in patient survival for most cancers over the decades, the patient survival rate for pancreatic cancer remains low with current therapeutic strategies. The Wnt/β-catenin pathway controls the maintenance of somatic stem cells in many tissues and organs and is implicated in pancreatic carcinogenesis by regulating cell cycle progression, apoptosis, epithelial-mesenchymal transition (EMT), angiogenesis, stemness, tumor immune microenvironment, etc. Further, dysregulated Wnt has been shown to cause drug resistance in pancreatic cancer. Although different Wnt antagonists are effective in pancreatic patients, limitations remain that must be overcome to increase the survival benefits associated with this emerging therapy. In this review, we have summarized the role of Wnt signaling in pancreatic cancer and suggested future directions to enhance the survival of pancreatic cancer patients.
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Affiliation(s)
- Monish Ram Makena
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Himavanth Gatla
- Department of Pediatric Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Dattesh Verlekar
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Sahithi Sukhavasi
- Center for Distance Learning, GITAM University, Visakhapatnam 530045, India
| | - Manoj K Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Kartick C Pramanik
- Department of Basic Sciences, Kentucky College of Osteopathic Medicine, University of Pikeville, Pikeville, KY 41501, USA.
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29
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A Role for the WNT Co-Receptor LRP6 in Pathogenesis and Therapy of Epithelial Cancers. Cancers (Basel) 2019; 11:cancers11081162. [PMID: 31412666 PMCID: PMC6721565 DOI: 10.3390/cancers11081162] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
The WNT/β-catenin signaling pathway controls stem and progenitor cell proliferation, survival and differentiation in epithelial tissues. Aberrant stimulation of this pathway is therefore frequently observed in cancers from epithelial origin. For instance, colorectal and hepatic cancers display activating mutations in the CTNNB1 gene encoding β-catenin, or inactivating APC and AXIN gene mutations. However, these mutations are uncommon in breast and pancreatic cancers despite nuclear β-catenin localization, indicative of pathway activation. Notably, the low-density lipoprotein receptor-related protein 6 (LRP6), an indispensable co-receptor for WNT, is frequently overexpressed in colorectal, liver, breast and pancreatic adenocarcinomas in association with increased WNT/β -catenin signaling. Moreover, LRP6 is hyperphosphorylated in KRAS-mutated cells and in patient-derived colorectal tumours. Polymorphisms in the LRP6 gene are also associated with different susceptibility to developing specific types of lung, bladder and colorectal cancers. Additionally, recent observations suggest that LRP6 dysfunction may be involved in carcinogenesis. Indeed, reducing LRP6 expression and/or activity inhibits cancer cell proliferation and delays tumour growth in vivo. This review summarizes current knowledge regarding the biological function and regulation of LRP6 in the development of epithelial cancers—especially colorectal, liver, breast and pancreatic cancers.
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