1
|
Chen X, Pan T, Guo G, Chen G, Cai Y, Tang Y, Wang Y, Wang Y, Deng Z, Li L, Zhou Y. LncRNA NORAD mediates KMT2D expression by targeting miR-204-5p and affects the growth of gastric cancer. J Gastrointest Oncol 2022; 13:2832-2844. [PMID: 36636064 PMCID: PMC9830370 DOI: 10.21037/jgo-22-1014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long non-coding ribonucleic acids (lncRNAs) are a class of non-coding RNAs implicated in the development of many malignancies, including gastric cancer (GC). In this study, we investigated the functions and molecular mechanisms of non-coding RNA activated by deoxyribonucleic acid damage (NORAD) in GC. METHODS NORAD expression at the messenger RNA levels was determined by quantitative reverse transcriptase (RT)-polymerase chain reaction assays. Cell proliferation, migration, and invasion were detected by Cell Counting Kit-8 assays, in-vivo tumor formation assays, and Transwell assays. Cell-cycle distribution was detected by a flow cytometry analysis. NORAD location was detected by nucleocytoplasmic fractionation assays. The interaction between NORAD and the microRNA-204-5p (miR-204-5p)/Lysine Methyltransferase 2D (KMT2D) axis was verified by dual-luciferase reporter gene assays and RNA binding protein immunoprecipitation (RIP) assays. Western blot was used to study the phosphatase and tensin homolog (PTEN)/phosphoinositide 3-kinases (PI3K)/protein kinase B (AKT) signaling pathway. RESULTS NORAD was upregulated in the GC tissues and cell lines. The silencing of NORAD repressed cell proliferation and the Growth 2 (G2)/Mitosis (M) cell-cycle transition in GC. NORAD also regulated KMT2D expression by targeting miR-204-5p and mediated PTEN/PI3K/AKT signaling in GC. CONCLUSIONS We found that NORAD acts as an oncogene in GC. Our findings might provide a novel therapeutic target for GC.
Collapse
Affiliation(s)
- Xinqi Chen
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Ting Pan
- Department of Blood Transfusion, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Guohu Guo
- Department of General Surgery, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Guohao Chen
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yongchang Cai
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yuxin Tang
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yijun Wang
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yucheng Wang
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Zhenwei Deng
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Libo Li
- Department of General Surgery, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yan Zhou
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
2
|
Liu Y, Cummins SF, Zhao M. A Genomics Resource for 12 Edible Seaweeds to Predict Seaweed-Secreted Peptides with Potential Anti-Cancer Function. BIOLOGY 2022; 11:biology11101458. [PMID: 36290362 PMCID: PMC9598510 DOI: 10.3390/biology11101458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Seaweeds are multicellular marine macroalgae with natural compounds that have potential anticancer activity. To date, the identification of those compounds has relied on purification and assay, yet few have been documented. Additionally, the genomes and associated proteomes of edible seaweeds that have been identified thus far are scattered among different resources and with no systematic summary available, which hinders the development of a large-scale omics analysis. To enable this, we constructed a comprehensive genomics resource for the edible seaweeds. These data could be used for systematic metabolomics and a proteome search for anti-cancer compound and peptides. In brief, we integrated and annotated 12 publicly available edible seaweed genomes (8 species and 268,071 proteins). In addition, we integrate the new seaweed genomic resources with established cancer bioinformatics pipelines to help identify potential seaweed proteins that could help mitigate the development of cancer. We present 7892 protein domains that were predicted to be associated with cancer proteins based on a protein domain-domain interaction. The most enriched protein families were associated with protein phosphorylation and insulin signalling, both of which are recognised to be crucial molecular components for patient survival in various cancers. In addition, we found 6692 seaweed proteins that could interact with over 100 tumour suppressor proteins, of which 147 are predicted to be secreted proteins. In conclusion, our genomics resource not only may be helpful in exploring the genomics features of these edible seaweed but also may provide a new avenue to explore the molecular mechanisms for seaweed-associated inhibition of human cancer development.
Collapse
Affiliation(s)
- Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 510180, China
| | - Scott F. Cummins
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Min Zhao
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
- Correspondence: ; Tel.: +61-07-54563402
| |
Collapse
|
3
|
Bioinformatic investigation and functional analysis of 214 hereditary genes identified non-coding RNAs as therapeautic tool for breast cancer management. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
4
|
Wei S, Dai S, Zhang C, Zhao R, Zhao Z, Song Y, Shan B, Zhao L. LncRNA NR038975, A Serum-Based Biomarker, Promotes Gastric Tumorigenesis by Interacting With NF90/NF45 Complex. Front Oncol 2021; 11:721604. [PMID: 34900675 PMCID: PMC8660099 DOI: 10.3389/fonc.2021.721604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/20/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is one of the deadliest cancers, and long noncoding RNAs (lncRNAs) have been reported to be the important regulators during the occurrence and development of GC. The present study identified a novel and functional lncRNA in GC, named NR038975, which was confirmed to be markedly upregulated in the Gene Expression Profiling Interactive Analysis (GEPIA) dataset and our independent cohort of GC tissues. We firstly characterized the full-length sequence and subcellular location of NR038975 in GC cells. Our data demonstrated that upregulated NR038975 expression was significantly related to lymph node metastasis and TNM stage. In addition, knockdown of NR038975 inhibited GC cell proliferation, migration, invasion, and clonogenicity and vice versa. Mechanistically, RNA pull-down and mass spectrometry assays identified the NR038975-binding proteins and NF90/NF45 complex, and the binding was also confirmed by RNA immunoprecipitation and confocal experiments. We further demonstrated that genetic deficiency of NR038975 abrogated the interaction between NF45 and NF90. Moreover, NF90 increased the stability of NR038975. Thus, NR038975-NF90/NF45 will be an important combinational target of GC. Finally, we detected NR038975 in serum exosomes and serum of GC patients. Our results indicated that NR038975 was a biomarker for gastric tumorigenesis. The current study demonstrated that NR038975 is a novel lncRNA that is clinically and functionally engaged in GC progression and might be a novel diagnostic marker and potential therapeutic target.
Collapse
Affiliation(s)
- Sisi Wei
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Suli Dai
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Cong Zhang
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ruinian Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zitong Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoen Shan
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
5
|
Qin J, Wang S, Shi J, Ma Y, Wang K, Ye H, Zhang X, Wang P, Wang X, Song C, Dai L, Wang K, Jiang B, Zhang J. Using recursive partitioning approach to select tumor-associated antigens in immunodiagnosis of gastric adenocarcinoma. Cancer Sci 2019; 110:1829-1841. [PMID: 30950146 PMCID: PMC6550128 DOI: 10.1111/cas.14013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022] Open
Abstract
The present study aimed to select anti‐tumor‐associated antigen (TAA) autoantibodies as biomarkers in the immunodiagnosis of gastric adenocarcinoma (GAC) by the recursive partitioning approach (RPA) and further construct and evaluate a predictive model. A case‐control study was designed including 407 GAC patients as the case group and 407 normal controls. In addition, 67 serial serum samples from 25 GAC patients were collected at different time points before and after gastrectomy treatment. Autoantibodies against 14 TAA were measured in sera from all subjects by enzyme immunoassay. Finally, RPA resulted in the selection of nine‐panel TAA (c‐Myc, p16, HSPD1, PTEN, p53, NPM1, ENO1, p62, HCC1.4) from all detected TAA in the case‐control study; the classification tree based on this nine‐TAA panel had area under curve (AUC) of 0.857, sensitivity of 71.5% and specificity of 71.3%; The optimal panel also can identify GAC patients at an early stage from normal individuals, with AUC of 0.737, sensitivity of 64.9% and specificity of 70.5%. However, frequencies of the nine autoantibodies showed no correlation with GAC stage, tumor size, lymphatic metastasis or differentiation. GAC patients positive for more than two autoantibodies in the nine‐TAA panel had a worse prognosis than that of the GAC patients positive for no or one antibody. Titers of 10 autoantibodies in serial serum samples were significantly higher in GAC patients after surgical resection than before. In conclusion, this study showed that the panel of nine multiple TAAs could enhance the detection of anti‐TAA antibodies in GAC, and may be potential prognostic biomarkers in GAC.
Collapse
Affiliation(s)
- Jiejie Qin
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Shuaibing Wang
- Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianxiang Shi
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yan Ma
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Keyan Wang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hua Ye
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaojun Zhang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiao Wang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chunhua Song
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Liping Dai
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Kaijuan Wang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Binghua Jiang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianying Zhang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China.,Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
6
|
Wang T, Liu Y, Liu Q, Cummins S, Zhao M. Integrative proteomic analysis reveals potential high-frequency alternative open reading frame-encoded peptides in human colorectal cancer. Life Sci 2018; 215:182-189. [PMID: 30419281 DOI: 10.1016/j.lfs.2018.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 11/30/2022]
Abstract
Identification of alternative open reading frame-encoded peptides (AEPs) for the diagnosis of colorectal cancer at the proteome level is largely unexplored because of a lack of comprehensive proteomics data. Here, we performed a comprehensive integrative analysis of mass spectral data published by Clinical Proteomic Tumor Analysis Consortium and characterized 93 high-confident AEPs encoded within 75 genes. There are four cancer-related genes appeared to have AEPs identified frequently in >20 out of 95 colorectal cancer samples, including ABCF2, AR, RBM10 and NRG1. Further network analysis of the identified AEPs found the enrichment of novel AEPs within hormone androgen receptor and a highly-modularised network with 42 genes associated with patient survival. Our results not only suggested a mechanistic view of how AEPs work in cancer progression, but also shed light on somatic amino acid mutations in AEPs, which might be overlooked previously because of their low frequencies. In particular, potential high-frequency mutations in 77 samples associated with EDARADD may contribute to the discovery of new biomarkers and the development of innovative therapeutic approaches.
Collapse
Affiliation(s)
- Tianfang Wang
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Qi Liu
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37232, United States; Center for Quantitative Sciences, School of Medicine, Vanderbilt University, Nashville, TN 37232, United States
| | - Scott Cummins
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Min Zhao
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.
| |
Collapse
|