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Abstract
With completing the whole genome sequencing project, awareness of lncRNA further deepened. The growth arrest-specific transcript 5 (GAS5) was initially identified in growth-inhibiting cells. GAS5 is a lncRNA (long non-coding RNA), and it plays a crucial role in various human cancers. There are small ORFs (open reading frames) in the exons of the GAS5 gene sequence, but they do not encode functional proteins. In addition, GAS5 is also the host gene of several small nucleolar RNAs (snoRNA). These snoRNAs are believed to play a suppressive role during tumor progression by methylating ribosomal RNA (rRNA). As a result, GAS5 expression levels in tumor tissues are significantly reduced, leading to increased malignancy, poor prognosis, and drug resistance. Recent studies have demonstrated that GAS5 can interact with miRNAs by base-pairing and other functional proteins to inhibit their biological functions, impacting signaling pathways and changing the level of intracellular autophagy, oxidative stress, and immune cell function in vivo. In addition, GAS5 participates in regulating proliferation, invasion, and apoptosis through the above molecular mechanisms. This article reviews the recent discoveries on GAS5, including its expression levels in different tumors, its biological behavior, and its molecular regulation mechanism in human cancers. The value of GAS5 as a molecular marker in the prevention and treatment of cancers is also discussed.
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Affiliation(s)
- Guohong Lin
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Tianzhun Wu
- Oncology Medical College, Guangxi Medical University, Nanning, China
| | - Xing Gao
- Oncology Medical College, Guangxi Medical University, Nanning, China
| | - Ziqin He
- Oncology Medical College, Guangxi Medical University, Nanning, China
| | - Wenwei Nong
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Wenwei Nong,
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Huang S, Ma L, Lan B, Liu N, Nong W, Huang Z. Comprehensive analysis of prognostic genes in gastric cancer. Aging (Albany NY) 2021; 13:23637-23651. [PMID: 34686626 PMCID: PMC8580339 DOI: 10.18632/aging.203638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/03/2021] [Indexed: 12/16/2022]
Abstract
Background: Gastric cancer is associated with high mortality, and effective methods for predicting prognosis are lacking. We aimed to identify potential prognostic markers associated with the development of gastric cancer through bioinformatic analyses. Methods: Gastric cancer-associated gene expression profiles were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The key genes involved in the development of gastric cancer were obtained by differential expression analysis, coexpression analysis, and short time-series expression miner (STEM) analysis. The potential prognostic value of differentially expressed genes was further evaluated using a Cox regression model and risk scores. Hierarchical clustering was applied to validate the impact of key genes on the overall survival of gastric cancer patients. Results: A total of 1381 genes were consistently dysregulated in the development of gastric cancer. Among them, 186 genes affected the overall survival of gastric cancer patients. The following genes had areas under the receiver operating characteristic curve greater than 0.9 in both datasets and were therefore considered key genes: ADAM12, CEP55, LRFN4, INHBA, ADH1B, DPT, FAM107A, and LOC100506388. LRFN4, DPT, and LOC100506388 were identified as potential prognostic genes for gastric cancer through a nomogram. Overexpression of LRFN4 and LOC100506388 was associated with a higher risk of gastric cancer. Finally, we found that tumors were infiltrated with high levels of Th2 cells and mast cells, and the infiltration levels were associated with overall survival in gastric cancer patients. Conclusions: We found that key dysregulated genes may have a prognostic value for the development of gastric cancer.
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Affiliation(s)
- Shaohua Huang
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Liping Ma
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Biyang Lan
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Ning Liu
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Wenwei Nong
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Zhihu Huang
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
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Nong W, Ma L, Lan B, Liu N, Yang H, Lao X, Deng Q, Huang Z. Comprehensive Identification of Bridge Genes to Explain the Progression from Chronic Hepatitis B Virus Infection to Hepatocellular Carcinoma. J Inflamm Res 2021; 14:1613-1624. [PMID: 33907440 PMCID: PMC8071210 DOI: 10.2147/jir.s298977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Background Hepatitis B virus infection co-occurs in 33% of individuals with hepatocellular carcinoma worldwide. However, the molecular link between hepatitis B virus and hepatocellular carcinoma is unknown. Thus, we aimed to elucidate molecular linkages underlying pathogenesis through in-depth data mining analysis. Materials and Methods Differentially expressed genes were identified from patients with chronic hepatitis B virus infection, hepatocellular carcinoma, or both. Gene set enrichment analysis revealed signaling pathways involving differentially expressed genes. Protein-protein interaction networks, protein crosstalk, and enrichment were analyzed to determine whether differentially expressed gene products might serve as a bridge from hepatitis B virus infection to hepatocellular carcinoma pathogenesis. Prognostic potential and transcriptional and post-transcriptional regulators of bridge genes were also examined. Results We identified vital bridge factors in hepatitis B virus infection-associated hepatocellular carcinoma. Differentially expressed genes were clustered into modules based on relative protein function. Signaling pathways associated with cancer, inflammation, immune system, and microenvironment showed significant crosstalk between modules. Thirty-two genes were dysregulated in hepatitis B virus infection-mediated hepatocellular carcinoma. CPEB3, RAB26, SLCO1B1, ST3GAL6 and XK had higher connectivity in the modular network, suggesting significant associations with survival. CDC20 and NUP107 were identified as driver genes as well as markers of poor prognosis. Conclusion Our results suggest that the sustained inflammatory environment created by hepatitis B virus infection is a risk factor for hepatocellular carcinoma. The identification of hepatitis B virus infection-related hepatocellular carcinoma bridge genes provides testable hypotheses about the pathogenesis of hepatocellular carcinoma.
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Affiliation(s)
- Wenwei Nong
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Liping Ma
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Biyang Lan
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Ning Liu
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hongzhi Yang
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xiaoxia Lao
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qiaomei Deng
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Zhihu Huang
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
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Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL. Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity (Edinb) 2016; 116:190-9. [PMID: 26419336 PMCID: PMC4806888 DOI: 10.1038/hdy.2015.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
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Affiliation(s)
- N J Kenny
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - K W Chan
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - W Nong
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - Z Qu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - I Maeso
- Centro Andaluz de Biología del
Desarrollo (CABD), Consejo Superior de Investigaciones
Científicas/Universidad Pablo de Olavide, Sevilla,
Spain
| | - H Y Yip
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - T F Chan
- School of Life Sciences, Center of
Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - H S Kwan
- School of Life Sciences, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - P W H Holland
- Department of Zoology, University of
Oxford, Oxford, UK
| | - K H Chu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, The Chinese University of Hong Kong,
Shatin, Hong Kong
| | - J H L Hui
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
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Nong W, Xie TS, Li LY, Lu AG, Mo J, Gou YF, Lan G, Jiang H, Len J, Li MM, Jiang QY, Huang B. Qualitative Analyses of Protein Phosphorylation in Bovine Pluripotent Stem Cells Generated from Embryonic Fibroblasts. Reprod Domest Anim 2015; 50:989-98. [DOI: 10.1111/rda.12619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/07/2015] [Indexed: 12/19/2022]
Affiliation(s)
- W Nong
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi University of Chinese Medicine; Nanning China
| | - TS Xie
- College of Animal Science and Technology; Guangxi University; Nanning China
- Nanning Languang Biotechnology Inc.; Nanning China
| | - LY Li
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
| | - AG Lu
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi Analysis and Testing Center; Nanning China
| | - J Mo
- Guangxi Analysis and Testing Center; Nanning China
| | - YF Gou
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - G Lan
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - H Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - J Len
- Guangxi University of Chinese Medicine; Nanning China
| | - MM Li
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - QY Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - B Huang
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
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