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Han X, Chen L, Sun P, Wang X, Zhao Q, Liao L, Lou D, Zhou N, Wang Y. A novel lncRNA-hidden polypeptide regulates malignant phenotypes and pemetrexed sensitivity in A549 pulmonary adenocarcinoma cells. Amino Acids 2024; 56:15. [PMID: 38351332 PMCID: PMC10864564 DOI: 10.1007/s00726-023-03361-7] [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: 09/22/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024]
Abstract
The advance of high-throughput sequencing enhances the discovery of short ORFs embedded in long non-coding RNAs (lncRNAs). Here, we uncovered the production and biological activity of lncRNA-hidden polypeptides in lung adenocarcinoma (LUAD). In the present study, bioinformatics was used to screen the lncRNA-hidden polypeptides in LUAD. Analysis of protein expression was done by western blot or immunofluorescence assay. The functions of the polypeptide were determined by detecting its effects on cell viability, proliferation, migration, invasion, and pemetrexed (PEM) sensitivity. The protein interactors of the polypeptide were analyzed by mass spectrometry after Co-immunoprecipitation (Co-IP) assay. The results showed that the lncRNA LINC00954 was confirmed to encode a novel polypeptide LINC00954-ORF. The polypeptide had tumor-suppressor features in A549 cells by repressing cell growth, motility and invasion. Moreover, the polypeptide enhanced PEM sensitivity and suppressed growth in A549/PEM cells. The protein interactors of this polypeptide had close correlations with RNA processing, amide metabolic process, translation, RNA binding, RNA transport, and DNA replication. As a conclusion, the LINC00954-ORF polypeptide embedded in lncRNA LINC00954 possesses tumor-suppressor features in A549 and PEM-resistant A549 cells and sensitizes PEM-resistant A549 cells to PEM, providing evidence that the LINC00954-ORF polypeptide is a potential anti-cancer agent in LUAD.
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Affiliation(s)
- Xiaobing Han
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China.
| | - Liangxin Chen
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Peng Sun
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Xiuqing Wang
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Qian Zhao
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Lingfeng Liao
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Dejin Lou
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Nan Zhou
- Department of Oncology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China
| | - Yujun Wang
- Department of Gastroenterology, Xinyang Central Hospital, No. 1 Siyi Road, Shihe District, Xinyang, 464000, Henan, China.
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An F, Wang X, Wang C, Liu Y, Sun B, Zhang J, Gao P, Yan C. Research progress on the role of lncRNA-miRNA networks in regulating adipogenic and osteogenic differentiation of bone marrow mesenchymal stem cells in osteoporosis. Front Endocrinol (Lausanne) 2023; 14:1210627. [PMID: 37645421 PMCID: PMC10461560 DOI: 10.3389/fendo.2023.1210627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023] Open
Abstract
Osteoporosis (OP) is characterized by a decrease in osteoblasts and an increase in adipocytes in the bone marrow compartment, alongside abnormal bone/fat differentiation, which ultimately results in imbalanced bone homeostasis. Bone marrow mesenchymal stem cells (BMSCs) can differentiate into osteoblasts and adipocytes to maintain bone homeostasis. Several studies have shown that lncRNAs are competitive endogenous RNAs that form a lncRNA-miRNA network by targeting miRNA for the regulation of bone/fat differentiation in BMSCs; this mechanism is closely related to the corresponding treatment of OP and is important in the development of novel OP-targeted therapies. However, by reviewing the current literature, it became clear that there are limited summaries discussing the effects of the lncRNA-miRNA network on osteogenic/adipogenic differentiation in BMSCs. Therefore, this article provides a review of the current literature to explore the impact of the lncRNA-miRNA network on the osteogenic/adipogenic differentiation of BMSCs, with the aim of providing a new theoretical basis for the treatment of OP.
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Affiliation(s)
- Fangyu An
- Teaching Experiment Training Center, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Xiaxia Wang
- School of Tradional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Chunmei Wang
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Ying Liu
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Bai Sun
- School of Tradional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Jie Zhang
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Peng Gao
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Chunlu Yan
- School of Tradional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
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Liu Z, Yan W, Liu S, Liu Z, Xu P, Fang W. Regulatory network and targeted interventions for CCDC family in tumor pathogenesis. Cancer Lett 2023; 565:216225. [PMID: 37182638 DOI: 10.1016/j.canlet.2023.216225] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
CCDC (coiled-coil domain-containing) is a coiled helix domain that exists in natural proteins. There are about 180 CCDC family genes, encoding proteins that are involved in intercellular transmembrane signal transduction and genetic signal transcription, among other functions. Alterations in expression, mutation, and DNA promoter methylation of CCDC family genes have been shown to be associated with the pathogenesis of many diseases, including primary ciliary dyskinesia, infertility, and tumors. In recent studies, CCDC family genes have been found to be involved in regulation of growth, invasion, metastasis, chemosensitivity, and other biological behaviors of malignant tumor cells in various cancer types, including nasopharyngeal carcinoma, lung cancer, colorectal cancer, and thyroid cancer. In this review, we summarize the involvement of CCDC family genes in tumor pathogenesis and the relevant upstream and downstream molecular mechanisms. In addition, we summarize the potential of CCDC family genes as tumor therapy targets. The findings discussed here help us to further understand the role and the therapeutic applications of CCDC family genes in tumors.
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Affiliation(s)
- Zhen Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
| | - Weiwei Yan
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China
| | - Shaohua Liu
- Department of General Surgery, Pingxiang People's Hospital, Pingxiang, Jiangxi, 337000, China
| | - Zhan Liu
- Department of Gastroenterology and Clinical Nutrition, The First Affiliated Hospital (People's Hospital of Hunan Province), Hunan Normal University, Changsha, 410002, China
| | - Ping Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China; Respiratory Department, Peking University Shenzhen Hospital, Shenzhen, 518034, China.
| | - Weiyi Fang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
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A review on the role of ADAMTS9-AS2 in different disorders. Pathol Res Pract 2023; 243:154346. [PMID: 36746036 DOI: 10.1016/j.prp.2023.154346] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Recent decade has seen a tremendous progress in identification of the role of different long non-coding RNAs (lncRNAs) in human pathologies. ADAMTS9-AS2 is an example of lncRNAs with different roles in human disorders. It is mostly acknowledged as a tumor suppressor lncRNA in different types of cancers. However, it has been reported to be up-regulated in tongue squamous cell carcinoma, salivary adenoid cystic carcinoma and glioblastoma. Moreover, ADAMTS9-AS2 is possibly involved in the pathoetiology of pulpitis, acute ischemic stroke, type 2 diabetes and its complications. This lncRNA sponges miR-196b-5p, miR-223-3p, miR-130a-5p, miR-600, miR-223-3p, miR-27a-3p, miR-32, miR-143-3p, miR-143-3p and miR-182-5p in order to regulate downstream mRNAs. This review aims at summarization of the role of ADAMTS9-AS2 in different disorders with a particular focus on its diagnostic and prognostic values.
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Chen Q, Pan Q, Gao H, Wang Y, Zhong X. miR-17-5p/ HOXA7 Is a Potential Driver for Brain Metastasis of Lung Adenocarcinoma Related to Ferroptosis Revealed by Bioinformatic Analysis. Front Neurol 2022; 13:878947. [PMID: 35693013 PMCID: PMC9174431 DOI: 10.3389/fneur.2022.878947] [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: 02/18/2022] [Accepted: 05/03/2022] [Indexed: 11/21/2022] Open
Abstract
Objectives Present study aims to identify the essential mRNAs responsible for the development of brain neurovascular-related metastases (BNM) among lung adenocarcinoma (LUAD) patients. Further, we attempted to predict brain metastases more accurately and prevent their development in LUAD patients. Methods Transcriptome data analysis was used to identify differentially expressed mRNAs (DEMs) associated with brain metastasis, and thereby the ferroptosis index (FPI) is calculated using a computational model. Meanwhile, the DEmRNAs linked with FPI, and brain metastasis were derived by the intersection of these two groups of DEMs. We also constructed a ceRNA network containing these DEmRNAs, identifying the HCP5 /hsa-miR-17-5p/HOXA7 axis for analysis. Further, a clinical cohort was employed to validate the regulatory roles of molecules involved in the ceRNA regulatory axis. Results Here we report the development of a ceRNA network based on BNM-associated DEMs and FPI-associated DEmRNAs which includes three core miRNAs (hsa-miR-338-3p, hsa-miR-429, and hsa-miR-17-5p), three mRNAs (HOXA7, TBX5, and TCF21), and five lncRNAs (HCP5, LINC00460, TP53TG1). Using gene set enrichment analysis (GSEA) and survival analysis, the potential axis of HCP5 /hsa-miR-17-5p/HOXA7 was further investigated. It is found that HOXA7 and ferroptosis index are positively correlated while inhibiting tumor brain metastasis. It may be that HCP5 binds competitively with miR-17-5p and upregulates HOXA7 to increase iron death limiting brain cancer metastases. Conclusions The expression of both HOXA7 and HCP5 is positively correlated with FPI, indicating a possible link between ferroptosis and BNM. According to the results of our study, the ferroptosis-related ceRNA HCP5 /hsa-miR-17-5p/HOXA7 axis may contribute to the development of BNM in LUAD patients.
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Affiliation(s)
| | | | | | | | - Xiaoning Zhong
- Department of Respiratory Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Yang Y, Zhang S, Guo L. Characterization of Cell Cycle-Related Competing Endogenous RNAs Using Robust Rank Aggregation as Prognostic Biomarker in Lung Adenocarcinoma. Front Oncol 2022; 12:807367. [PMID: 35186743 PMCID: PMC8853726 DOI: 10.3389/fonc.2022.807367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD), one of the most common pathological subtypes in lung cancer, has been of concern because it is the leading cause of cancer-related deaths. Due to its poor prognosis, to identify a prognostic biomarker, this study performed an integrative analysis to screen curial RNAs and discuss their cross-talks. The messenger RNA (mRNA) profiles were primarily screened using robust rank aggregation (RRA) through several datasets, and these deregulated genes showed important roles in multiple biological pathways, especially for cell cycle and oocyte meiosis. Then, 31 candidate genes were obtained via integrating 12 algorithms, and 16 hub genes (containing homologous genes) were further screened according to the potential prognostic values. These hub genes were used to search their regulators and biological-related microRNAs (miRNAs). In this way, 10 miRNAs were identified as candidate small RNAs associated with LUAD, and then miRNA-related long non-coding RNAs (lncRNAs) were further obtained. In-depth analysis showed that 4 hub mRNAs, 2 miRNAs, and 2 lncRNAs were potential crucial RNAs in the occurrence and development of cancer, and a competing endogenous RNA (ceRNA) network was then constructed. Finally, we identified CCNA2/MKI67/KIF11:miR-30a-5p:VPS9D1-AS1 axis-related cell cycle as a prognostic biomarker, which provided RNA cross-talks among mRNAs and non-coding RNAs (ncRNAs), especially at the multiple isomiR levels that further complicated the coding–non-coding RNA regulatory network. Our findings provide insight into complex cross-talks among diverse RNAs particularly involved in isomiRs, which will enrich our understanding of mRNA–ncRNA interactions in coding–non-coding RNA regulatory networks and their roles in tumorigenesis.
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Affiliation(s)
- Yifei Yang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Shiqi Zhang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
- *Correspondence: Li Guo,
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