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Zhou L, Liu X, Wu T, Liu Q, Jing M, Li H, Xu N, Tang H. Identification of survival related key genes and long-term survival specific differentially expressed genes related key miRNA network of primary glioblastoma. Heliyon 2024; 10:e28439. [PMID: 38601561 PMCID: PMC11004527 DOI: 10.1016/j.heliyon.2024.e28439] [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: 05/12/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Primary glioblastoma(pGBM) is the most malignant tumor of the central nervous system. Radiotherapy, chemotherapy and surgical treatment have little effect on the survival of pGBM patients. The prognosis is often poorly once the tumor recurs. It is urgent to develop new therapies for patients. In recent years, studies have been clarified that miRNA have a powerful regulating effect on the genes. However, the main group of miRNAs in regulating long-term survival specific related genes of pGBM is still unclear. Given that the survival period of most glioma patients is relatively short, studying long-term survival patients with pGBM is of great value for this disease. Our study aim to identify key miRNAs with long-term survival related genes present in pGBM and uncover their potential mechanisms. The gene expression profiles of GSE53733, GSE15824, GSE30563, GSE50161 were obtained from the Gene Expression Omnibus database. Firstly, samples were divided into 3 groups according to its survival time and each group compare to the normal control group. Then we obtained differential expression genes (DEGs) with a long-term survival specific (LTSDEGs) and a short-term survival specific DEGs (STSDEGs). Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted with LTSDEGs and STSDEGs together. Moreover, we used the UALCAN database to verify LTSDEGs and STSDEGs, and obtained long-term verified survival specific DEGs(LTVSDEGs) and short-term verified survival specific DEGs(STVSDEGs). Finally, we established the predicted key miRNAs-LTVSDEGs interaction network. The protein expressions of the top 4 LTVSDEGs were verified in the HPA database with immunohistochemical staining. In total, we found 260 genes changed in LTSDEGs and 822 genes changed in STSDEGs. GO and KEGG results shown that the major changes are focused on tumor metabolism. 9 LTVSDEGs and 18 STVSDEGs were verified in UALCAN database. As for protein expression verification in top 4 LTVSDEGs, ZNF630, BLVRB and RPA3 were verified, while TPBG was not detected. We obtained 59 key miRNA from the predicted key miRNAs-LTVSDEGs interaction network. 25 key miRNAs were verified using GSE90603. Finally, we constructed the key miRNAs-LTVSDEGs network using a Sankey diagram, including 25 miRNAs and 7 LTVSDEGs. In conclusion, our study shows that there is a close relationship between metabolic changes and survival in pGBM. Besides, we established a key miRNAs-LTVSDEGs network for pGBM, which could be the key path in prolonging the life of pGBM patients.
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Affiliation(s)
- Lingqi Zhou
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
- Guangzhou Key Laboratory of Child Neurodevelopment, Guangzhou, 510623, China
- Institute Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China
| | - Xuemei Liu
- Department of Gynecology, Shunde Hospital,Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, 528308, China
| | - Tong Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080,China
| | - Qundi Liu
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Meilian Jing
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Huahan Li
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Ning Xu
- Department of Clinical Laboratory, South China Hospital, Medical School, Shenzhen University, Shenzhen, 518111, China
| | - Hai Tang
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080,China
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Gao J, Pan H, Li J, Jiang J, Wang W. A peptide encoded by the circular form of the SHPRH gene induces apoptosis in neuroblastoma cells. PeerJ 2024; 12:e16806. [PMID: 38282862 PMCID: PMC10812589 DOI: 10.7717/peerj.16806] [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: 08/30/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Background Circular RNAs (circRNAs) and their derived peptides represent largely unchartered areas in cellular biology, with many potential roles yet to be discovered. This study aimed to elucidate the role and molecular interactions of circSHPRH and its peptide derivative SHPRH-146aa in the pathogenesis of neuroblastoma (NB). Methods NB samples in the GSE102285 dataset were analyzed to measure circSHPRH expression, followed by in vitro experiments for validation. The role of SHPRH-146aa in NB cell proliferation, migration, and invasion was then examined, and luciferase activity assay was performed after SHPRH-146aa and RUNX1 transfection. Finally, the regulation of NB cell apoptosis by SHPRH-146aa combined with NFKBIA was tested. Results The GSE102285 dataset indicated overexpression of circSHPRH in NB samples, further supported by in vitro findings. Overexpression of circ-SHPRH and SHPRH-146aa inhibited proliferation, migration, and invasion of NB cells. A significant increase in apoptosis was observed, with upregulation of Caspase-3 and downregulation of Bcl-2. Furthermore, the peptide derivative SHPRH-146aa, derived from circSHPRH, suppressed NB cell malignancy traits, suggesting its role as a therapeutic target. A direct interaction between SHPRH-146aa and the transcription factor RUNX1 was identified, subsequently leading to increased NFKBIA expression. Notably, NFKBIA knockdown inhibited the pro-apoptotic effect of SHPRH-146aa on NB cells. Conclusion The study demonstrates that circ-SHPRH and SHPRH-146aa play significant roles in inhibiting the malignant progression of NB. They induce apoptosis primarily by modulating key apoptotic proteins Caspase-3 and Bcl-2, a process that appears to be regulated by NFKBIA. The SHPRH-146aa-RUNX1 interaction further elucidates a novel pathway in the regulation of apoptosis in NB. These findings indicate that circ-SHPRH and its derived peptide SHPRH-146aa could be potential therapeutic targets for NB treatment.
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Affiliation(s)
- Jingjing Gao
- Department of Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Pan
- Department of Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Li
- Department of Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Jiang
- Endoscopy Center, Minhang District Central Hospital of Fudan University, Shanghai, China
| | - Wenxian Wang
- Department of Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Wu K, Tan J, Yang C. Recent advances and application value of circRNA in neuroblastoma. Front Oncol 2023; 13:1180300. [PMID: 37091173 PMCID: PMC10116045 DOI: 10.3389/fonc.2023.1180300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Neuroblastoma (NB) is children’s most prevalent solid malignant tumor, accounting for 15% of childhood cancer mortality. Non-coding RNA is important in NB pathogenesis. As a newly identified non-coding RNA, abnormal regulation (abnormal up-regulation or down-regulation) of the circRNAs expression is implicated in the tumorigenesis of various tumors, including NB. CircRNAs primarily regulate the expression of microRNA (miRNA) target genes by microRNA (miRNA) sponge adsorption. Clinical evidence suggests that the expression of certain circRNAs is associated with the prognosis and clinical features of NB and hence may be exploited as a biomarker or therapeutic target. This review examines circRNAs that have been demonstrated to play a function in NB.
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Affiliation(s)
- Ke Wu
- Department of Pharmacology, Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Juan Tan
- Child Healthcare Department, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Chao Yang
- Child Healthcare Department, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatric Surgical Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Chao Yang,
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MicroRNAs as prospective biomarkers, therapeutic targets and pharmaceuticals in neuroblastoma. Mol Biol Rep 2023; 50:1895-1912. [PMID: 36520359 DOI: 10.1007/s11033-022-08137-y] [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: 06/14/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Neuroblastomas, the most prevalent malignant solid neoplasms of childhood, originate from progenitor cells of the sympathetic nervous system. Their genetic causation is diverse and involves multiple molecular mechanisms. This review highlights multiple roles of microRNA in neuroblastoma pathogenesis and discusses the prospects of harnessing these important natural regulator molecules as biomarkers, therapeutic targets and pharmaceuticals in neuroblastoma.
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Galardi A, Colletti M, Palma A, Di Giannatale A. An Update on Circular RNA in Pediatric Cancers. Biomedicines 2022; 11:biomedicines11010036. [PMID: 36672544 PMCID: PMC9856195 DOI: 10.3390/biomedicines11010036] [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: 11/21/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded closed noncoding RNA molecules which are formed as a result of reverse splicing of mRNAs. Despite their relative abundance, only recently there appeared an increased interest in the understanding of their regulatory importance. Among their most relevant characteristics are high stability, abundance and evolutionary conservation among species. CircRNAs are implicated in several cellular functions, ranging from miRNA and protein sponges to transcriptional modulation and splicing. Additionally, circRNAs' aberrant expression in pathological conditions is bringing to light their possible use as diagnostic and prognostic biomarkers. Their use as indicator molecules of pathological changes is also supported by their peculiar covalent closed cyclic structure which bestows resistance to RNases. Their regulatory role in cancer pathogenesis and metastasis is supported by studies involving human tumors that have investigated different expression profiles of these molecules. As endogenous competitive RNA, circRNAs can regulate tumor proliferation and invasion and they arouse great consideration as potential therapeutic biomarkers and targets for cancer. In this review, we describe the most recent findings on circRNAs in the most common pediatric solid cancers (such as brain tumors, neuroblastomas, and sarcomas) and in more rare ones (such as Wilms tumors, hepatoblastomas, and retinoblastomas).
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Affiliation(s)
- Angela Galardi
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
| | - Marta Colletti
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
| | - Alessandro Palma
- Translational Cytogenomics Research Unit, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
| | - Angela Di Giannatale
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
- Correspondence:
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Karami Fath M, Pourbagher Benam S, Salmani K, Naderi S, Fahham Z, Ghiabi S, Houshmand Kia SA, Naderi M, Darvish M, Barati G. Circular RNAs in neuroblastoma: Pathogenesis, potential biomarker, and therapeutic target. Pathol Res Pract 2022; 238:154094. [PMID: 36087416 DOI: 10.1016/j.prp.2022.154094] [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: 07/24/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 10/15/2022]
Abstract
Neuroblastoma (NB) is a common cancer in childhood responsible for 15 % of fatalities by pediatric cancers. Epigenetic factors play an important role in the pathogenesis of NB. Recently, it has been demonstrated that circular RNAs (circRNAs, ciRNAs), a newly identified class of non-coding RNAs, are also dysregulated in NB. CircRNAs mediate their functions by regulating gene expression mainly through microRNA (miRNA) sponging. The dysregulation (abnormal upregulation or downregulation) of circRNAs is involved in tumorigenesis of a variety of tumors including NB. It seems that the expression of some circRNAs is correlated with NB prognosis and clinical features. CircRNAs might be favorable as a diagnostic/prognostic biomarker and therapeutic target. However, due to the lack of studies, it is difficult to make a conclusion regarding the clinical benefits of circRNAs. In this review, we discussed the circRNAs that experimentally have been proved to be dysregulated in NB tissues and cancer cells.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Kiana Salmani
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sina Naderi
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Fahham
- Faculty of Biology, Technische Universitat Dresden, Dresden, Germany
| | - Shamim Ghiabi
- Department of Medical Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Malihe Naderi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Maryam Darvish
- Department of Medical Biotechnology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
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