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Shi X, Hu Z, Bai S, Zong C, Xue H, Li Y, Li F, Chen L, Xuan J, Xia Y, Wei L, Shen F, Wang K. YBX1 promotes stemness and cisplatin insensitivity in intrahepatic cholangiocarcinoma via the AKT/β-catenin axis. J Gene Med 2024; 26:e3689. [PMID: 38676365 DOI: 10.1002/jgm.3689] [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: 02/18/2024] [Revised: 03/13/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive malignancy characterized by a poor prognosis and closely linked to tumor stemness. However, the key molecules that regulate ICC stemness remain elusive. Although Y-box binding protein 1 (YBX1) negatively affects prognosis in various cancers by enhancing stemness and chemoresistance, its effect on stemness and cisplatin sensitivity in ICC remains unclear. METHODS Three bulk and single-cell RNA-seq datasets were analyzed to investigate YBX1 expression in ICC and its association with stemness. Clinical samples and colony/sphere formation assays validated the role of YBX1 in stemness and sensitivity to cisplatin. AZD5363 and KYA1979K explored the interaction of YBX1 with the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB/AKT) and WNT/β-catenin pathways. RESULTS YBX1 was significantly upregulated in ICC, correlated with worse overall survival and shorter postoperative recurrence time, and was higher in chemotherapy-non-responsive ICC tissues. The YBX1-high group exhibited significantly elevated stemness scores, and genes linked to YBX1 upregulation were enriched in multiple stemness-related pathways. Moreover, YBX1 expression is significantly correlated with several stemness-related genes (SOX9, OCT4, CD133, CD44 and EPCAM). Additionally, YBX1 overexpression significantly enhanced the colony- and spheroid-forming abilities of ICC cells, accelerated tumor growth in vivo and reduced their sensitivity to cisplatin. Conversely, the downregulation of YBX1 exerted the opposite effect. The transcriptomic analysis highlighted the link between YBX1 and the PI3K/AKT and WNT/β-catenin pathways. Further, AZD5363 and KYA1979K were used to clarify that YBX1 promoted ICC stemness through the regulation of the AKT/β-catenin axis. CONCLUSIONS YBX1 is upregulated in ICC and promotes stemness and cisplatin insensitivity via the AKT/β-catenin axis. Our study describes a novel potential therapeutic target for improving ICC prognosis.
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Affiliation(s)
- Xiaodong Shi
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Zhiliang Hu
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Shilei Bai
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Chen Zong
- Department of Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Naval Medical University, Shanghai, China
- National Center for Liver Cancer, Shanghai, China
| | - Hui Xue
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yao Li
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Fengwei Li
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Liangrui Chen
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Jianbing Xuan
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yong Xia
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Lixin Wei
- Department of Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Naval Medical University, Shanghai, China
- National Center for Liver Cancer, Shanghai, China
| | - Feng Shen
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Kui Wang
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
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Babayev M, Silveyra P. Role of circular RNAs in lung cancer. Front Genet 2024; 15:1346119. [PMID: 38501058 PMCID: PMC10944888 DOI: 10.3389/fgene.2024.1346119] [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: 11/29/2023] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Lung cancer remains a global public health concern with significant research focus on developing better diagnosis/prognosis biomarkers and therapeutical targets. Circular RNAs (circRNAs) are a type of single-stranded RNA molecules that covalently closed and have ubiquitous expression. These molecules have been implicated in a variety of disease mechanisms, including lung cancer, as they exhibit oncogenic or tumor suppressor characteristics. Recent research has shown an important role that circRNAs play at different stages of lung cancer, particularly in lung adenocarcinoma. In this review, we summarize the latest research on circRNAs and their roles within lung cancer diagnosis, as well as on disease mechanisms. We also discuss the knowledge gaps on these topics and possible future research directions.
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Affiliation(s)
| | - Patricia Silveyra
- Department of Environmental and Occupational Health, Indiana University School of Public Health Bloomington, Bloomington, IN, United States
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Dinh NTM, Nguyen TM, Park MK, Lee CH. Y-Box Binding Protein 1: Unraveling the Multifaceted Role in Cancer Development and Therapeutic Potential. Int J Mol Sci 2024; 25:717. [PMID: 38255791 PMCID: PMC10815159 DOI: 10.3390/ijms25020717] [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: 11/11/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Y-box binding protein 1 (YBX1), a member of the Cold Shock Domain protein family, is overexpressed in various human cancers and is recognized as an oncogenic gene associated with poor prognosis. YBX1's functional diversity arises from its capacity to interact with a broad range of DNA and RNA molecules, implicating its involvement in diverse cellular processes. Independent investigations have unveiled specific facets of YBX1's contribution to cancer development. This comprehensive review elucidates YBX1's multifaceted role in cancer across cancer hallmarks, both in cancer cell itself and the tumor microenvironment. Based on this, we proposed YBX1 as a potential target for cancer treatment. Notably, ongoing clinical trials addressing YBX1 as a target in breast cancer and lung cancer have showcased its promise for cancer therapy. The ramp up in in vitro research on targeting YBX1 compounds also underscores its growing appeal. Moreover, the emerging role of YBX1 as a neural input is also proposed where the high level of YBX1 was strongly associated with nerve cancer and neurodegenerative diseases. This review also summarized the up-to-date advanced research on the involvement of YBX1 in pancreatic cancer.
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Affiliation(s)
- Ngoc Thi Minh Dinh
- College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea; (N.T.M.D.); (T.M.N.)
| | - Tuan Minh Nguyen
- College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea; (N.T.M.D.); (T.M.N.)
| | - Mi Kyung Park
- Department of BioHealthcare, Hwasung Medi-Science University, Hwaseong-si 18274, Republic of Korea
| | - Chang Hoon Lee
- College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea; (N.T.M.D.); (T.M.N.)
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Li F, Song W, Wu L, Liu B, Du X. EIF4A3 induced circGRIK2 promotes the malignancy of glioma by regulating the miR-1303/HOXA10 axis. Am J Cancer Res 2023; 13:5868-5886. [PMID: 38187044 PMCID: PMC10767333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/13/2023] [Indexed: 01/09/2024] Open
Abstract
In recent years, the role of circular RNAs (circRNAs) in glioma has become increasingly important. However, there are still many newly discovered circRNAs with unknown functions that require further study. In this study, circRNA sequencing, qPCR, MTS, EdU, Transwell, and other assays were conducted to detect the expression and malignant effects of a novel circRNA molecule, circGRIK2, in glioma. qPCR, western blotting, RIP, and luciferase reporter gene experiments were used to investigate the downstream molecular mechanisms of circGRIK2. Our study found that circGRIK2 was highly expressed in glioma and promoted glioma cell viability, proliferation, invasion, and migration. Mechanistically, circGRIK2 acted as a competitive sponge for miR-1303, upregulating the expression of HOXA10 to exert its oncogenic effects. Additionally, the RNA-binding protein EIF4A3 could bind to and stabilize circGRIK2, leading to its high expression in glioblastoma. The discovery of circGRIK2 in this study not only contributes to a better understanding of the biological mechanisms of circGRIK2 in glioma but also provides a new target for molecular targeted therapy.
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Affiliation(s)
- Fubin Li
- Department of Neurosurgery, Zibo Central HospitalZibo 255036, Shandong, China
| | - Wei Song
- Department of Breast and Thyroid Surgery, Zibo Central HospitalZibo 255036, Shandong, China
| | - Lin Wu
- Department of Pediatrics, Zhangdian Maternal and Child Health Care HospitalZibo 255036, Shandong, China
| | - Bin Liu
- Department of Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
| | - Xinrui Du
- Department of Neurosurgery, Zibo Central HospitalZibo 255036, Shandong, China
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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [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: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
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Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
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Yi Q, Yue J, Liu Y, Shi H, Sun W, Feng J, Sun W. Recent advances of exosomal circRNAs in cancer and their potential clinical applications. J Transl Med 2023; 21:516. [PMID: 37525158 PMCID: PMC10388565 DOI: 10.1186/s12967-023-04348-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Circular RNA (circRNA) is a type of non-coding RNA that forms a covalently closed, uninterrupted loop. The expression of circRNA differs among cell types and tissues, and various circRNAs are aberrantly expressed in a variety of diseases, including cancer. Aberrantly expressed circRNAs contribute to disease progression by acting as microRNA sponges, functional protein sponges, or novel templates for protein translation. Recent studies have shown that circRNAs are enriched in exosomes. Exosomes are spherical bilayer vesicles released by cells into extracellular spaces that mediate intercellular communication by delivering cargoes. These cargoes include metabolites, proteins, lipids, and RNA molecules. Exosome-mediated cell-cell or cell-microenvironment communications influence the progression of carcinogenesis by regulating cell proliferation, angiogenesis, metastasis as well as immune escape. In this review, we summarize the current knowledge about exosomal circRNAs in cancers and discuss their specific functions in tumorigenesis. Additionally, we discuss the potential value of exosomal circRNAs as diagnostic biomarkers and the potential applications of exosomal circRNA-based cancer therapy.
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Affiliation(s)
- Qian Yi
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, 646000, China
| | - Jiaji Yue
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Yang Liu
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Houyin Shi
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Wei Sun
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - Weichao Sun
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China.
- The Central Laboratory, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China.
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