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Li H, Jin X, Li W, Ren F, Li T, Li X, Yu H, Fu D, Song Z, Xu S. Construction of a circRNA-miRNA-mRNA Regulatory Network for the Immune Regulation of Lung Adenocarcinoma. Biol Proced Online 2025; 27:13. [PMID: 40211126 PMCID: PMC11983969 DOI: 10.1186/s12575-025-00275-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Accepted: 03/24/2025] [Indexed: 04/12/2025] Open
Abstract
BACKGROUND Recent research has highlighted the significance of circular RNAs (circRNAs) as pivotal regulators in the progression of tumors and the therapeutic response in non-small cell lung cancer (NSCLC). These circRNAs function through a sponge mechanism, interacting with microRNAs (miRNAs) to modulate mRNA expression levels. Nevertheless, the precise role of the circRNA-miRNA-mRNA regulatory network in immune regulation within lung adenocarcinoma (LUAD) remains inadequately understood. METHODS AND MATERIALS We utilized microarray datasets from the GEO NCBI database (GSE101586) to identify differentially expressed circRNAs (DEcircRNAs) in LUAD. CircBank was employed to predict the target miRNAs of DEcircRNAs, which were subsequently intersected with miRNAs from the GSE36681 database. The identified miRNAs were then predicted to target mRNAs using miRDB and miWalk, and intersections with immune-related genes from the IMMPORT database were analyzed. Protein-protein interaction (PPI) networks were constructed using Cytoscape software. The DAVID functional annotation tool was utilized to explore potential biological processes, molecular functions, and KEGG pathways associated with LUAD. Gene expression and Kaplan-Meier survival analyses were conducted to establish a key regulatory network and to assess immune cell infiltration and Pearson correlation for significant target genes. Finally, we selected the most significantly upregulated circRNA with differential expression for validation through in vitro experiments. RESULTS Our analysis identified a total of 7 upregulated and 42 downregulated circRNAs, along with 10 significant miRNAs and 20 target mRNAs. KEGG enrichment analysis indicated that these components are primarily enriched in the ErbB signaling pathway. Furthermore, Gene Ontology (GO) analysis revealed significant enrichment in responses to organic substances, cytokine-mediated signaling pathways, cellular responses to cytokines, responses to chemical stimuli, steroid hormone receptor activity, ErbB-3 class receptor binding, oxysterol binding, signal receptor activity, and molecular transducer activity. Notable core mRNAs identified included OAS1, VIPR1, and PIK3R1. Subsequently, we constructed a regulatory network comprising 6 DEcircRNAs, 3 DEmiRNAs, and 3 DEmRNAs. Through ssGSEA and CIBERSORT analyses, we observed significant differences in immune cell infiltration levels between the NSCLC cohort and the control group. Knocking down the expression of hsa_circ_0079557 significantly inhibited the viability, proliferation, migration, and invasion of LUAD cells. CONCLUSION We have established a circRNA-miRNA-mRNA regulatory network that offers novel insights into the molecular mechanisms governing immune regulation in LUAD. Future research should aim to translate these findings into clinical applications to enhance patient outcomes.
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Affiliation(s)
- Hanyi Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Jin
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Wei Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Fan Ren
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Tong Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuanguang Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Haochuan Yu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Dianxun Fu
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Zuoqing Song
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.
| | - Song Xu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.
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Mosca N, Alessio N, Di Paola A, Marrapodi MM, Galderisi U, Russo A, Rossi F, Potenza N. Osteosarcoma in a ceRNET perspective. J Biomed Sci 2024; 31:59. [PMID: 38835012 DOI: 10.1186/s12929-024-01049-y] [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: 12/27/2023] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
Osteosarcoma (OS) is the most prevalent and fatal type of bone tumor. It is characterized by great heterogeneity of genomic aberrations, mutated genes, and cell types contribution, making therapy and patients management particularly challenging. A unifying picture of molecular mechanisms underlying the disease could help to transform those challenges into opportunities.This review deeply explores the occurrence in OS of large-scale RNA regulatory networks, denominated "competing endogenous RNA network" (ceRNET), wherein different RNA biotypes, such as long non-coding RNAs, circular RNAs and mRNAs can functionally interact each other by competitively binding to shared microRNAs. Here, we discuss how the unbalancing of any network component can derail the entire circuit, driving OS onset and progression by impacting on cell proliferation, migration, invasion, tumor growth and metastasis, and even chemotherapeutic resistance, as distilled from many studies. Intriguingly, the aberrant expression of the networks components in OS cells can be triggered also by the surroundings, through cytokines and vesicles, with their bioactive cargo of proteins and non-coding RNAs, highlighting the relevance of tumor microenvironment. A comprehensive picture of RNA regulatory networks underlying OS could pave the way for the development of innovative RNA-targeted and RNA-based therapies and new diagnostic tools, also in the perspective of precision oncology.
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Affiliation(s)
- Nicola Mosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Nicola Alessio
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alessandra Di Paola
- Department of Woman, Child and General and Specialist Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Maddalena Marrapodi
- Department of Woman, Child and General and Specialist Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Umberto Galderisi
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Aniello Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Francesca Rossi
- Department of Woman, Child and General and Specialist Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Nicoletta Potenza
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy.
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de Brot S, Cobb J, Alibhai AA, Jackson-Oxley J, Haque M, Patke R, Harris AE, Woodcock CL, Lothion-Roy J, Varun D, Thompson R, Gomes C, Kubale V, Dunning MD, Jeyapalan JN, Mongan NP, Rutland CS. Immunohistochemical Investigation into Protein Expression Patterns of FOXO4, IRF8 and LEF1 in Canine Osteosarcoma. Cancers (Basel) 2024; 16:1945. [PMID: 38792023 PMCID: PMC11120020 DOI: 10.3390/cancers16101945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024] Open
Abstract
Osteosarcoma (OSA) is the most common type of primary bone malignancy in people and dogs. Our previous molecular comparisons of canine OSA against healthy bone resulted in the identification of differentially expressed protein-expressing genes (forkhead box protein O4 (FOXO4), interferon regulatory factor 8 (IRF8), and lymphoid enhancer binding factor 1 (LEF1)). Immunohistochemistry (IHC) and H-scoring provided semi-quantitative assessment of nuclear and cytoplasmic staining alongside qualitative data to contextualise staining (n = 26 patients). FOXO4 was expressed predominantly in the cytoplasm with significantly lower nuclear H-scores. IRF8 H-scores ranged from 0 to 3 throughout the cohort in the nucleus and cytoplasm. LEF1 was expressed in all patients with significantly lower cytoplasmic staining compared to nuclear. No sex or anatomical location differences were observed. While reduced levels of FOXO4 might indicate malignancy, the weak or absent protein expression limits its primary use as diagnostic tumour marker. IRF8 and LEF1 have more potential for prognostic and diagnostic uses and facilitate further understanding of their roles within their respective molecular pathways, including Wnt/beta-catenin/LEF1 signalling and differential regulation of tumour suppressor genes. Deeper understanding of the mechanisms involved in OSA are essential contributions towards the development of novel diagnostic, prognostic, and treatment options in human and veterinary medicine contexts.
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Affiliation(s)
- Simone de Brot
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
- Comparative Pathology Platform of the University of Bern (COMPATH), Institute of Animal Pathology, University of Bern, 3012 Bern, Switzerland
| | - Jack Cobb
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Aziza A. Alibhai
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Jorja Jackson-Oxley
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Maria Haque
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Rodhan Patke
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Anna E. Harris
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Corinne L. Woodcock
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Jennifer Lothion-Roy
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Dhruvika Varun
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Rachel Thompson
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Claudia Gomes
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
| | - Valentina Kubale
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Mark D. Dunning
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
- Willows Veterinary Centre and Referral Service, Solihull B90 4NH, UK
| | - Jennie N. Jeyapalan
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
- Faculty of Medicine and Health Science, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Nigel P. Mongan
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
- Willows Veterinary Centre and Referral Service, Solihull B90 4NH, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10075, USA
| | - Catrin S. Rutland
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (S.d.B.); (J.C.); (A.A.A.); (J.J.-O.); (M.H.); (R.P.); (A.E.H.); (C.L.W.); (J.L.-R.); (D.V.); (R.T.); (C.G.); (M.D.D.); (J.N.J.)
- Faculty of Medicine and Health Science, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
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Zhang Y, Zhan Y, Liu Z, Guo H, Liu D, Chen C. Circ_0002669 promotes osteosarcoma tumorigenesis through directly binding to MYCBP and sponging miR-889-3p. Biol Direct 2024; 19:25. [PMID: 38570856 PMCID: PMC10988859 DOI: 10.1186/s13062-024-00466-1] [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: 11/30/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Circular RNAs (circRNAs) are a class of highly multifunctional single-stranded RNAs that play crucial roles in cancer progression, including osteosarcoma (OS). Circ_0002669, generated from the dedicator of cytokinesis (DOCK) gene, was highly expressed in OS tissues, and negatively correlated with OS patient survival. Elevated circ_0002669 promoted OS cell growth and invasion in vivo and in vitro. By biotin pulldown and mass spectroscopy, we found that circ_0002669 directly bound to MYCBP, a positive regulator of c-myc, to prevent MYCBP from ubiquitin-mediated proteasome degradation. In addition, circ_0002669 interacted with miR-889-3p and served as a miRNA sponge to increase the expression of MYCBP, as determined by luciferase assays and RNA immunoprecipitation. Functional rescue experiments indicated MYCBP acted as a key factor for circ_0002669- and miR-889-3p-regulated OS cell proliferation and migration. Increased expression of c-myc-associated genes, such as CCND1, c-Jun and CDK4, were found in circ_0002669- and MYCBP-overexpressing OS cells. Our data thus provide evidence that circ_0002669 promotes OS malignancy by protecting MYCBP from protein ubiquitination and degradation and blocking miR-889-3p-mediated inhibition of MYCBP expression.
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Affiliation(s)
- Ying Zhang
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, 515041, Shantou, Guangdong, PR China.
- Department of Clinical Research Center, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, 515041, Shantou, Guangdong, China.
| | - Yizhou Zhan
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, 515041, Shantou, Guangdong, PR China
| | - Zhaoyong Liu
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, 515041, Shantou, Guangdong, China
| | - Huancheng Guo
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, 515041, Shantou, Guangdong, China
| | - Dongchen Liu
- Department of Clinical Research Center, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, 515041, Shantou, Guangdong, China
| | - Chuangzhen Chen
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, 515041, Shantou, Guangdong, PR China
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