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Zhou J, Wang X, Niu R, Shang X, Wen J. Predicting circRNA-miRNA interactions utilizing transformer-based RNA sequential learning and high-order proximity preserved embedding. iScience 2024; 27:108592. [PMID: 38205240 PMCID: PMC10777065 DOI: 10.1016/j.isci.2023.108592] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/20/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
A key regulatory mechanism involves circular RNA (circRNA) acting as a sponge to modulate microRNA (miRNA), and thus, studying their interaction has significant medical implications. In this field, there are currently two pressing issues that remain unresolved. Firstly, due to the scarcity of verified interactions, we require a minimal amount of samples for training. Secondly, the current models lack interpretability. Therefore, we propose SPBCMI, a method that combines sequence features extracted using the Bidirectional Encoder Representations from Transformer (BERT) model and structural features of biological molecule networks extracted through graph embedding to train a GBDT (Gradient-boosted decision trees) classifier for prediction. Our method yielded an AUC of 0.9143, which is currently the best for this problem. Furthermore, in the case study, SPBCMI accurately predicted 7 out of 10 circRNA-miRNA interactions. These results show that our method provides an innovative and high-performing approach to understanding the interaction between circRNA and miRNA.
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Affiliation(s)
- Jiren Zhou
- School of Computer Science, Northwestern Polytechnical University, Xi’an, China
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Xinfei Wang
- School of Information Engineering, Xijing University, Xi’an, China
| | - Rui Niu
- School of Computer Science, Northwestern Polytechnical University, Xi’an, China
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an, China
| | - Jiayu Wen
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for the Mathematical Analysis of Cellular Systems
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Chen C, Naveed H, Chen K. Research progress on branched-chain amino acid aminotransferases. Front Genet 2023; 14:1233669. [PMID: 38028625 PMCID: PMC10658711 DOI: 10.3389/fgene.2023.1233669] [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: 06/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Branched-chain amino acid aminotransferases, widely present in natural organisms, catalyze bidirectional amino transfer between branched-chain amino acids and branched-chain α-ketoacids in cells. Branched-chain amino acid aminotransferases play an important role in the metabolism of branched-chain amino acids. In this paper, the interspecific evolution and biological characteristics of branched-chain amino acid aminotransferases are introduced, the related research of branched-chain amino acid aminotransferases in animals, plants, microorganisms and humans is summarized and the molecular mechanism of branched-chain amino acid aminotransferase is analyzed. It has been found that branched-chain amino acid metabolism disorders are closely related to various diseases in humans and animals and plants, such as diabetes, cardiovascular diseases, brain diseases, neurological diseases and cancer. In particular, branched-chain amino acid aminotransferases play an important role in the development of various tumors. Branched-chain amino acid aminotransferases have been used as potential targets for various cancers. This article reviews the research on branched-chain amino acid aminotransferases, aiming to provide a reference for clinical research on targeted therapy for various diseases and different cancers.
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Affiliation(s)
- Can Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hassan Naveed
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Ghaedrahmati F, Nasrolahi A, Najafi S, Mighani M, Anbiyaee O, Haybar H, Assareh AR, Kempisty B, Dzięgiel P, Azizidoost S, Farzaneh M. Circular RNAs-mediated angiogenesis in human cancers. Clin Transl Oncol 2023; 25:3101-3121. [PMID: 37039938 DOI: 10.1007/s12094-023-03178-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/16/2023] [Indexed: 04/12/2023]
Abstract
Circular RNAs (circRNAs) as small non-coding RNAs with cell, tissue, or organ-specific expression accomplish a broad array of functions in physiological and pathological processes such as cancer development. Angiogenesis, a complicated multistep process driving a formation of new blood vessels, speeds up tumor progression by supplying nutrients as well as energy. Abnormal expression of circRNAs reported to affect tumor development through impressing angiogenesis. Such impacts are introduced as constant with different tumorigenic features known as "hallmarks of cancer". In addition, deregulated circRNAs show possibilities to prognosis and diagnosis both in the prophecy of prognosis in malignancies and also their prejudice from healthy individuals. In the present review article, we have evaluated the angiogenic impacts and anti-angiogenic managements of circRNAs in human cancers.
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Affiliation(s)
- Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Mighani
- School of Medicine, Golestan University of Medical Sciences, Golestan, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Nemazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Habib Haybar
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ahmad Reza Assareh
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bartosz Kempisty
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wrocław, Poland
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, US
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368, Wroclaw, Poland
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Tirpe A, Streianu C, Tirpe SM, Kocijancic A, Pirlog R, Pirlog B, Busuioc C, Pop OL, Berindan-Neagoe I. The Glioblastoma CircularRNAome. Int J Mol Sci 2023; 24:14545. [PMID: 37833993 PMCID: PMC10572686 DOI: 10.3390/ijms241914545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Glioblastoma remains one of the most aggressive cancers of the brain, warranting new methods for early diagnosis and more efficient treatment options. Circular RNAs (circRNAs) are rather new entities with increased stability compared to their linear counterparts that interact with proteins and act as microRNA sponges, among other functions. Herein, we provide a critical overview of the recently described glioblastoma-related circRNAs in the literature, focusing on their roles on glioblastoma cancer cell proliferation, survival, migration, invasion and metastasis, metabolic reprogramming, and therapeutic resistance. The main roles of circRNAs in regulating cancer processes are due to their regulatory roles in essential oncogenic pathways, including MAPK, PI3K/AKT/mTOR, and Wnt, which are influenced by various circRNAs. The present work pictures the wide implication of circRNAs in glioblastoma, thus highlighting their potential as future biomarkers and therapeutic targets/agents.
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Affiliation(s)
- Alexandru Tirpe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.T.); (R.P.)
- The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania;
| | - Cristian Streianu
- The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania;
| | - Stefana Maria Tirpe
- Department of Neurology, Ortenau-Klinikum Lahr, Klostenstrasse 19, 7933 Lahr, Germany;
| | - Anja Kocijancic
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway;
| | - Radu Pirlog
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.T.); (R.P.)
| | - Bianca Pirlog
- Department of Neurology, County Emergency Hospital, 400012 Cluj-Napoca, Romania;
| | - Constantin Busuioc
- Department of Pathology, National Institute of Infectious Disease, 021105 Bucharest, Romania;
- Department of Pathology, Onco Team Diagnostic, 010719 Bucharest, Romania
| | - Ovidiu-Laurean Pop
- Department of Morphological Sciences, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania;
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.T.); (R.P.)
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Zhao S, Li B, Gao H, Zhang Y. MiR-320a Acts as a Tumor Suppressor in Somatotroph Pituitary Neuroendocrine Tumors by Targeting BCAT1. Neuroendocrinology 2023; 114:14-24. [PMID: 37591221 DOI: 10.1159/000533549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
INTRODUCTION Aberrant miR-320a has been reported to be involved in the tumorigenesis of several cancers. In our previous study, we identified the low expression of circulating miR-320a in patients with somatotroph pituitary neuroendocrine tumor (PitNET); however, the role of miR-320a in somatotroph PitNET proliferation is still unclear. METHODS Cell viability and colony formation assays were used to detect the effect of miR-320a and BCAT1 on GH3 cells. TargetScan was used to identify the target genes of miR-320a. Dual-luciferase reporter gene assay was used to explore the relation between miR-320a and BCAT1. Transcriptome and proteome analyses were performed between somatotroph PitNETs and healthy controls. The expression level of miR-320a in somatotroph PitNETs were detected by RT-qPCR and Western blot. RESULTS miR-320a mimics inhibit cell proliferation, while miR-320a inhibitors promote cell proliferation in GH3 cells. An overlap analysis using a Venn diagram revealed that BCAT1 is the only target gene of miR-320a overexpressed in somatotroph PitNETs compared to healthy controls, as revealed by both microarray and proteomics results. A dual-luciferase reporter gene assay showed that miR-320a may bind to the BCAT1-3'UTR. The transfection of miR-320a mimics downregulated the expression and miR-320a inhibitors and upregulated the expression of BCAT1 in GH3 cells. The interference of BCAT1 expression in GH3 cells downregulated cell proliferation and growth. Pan-cancer analyses demonstrated that high BCAT1 expression often indicates a poor prognosis. CONCLUSION Our findings illustrate that miR-320a may function as a tumor suppressor and BCAT1 may promote tumor progression. miR-320a may inhibit the growth of somatotroph PitNETs by targeting BCAT1.
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Affiliation(s)
- Sida Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Bin Li
- Department of Neurosurgery, Peking University People's Hospital, Beijing, China
| | - Hua Gao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
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Secretory phosphoprotein 1 secreted by fibroblast-like synoviocytes promotes osteoclasts formation via PI3K/AKT signaling in collagen-induced arthritis. Biomed Pharmacother 2022; 155:113687. [PMID: 36088855 DOI: 10.1016/j.biopha.2022.113687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Synovial tissue hyperplasia is a major cause of bone damage in rheumatoid arthritis (RA). Over-proliferation and secretion of cytokines of fibroblast-like synoviocytes (FLSs) are key contributors to bone damage in the joint microenvironment. Therefore, inhibition of FLSs-mediated bone damage is of great significance in RA patients. The aim of this study was to investigate the molecular mechanisms by which FLSs-mediated bone damage in the joint microenvironment. The results of whole transcriptome sequencing showed that Spp1 gene expression was significantly upregulated in collagen-induced arthritis FLSs compared to Normal FLSs. KEGG enrichment analysis revealed up-regulated Spp1 gene expression, associated with PI3K/AKT signaling. Animal and cellular experiments were designed to validate and explore the results of sequencing. Briefly, the data demonstrated secretory phosphoprotein 1 (SPP1) (encoded by Spp1 gene) secreted by FLSs promotes osteoclasts differentiation in vivo and in vitro and exacerbates articular bone damage in collagen-induced arthritis mice. Interestingly, SPP1 secreted by FLSs does not affect its own proliferation and apoptosis. The results of co-culture of FLSs with bone marrow-derived monocytes indicated the level of SPP1 secreted by FLSs positively correlates with the frequency of p-PI3K+PI3K+ osteoclasts, whereas not with the frequency of p-AKT+AKT+ osteoclasts. This may suggest that SPP1 secreted by FLSs acts directly on PI3K while indirectly on AKT. Together, the results revealed SPP1 secreted by FLSs promotes osteoclasts formation via PI3K/AKT signaling in collagen-induced arthritis. Regulation of Spp1 gene expression in FLSs may be a potential approach to treat RA bone damage in the joint microenvironment.
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