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Fu L, Yao Z, Zhou Y, Peng Q, Lyu H. ACLNDA: an asymmetric graph contrastive learning framework for predicting noncoding RNA-disease associations in heterogeneous graphs. Brief Bioinform 2024; 25:bbae533. [PMID: 39441244 PMCID: PMC11497849 DOI: 10.1093/bib/bbae533] [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: 06/29/2024] [Revised: 08/27/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), play crucial roles in gene expression regulation and are significant in disease associations and medical research. Accurate ncRNA-disease association prediction is essential for understanding disease mechanisms and developing treatments. Existing methods often focus on single tasks like lncRNA-disease associations (LDAs), miRNA-disease associations (MDAs), or lncRNA-miRNA interactions (LMIs), and fail to exploit heterogeneous graph characteristics. We propose ACLNDA, an asymmetric graph contrastive learning framework for analyzing heterophilic ncRNA-disease associations. It constructs inter-layer adjacency matrices from the original lncRNA, miRNA, and disease associations, and uses a Top-K intra-layer similarity edges construction approach to form a triple-layer heterogeneous graph. Unlike traditional works, to account for both node attribute features (ncRNA/disease) and node preference features (association), ACLNDA employs an asymmetric yet simple graph contrastive learning framework to maximize one-hop neighborhood context and two-hop similarity, extracting ncRNA-disease features without relying on graph augmentations or homophily assumptions, reducing computational cost while preserving data integrity. Our framework is capable of being applied to a universal range of potential LDA, MDA, and LMI association predictions. Further experimental results demonstrate superior performance to other existing state-of-the-art baseline methods, which shows its potential for providing insights into disease diagnosis and therapeutic target identification. The source code and data of ACLNDA is publicly available at https://github.com/AI4Bread/ACLNDA.
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Affiliation(s)
- Laiyi Fu
- School of Automation Science and Engineering, Xi’an Jiaotong University, Xi’an, Shannxi 710049, China
- Research Institute, Xi’an Jiaotong University, Zhejiang, Hangzhou, Zhejiang 311200, China
- Sichuan Digital Economy Industry Development Research Institute, Chengdu, Sichuan 610036, China
| | - ZhiYuan Yao
- School of Automation Science and Engineering, Xi’an Jiaotong University, Xi’an, Shannxi 710049, China
| | - Yangyi Zhou
- School of Automation Science and Engineering, Xi’an Jiaotong University, Xi’an, Shannxi 710049, China
| | - Qinke Peng
- School of Automation Science and Engineering, Xi’an Jiaotong University, Xi’an, Shannxi 710049, China
| | - Hongqiang Lyu
- School of Automation Science and Engineering, Xi’an Jiaotong University, Xi’an, Shannxi 710049, China
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2
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Sadeghsoltani F, Avci ÇB, Hassanpour P, Haiaty S, Rahmati M, Mota A, Rahbarghazi R, Nemati M, Mahdipour M, Talebi M, Takanlou LS, Takanlou MS, Mehdizadeh A. Autophagy modulation effect on homotypic transfer of intracellular components via tunneling nanotubes in mesenchymal stem cells. Stem Cell Res Ther 2024; 15:189. [PMID: 38956646 PMCID: PMC11218273 DOI: 10.1186/s13287-024-03813-1] [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: 04/26/2024] [Accepted: 06/23/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Recent studies have proved the role of autophagy in mesenchymal stem cell (MSCs) function and regenerative properties. How and by which mechanism autophagy modulation can affect the juxtacrine interaction of MSCs should be addressed. Here, the role of autophagy was investigated in the formation of tunneling nanotubes (TNTs) and homotypic mitochondrial donation. METHODS MSCs were incubated with 15 µM Metformin (Met) and/or 3 µM 3-methyladenine (3-MA) for 48 h. The formation of TNTs was assessed using bright-field and SEM images. The mitochondria density and ΔΨ values were monitored using flow cytometry analysis. Using RT-PCR and protein array, the close interaction and shared mediators between autophagy, apoptosis, and Wnt signaling pathways were also monitored. The total fatty acid profile was assessed using gas chromatography. RESULT Data indicated the increase of TNT length and number, along with other cell projections after the induction of autophagy while these features were blunted in 3-MA-treated MSCs (p < 0.05). Western blotting revealed the significant reduction of Rab8 and p-FAK in 3-MA-treated MSCs (p < 0.05), indicating the inhibition of TNT assembly and vesicle transport. Likewise, the stimulation of autophagy increased autophagic flux and mitochondrial membrane integrity compared to 3-MA-treated MSCs. Despite these findings, protein levels of mitochondrial membrane Miro1 and 2 were unchanged after autophagy inhibition/stimulation (p > 0.05). We found that the inhibition/stimulation of autophagy can affect the protein, and transcription levels of several mediators related to Wnt and apoptosis signaling pathways involved in different cell bioactivities. Data confirmed the profound increase of mono and polyunsaturated/saturated fatty acid ratio in MSCs exposed to autophagy stimulator. CONCLUSIONS In summary, autophagy modulation could affect TNT formation which is required for homotypic mitochondrial donation. Thus, the modulation of autophagy creates a promising perspective to increase the efficiency of cell-based therapies.
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Affiliation(s)
- Fatemeh Sadeghsoltani
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, 5166614766, Iran
| | - Çığır Biray Avci
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Parisa Hassanpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, 5166614766, Iran
| | - Sanya Haiaty
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohamad Rahmati
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, 5166614766, Iran
| | - Ali Mota
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, 5166614766, Iran.
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, 5166653431, Iran.
| | - Maryam Nemati
- Department of Genetic, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Talebi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Amir Mehdizadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Wang K, Lu Y, Li H, Zhang J, Ju Y, Ouyang M. Role of long non-coding RNAs in metabolic reprogramming of gastrointestinal cancer cells. Cancer Cell Int 2024; 24:15. [PMID: 38184562 PMCID: PMC10770979 DOI: 10.1186/s12935-023-03194-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024] Open
Abstract
Metabolic reprogramming, which is recognized as a hallmark of cancer, refers to the phenomenon by which cancer cells change their metabolism to support their increased biosynthetic demands. Tumor cells undergo substantial alterations in metabolic pathways, such as glycolysis, oxidative phosphorylation, pentose phosphate pathway, tricarboxylic acid cycle, fatty acid metabolism, and amino acid metabolism. Latest studies have revealed that long non-coding RNAs (lncRNAs), a group of non-coding RNAs over 200 nucleotides long, mediate metabolic reprogramming in tumor cells by regulating the transcription, translation and post-translational modification of metabolic-related signaling pathways and metabolism-related enzymes through transcriptional, translational, and post-translational modifications of genes. In addition, lncRNAs are closely related to the tumor microenvironment, and they directly or indirectly affect the proliferation and migration of tumor cells, drug resistance and other processes. Here, we review the mechanisms of lncRNA-mediated regulation of glucose, lipid, amino acid metabolism and tumor immunity in gastrointestinal tumors, aiming to provide more information on effective therapeutic targets and drug molecules for gastrointestinal tumors.
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Affiliation(s)
- Kang Wang
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University, The First People's Hospital of Shunde Foshan), Shunde, Foshan, 528300, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Yan Lu
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University, The First People's Hospital of Shunde Foshan), Shunde, Foshan, 528300, Guangdong, China
| | - Haibin Li
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University, The First People's Hospital of Shunde Foshan), Shunde, Foshan, 528300, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Jun Zhang
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University, The First People's Hospital of Shunde Foshan), Shunde, Foshan, 528300, Guangdong, China
- Guangdong Medical University, Dongguan, 523808, China
| | - Yongle Ju
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University, The First People's Hospital of Shunde Foshan), Shunde, Foshan, 528300, Guangdong, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510080, Guangdong, China.
| | - Manzhao Ouyang
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University, The First People's Hospital of Shunde Foshan), Shunde, Foshan, 528300, Guangdong, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510080, Guangdong, China.
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Tian Y, Han W, Fu L, Zhang J, Zhou X. IGF2 is upregulated by its antisense RNA to potentiate pancreatic cancer progression. Funct Integr Genomics 2023; 23:348. [PMID: 38036690 DOI: 10.1007/s10142-023-01277-9] [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: 09/04/2023] [Revised: 10/24/2023] [Accepted: 11/26/2023] [Indexed: 12/02/2023]
Abstract
Pancreatic cancer is a deadly cancer. More and more long noncoding RNAs (lncRNAs) have received confirmation to be dysregulated in tumors and exert the regulatory function. Studies have suggested that lncRNA insulin-like growth factor 2 antisense RNA (IGF2-AS) participates in the development of some cancers. Thus, we attempted to clarify its function in pancreatic cancer. Reverse-transcription quantitative polymerase chain reaction was applied for testing IGF2-AS expression in pancreatic cancer cells. Colony formation and Transwell wound experiments were applied for determining cell proliferative, migratory, and invasive capabilities. The alteration of epithelial-mesenchymal transition (EMT)-related gene level was tested via western blot. The mice model was established for measuring the tumor growth and metastasis. RIP validated the interaction of RNAs. IGF2-AS displays high expression in pancreatic cancer cells. IGF2-AS depletion repressed PC cell proliferative, migratory, invasive capabilities, and EMT process. Furthermore, pancreatic cancer tumor growth and metastasis were also inhibited by IGF2-AS depletion. Additionally, IGF2-AS positively regulated IGF2 level via recruiting HNRNPC. IGF2 overexpression counteracted the functions of IGF2-AS deficiency on pancreatic cancer cell behaviors. Moreover, IGF2R deletion was found to inhibit the positive effect of IGF2 on pancreatic cancer progression. IGF2-AS potentiates pancreatic cancer cell proliferation, tumor growth, and metastasis by recruiting HNRNPC via the IGF2-IGF2R regulatory pathway. These discoveries might offer a novel insight for treatment of PC, which may facilitate targeted therapies of PC in clinical practice.
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Affiliation(s)
- Yuan Tian
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, 315100, China
| | - Wenwen Han
- Department of Emergency, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, 315100, China
| | - Long Fu
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, 315100, China
| | - Jing Zhang
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, 315100, China
| | - Xinhua Zhou
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, 315100, China.
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5
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Sheng N, Wang Y, Huang L, Gao L, Cao Y, Xie X, Fu Y. Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases. Brief Bioinform 2023; 24:bbad276. [PMID: 37529914 DOI: 10.1093/bib/bbad276] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION Identifying the relationships among long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and diseases is highly valuable for diagnosing, preventing, treating and prognosing diseases. The development of effective computational prediction methods can reduce experimental costs. While numerous methods have been proposed, they often to treat the prediction of lncRNA-disease associations (LDAs), miRNA-disease associations (MDAs) and lncRNA-miRNA interactions (LMIs) as separate task. Models capable of predicting all three relationships simultaneously remain relatively scarce. Our aim is to perform multi-task predictions, which not only construct a unified framework, but also facilitate mutual complementarity of information among lncRNAs, miRNAs and diseases. RESULTS In this work, we propose a novel unsupervised embedding method called graph contrastive learning for multi-task prediction (GCLMTP). Our approach aims to predict LDAs, MDAs and LMIs by simultaneously extracting embedding representations of lncRNAs, miRNAs and diseases. To achieve this, we first construct a triple-layer lncRNA-miRNA-disease heterogeneous graph (LMDHG) that integrates the complex relationships between these entities based on their similarities and correlations. Next, we employ an unsupervised embedding model based on graph contrastive learning to extract potential topological feature of lncRNAs, miRNAs and diseases from the LMDHG. The graph contrastive learning leverages graph convolutional network architectures to maximize the mutual information between patch representations and corresponding high-level summaries of the LMDHG. Subsequently, for the three prediction tasks, multiple classifiers are explored to predict LDA, MDA and LMI scores. Comprehensive experiments are conducted on two datasets (from older and newer versions of the database, respectively). The results show that GCLMTP outperforms other state-of-the-art methods for the disease-related lncRNA and miRNA prediction tasks. Additionally, case studies on two datasets further demonstrate the ability of GCLMTP to accurately discover new associations. To ensure reproducibility of this work, we have made the datasets and source code publicly available at https://github.com/sheng-n/GCLMTP.
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Affiliation(s)
- Nan Sheng
- Key laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 130012 Changchun, China
| | - Yan Wang
- Key laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 130012 Changchun, China
- School of Artificial Intelligence, Jilin University, 130012 Changchun, China
| | - Lan Huang
- Key laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 130012 Changchun, China
| | - Ling Gao
- Key laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 130012 Changchun, China
| | - Yangkun Cao
- School of Artificial Intelligence, Jilin University, 130012 Changchun, China
| | - Xuping Xie
- Key laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 130012 Changchun, China
| | - Yuan Fu
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
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6
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Zhang X, Zhang X, Yang G, Wan L, Yin F, Li H, Yin D. LncRNA SOCS2-AS1 promotes the progression of papillary thyroid cancer by destabilizing p53 protein. Biochem Biophys Res Commun 2023; 669:95-102. [PMID: 37267865 DOI: 10.1016/j.bbrc.2023.05.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/21/2023] [Indexed: 06/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to contribute to tumorigenesis and cancer progression. However, neither the dysregulation nor the functions of anti-sense lncRNAs in papillary thyroid carcinoma (PTC) have been exhaustively studied. In this study, we accessed The Cancer Genome Atlas (TCGA) database and discovered that the natural antisense lncRNA SOCS2-AS1 is highly expressed in PTC and that patients with a higher level of SOCS2-AS1 had a poor prognosis. Furthermore, loss- and gain-function assays demonstrated that SOCS2-AS1 promotes PTC cell proliferation and growth both in vitro and in vivo. In addition, we demonstrated that SOCS2-AS1 regulates the rate of fatty acid oxidation (FAO) in PTC cells. Analysis of the mechanism revealed that SOCS2-AS1 binds to p53 and controls its stability in PTC cell lines. Overall, our findings showed that the natural antisense lncRNA SOCS2-AS1 stimulates the degradation of p53 and enhances PTC cell proliferation and the FAO rate.
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Affiliation(s)
- Xiaojian Zhang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, P.R. China; Department of Thyroid Surgery, The Affiliated Taian City Central Hospital of Qingdao University, 271000, Taian, China
| | - Xiaozhou Zhang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, P.R. China; Department of Thyroid Surgery, The Affiliated Taian City Central Hospital of Qingdao University, 271000, Taian, China
| | - Guang Yang
- Department of Thyroid Surgery, The Affiliated Taian City Central Hospital of Qingdao University, 271000, Taian, China
| | - Long Wan
- Department of Clinical Oncology, The Affiliated Taian City Central Hospital of Qingdao University, 271000, Taian, China
| | - Fengyan Yin
- Department of Thyroid Surgery, The Affiliated Taian City Central Hospital of Qingdao University, 271000, Taian, China
| | - Hongqiang Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, P.R. China
| | - Detao Yin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, P.R. China.
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7
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Hou XR, Zhang ZD, Cao XL, Wang XP. Long noncoding RNAs, glucose metabolism and cancer (Review). Oncol Lett 2023; 26:340. [PMID: 37427347 PMCID: PMC10326653 DOI: 10.3892/ol.2023.13925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Cancer is a serious and potentially life-threatening disease, which, despite numerous advances over several decades, remains a challenge to treat that challenging to detect at an early stage or treat during the later stages. Long noncoding RNAs are >200 nucleotides long and do not possess protein-coding capacity, instead regulating cellular processes, such as proliferation, differentiation, maturation, apoptosis, metastasis, and sugar metabolism. Several studies have shown the role of lncRNAs and glucose metabolism in regulating several key glycolytic enzymes and the activity of multiple functional signaling pathways during tumor progression. Thus, it is possible to further learn about the effects of lncRNA and glycolytic metabolism on tumor diagnosis, treatment, and prognosis through a thorough investigation of the lncRNA expression profiles and glycolytic metabolism in tumors. This may provide a novel strategy for improving the management of several types of cancer.
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Affiliation(s)
- Xin-Rui Hou
- Graduate School, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
| | - Zhen-Dong Zhang
- Graduate School, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
| | - Xiao-Lan Cao
- Graduate School, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
| | - Xiao-Ping Wang
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, P.R. China
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8
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Davoodvandi A, Rafiyan M, Asemi Z, Matini SA. An epigenetic modulator with promising therapeutic impacts against gastrointestinal cancers: A mechanistic review on microRNA-195. Pathol Res Pract 2023; 248:154680. [PMID: 37467635 DOI: 10.1016/j.prp.2023.154680] [Citation(s) in RCA: 2] [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: 06/20/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Due to their high prevalence, gastrointestinal cancers are one of the key causes of cancer-related death globally. The development of drug-resistant cancer cell populations is a major factor in the high mortality rate, and it affects about half of all cancer patients. Because of advances in our understanding of cancer molecular biology, non-coding RNAs (ncRNAs) have emerged as critical factors in the initiation and development of gastrointestinal cancers. Gene expression can be controlled in several ways by ncRNAs, including through epigenetic changes, interactions between microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and proteins, and the function of lncRNAs as miRNA precursors or pseudogenes. As lncRNAs may be detected in the blood, circulating ncRNAs have emerged as a promising new class of non-invasive cancer biomarkers for use in the detection, staging, and prognosis of gastrointestinal cancers, as well as in the prediction of therapy efficacy. In this review, we assessed the role lncRNAs play in the progression, and maintenance of colorectal cancer, and how they might be used as therapeutic targets in the future.
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Affiliation(s)
- Amirhossein Davoodvandi
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. Iran.
| | - Mahdi Rafiyan
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. Iran.
| | - Seyed Amirhassan Matini
- Department of Pathology, School of Medicine, Kashan University of Medical Sciences, Kashan, I.R. Iran.
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Effects of mir-195 Targeted Regulation of JAK2 on Proliferation, Invasion, and Apoptosis of Gastric Cancer Cells. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5873479. [PMID: 35928970 PMCID: PMC9345721 DOI: 10.1155/2022/5873479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022]
Abstract
Background. Overexpression of miR-195 can make gastric cancer cells stay in G1/G2 phase. miR-195 has been shown to inhibit gastric cancer cell replication and accelerate cell death by targeting JAK2. However, the relationship between miR-195, JAK2, and gastric cancer is not clear. Objective. To observe the effect of mir-195 regulated by JAK2 on the growth, invasion, and death of gastric cancer cells. Methods. MGC803 and NCI gastric N87 cells were introduced into the negative control sequences of miR-195 and RNA, respectively. To detect the expression of miR-195 in cells, to detect the effect of miR-195 on mitosis and proliferation of tumor cells, to analyze the effect of miR-195 on cell invasion and metastasis, and to detect the regulation of miR-195 on JAK2 expression. Results. The level of miR-195 in miR-195-MIMICS group was significantly higher than that in miR-NC group. The cell survival rate of miR-195 mimic group was lower than that of miR-NC group (
). Compared with miR-NC group, the number of cells in G1 phase increased, the cells in G2 phase and S phase decreased, and the proportion of cells in G2 and S phase decreased in miR-195 mimic group. The scratch distance of miR-195 simulator group was larger than that of control group. The number of invasive cells in the miR-195 mimic group was significantly lower than that in the control group. The expression of JAK2 protein in miR-195 mimic group was lower than that in miR-NC group. There was a significant negative correlation between the expression level of miR-195 and JAK2 (rhabdomile 0.326 and record 0.00). There are continuous interaction fragments between JAK2 and miR-195. The luciferase activity of miR-195 mimic and wild type JAK2 sequence expression vector was significantly lower than that of wild type JAK2 sequence expression vector. Conclusion. miR-195 may inhibit the occurrence, metastasis, and invasion of gastric tumor by downregulating the expression of JAK2. miR-195/JAK2 may be a new molecular target for the treatment of gastrointestinal tumors.
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10
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Exosomal CTCF Confers Cisplatin Resistance in Osteosarcoma by Promoting Autophagy via the IGF2-AS/miR-579-3p/MSH6 Axis. JOURNAL OF ONCOLOGY 2022; 2022:9390611. [PMID: 35693981 PMCID: PMC9175095 DOI: 10.1155/2022/9390611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022]
Abstract
Cancer-derived exosomes participate in carcinogenesis and progression of cancers, including metastasis and drug-resistance. Of note, CTCF has been suggested to induce drug resistance in various cancers. Herein, we aim to investigate the role of cisplatin- (CDDP-) resistant osteosarcoma- (OS-) derived exosomal CTCF in OS cell resistance to CDDP and its mechanistic basis. Differentially expressed transcription factors, long noncoding RNAs (lncRNAs), miRNAs, and genes in OS were retrieved using bioinformatics approaches. Exosomes were extracted from CDDP-resistant OS cells and then cocultured with parental OS cells, followed by lentiviral transduction to manipulate the expression of CTCF, IGF2-AS, miR-579-3p, and MSH6. We assessed the in vitro and in vivo effects on malignant phenotypes, autophagy, CDDP sensitivity, and tumor formation of OS cells. It was established that CTCF and IGF2-AS were highly expressed in CDDP-resistant OS cells, and the CDDP-resistant OS cell-derived exosomal CTCF enhanced IGF2-AS transcription. CDDP-resistant OS-derived exosomes transmitted CTCF to OS cells and increased CDDP resistance in OS cells by activating an autophagy-dependent pathway. Mechanistically, CTCF activated IGF2-AS transcription and IGF2-AS competitively bound to miR-579-3p to upregulate MSH6 expression. Additionally, the promoting function of exosomal CTCF-mediated IGF2-AS/miR-579-3p/MSH6 in OS cell resistance to CDDP was confirmed in vivo. Taken together, CDDP-resistant OS-derived exosomal CTCF enhanced resistance of OS cells to CDDP via activating the autophagy-dependent pathway, providing a potential therapeutic consideration for OS treatment.
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11
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Wang S, Zhang H, Xia L, Lan F. Circular RNA circ_0061140 accelerates hypoxia-induced glycolysis, migration, and invasion in lung adenocarcinoma through the microRNA-653/hexokinase 2 (HK2) axis. Bioengineered 2022; 13:7156-7166. [PMID: 35379058 PMCID: PMC9208531 DOI: 10.1080/21655979.2021.2000743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Circular RNA (circRNA) is considered to be an essential regulator of multiple human malignancies. However, the role and molecular mechanism of circ_0061140 in lung adenocarcinoma ((LUAD) remain elusive. The levels of circ_0061140, microRNA (miR)-653 and hexokinase 2 (HK2) were examined by RT-qPCR. Downstream targets of circ_0061140 were predicted by circinteractome website and verified by luciferase reporter and RIP assays. HK2 protein level was assessed via Western blotting. The migratory and invasive abilities of LUAD cells were assessed via wound healing and transwell assays. It was uncovered that circ_0061140 level was elevated in LUAD samples, and the high level of circ_0061140 was related to poor survival rate of LUAD patients. Circ_0061140 deletion inhibited glycolysis, migration and invasion of hypoxia-treated LUAD cells. Moreover, circ_0061140 could modulate HK2 level by absorbing miR-653. Furthermore, miR-653 silence or HK2 addition neutralized the effects of circ_0061140 knockdown on LUAD progression under hypoxia. This study elaborated that circ_0061140 accelerated hypoxia-triggered glycolysis, migration and invasion in LUAD cells via downregulating miR-653 and increasing HK2 expression.
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Affiliation(s)
- Shaobin Wang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Hao Zhang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Lixia Xia
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Fen Lan
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
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Hu Z, Zhou X, Zeng D, Lai J. Shikonin induces cell autophagy via modulating the microRNA -545-3p/guanine nucleotide binding protein beta polypeptide 1 axis, thereby disrupting cellular carcinogenesis in colon cancer. Bioengineered 2022; 13:5928-5941. [PMID: 35192430 PMCID: PMC8973937 DOI: 10.1080/21655979.2021.2024638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 01/22/2023] Open
Abstract
Shikonin (SHK), a major component of shiverweed, was provided with anti-tumor effects via multiple targets and signal pathways. Nevertheless, the specific mechanism of its function in colorectal cancer (CRC) still needed to be further explored. The study was designed to examine the role of SHK in CRC and its specific mechanism on the cell tumor behavior of CRC. Collection of clinical samples was performed, and test of microRNA (miR)-545-3p and guanine nucleotide-binding protein beta polypeptide 1 (GNB1) in the samples was conducted; Selection of CRC cell line was exerted, and examination of miR-545-3p and GNB1 was performed; After treatment of shikonin (SHK), correlated plasmids were transfected, test of cell advancement was performed. Test of the protein of autophagy-correlated proteins light chain 3-II/light chain 3I and p63 was performed. The interaction of miR-545-3p with GNB1 was explored, and the action of SHK in vivo was tested. SHK repressed the advancement of SW480 cells with elevated apoptosis and autophagy and the cells quantities in G0/G1 phase. MiR-545-3p was elevated in CRC. SHK boosted miR-545-3p, repression of miR-545-3p or augmentation of GNB1 was able to turn around the function of SHK on CRC, and GNB1 was the target gene of miR-545-3p.All in all, SHK stimulates apoptosis and autophagy in CRC via miR-545-3p/GNB1 signaling axis, firstly demonstrating the regulatory mechanism of SHK in CRC via miR-545-3p/GNB1 axis.
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Affiliation(s)
- ZhiWei Hu
- Department of Gastrointestinal Surgery, The Yuebei People’s Hospital of ShaoGuan, ShaoGuan, GuangDong, China
| | - XinDong Zhou
- Department of Gastrointestinal Surgery, The Yuebei People’s Hospital of ShaoGuan, ShaoGuan, GuangDong, China
| | - DeQiang Zeng
- Department of Gastrointestinal Surgery, The Yuebei People’s Hospital of ShaoGuan, ShaoGuan, GuangDong, China
| | - JiaJun Lai
- Department of Gastrointestinal Surgery, The Yuebei People’s Hospital of ShaoGuan, ShaoGuan, GuangDong, China
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lncRNA IGF2-AS Regulates Nucleotide Metabolism by Mediating HMGA1 to Promote Pyroptosis of Endothelial Progenitor Cells in Sepsis Patients. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9369035. [PMID: 35082972 PMCID: PMC8786475 DOI: 10.1155/2022/9369035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022]
Abstract
Background Sepsis is one of the major causes of death worldwide, and its high mortality and pathological complexity hinder early accurate diagnosis. We aimed to investigate lncRNA IGF2-AS and HMGA1 effects on pyroptosis of endothelial progenitor cells (EPCs) in sepsis patients and the mechanisms involved. Methods Blood samples from sepsis patients and healthy subjects were collected, and EPCs were isolated and identified. We constructed cell lines that knocked down lncRNA IGF2-AS, HMGA1, and TYMS. Furthermore, lncRNA IGF2-AS was overexpressed. Subsequently, dNTP treatment with different concentrations was performed to investigate lncRNA IGF2-AS and HMGA1 effects on pyroptosis of EPCs in sepsis patients. Finally, exosomes were isolated from bone marrow mesenchymal stem cells (MSCs) to detect lncRNA IGF2-AS expression, and the influence of MSC-derived exosomal lncRNA IGF2-AS on sepsis was preliminarily discussed. Results Compared with Healthy group, lncRNA IGF2-AS, HMGA1, and TYMS were highly expressed in Sepsis group. Compared with si-NC group, si-lncRNA IGF2-AS group had increased proliferation ability, decreased pyroptosis, decreased HMGA1, RRM2, TK1, and TYMS expressions. lncRNA IGF2-AS played a regulatory role by binding HMGA1. Compared with si-NC group, the proliferation ability of si-HMGA1 group increased, pyroptosis decreased, and RRM2, TK1, and TYMS expressions also decreased. Compared with si-NC group, pyroptosis in si-TYMS group was reduced. In addition, HMGA1 was related and bound to TYMS. After overexpressing lncRNA IGF2-AS, dNTP level decreased, while the proliferation increased and pyroptosis decreased with higher concentration of dNTP. In addition, we found that EPCs took up MSC-exosomes. Compared with supernatant group, lncRNA IGF2-AS was expressed in exosomes group. Compared with EPCs group, EPCs+exosomes group had increased lncRNA IGF2-AS expression and increased pyroptosis. Conclusions lncRNA IGF2-AS regulated nucleotide metabolism by mediating HMGA1 to promote pyroptosis of EPCs in sepsis patients. This study provided important clues for finding new therapeutic targets for sepsis.
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Zeng L, Yuan S, Zhou P, Gong J, Kong X, Wu M. Circular RNA Pvt1 oncogene (CircPVT1) promotes the progression of papillary thyroid carcinoma by activating the Wnt/β-catenin signaling pathway and modulating the ratio of microRNA-195 (miR-195) to vascular endothelial growth factor A (VEGFA) expression. Bioengineered 2021; 12:11795-11810. [PMID: 34927541 PMCID: PMC8810178 DOI: 10.1080/21655979.2021.2008639] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) have been reported to be involved in the progression of papillary thyroid carcinoma (PTC). However, the role of circular RNA Pvt1 oncogene (circPVT1) in PTC has rarely been reported. In this study, we aimed to investigate the function and mechanism of circPVT1 in PTC. The expression level of circPVT1, miR-195 and VEGFA were determined by reverse transcription‑quantitative PCR (RT‑qPCR). Fisher's exact test was used to analyze the correlation between circPVT1 expression and PTC clinical features. Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (EdU) staining assay and transwell assay were conducted to evaluate the cell proliferation, migration and invasion ability. Dual-luciferase reporter and Western blot assay were conducted for evaluating the correlation between miR-195 and circPVT1 or VEGFA. The results of RT-PCR showed that the expression level of circPVT1 was significantly upregulated in PTC tissues and cell lines. After downregulating circPVT1 expression in PTC cells, the abilities of cell proliferation, migration, and invasion were obviously suppressed, and the Wnt/β-catenin signaling pathway was also repressed. Besides, miR-195 could both bind to PVT1 and VEGFA, while PVT1 could promote the expression of VEGFA by binding to miR-195. Downregulation of VEGFA expression in PTC cells revealed weakened cell proliferation, migration, and invasion capacities, and restrained Wnt/β-catenin signaling pathway. Therefore, we demonstrated that circPVT1 could promote VEGFA expression by sponging miR-195. CircPVT1 could serve as a molecule sponge for miR-195 and mediate the ceRNA network to promote the expression of VEGFA, thus contributed to the malignant progression of PTC.
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Affiliation(s)
- Linwen Zeng
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Shaofeng Yuan
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Pengfei Zhou
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Jianming Gong
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Xiangdong Kong
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Ming Wu
- Department of Surgery, Tinglin Hospital of Jinshan District, Shanghai, China
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15
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Huang Z, Su G, Bi X, Zhang L, Xu Z, Wang G. Over-expression of long non-coding RNA insulin-like growth factor 2-antisense suppressed hepatocellular carcinoma cell proliferation and metastasis by regulating the microRNA-520h/cyclin-dependent kinase inhibitor 1A signaling pathway. Bioengineered 2021; 12:6952-6966. [PMID: 34516353 PMCID: PMC8806836 DOI: 10.1080/21655979.2021.1975016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Primary liver cancer is the sixth most common cancer and the third leading cause of malignancy-related death worldwide in 2020, with 75–85% of hepatocellular carcinoma (HCC). Evidences have verified that long noncoding RNAs (lncRNAs) play key roles in HCC onset and development. However, the function and mechanism of lncRNA insulin-like growth factor 2-antisense (IGF2-AS) in HCC remain unclear. Herein, IGF2-AS expression profile in HCC patients was first investigated based on The Cancer Genome Atlas (TCGA) database and local HCC patients, followed by prognostic value evaluation using Kaplan–Meier method; then, the bioinformatics analysis, dual-luciferase reporter assay, Spearman correlation assay, function gain, and loss with rescue experiments were applied to investigate the biological function and the involved molecular mechanisms of IGF2-AS in HCC oncogenesis and development. Our results showed that IGF2-AS expression was significantly down-regulated in HCC cells and tissues; lower IGF2-AS expression was significantly associated with poor prognosis of HCC patients; IGF2-AS over-expression inhibited the viability, colony formation, invasion, and migration, while promoted apoptosis in vitro, and inhibited HCC xenograft growth in vivo; IGF2-AS sponged microRNA-520h (miR-520h) to up-regulate IGF2-AS expression, and miR-520h over-expression or cyclin-dependent kinase inhibitor 1A (CDKN1A) silencing reversed IGF2-AS reduced aggressive behaviors of HCC cells. In conclusion, IGF2-AS is a tumor-suppressor in HCC, and lower IGF2-AS expression is associated with poor prognosis of HCC patients; IGF2-AS inhibits HCC oncogenesis and development by IGF2-AS/miR-520h/CDKN1A pathway. Therefore, IGF2-AS may serve as a new biomarker for HCC management.
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Affiliation(s)
- Zhen Huang
- Department of Interventional Radiology, Huizhou First Hospital, Guangdong, China
| | - Guofeng Su
- Department of Interventional Radiology, Huizhou First Hospital, Guangdong, China
| | - Xiaoxia Bi
- Department of Medical Oncology, Huizhou First Hospital, Guangdong, China
| | - Libo Zhang
- Department of Interventional Radiology, Huizhou First Hospital, Guangdong, China
| | - Zhuohui Xu
- Department of Interventional Radiology, Huizhou First Hospital, Guangdong, China
| | - Ge Wang
- Department of Interventional Radiology, Huizhou First Hospital, Guangdong, China
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Zhang S, Wang C, Shi L, Xue Q. Beware of Steroid-Induced Avascular Necrosis of the Femoral Head in the Treatment of COVID-19-Experience and Lessons from the SARS Epidemic. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:983-995. [PMID: 33692615 PMCID: PMC7939498 DOI: 10.2147/dddt.s298691] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 01/08/2023]
Abstract
Summary The recent outbreak of coronavirus disease 2019 (COVID-19) has become a global epidemic. Corticosteroids have been widely used in the treatment of severe acute respiratory syndrome (SARS), and the pathological findings seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are very similar to those observed in severe acute respiratory syndrome-related coronavirus (SARS-CoV) infection. However, the long-term use of corticosteroids (especially at high doses) is associated with potentially serious adverse events, particularly steroid-induced avascular necrosis of the femoral head (SANFH). In today’s global outbreak, whether corticosteroid therapy should be used, the dosage and duration of treatment, and ways for the prevention, early detection, and timely intervention of SANFH are some important issues that need to be addressed. This review aims to provide a reference for health care providers in COVID-19 endemic countries and regions. Article Focus Hormones are a double-edged sword. This review aims to provide a reference for health care providers in coronavirus disease 2019 (COVID-19) endemic countries and regions, especially with respect to the pros and cons of corticosteroid use in the treatment of patients with COVID-19. Key Messages In today’s global outbreak, whether corticosteroid therapy should be used, the dosage and duration of treatment, and ways for the prevention, early detection, and timely intervention of SANFH are some important issues that need to be addressed. Strengths and Limitations Since SARS was mainly prevalent in China at that time, many evidences in this paper came from the reports of Chinese scholars. There is a bias in the selection of data, which may ignore the differences in environment, race, living habits, medical level and so on. SANFH may be the result of multiple factors. Whether the virus itself is an independent risk factor for SANFH has not been confirmed. In this paper, through literature retrieval, some reference opinions on glucocorticoid usage, diagnosis and treatment of SANFH are given. However, due to the lack of large-scale research data support, it can not be used as the gold standard for the above problems.
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Affiliation(s)
- Shenqi Zhang
- Department of Orthopedics, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Department of Joint and Sports Medicine, Zaozhuang Municipal Hospital Affiliated to Jining Medical University, Shandong, People's Republic of China
| | - Chengbin Wang
- Department of Joint and Sports Medicine, Zaozhuang Municipal Hospital Affiliated to Jining Medical University, Shandong, People's Republic of China
| | - Lei Shi
- Department of Orthopedics, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Qingyun Xue
- Department of Orthopedics, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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