201
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Zheng W, Wang X, Yu Y, Ji C, Fang L. CircRNF10-DHX15 interaction suppressed breast cancer progression by antagonizing DHX15-NF-κB p65 positive feedback loop. Cell Mol Biol Lett 2023; 28:34. [PMID: 37101128 PMCID: PMC10131429 DOI: 10.1186/s11658-023-00448-7] [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: 02/11/2023] [Accepted: 04/11/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is a common threat to women. The continuous activation of nuclear factor kappa B (NF-κB) signaling pathway contributes to the development of BC. This study aimed to investigate the role of a circular RNA (circRNF10) in BC progression and regulating NF-κB signaling pathway. METHODS Bioinformatics analysis, RT-qPCR, subcellular fractionation, FISH, RNase R treatment, and actinomycin D assay were used to explore the expression and characteristics of circRNF10 in BC. The biological functions of circRNF10 in BC were analyzed by MTT assay, colony formation assay, wound healing assay, and Transwell assay. RNA pulldown and RIP assay were used to identify the interaction between circRNF10 and DEAH (Asp-Glu-Ala-His) box helicase 15 (DHX15). The impact of circRNF10-DHX15 interaction on NF-κB signaling pathway was explored by western blot, IF, and co-IP. Furthermore, dual-luciferase reporter assay, ChIP, and EMSA were performed to assess the effect of NF-κB p65 on DHX15 transcription. RESULTS CircRNF10 was downregulated in BC, and lower expression of circRNF10 was related to poor prognosis of patients with BC. CircRNF10 inhibited the proliferation and migration of BC. Mechanically, circRNF10-DHX15 interaction sequestered DHX15 from NF-κB p65, thereby inhibiting the activation of NF-κB signaling pathway. On the other hand, NF-κB p65 enhanced DHX15 transcription by binding to the promoter of DHX15. Altogether, circRNF10 impaired the DHX15-NF-κB p65 positive feedback loop and suppressed the progression of BC. CONCLUSION CircRNF10-DHX15 interaction suppressed the DHX15-NF-κB p65 positive feedback loop, thereby inhibiting BC progression. These findings provide new insights in the continuous activation of NF-κB signaling pathway and raised potential therapeutic approach for BC treatment.
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Affiliation(s)
- Wenfang Zheng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yanchangzhong Road, Shanghai, 200072, People's Republic of China
| | - Xuehui Wang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yanchangzhong Road, Shanghai, 200072, People's Republic of China
| | - Yunhe Yu
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yanchangzhong Road, Shanghai, 200072, People's Republic of China
| | - Changle Ji
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yanchangzhong Road, Shanghai, 200072, People's Republic of China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yanchangzhong Road, Shanghai, 200072, People's Republic of China.
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202
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Niazi SK. RNA Therapeutics: A Healthcare Paradigm Shift. Biomedicines 2023; 11:biomedicines11051275. [PMID: 37238946 DOI: 10.3390/biomedicines11051275] [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: 03/30/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
COVID-19 brought about the mRNA vaccine and a paradigm shift to a new mode of treating and preventing diseases. Synthetic RNA products are a low-cost solution based on a novel method of using nucleosides to act as an innate medicine factory with unlimited therapeutic possibilities. In addition to the common perception of vaccines preventing infections, the newer applications of RNA therapies include preventing autoimmune disorders, such as diabetes, Parkinson's disease, Alzheimer's disease, and Down syndrome; now, we can deliver monoclonal antibodies, hormones, cytokines, and other complex proteins, reducing the manufacturing hurdles associated with these products. Newer PCR technology removes the need for the bacterial expression of DNA, making mRNA a truly synthetic product. AI-driven product design expands the applications of mRNA technology to repurpose therapeutic proteins and test their safety and efficacy quickly. As the industry focuses on mRNA, many novel opportunities will arise, as hundreds of products under development will bring new perspectives based on this significant paradigm shift-finding newer solutions to existing challenges in healthcare.
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Affiliation(s)
- Sarfaraz K Niazi
- College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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203
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Mazzeo F, Meccariello R, Guatteo E. Molecular and Epigenetic Aspects of Opioid Receptors in Drug Addiction and Pain Management in Sport. Int J Mol Sci 2023; 24:ijms24097831. [PMID: 37175536 PMCID: PMC10178540 DOI: 10.3390/ijms24097831] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Opioids are substances derived from opium (natural opioids). In its raw state, opium is a gummy latex extracted from Papaver somniferum. The use of opioids and their negative health consequences among people who use drugs have been studied. Today, opioids are still the most commonly used and effective analgesic treatments for severe pain, but their use and abuse causes detrimental side effects for health, including addiction, thus impacting the user's quality of life and causing overdose. The mesocorticolimbic dopaminergic circuitry represents the brain circuit mediating both natural rewards and the rewarding aspects of nearly all drugs of abuse, including opioids. Hence, understanding how opioids affect the function of dopaminergic circuitry may be useful for better knowledge of the process and to develop effective therapeutic strategies in addiction. The aim of this review was to summarize the main features of opioids and opioid receptors and focus on the molecular and upcoming epigenetic mechanisms leading to opioid addiction. Since synthetic opioids can be effective for pain management, their ability to induce addiction in athletes, with the risk of incurring doping, is also discussed.
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Affiliation(s)
- Filomena Mazzeo
- Department of Economics, Law, Cybersecurity and Sports Sciences, University of Naples "Parthenope", 80133 Naples, Italy
- Department of Movement Sciences and Wellbeing, University of Naples "Parthenope", 80133 Naples, Italy
| | - Rosaria Meccariello
- Department of Movement Sciences and Wellbeing, University of Naples "Parthenope", 80133 Naples, Italy
| | - Ezia Guatteo
- Department of Movement Sciences and Wellbeing, University of Naples "Parthenope", 80133 Naples, Italy
- IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64, 00143 Rome, Italy
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204
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Tian Y, Ma X, Jiang Y, Han J, Zhang R, Xu X, Zhang W, Man C. Circular RNA circAKIRIN2 participates in the process of stress-induced immunosuppression affecting immune response to infectious bursal disease virus vaccine in chicken. Vet Microbiol 2023; 281:109746. [PMID: 37075663 DOI: 10.1016/j.vetmic.2023.109746] [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: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
At present, stress-induced immunosuppression is still a hidden threat that leads to immunization failure and outbreaks of poultry diseases, and causes huge economic losses to the modern poultry industry. However, the molecular mechanisms of stress-induced immunosuppression affecting viral vaccine immunity are still poorly understood. Here, we identified circAKIRIN2 as a conserved circular transcript in chicken, and explored its expression patterns in different immune states by quantitative real-time PCR (qRT-PCR), then conducted bioinformatics analysis. The results showed that circAKIRIN2 actively participated in the process of stress-induced immunosuppression affecting the immune response to infectious bursal disease virus (IBDV) vaccine. The key time points for circAKIRIN2 involving in the process were 2 day post immunization (dpi), 5 dpi, and 28 dpi, especially at the acquired immune stage. The important tissues that responded to the process included the heart, liver, and lung, all of which changed significantly. In addition, circAKIRIN2 as a competing endogenous RNA (ceRNA) sponging zinc finger and BTB domain containing 20 (ZBTB20) was a potential molecular mechanism for regulating immune functions in the process. In conclusion, circAKIRIN2 is a key regulatory factor for stress-induced immunosuppression affecting the IBDV vaccine immune response, and this study can provide a new perspective for exploring the molecular regulatory mechanisms of stress-induced immunosuppression affecting immune response.
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Affiliation(s)
- Yufei Tian
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Xiaoli Ma
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Yi Jiang
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Jianwei Han
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Rui Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Xinxin Xu
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Wei Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China
| | - Chaolai Man
- College of Life Science and Technology, Harbin Normal University, Harbin 150001, PR China.
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205
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Hou L, Zhang J, Zhao F. Full-length circular RNA profiling by nanopore sequencing with CIRI-long. Nat Protoc 2023:10.1038/s41596-023-00815-w. [PMID: 37045995 DOI: 10.1038/s41596-023-00815-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
Abstract
Circular RNAs (circRNAs) have important roles in regulating developmental processes and disease progression. As most circRNA sequences are highly similar to their cognate linear transcripts, the current short-read sequencing-based methods rely on the back-spliced junction signal for distinguishing circular and linear reads, which does not allow circRNAs' full-length structure to be effectively reconstructed. Here we describe a long-read sequencing-based protocol, CIRI-long, for the detection of full-length circular RNAs. The CIRI-long protocol combines rolling circular reverse transcription and nanopore sequencing to capture full-length circRNA sequences. After poly(A) tailing, RNase R treatment, and size selection of polymerase chain reaction products, CIRI-long achieves an increased percentage (6%) of circular reads in the constructed library, which is 20-fold higher compared with previous Illumina-based strategies. This method can be applied in cell lines or tissue samples, enabling accurate detection of full-length circRNAs in the range of 100-3,000 bp. The entire protocol can be completed in 1 d, and can be scaled up for large-scale analysis using the nanopore barcoding kit and PromethION sequencing device. CIRI-long can serve as an effective and user-friendly protocol for characterizing full-length circRNAs, generating direct and convincing evidence for the existence of detected circRNAs. The analytical pipeline offers convenient functions for identification of full-length circRNA isoforms and integration of multiple datasets. The assembled full-length transcripts and their splicing patterns provide indispensable information to explore the biological function of circRNAs.
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Affiliation(s)
- Lingling Hou
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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206
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Ju LS, Morey TE, Seubert CN, Martynyuk AE. Intergenerational Perioperative Neurocognitive Disorder. BIOLOGY 2023; 12:biology12040567. [PMID: 37106766 PMCID: PMC10135810 DOI: 10.3390/biology12040567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
Accelerated neurocognitive decline after general anesthesia/surgery, also known as perioperative neurocognitive disorder (PND), is a widely recognized public health problem that may affect millions of patients each year. Advanced age, with its increasing prevalence of heightened stress, inflammation, and neurodegenerative alterations, is a consistent contributing factor to the development of PND. Although a strong homeostatic reserve in young adults makes them more resilient to PND, animal data suggest that young adults with pathophysiological conditions characterized by excessive stress and inflammation may be vulnerable to PND, and this altered phenotype may be passed to future offspring (intergenerational PND). The purpose of this narrative review of data in the literature and the authors' own experimental findings in rodents is to draw attention to the possibility of intergenerational PND, a new phenomenon which, if confirmed in humans, may unravel a big new population that may be affected by parental PND. In particular, we discuss the roles of stress, inflammation, and epigenetic alterations in the development of PND. We also discuss experimental findings that demonstrate the effects of surgery, traumatic brain injury, and the general anesthetic sevoflurane that interact to induce persistent dysregulation of the stress response system, inflammation markers, and behavior in young adult male rats and in their future offspring who have neither trauma nor anesthetic exposure (i.e., an animal model of intergenerational PND).
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Affiliation(s)
- Ling-Sha Ju
- Department of Anesthesiology, College of Medicine, University of Florida, P.O. Box 100254, JHMHC, 1600 SW Archer Road, Gainesville, FL 32610, USA
| | - Timothy E Morey
- Department of Anesthesiology, College of Medicine, University of Florida, P.O. Box 100254, JHMHC, 1600 SW Archer Road, Gainesville, FL 32610, USA
| | - Christoph N Seubert
- Department of Anesthesiology, College of Medicine, University of Florida, P.O. Box 100254, JHMHC, 1600 SW Archer Road, Gainesville, FL 32610, USA
| | - Anatoly E Martynyuk
- Department of Anesthesiology, College of Medicine, University of Florida, P.O. Box 100254, JHMHC, 1600 SW Archer Road, Gainesville, FL 32610, USA
- Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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207
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Wang XB, Luo T, Lu SL, Lu HZ, Zhao TY, Jiang ZJ, Liu XY, Zhao C, Li LQ, Chen J. Circular RNA hsa_circ_0005218 promotes the early recurrence of hepatocellular carcinoma by targeting the miR-31-5p/CDK1 pathway. Heliyon 2023; 9:e14816. [PMID: 37035389 PMCID: PMC10073894 DOI: 10.1016/j.heliyon.2023.e14816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/28/2023] Open
Abstract
Increasing evidence has manifested that circular RNAs (circRNAs) exhibited critical function in regulating various signaling pathways related to hepatocellular carcinoma (HCC) recurrence. However, the role and mechanism of the circRNAs in the HCC early recurrence remain elusive. In this study, high-throughput RNA-sequencing (RNA-seq) analysis was conducted to identify the expression profile of circRNAs in HCC tissues and circ_0005218 was identified as one circRNA that significantly up-regulated in early recurrent HCC tissues. And patients with high expression of circ_0005218 showed worsen overall survival (OS) and disease-free survival (DFS). Moreover, the promotion effects of circ_0005218 on HCC cells in term of proliferation, invasion and metastasis were confirmed both in vitro and vivo by gain- and loss-of function assays. In addition, dual-luciferase reporter assays showed that circ_0005218 could competitively bind to micro-RNA (miR)-31-5p. Furthermore, we showed that suppression of CDK1 by miR-31-5p could be partially rescued by up-regulating circ_0005218. Taken together, the present study indicates that circ_0005218 absorbed miR-31-5p as a sponge to weaken its suppression on CDK1 expression, and thus boost HCC cell invasion and migration, which would act as a potential biomarker to predict the HCC early recurrence and as a new therapeutic target for treatment of HCC.
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Affiliation(s)
- Xiao-bo Wang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Tao Luo
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Shao-long Lu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Hua-ze Lu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Tai-yun Zhao
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Nanning, China
| | - Zhi-jun Jiang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xin-yu Liu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Chang Zhao
- Department of Interventional Therapy, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Le-qun Li
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Corresponding author. Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021 China.
| | - Jie Chen
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Corresponding author. Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021 China.
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208
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Fan B, Zheng C, Wang N, Chang Z, Liu Y, Wang C, Xiang J, Tao Y, Wang G, Zhang Q. CircSTK3 drives the metastasis of colorectal cancer by regulating epithelial-mesenchymal transition. iScience 2023; 26:106170. [PMID: 36922993 PMCID: PMC10009203 DOI: 10.1016/j.isci.2023.106170] [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: 07/12/2022] [Revised: 11/24/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Circular RNAs (circRNAs) play crucial roles in malignancies. We aimed to delineate the functions and clinical importance of dysregulated circRNAs in colorectal cancer (CRC). We determined the circRNA expression profile from five CRC and paired adjacent normal tissues using circRNA microarray. We found that a novel circRNA, hsa_circ_0004592 (named circSTK3), was significantly upregulated in CRC tissues and correlated with decreased survival. Loss- and gain-of-function assays revealed that circSTK3 promoted the migration and invasion but not proliferation of cells. Whole genome expression microarray identified potential downstream targets and the regulatory networks of circSTK3; Gene Ontology analysis confirmed circSTK3 involvement in the CRC metastasis phenotype. Abnormal circSTK3 expression affected a subset of genes associated with CRC metastasis and triggered epithelial-mesenchymal transition programming, maintaining a tumor-promoting signature. Moreover, circSTK3 was transcriptionally regulated by CTCF. These findings reveal the functional and prognostic roles of circSTK3 and expose circRNAs as key players in metastasis.
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Affiliation(s)
- Boyang Fan
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Chaojing Zheng
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ning Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Zewen Chang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yunxiao Liu
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Chunlin Wang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Jun Xiang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yangbao Tao
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Guiyu Wang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qian Zhang
- Department of Colorectal Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310000, China
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209
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Campos-Melo D, Droppelmann CA, Zhu LQ. Editorial: MiRNAs as pivotal components of ncRNA networks associated with CNS injuries and neurodegeneration, and their therapeutic potential. Front Mol Neurosci 2023; 16:1166943. [PMID: 36993783 PMCID: PMC10040871 DOI: 10.3389/fnmol.2023.1166943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Affiliation(s)
- Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Western University, London, ON, Canada
- *Correspondence: Danae Campos-Melo
| | - Cristian A. Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Western University, London, ON, Canada
| | - Ling Q. Zhu
- Huazhong University of Science and Technology, Wuhan, China
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210
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Wang X, Wang J, An Z, Yang A, Qiu M, Tan Z. CircXPO1 Promotes Glioblastoma Malignancy by Sponging miR-7-5p. Cells 2023; 12:831. [PMID: 36980172 PMCID: PMC10047377 DOI: 10.3390/cells12060831] [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: 12/13/2022] [Revised: 02/08/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Mounting evidence suggests that circular RNAs play important roles in the development and progression of cancers. However, their function in glioblastomas (GBM) is still unclear. By circRNA array analysis, we found that circXPO1 (hsa_circ_102737) was significantly upregulated in GBM, and qPCR analysis verified that the circXPO1 expression level was increased in both GBM tissues and cell lines. Functional studies demonstrated that the knockdown of circXPO1 in GBM cell lines repressed cell proliferation and migration; conversely, the overexpression of circXPO1 promoted the malignancy of GBM cells. In line with these findings, circXPO1 inhibition effectively suppressed gliomagenesis in the in situ transplantation model of nude mice. Through bioinformatic analyses and dual-luciferase reporter assays, we showed that circXPO1 directly bound to miR-7-5p, which acted as a tumor suppressor through the negative regulation of RAF1. In conclusion, our studies suggest that the circXPO1/miR-7-5p/RAF1 axis promotes brain tumor formation and may be a potential therapeutic target for GBM treatment.
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211
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Li QY, Gong T, Huang YK, Kang L, Warner CA, Xie H, Chen LM, Duan XQ. Role of noncoding RNAs in liver fibrosis. World J Gastroenterol 2023; 29:1446-1459. [PMID: 36998425 PMCID: PMC10044853 DOI: 10.3748/wjg.v29.i9.1446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/27/2022] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Liver fibrosis is a wound-healing response following chronic liver injury caused by hepatitis virus infection, obesity, or excessive alcohol. It is a dynamic and reversible process characterized by the activation of hepatic stellate cells and excess accumulation of extracellular matrix. Advanced fibrosis could lead to cirrhosis and even liver cancer, which has become a significant health burden worldwide. Many studies have revealed that noncoding RNAs (ncRNAs), including microRNAs, long noncoding RNAs and circular RNAs, are involved in the pathogenesis and development of liver fibrosis by regulating signaling pathways including transforming growth factor-β pathway, phosphatidylinositol 3-kinase/protein kinase B pathway, and Wnt/β-catenin pathway. NcRNAs in serum or exosomes have been reported to tentatively applied in the diagnosis and staging of liver fibrosis and combined with elastography to improve the accuracy of diagnosis. NcRNAs mimics, ncRNAs in mesenchymal stem cell-derived exosomes, and lipid nanoparticles-encapsulated ncRNAs have become promising therapeutic approaches for the treatment of liver fibrosis. In this review, we update the latest knowledge on ncRNAs in the pathogenesis and progression of liver fibrosis, and discuss the potentials and challenges to use these ncRNAs for diagnosis, staging and treatment of liver fibrosis. All these will help us to develop a comprehensive understanding of the role of ncRNAs in liver fibrosis.
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Affiliation(s)
- Qing-Yuan Li
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Tao Gong
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yi-Ke Huang
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
| | - Lan Kang
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
| | - Charlotte A Warner
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - He Xie
- Department of Clinical Laboratory, The Hospital of Xidian Group, Xi’an 710077, Shaanxi Province, China
| | - Li-Min Chen
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
- Department of Clinical Laboratory, The Hospital of Xidian Group, Xi’an 710077, Shaanxi Province, China
| | - Xiao-Qiong Duan
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
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212
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An F, Meng X, Yuan L, Niu Y, Deng J, Li Z, Liu Y, Xia R, Liu S, Yan C. Network regulatory mechanism of ncRNA on the Wnt signaling pathway in osteoporosis. Cell Div 2023; 18:3. [PMID: 36879309 PMCID: PMC9990358 DOI: 10.1186/s13008-023-00086-7] [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: 11/14/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Non-coding RNA (ncRNA) is a type of non-protein-coding RNA molecule transcribed from the genome which performs broad regulation of a variety of biological functions in human cells. The Wnt signaling pathway is highly conserved in multicellular organisms, playing an important role in their growth and development. Increasing evidence suggests that ncRNA can regulate cell biological function, enhance bone metabolism, and maintain normal bone homeostasis by interacting with the Wnt pathway. Studies have also demonstrated that the association of ncRNA with the Wnt pathway may be a potential biomarker for the diagnosis, evaluation of prognosis, and treatment of osteoporosis. The interaction of ncRNA with Wnt also performs an important regulatory role in the occurrence and development of osteoporosis. Targeted therapy of the ncRNA/Wnt axis may ultimately be the preferred choice for the treatment of osteoporosis in the future. The current article reviews the mechanism of the ncRNA/Wnt axis in osteoporosis and reveals the relationship between ncRNA and Wnt, thereby exploring novel molecular targets for the treatment of osteoporosis and providing theoretical scientific guidance for its clinical treatment.
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Affiliation(s)
- Fangyu An
- Teaching Experiment Training Center, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Xiangrui Meng
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Lingqing Yuan
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Yanqiang Niu
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Jie Deng
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Zhaohui Li
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Yongqi Liu
- School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China.
| | - Ruoliu Xia
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Shiqing Liu
- The First Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China
| | - Chunlu Yan
- School of Traditional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, Gansu, China.
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213
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Chien PY, Gao L, Liu Y. Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method. Int J Mol Sci 2023; 24:ijms24054934. [PMID: 36902367 PMCID: PMC10003555 DOI: 10.3390/ijms24054934] [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: 01/26/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
T7 RNA polymerase is the most widely used enzyme in RNA synthesis, and it is also used for RNA labeling in position-selective labeling of RNA (PLOR). PLOR is a liquid-solid hybrid phase method that has been developed to introduce labels to specific positions of RNA. Here, we applied PLOR as a single-round transcription method to quantify the terminated and read-through products in transcription for the first time. Various factors, including pausing strategies, Mg2+, ligand and the NTP concentration at the transcriptional termination of adenine riboswitch RNA have been characterized. This helps to understand transcription termination, which is one of the least understood processes in transcription. Additionally, our strategy can potentially be used to study the co-transcription behavior of general RNA, especially when continuous transcription is not desired.
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214
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Li Q, Zhao Y, Xu C, Liang Y, Zhao Y, He Q, Li J, Chen K, Qiao H, Liu N, Ma J, Chen L, Li Y. Chemotherapy-Induced Senescence Reprogramming Promotes Nasopharyngeal Carcinoma Metastasis by circRNA-Mediated PKR Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205668. [PMID: 36683218 PMCID: PMC10015868 DOI: 10.1002/advs.202205668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/23/2022] [Indexed: 05/13/2023]
Abstract
Senescence is associated with tumor metastasis and chemotherapy resistance, yet the mechanisms remain elusive. Here, it is identified that nasopharyngeal carcinoma (NPC) patients who developed distant metastasis are characterized by senescence phenotypes, in which circWDR37 is a key regulator. CircWDR37 deficiency limits cisplatin or gemcitabine-induced senescent NPC cells from proliferation, migration, and invasion. Mechanistically, circWDR37 binds to and dimerizes double-stranded RNA-activated protein kinase R (PKR) to initiate PKR autophosphorylation and activation. Independent of its kinase activity, phosphorylated PKR induces I-kappaB kinase beta (IKKβ) phosphorylation, binds to and releases RELA from NF-κB inhibitor alpha (IκBα) to trigger nuclear factor kappa B (NF-κB) activation, thereby stimulating cyclin D1 (CCND1) and senescence-associated secretory phenotype component gene transcription in a circWDR37-dependent manner. Low circWDR37 levels correlate with chemotherapy response and favorable survival in NPC patients treated with gemcitabine or cisplatin induction chemotherapy. This study uncovers a new mechanism of circWDR37 activated PKR in senescence-driven metastasis and provides appealing therapeutic targets in NPC.
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Affiliation(s)
- Qian Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yu‐Heng Zhao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Cheng Xu
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ye‐Lin Liang
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yin Zhao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Qing‐Mei He
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jun‐Yan Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Kai‐Lin Chen
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Han Qiao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Na Liu
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jun Ma
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Lei Chen
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ying‐Qin Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
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Ye L, Shi Y, Zhang H, Chen C, Niu J, Yang J, Li Z, Shao H, Qin B. circFLNA promotes intestinal injury during abdominal sepsis through Fas-mediated apoptosis pathway by sponging miR-766-3p. Inflamm Res 2023; 72:509-529. [PMID: 36625877 PMCID: PMC10023616 DOI: 10.1007/s00011-023-01688-1] [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: 11/04/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Intra-abdominal infections are the second most common cause of sepsis in the intensive care unit. Intestinal epithelial injury due to abdominal sepsis results in a variety of pathological changes, such as intestinal bacteria and toxins entering the blood, leading to persistent systemic inflammation and multiple organ dysfunction. The increased apoptosis of intestinal epithelial cells induced by sepsis further exacerbates the progression of sepsis. Although several studies have revealed that circRNAs are involved in intestinal epithelial injury in sepsis, few studies have identified the roles of circRNAs in intestinal epithelial apoptosis. METHODS We used laser capture microdissection to obtain purified epithelial cells located in intestinal crypts from four patients with abdominal sepsis induced by intestinal perforation and four samples from age and sex-matched non-septic patients. Microarray analysis of circRNAs was conducted to assess differentially expressed circRNAs between patients with and without sepsis. Lastly, in vitro and in vivo assays were performed to study the mechanism of circFLNA in intestinal epithelial apoptosis during sepsis. RESULTS circFLNA was upregulated in the intestinal epithelium after abdominal sepsis induced by intestinal perforation. Inhibition of miR-766-3p impaired si-circFLNA-mediated inhibition of apoptosis and inflammation factor levels in lipopolysaccharide (LPS)-treated HIEC-6 cells. circFLNA aggravated apoptosis and inflammation through the Fas-mediated apoptosis pathway in both LPS-treated HIEC-6 cells and a mouse cecal ligation and puncture model. CONCLUSION Our findings showed that circFLNA promotes intestinal injury in abdominal sepsis through the Fas-mediated apoptosis pathway by sponging miR-766-3p. The circFLNA/miR-766-3p/Fas axis has potential as a novel therapeutic target for treating intestinal injury in sepsis.
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Affiliation(s)
- Ling Ye
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yuan Shi
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Huifeng Zhang
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Chao Chen
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Jingjing Niu
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Jianxu Yang
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Zhifeng Li
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Huanzhang Shao
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
| | - Bingyu Qin
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
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216
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Zhang YC, Yuan C, Chen YQ. Noncoding RNAs and their roles in regulating the agronomic traits of crops. FUNDAMENTAL RESEARCH 2023. [DOI: 10.1016/j.fmre.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
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217
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Epigenetic Regulation of Ferroptosis in Central Nervous System Diseases. Mol Neurobiol 2023; 60:3584-3599. [PMID: 36847936 DOI: 10.1007/s12035-023-03267-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/14/2023] [Indexed: 03/01/2023]
Abstract
Ferroptosis, a newly identified form of cell death, is characterized by iron overload and accumulation of lipid reactive oxygen species. Inactivation of pathways, such as glutathione/glutathione peroxidase 4, NAD(P)H/ferroptosis suppressor protein 1/ubiquinone, dihydroorotate dehydrogenase/ubiquinol, or guanosine triphosphate cyclohydrolase-1/6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin pathways, have been found to induce ferroptosis. The accumulating data suggest that epigenetic regulation can determine cell sensitivity to ferroptosis at both the transcriptional and translational levels. While many of the effectors that regulate ferroptosis have been mapped, epigenetic regulation in ferroptosis is not yet fully understood. Neuronal ferroptosis is a driver in several central nervous system (CNS) diseases, such as stroke, Parkinson's disease, traumatic brain injury, and spinal cord injury, and thus, research on how to inhibit neuronal ferroptosis is required to develop novel therapies for these diseases. In this review, we have summarized epigenetic regulation of ferroptosis in these CNS diseases, focusing in particular on DNA methylation, non-coding RNA regulation, and histone modification. Understanding epigenetic regulation in ferroptosis will hasten the development of promising therapeutic strategies in CNS diseases associated with ferroptosis.
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218
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Wang H, Yuan H, Guo Q, Zeng X, Liu M, Ji R, Chen Z, Guan Q, Zheng Y, Wang Y, Zhou Y. A novel circRNA, hsa_circ_0069382, regulates gastric cancer progression. Cancer Cell Int 2023; 23:35. [PMID: 36841760 PMCID: PMC9960672 DOI: 10.1186/s12935-023-02871-4] [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: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 02/27/2023] Open
Abstract
Aberrant expression of circRNAs is closely associated with the progression of gastric cancer; however, the specific mechanisms involved remain unclear. Our aim was to identify new gastric cancer biomarkers and explore the molecular mechanisms of gastric cancer progression. Therefore, we analyzed miRNA and circRNA microarrays of paired early-stage gastric cancer samples. Our study identified a new circRNA called hsa_circ_0069382, that had not been reported before and was expressed at low levels in gastric cancer tissues. Our study also included bioinformatics analyses which determined that the high expression of hsa_circ_0069382 regulated the BTG anti-proliferation factor 2 (BTG2)/ focal adhesion kinase (FAK) axis in gastric cancer lines by sponging for miR-15a-5p. Therefore, proliferation, invasion, and migration of gastric cancer is impacted. miR-15a-5p overexpression partially restored the effects of hsa_circ_0069382. This study provides potential new therapeutic options and a future direction to explore for gastric cancer treatment, and biomarkers.
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Affiliation(s)
- Haoying Wang
- grid.32566.340000 0000 8571 0482The First Clinical Medical College, Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Hao Yuan
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Qinghong Guo
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Xi Zeng
- grid.32566.340000 0000 8571 0482The First Clinical Medical College, Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Mengxiao Liu
- grid.32566.340000 0000 8571 0482The First Clinical Medical College, Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Rui Ji
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Zhaofeng Chen
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Quanlin Guan
- grid.412643.60000 0004 1757 2902Department of Oncology Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Ya Zheng
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000, China. .,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000, China. .,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
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219
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CircRNA_0017076 acts as a sponge for miR-185-5p in the control of epithelial-to-mesenchymal transition of tubular epithelial cells during renal interstitial fibrosis. Hum Cell 2023; 36:1024-1040. [PMID: 36828974 DOI: 10.1007/s13577-023-00877-8] [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: 10/03/2022] [Accepted: 02/04/2023] [Indexed: 02/26/2023]
Abstract
Renal interstitial fibrosis (RIF) is a common pathological hallmark of progressive chronic kidney disease (CKD). Circular RNAs (circRNAs) are involved in certain renal diseases, but their role in RIF is largely unknown. The present study investigated the effects and potential mechanisms of circRNA_0017076 in RIF. CircRNA_0017076 expression was markedly upregulated in transforming growth factor-β1 (TGF-β1)-treated renal tubular epithelial cells (RTECs) and kidney biopsy samples from patients with RIF. Functional assays showed that circRNA_0017076 colocalized with microRNA-185-5p (miR-185-5p) and inhibited miR-185-5p function via direct binding to miR-185-5p. In vitro, the knockdown of circRNA_0017076 inhibited the calcium ion (Ca2+) influx-mediated epithelial-to-mesenchymal transition (EMT) of RTECs and downregulated the expression of stromal interaction molecule 1 (STIM1), which is a target protein of miR-185-5p. Silencing mmu_circ_0004488 reduced fibrotic lesions in the kidneys of unilateral ureteral obstruction (UUO) mice by targeting the miR-185-5p/Stim1 axis. For the first time, we identified circRNA_0017076 as a sponge for miR-185-5p, which regulates STIM1 gene expression and is involved in RIF. Our results support circRNA_0017076 as a potential therapeutic target for RIF disease.
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220
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Liu L, Sang M, Shi J, Zheng Y, Meng L, Gu L, Li Z, Liu F, Bu J, Duan X, Zhao F, Zhang W, Shan B. CircRNA mannosidase alpha class 1A member 2 promotes esophageal squamous cell carcinoma progression by regulating C-C chemokine ligand 5. Biochem Biophys Res Commun 2023; 645:61-70. [PMID: 36680938 DOI: 10.1016/j.bbrc.2023.01.043] [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: 12/23/2022] [Revised: 01/04/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignancy with high morbidity and mortality. Although circular RNAs (circRNAs) play important roles in various cancers including ESCC, the role of the circRNA mannosidase alpha class 1A member 2 (circMAN1A2) in ESCC has been rarely studied. This study aimed to explore the role of circMAN1A2 in ESCC. CircMAN1A2 expression in ESCC tissues and cells was evaluated, and the relationship between circMAN1A2 expression and prognosis in patients with ESCC was analyzed. C-C chemokine ligand 5 (CCL5) was found to be a downstream target of circMAN1A2 by analysing the Agilent Microarray. Next, we performed in vitro and in vivo xenotransplantation assays to explore the role of circMAN1A2 in ESCC. We observed that high circMAN1A2 expression is associated with poor prognosis in patients with ESCC. Suppression of circMAN1A2 expression inhibits the proliferation, migration, and invasiveness of ESCC via regulating CCL5. Our results suggest that circMAN1A2 can promote the progression of ESCC by regulating CCL5. Thus, circMAN1A2 might be a novel diagnostic biomarker of ESCC, and targeting circMAN1A2 using inhibitors could be a potential therapeutic strategy to treat ESCC.
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Affiliation(s)
- Lie Liu
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Meixiang Sang
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China; Department of Tumor Research Institute, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Jian Shi
- Department of Medical Oncology, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Yang Zheng
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Lingjiao Meng
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Lina Gu
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Ziyi Li
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Fei Liu
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Jing Bu
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Xiaoyang Duan
- Department of Medical Oncology, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Feifei Zhao
- Department of Hematology, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Wentian Zhang
- Department of Medical Oncology, Lingshou County Hospital of Integrated Traditional Chinese and Western Medicine, Shijiazhuang, Hebei, 050500, People's Republic of China
| | - Baoen Shan
- Department of Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China; Department of Tumor Research Institute, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China.
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Sun K, Yao H, Zhang P, Sun Y, Ma J, Xia Q. Emerging landscape of circFNDC3B and its role in human malignancies. Front Oncol 2023; 13:1097956. [PMID: 36793611 PMCID: PMC9924128 DOI: 10.3389/fonc.2023.1097956] [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: 11/14/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023] Open
Abstract
In recent years, more attention has been paid to expanding the abundance of Circular RNAs (circRNAs), while the circRNAs that have been found to have significant functions have not been studied in different diseases. CircFNDC3B is one of the most researched circRNAs generated from fibronectin type III domain-containing protein 3B (FNDC3B) gene. Accumulating researches have reported the multiple functions of circFNDC3B in different cancer types and other non-neoplastic diseases, and predicted that circFNDC3B might be a potential biomarker. Notably, circFNDC3B can play roles in different diseases by binding to various microRNAs (miRNAs), binding to RNA-binding proteins (RBPs), or encoding functional peptides. This paper systematically summarizes the biogenesis and function of circRNAs, reviews and discusses the roles and molecular mechanisms of circFNDC3B and its target genes in different cancers and non-neoplastic diseases, which will do favor to broaden our comprehension of the function of circRNAs and facilitate subsequent research on circFNDC3B.
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Affiliation(s)
- Kai Sun
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
| | - Huibao Yao
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Peizhi Zhang
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
| | - Yanning Sun
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
| | - Jian Ma
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Qinghua Xia
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
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Wu J, Shi Y, Xing M, Deng M, Cao W, Guo Q, Zou W. CircRalgapa1 facilitates morphine tolerance via miR-873a-5p/A20 axis in mice. Neuropharmacology 2023; 224:109353. [PMID: 36455645 DOI: 10.1016/j.neuropharm.2022.109353] [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: 10/04/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Morphine tolerance (MT) caused by long-term use of morphine is a major medical problem. The underlying molecular mechanisms of morphine tolerance remain unclear. Here, we establish the morphine tolerance model in mice and verify whether a novel circRNA, circRalgapa1 is involved in morphine tolerance and its specific molecular mechanism. We show that the expression of circRalgapa1 in the spinal cord is significantly down-expressed in the spinal cord of morphine-tolerant mice. CircRalgapa1 is mainly located in the neuronal cytoplasm and co-localizes with miR-873a-5p. Mechanically, circRalgapa1 acts as competing endogenous RNAs (ceRNAs) to regulate the inhibitory of miR-873a-5p on A20 (also known as tumor necrosis factor α-induced protein 3, TNFAIP3). Functionally, overexpression of circRalgapa1 by intrathecal injection of adeno-associated virus (AAV- circRalgapa1) attenuated the formation of morphine tolerance and partially reversed the development of morphine tolerance. Moreover, overexpression of miR-873a-5p blocked the effect of AAV-circRalgapa1 on alleviating morphine tolerance in mice. In conclusion, chronic morphine administration-mediated down-regulation of circRalgapa1 in the spinal cord contributes to morphine tolerance via miR-873a-5p/A20 axis in mice. Overexpression of circRalgapa1 may be a promising RNA-based therapy for morphine tolerance.
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Affiliation(s)
- Jing Wu
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yufei Shi
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Manyu Xing
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Meiling Deng
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Cao
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qulian Guo
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wangyuan Zou
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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223
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Ren C, Fan P, Li S, Liang Z. Advances in understanding cold tolerance in grapevine. PLANT PHYSIOLOGY 2023:kiad092. [PMID: 36789447 DOI: 10.1093/plphys/kiad092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/06/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
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224
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Wang F, Li W, Li B, Xie L, Tong Y, Xu X. cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities. Int J Mol Sci 2023; 24:ijms24043822. [PMID: 36835231 PMCID: PMC9959564 DOI: 10.3390/ijms24043822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/29/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5' and 3' ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in clinical and research fields. The accurate modeling of circRNAs structure and stability has far-reaching impact on our understanding of their functions and our ability to develop RNA-based therapeutics. The cRNAsp12 server offers a user-friendly web interface to predict circular RNA secondary structures and folding stabilities from the sequence. Through the helix-based landscape partitioning strategy, the server generates distinct ensembles of structures and predicts the minimal free energy structures for each ensemble with the recursive partition function calculation and backtracking algorithms. For structure predictions in the limited structural ensemble, the server also provides users with the option to set the structural constraints of forcing the base pairs and/or forcing the unpaired bases, such that only structures that meet the criteria are enumerated recursively.
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Affiliation(s)
- Fengfei Wang
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Wei Li
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Baiyi Li
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Yunguang Tong
- Department of Pharmacy, China Jiliang University, Hangzhou 310000, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
- Correspondence:
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225
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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226
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Circular RNAs and Untranslated Regions in Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24043215. [PMID: 36834627 PMCID: PMC9967498 DOI: 10.3390/ijms24043215] [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: 11/15/2022] [Revised: 01/05/2023] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
Before the advent of next-generation sequencing, research on acute myeloid leukemia (AML) mostly centered on protein-coding genes. In recent years, breakthroughs in RNA sequencing technologies and whole transcriptome analysis have led to the discovery that approximately 97.5% of the human genome is transcribed into non-coding RNAs (ncRNAs). This paradigm shift has led to an explosion of research interest in different classes of non-coding RNAs, such as circular RNAs (circRNAs) as well as non-coding untranslated regions (UTRs) of protein-coding messenger RNAs. The critical roles of circRNAs and UTRs in AML pathogenesis have become increasingly apparent. In this review, we discuss the cellular mechanisms of circRNAs and summarize recent studies that reveal their biological roles in AML. Furthermore, we also review the contribution of 3'UTRs to disease progression. Finally, we discuss the potential of circRNAs and 3'UTRs as new biomarkers for disease stratification and/or the prediction of treatment response and targets for the development of RNA-directed therapeutic applications.
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227
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Li H, Liu C, Wu H. Reply. Hepatology 2023; 77:E25. [PMID: 35810445 DOI: 10.1002/hep.32661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Li
- Liver Transplantation Division, Department of Liver Surgery , West China Hospital, Sichuan University , Chengdu , China.,Laboratory of Liver Surgery , West China Hospital, Sichuan University , Chengdu , China.,Department of Hepatobiliary Pancreatic Tumor Center , Chongqing University Cancer Hospital , Chongqing , China
| | - Chang Liu
- Liver Transplantation Division, Department of Liver Surgery , West China Hospital, Sichuan University , Chengdu , China
| | - Hong Wu
- Liver Transplantation Division, Department of Liver Surgery , West China Hospital, Sichuan University , Chengdu , China.,Laboratory of Liver Surgery , West China Hospital, Sichuan University , Chengdu , China
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228
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BMSC-Derived Exosomal CircHIPK3 Promotes Osteogenic Differentiation of MC3T3-E1 Cells via Mitophagy. Int J Mol Sci 2023; 24:ijms24032785. [PMID: 36769123 PMCID: PMC9917928 DOI: 10.3390/ijms24032785] [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: 01/03/2023] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Exosome-based therapy is emerging as a promising strategy to promote bone regeneration due to exosomal bioactive cargos, among which circular RNA (circRNA) has recently been recognized as the key effector. The role of exosomal circRNA derived from bone marrow mesenchymal stem cells (BMSCs) has not been well-defined. The present study aimed to clarify the regulatory function and molecular mechanism of BMSC-derived exosomal circRNA in osteogenesis. Exosomes derived from bone marrow mesenchymal stem cells (BMSC-Exos) were isolated and identified. BMSC-Exos' pro-osteogenic effect on MC3T3-E1 cells was validated by alkaline phosphatase (ALP) activity and Alizarin Red staining. Through bioinformatic analysis and molecular experiments, circHIPK3 was selected and verified as the key circRNA of BMSC-Exos to promote osteoblast differentiation of MC3T3-E1 cells. Mechanistically, circHIPK3 acted as an miR-29a-5p sponge and functioned in mitophagy via targeting miR-29a-5p and PINK1. Additionally, we showed that the mitophagy level of MC3T3-E1 cells were mediated by BMSC-Exos, which promoted the osteogenic differentiation. Collectively, our results revealed an important role for BMSC-derived exosomal circHIPK3 in osteogenesis. These findings provide a potentially effective therapeutic strategy for bone regeneration.
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229
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Teng M, Zhu ZJ, Yao Y, Nair V, Zhang GP, Luo J. Critical roles of non-coding RNAs in lifecycle and biology of Marek's disease herpesvirus. SCIENCE CHINA. LIFE SCIENCES 2023; 66:251-268. [PMID: 36617590 PMCID: PMC9838510 DOI: 10.1007/s11427-022-2258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 01/10/2023]
Abstract
Over the past two decades, numerous non-coding RNAs (ncRNAs) have been identified in different biological systems including virology, especially in large DNA viruses such as herpesviruses. As a representative oncogenic alphaherpesvirus, Marek's disease virus (MDV) causes an important immunosuppressive and rapid-onset neoplastic disease of poultry, namely Marek's disease (MD). Vaccinations can efficiently prevent the onset of MD lymphomas and other clinical disease, often heralded as the first successful example of vaccination-based control of cancer. MDV infection is also an excellent model for research into virally-induced tumorigenesis. Recently, great progress has been made in understanding the functions of ncRNAs in MD biology. Herein, we give a review of the discovery and identification of MDV-encoded viral miRNAs, focusing on the genomics, expression profiles, and emerging critical roles of MDV-1 miRNAs as oncogenic miRNAs (oncomiRs) or tumor suppressor genes involved in the induction of MD lymphomas. We also described the involvements of host cellular miRNAs, lincRNAs, and circRNAs participating in MDV life cycle, pathogenesis, and/or tumorigenesis. The prospects, strategies, and new techniques such as the CRISPR/Cas9-based gene editing applicable for further investigation into the ncRNA-mediated regulatory mechanisms in MDV pathogenesis/oncogenesis were also discussed, together with the possibilities of future studies on antiviral therapy and the development of new efficient MD vaccines.
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Affiliation(s)
- Man Teng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhi-Jian Zhu
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, 463000, China
| | - Yongxiu Yao
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, GU24 0NF, UK
| | - Venugopal Nair
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, GU24 0NF, UK
| | - Gai-Ping Zhang
- International Joint Research Center of National Animal Immunology & College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Jun Luo
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- Key Laboratory of Animal Disease and Public Safety, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China.
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230
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Identification of a Novel Angiogenesis Signalling circSCRG1/miR-1268b/NR4A1 Pathway in Atherosclerosis and the Regulatory Effects of TMP-PF In Vitro. Molecules 2023; 28:molecules28031271. [PMID: 36770940 PMCID: PMC9919304 DOI: 10.3390/molecules28031271] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/14/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Angiogenesis contributes to plaque instability in atherosclerosis and further increases cardio-cerebrovascular risk. Circular RNAs (circRNAs) are promising biomarkers and potential therapeutic targets for atherosclerosis. Previous studies have demonstrated that tetramethylpyrazine (TMP) and paeoniflorin (PF) combination treatment (TMP-PF) inhibited oxidized low-density lipoprotein (ox-LDL)-induced angiogenesis in vitro. However, whether circRNAs regulate angiogenesis in atherosclerosis and whether TMP-PF can regulate angiogenesis-related target circRNAs in atherosclerosis are unknown. In this study, human RNA sequencing (RNA-seq) data were analysed to identify differentially expressed (DE) circRNAs in atherosclerosis and to obtain angiogenesis-associated circRNA-microRNA (miRNA)-messenger RNA (mRNA) networks. Target circRNA-related mechanisms in angiogenesis in atherosclerosis and the regulatory effects of TMP-PF on target circRNA signalling were studied in ox-LDL-induced human umbilical vein endothelial cells (HUVECs) by cell proliferation, migration, tube formation, and luciferase reporter assays, real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting. A novel circRNA (circular stimulator of chondrogenesis 1, circSCRG1) was initially identified associated with angiogenesis in atherosclerosis, and circSCRG1 silencing up-regulated miR-1268b expression, increased nuclear receptor subfamily 4 group A member 1 (NR4A1) expression and then promoted ox-LDL-induced angiogenesis. TMP-PF (1 μmol/L TMP combined with 10 μmol/L PF) up-regulated circSCRG1 expression, mediated miR-1268b to suppress NR4A1 expression and then inhibited ox-LDL-induced angiogenesis. However, circSCRG1 silencing abolished the inhibitory effects of TMP-PF on ox-LDL-induced angiogenesis, which were rescued by the miR-1268b inhibitor. In conclusion, circSCRG1 might serve as a new target regulating angiogenesis in atherosclerosis via the circSCRG1/miR-1268b/NR4A1 axis and TMP-PF could regulate the circSCRG1/miR-1268b/NR4A1 axis to inhibit angiogenesis in atherosclerosis in vitro, indicating a novel angiogenesis signalling circSCRG1/miR-1268b/NR4A1 pathway in atherosclerosis and the regulatory effects of TMP-PF, which might provide a new pharmaceutical strategy to combat atherosclerotic plaque instability.
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231
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Zhang L, Lu C, Zeng M, Li Y, Wang J. CRMSS: predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features. Brief Bioinform 2023; 24:6889442. [PMID: 36511222 DOI: 10.1093/bib/bbac530] [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: 07/21/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are reverse-spliced and covalently closed RNAs. Their interactions with RNA-binding proteins (RBPs) have multiple effects on the progress of many diseases. Some computational methods are proposed to identify RBP binding sites on circRNAs but suffer from insufficient accuracy, robustness and explanation. In this study, we first take the characteristics of both RNA and RBP into consideration. We propose a method for discriminating circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features, called CRMSS. For circRNAs, we use sequence ${k}\hbox{-}{mer}$ embedding and the forming probabilities of local secondary structures as features. For RBPs, we combine sequence and structure frequencies of RNA-binding domain regions to generate features. We capture binding patterns with multi-scale residual blocks. With BiLSTM and attention mechanism, we obtain the contextual information of high-level representation for circRNA-RBP binding. To validate the effectiveness of CRMSS, we compare its predictive performance with other methods on 37 RBPs. Taking the properties of both circRNAs and RBPs into account, CRMSS achieves superior performance over state-of-the-art methods. In the case study, our model provides reliable predictions and correctly identifies experimentally verified circRNA-RBP pairs. The code of CRMSS is freely available at https://github.com/BioinformaticsCSU/CRMSS.
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Affiliation(s)
- Lishen Zhang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, China
| | - Chengqian Lu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, China
| | - Min Zeng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, China
| | - Yaohang Li
- Department of Computer Science at Old Dominion University, USA
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, China
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232
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The Differential Expression of Circular RNAs and the Role of circAFF1 in Lens Epithelial Cells of High-Myopic Cataract. J Clin Med 2023; 12:jcm12030813. [PMID: 36769461 PMCID: PMC9918043 DOI: 10.3390/jcm12030813] [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: 11/23/2022] [Revised: 01/02/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
High-myopic cataract (HMC) is a complex cataract with earlier onset and more rapid progress than age-related cataract (ARC). Circular RNAs (circRNAs) have been implicated in many diseases. However, their involvement in HMC remain largely unexplored. To investigate the role of dysregulated circRNAs in HMC, lens epithelium samples from 24 HMC and 24 ARC patients were used for whole transcriptome sequencing. Compared with ARC, HMC had 3687 uniquely expressed circRNAs and 1163 significantly differentially expressed circRNAs (DEcRs) (|log2FC| > 1, p < 0.05). A putative circRNA-miRNA-mRNA network was constructed based on correlation analysis. We validated the differential expression of 3 DEcRs by quantitative polymerase chain reaction (qPCR) using different sets of samples. We further investigated the role of circAFF1 in cultured lens epithelial cells (LECs) and found that the overexpression of circAFF1 promoted cell proliferation, migration and inhibited apoptosis. We also showed that circAFF1 upregulated Tropomyosin 1 (TPM1) expression by sponging miR-760, which was consistent with the network prediction. Collectively, our study suggested the involvement of circRNAs in the pathogenesis of HMC and provide a resource for further study on this topic.
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233
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Yao M, Liang S, Cheng B. Role of exosomes in hepatocellular carcinoma and the regulation of traditional Chinese medicine. Front Pharmacol 2023; 14:1110922. [PMID: 36733504 PMCID: PMC9886889 DOI: 10.3389/fphar.2023.1110922] [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: 12/01/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) usually occurs on the basis of chronic liver inflammatory diseases and cirrhosis. The liver microenvironment plays a vital role in the tumor initiation and progression. Exosomes, which are nanometer-sized membrane vesicles are secreted by a number of cell types. Exosomes carry multiple proteins, DNAs and various forms of RNA, and are mediators of cell-cell communication and regulate the tumor microenvironment. In the recent decade, many studies have demonstrated that exosomes are involved in the communication between HCC cells and the stromal cells, including endothelial cells, macrophages, hepatic stellate cells and the immune cells, and serve as a regulator in the tumor proliferation and metastasis, immune evasion and immunotherapy. In addition, exosomes can also be used for the diagnosis and treatment HCC. They can potentially serve as specific biomarkers for early diagnosis and drug delivery vehicles of HCC. Chinese herbal medicine, which is widely used in the prevention and treatment of HCC in China, may regulate the release of exosomes and exosomes-mediated intercellular communication. In this review, we summarized the latest progresses on the role of the exosomes in the initiation, progression and treatment of HCC and the potential value of Traditional Chinese medicine in exosomes-mediated biological behaviors of HCC.
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Affiliation(s)
- Man Yao
- Oncology Department of Traditional Chinese Medicine, Changhai Hospital, Naval Medical University (The Second Military Medical University), Shanghai, China
| | - Shufang Liang
- Oncology Department of Traditional Chinese Medicine, Changhai Hospital, Naval Medical University (The Second Military Medical University), Shanghai, China
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, Changhai Hospital, Naval Medical University (The Second Military Medical University), Shanghai, China,Faculty of Traditional Chinese Medicine, Naval Medical University (The Second Military Medical University), Shanghai, China,*Correspondence: Binbin Cheng,
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234
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Chen X, Wei C, Huang L, Syrigos K, Li Y, Li P. Non-coding RNAs regulate mitochondrial dynamics in the development of gastric cancer. Front Mol Biosci 2023; 10:1107651. [PMID: 36714260 PMCID: PMC9877238 DOI: 10.3389/fmolb.2023.1107651] [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: 11/25/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Gastric cancer (GC) is a malignant cancer that reduces life expectancy worldwide. Although treatment strategies have improved, patients with GC still have poor prognoses. Hence, it is necessary to understand the molecular mechanisms of GC and to find new therapeutic targets. Mitochondrial dynamics and mitochondrial dysfunction are associated with cancer cell growth and progression. Numerous studies have reported that non-coding RNAs (ncRNAs) can participate in the occurrence and development of GC by regulating mitochondrial dynamics. Elucidating the crosstalk between ncRNAs and mitochondria would be helpful in preventing and treating GC. Herein, we review and summarize the functions of oncogenes and tumor suppressors in suppressing ncRNAs and regulating mitochondrial dynamics in GC tumor growth, proliferation, invasion and metastasis. This review provides new insights into the pathogenesis of and intervention for GC.
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Affiliation(s)
- Xiatian Chen
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Chuang Wei
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Liting Huang
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China,School of Basic Medicine, Qingdao University, Qingdao, China
| | | | - Yuzhen Li
- Basic Medical Department, Graduate School, Chinese PLA General Hospital, Beijing, China,*Correspondence: Yuzhen Li, ; Peifeng Li,
| | - Peifeng Li
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China,*Correspondence: Yuzhen Li, ; Peifeng Li,
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235
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Bai Y, Liu D, He Q, Liu J, Mao Q, Liang Z. Research progress on circular RNA vaccines. Front Immunol 2023; 13:1091797. [PMID: 36713460 PMCID: PMC9878156 DOI: 10.3389/fimmu.2022.1091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Owing to the success of linear mRNA coronavirus disease 2019 (COVID-19) vaccines, biopharmaceutical companies and research teams worldwide have attempted to develop more stable circular RNA (circRNA) vaccines and have achieved some preliminary results. This review aims to summarize key findings and important progress made in circRNA research, the in vivo metabolism and biological functions of circRNAs, and research progress and production process of circRNA vaccines. Further, considerations regarding the quality control of circRNA vaccines are highlighted herein, and the main challenges and problem-solving strategies in circRNA vaccine development and quality control are outlined to provide a reference for circRNA vaccine-related research.
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Affiliation(s)
- Yu Bai
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Dong Liu
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qian He
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Jianyang Liu
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China,*Correspondence: Zhenglun Liang, ; Qunying Mao,
| | - Zhenglun Liang
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China,*Correspondence: Zhenglun Liang, ; Qunying Mao,
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Chen G, Wang R, Jiang Y, Dong X, Xu J, Xu Q, Kan Q, Luo Z, Springer N, Li Q. A novel active transposon creates allelic variation through altered translation rate to influence protein abundance. Nucleic Acids Res 2023; 51:595-609. [PMID: 36629271 PMCID: PMC9881132 DOI: 10.1093/nar/gkac1195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 01/12/2023] Open
Abstract
Protein translation is tightly and precisely controlled by multiple mechanisms including upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are largely unexplored. In this study, an active transposition event was identified during the propagation of maize inbred line B73. The transposon, which was named BTA for 'B73 active transposable element hAT', creates a novel dosage-dependent hypomorphic allele of the hexose transporter gene ZmSWEET4c through insertion within the coding sequence in the first exon, and results in reduced kernel size. The BTA insertion does not affect transcript abundance but reduces protein abundance of ZmSWEET4c, probably through the introduction of a uORF. Furthermore, the introduction of BTA sequence in the exon of other genes can regulate translation efficiency without affecting their mRNA levels. A transposon capture assay revealed 79 novel insertions for BTA and BTA-like elements. These insertion sites have typical euchromatin features, including low levels of DNA methylation and high levels of H3K27ac. A putative autonomous element that mobilizes BTA and BTA-like elements was identified. Together, our results suggest a transposon-based origin of uORFs and document a new role for transposable elements to influence protein abundance and phenotypic diversity by affecting the translation rate.
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Affiliation(s)
| | | | | | - Xiaoxiao Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuxin Kan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixiang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Qing Li
- To whom correspondence should be addressed.
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237
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Toribio ML, González-García S. Notch Partners in the Long Journey of T-ALL Pathogenesis. Int J Mol Sci 2023; 24:ijms24021383. [PMID: 36674902 PMCID: PMC9866461 DOI: 10.3390/ijms24021383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological disease that arises from the oncogenic transformation of developing T cells during T-lymphopoiesis. Although T-ALL prognosis has improved markedly in recent years, relapsing and refractory patients with dismal outcomes still represent a major clinical issue. Consequently, understanding the pathological mechanisms that lead to the appearance of this malignancy and developing novel and more effective targeted therapies is an urgent need. Since the discovery in 2004 that a major proportion of T-ALL patients carry activating mutations that turn NOTCH1 into an oncogene, great efforts have been made to decipher the mechanisms underlying constitutive NOTCH1 activation, with the aim of understanding how NOTCH1 dysregulation converts the physiological NOTCH1-dependent T-cell developmental program into a pathological T-cell transformation process. Several molecular players have so far been shown to cooperate with NOTCH1 in this oncogenic process, and different therapeutic strategies have been developed to specifically target NOTCH1-dependent T-ALLs. Here, we comprehensively analyze the molecular bases of the cross-talk between NOTCH1 and cooperating partners critically involved in the generation and/or maintenance and progression of T-ALL and discuss novel opportunities and therapeutic approaches that current knowledge may open for future treatment of T-ALL patients.
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238
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Wang X, Zhang C, Song H, Yuan J, Zhang L, He J. CircCCDC66: Emerging roles and potential clinical values in malignant tumors. Front Oncol 2023; 12:1061007. [PMID: 36698408 PMCID: PMC9869039 DOI: 10.3389/fonc.2022.1061007] [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: 10/04/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Circular RNAs (circRNAs) are endogenous non-coding RNAs (ncRNAs) with a closed-loop structure. In recent years, circRNAs have become the focus of much research into RNA. CircCCDC66 has been identified as a novel oncogenic circRNA and is up-regulated in a variety of malignant tumors including thyroid cancer, non-small cell carcinoma, gastric cancer, colorectal cancer, renal cancer, cervical cancer, glioma, and osteosarcoma. It mediates cancer progression by regulating epigenetic modifications, variable splicing, transcription, and protein translation. The oncogenicity of circCCDC66 suppresses or promotes the expression of related genes mainly through direct or indirect pathways. This finding suggests that circCCDC66 is a biomarker for cancer diagnosis, prognosis assessment and treatment. However, there is no review on the relationship between circCCDC66 and cancers. Thus, the expression, biological functions, and regulatory mechanisms of circCCDC66 in malignant tumor and non-tumor diseases are summarized. The clinical value and prognostic significance of circCCDC66 are also evaluated, which can provide insights helpful to those exploring new strategies for the early diagnosis and targeted treatment of malignancies.
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Affiliation(s)
- Xiaoxiao Wang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Chao Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Huangqin Song
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Junlong Yuan
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Lei Zhang
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China,Hepatic Surgery Center, Institute of Hepato-Pancreato-Biliary Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiefeng He
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China,Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China,*Correspondence: Jiefeng He,
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Luo ZD, Wang YF, Zhao YX, Yu LC, Li T, Fan YJ, Zeng SJ, Zhang YL, Zhang Y, Zhang X. Emerging roles of non-coding RNAs in colorectal cancer oxaliplatin resistance and liquid biopsy potential. World J Gastroenterol 2023; 29:1-18. [PMID: 36683709 PMCID: PMC9850945 DOI: 10.3748/wjg.v29.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/11/2022] [Accepted: 11/04/2022] [Indexed: 01/04/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies of the digestive tract, with the annual incidence and mortality increasing consistently. Oxaliplatin-based chemotherapy is a preferred therapeutic regimen for patients with advanced CRC. However, most patients will inevitably develop resistance to oxaliplatin. Many studies have reported that non-coding RNAs (ncRNAs), such as microRNAs, long non-coding RNAs, and circular RNAs, are extensively involved in cancer progression. Moreover, emerging evidence has revealed that ncRNAs mediate chemoresistance to oxaliplatin by transcriptional and post-transcriptional regulation, and by epigenetic modification. In this review, we summarize the mechanisms by which ncRNAs regulate the initiation and development of CRC chemoresistance to oxaliplatin. Furthermore, we investigate the clinical application of ncRNAs as promising biomarkers for liquid CRC biopsy. This review provides new insights into overcoming oxaliplatin resistance in CRC by targeting ncRNAs.
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Affiliation(s)
- Zheng-Dong Luo
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Yi-Feng Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Yu-Xiao Zhao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Long-Chen Yu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Tian Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Ying-Jing Fan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Shun-Jie Zeng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Yan-Li Zhang
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250012, Shandong Province, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
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240
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Wang X, Cheng Q. Suppression of exosomal hsa_circ_0001005 eliminates the Vemurafenib resistance of melanoma. J Cancer Res Clin Oncol 2023:10.1007/s00432-022-04434-y. [PMID: 36598578 DOI: 10.1007/s00432-022-04434-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/18/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVES More and more evidences show that circular RNAs (circRNAs) can be used as miRNA sponge to regulate the drug resistance of malignancies, including melanoma. However, how exosomal circRNAs participate in the therapeutic resistance of melanoma remains ambiguous. METHODS Vemurafenib-resistant A375 cells were cultured and then the circRNA profile of exosomes from the parental A375 and A375-resistant cells were sequenced. Transmission electron microscopy (TEM), exogenous nanoparticle tracking analysis (NTA) and Western Blot assays were leveraged to confirm the successful collection of exosomes from A375 and A375R cells. Another five published RNA-seq data and microRNA-seq data, and seven miRNA databases were collected to construct a competing endogenous RNA (ceRNA) network. Comprehensive bioinformatic analysis was adopted to identify key molecules related to the drug resistance, including multiscale embedded gene co-expression network analysis (MEGENA). Then, qRT-PCR, cell viability and colony formation were used to estimate the function of hub circRNAs. The role of has_circ_0001005 in vivo was verified via xenograft assay. The Tumor online Prognostic analyses Platform (ToPP) was leveraged to develop the has_circ_0001005-related prognostic models for melanoma patients based on TCGA data. RESULTS Compared with parental cells, hsa_circ_0001005 expression was significantly increased in resistant cells and their exosomes. The elevated level of hsa_circ_0001005 was related to the poor clinical prognosis of melanoma patients. Hsa_circ_0001005 found in melanoma was mainly secreted by drug-resistant cells as exosomes. Exosomal hsa_circ_0001005 activated multiple canonical pathways related to drug resistance through sponging four miRNAs, thus suppressing the drug sensitivity of melanoma. Knocking down hsa_circ_0001005 in vitro, we found that the inhibition of hsa_circ_0001005 could hinder the clone formation of melanoma. Further in vivo animal experiments suggested that suppression of hsa_circ_0001005 can increase the sensitivity to Vemurafenib of melanoma cells. Finally, we also constructed the functional regulatory ceRNA network and prognostic risk models for hsa_circ_0001005, and further survival analysis reveals that the regulatory network and prognostic risk models obviously affected the prognosis of melanoma patients. CONCLUSIONS This study confirmed that the level of hsa_circ_0001005 in exosomes is the key factor affecting drug resistance of melanoma, which provides a new potential therapeutic target for melanoma patients.
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Affiliation(s)
- Xicheng Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Qiong Cheng
- Department of Dermatology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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241
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Letter to the Editor: There may be a misunderstanding about the function of circular RNA as miRNA sponges. Hepatology 2023; 77:E102. [PMID: 36680401 DOI: 10.1097/hep.0000000000000233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 01/22/2023]
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242
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Buratin A, Bortoluzzi S, Gaffo E. Systematic benchmarking of statistical methods to assess differential expression of circular RNAs. Brief Bioinform 2023; 24:6966517. [PMID: 36592056 PMCID: PMC9851295 DOI: 10.1093/bib/bbac612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/28/2022] [Accepted: 12/11/2022] [Indexed: 01/03/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data's statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs' performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments.
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Affiliation(s)
- Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Enrico Gaffo
- Corresponding author: Enrico Gaffo, Department of Molecular Medicine, University of Padova - Via G. Colombo, 3—35131 Padova, Italy. Phone +39 049 827 6502; Fax +39 049 827 6209; E-mail:
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243
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Liu H, Huang Q, Tang H, Luo K, Qin Y, Li F, Tang F, Zheng J, Feng W, Li B, Xie T, Liu Y. Circ_0001060 Upregulates and Encourages Progression in Osteosarcoma. DNA Cell Biol 2023; 42:53-64. [PMID: 36580535 DOI: 10.1089/dna.2022.0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Circular RNA (circRNA) is involved in the occurrence and development of various cancers. To this day, the expression and mechanism of circRNA in osteosarcoma (OS) remain unclear. We previously found that circ_0001060 was highly expressed in OS tumor tissues. In this work, we identified that high level expression of circ_0001060 was significantly associated with late clinical stage, larger tumor volume, higher frequency of metastasis, and poor prognosis in OS patients. Furthermore, we confirmed that silencing circ_0001060 inhibited the proliferation and migration of OS cell. Using bioinformatics analysis, we built three circRNA-miRNA-mRNA regulatory modules (circ_0001060-miR-203a-5p-TRIM21, circ_0001060-miR-208b-5p-MAP3K5, and circ_0001060-miR-203a-5p-PRKX), suggesting that these signaling axes may be involved in the inhibitory effect of circ_0001060 on OS. To sum up, circ_0001060 is a novel tumor biomarker for OS as well as a potential therapeutic target.
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Affiliation(s)
- Huijiang Liu
- Department of Spinal Bone Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopedics, The First People's Hospital of Nanning, Nanning, China
| | - Qian Huang
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haijun Tang
- Department of Spinal Bone Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Kai Luo
- Department of Spinal Bone Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yiwu Qin
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Feicui Li
- Department of Spinal Bone Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Fuxing Tang
- Department of Spinal Bone Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiqing Zheng
- Department of Rehabilitation and The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenyu Feng
- Department of Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Boxiang Li
- Department of Orthopedics, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, China
| | - Tianyu Xie
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yun Liu
- Department of Spinal Bone Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Yang R, Ma L, Wan J, Li Z, Yang Z, Zhao Z, Ming L. Ferroptosis-associated circular RNAs: Opportunities and challenges in the diagnosis and treatment of cancer. Front Cell Dev Biol 2023; 11:1160381. [PMID: 37152286 PMCID: PMC10157116 DOI: 10.3389/fcell.2023.1160381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Ferroptosis is an emerging form of non-apoptotic regulated cell death which is different from cell death mechanisms such as autophagy, apoptosis and necrosis. It is characterized by iron-dependent lipid peroxide accumulation. Circular RNA (circRNA) is a newly studied evolutionarily conserved type of non-coding RNA with a covalent closed-loop structure. It exhibits universality, conservatism, stability and particularity. At present, the functions that have been studied and found include microRNA sponge, protein scaffold, transcription regulation, translation and production of peptides, etc. CircRNA can be used as a biomarker of tumors and is a hotspot in RNA biology research. Studies have shown that ferroptosis can participate in tumor regulation through the circRNA molecular pathway and then affect cancer progression, which may become a direction of cancer diagnosis and treatment in the future. This paper reviews the molecular biological mechanism of ferroptosis and the role of circular RNA in tumors and summarizes the circRNA related to ferroptosis in tumors, which may inspire research prospects for the precise prevention and treatment of cancer in the future.
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Affiliation(s)
- Ruotong Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Liwei Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhuofang Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhengwu Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhuochen Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
- *Correspondence: Liang Ming,
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Yin W, Luo S, Qiu J, Xiao Z, Zhang Z, Xie Z, Li X, Zhou Z. Identification of hsa_circRNA_100632 as a novel molecular biomarker for fulminant type 1 diabetes. Front Immunol 2023; 14:1075970. [PMID: 36911697 PMCID: PMC9996325 DOI: 10.3389/fimmu.2023.1075970] [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: 10/21/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Objective Circular RNAs (circRNAs) are associated with diabetes, but their role in fulminant type 1 diabetes (FT1D) is unclear. Thus, we characterized the role of circRNAs in FT1D. Research design and methods CircRNA expression profiles were detected in peripheral blood mononuclear cells (PBMCs) of five FT1D patients and five controls using a circRNA microarray. An independent cohort comprised of 40 FT1D cases, 75 type 1 diabetes (T1D) cases, and 115 controls was used to verify the circRNAs using quantitative real-time polymerase chain reaction (qRT-PCR). Spearman's correlation analysis and receiver operating characteristic (ROC) curve analysis were performed to determine the clinical diagnostic capability of circRNAs. Bioinformatics was used to identify potential biological functions and circRNA-miRNA-mRNA interactions. Results There were 13 upregulated and 13 downregulated circRNAs in PBMCs of patients with FT1D. Five circRNAs were further verified in a second cohort. Hsa_circRNA_100632 was significantly upregulated in the FT1D and T1D groups. Hsa_circRNA_100632 was differentiated between patients with FT1D and controls [area under the curve (AUC) 0.846; 95% CI 0.776-0.916; P<0.0001] as well as between patients with FT1D and patients with T1D (AUC 0.726; 95% CI 0.633-0.820; P<0.0001). Bioinformatics analysis showed that hsa_circRNA_100632 may be involved in 47 circRNA-miRNA-mRNA signaling pathways associated with diabetes. Conclusions CircRNAs were aberrantly expressed in PBMCs of patients with FT1D, and hsa_circRNA_100632 may be a diagnostic marker of FT1D.
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Affiliation(s)
- Wenfeng Yin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Junlin Qiu
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zilin Xiao
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ziwei Zhang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Seelan RS, Greene RM, Pisano MM. Role of lncRNAs and circRNAs in Orofacial Clefts. Microrna 2023; 12:171-176. [PMID: 38009000 DOI: 10.2174/2211536612666230524153442] [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: 09/16/2022] [Revised: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 11/28/2023]
Abstract
Different modes of gene regulation, such as histone modification, transcription factor binding, DNA methylation, and microRNA (miRNA) expression, are critical for the spatiotemporal expression of genes in developing orofacial tissues. Aberrant regulation in any of these modes may contribute to orofacial defects. Noncoding RNAs (ncRNAs), such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs), have been shown to alter miRNA expression, and are thus emerging as novel contributors to gene regulation. Some of these appear to function as 'miRNA sponges', thereby diminishing the availability of these miRNAs to inhibit the expression of target genes. Such ncRNAs are also termed competitive endogenous RNAs (ceRNAs). Here, we examine emerging data that shed light on how lncRNAs and circRNAs may alter miRNA regulation, thus affecting orofacial development and potentially contributing to orofacial clefting.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - M Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, KY 40202, USA
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247
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Fang Y, Liu J. Novel regulatory role of non-coding RNAs in ankylosing spondylitis. Front Immunol 2023; 14:1131355. [PMID: 36911689 PMCID: PMC9998703 DOI: 10.3389/fimmu.2023.1131355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Ankylosing spondylitis (AS) is a type of arthritis that primarily affects the spine and involves disorders of the immune and skeletal systems. However, the exact pathogenesis of AS is not fully understood. Non-coding RNAs (ncRNAs), particularly, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and micro RNAs (miRNAs) and their interactions have been shown to influence many biological processes such as inflammatory responses, osteogenic differentiation and apoptosis, pyroptosis, and proliferation. In addition, ncRNAs reflect the disease activity of AS. In this review, we discuss the regulatory roles of ncRNAs in AS cell functions (inflammatory responses, cellular osteogenic differentiation and apoptosis, pyroptosis, and proliferation) and their potential applications in AS diagnosis and treatment. Understanding the role of ncRNAs in the pathogenesis of AS will lay the foundation for exploring potential new therapeutic approaches for AS.
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Affiliation(s)
- Yanyan Fang
- The First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China.,Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, China
| | - Jian Liu
- The First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, China.,Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, China.,Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, China
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248
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Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L, Zhao F. A guide to naming eukaryotic circular RNAs. Nat Cell Biol 2023; 25:1-5. [PMID: 36658223 PMCID: PMC10114414 DOI: 10.1038/s41556-022-01066-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Alternative splicing of eukaryotic transcripts often leads to production of multiple mature RNAs from a single gene locus. In addition to encoding linear RNAs, genes can produce stable circular RNAs (circRNAs) that are often co-expressed with their cognate linear RNAs. Multiple distinct circRNAs are frequently generated from a gene locus via back-splicing, with each mature transcript having a potentially unique function due to its distinct combination of exons and sometimes retained introns. However, names currently given to circRNAs are often ambiguous and lack consistency across studies. Here, we call on the community to embrace standards for naming circRNAs so that a common nomenclature is used to ensure clarity and reproducibility.
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Affiliation(s)
- Ling-Ling Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Albrecht Bindereif
- Institute of Biochemistry, Faculty of Biology and Chemistry, Justus Liebig University of Giessen, Giessen, Germany
| | - Irene Bozzoni
- Department of Biology and Biotechnologies 'Charles Darwin' and IIT Center for Life Nano- & Neuro-Science@Sapienza, Sapienza University of Rome, Rome, Italy
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - A Gregory Matera
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Thomas B Hansen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, Singapore
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Hemholtz Association, Berlin, Germany
| | - Julia Salzman
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA.
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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249
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Meng Y, Cao J, Li Y, Duan S, Zhou Z, Li J, Ousmane D, Ou C, Wang J. Emerging role of ferroptosis-related circular RNA in tumor metastasis. Front Pharmacol 2023; 14:1168458. [PMID: 37168995 PMCID: PMC10164976 DOI: 10.3389/fphar.2023.1168458] [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: 02/17/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023] Open
Abstract
Tumor metastasis is an important factor that contributes to the poor prognosis of patients with tumors. Therefore, to solve this problem, research on the mechanism of metastasis is essential. Ferroptosis, a new mode of cell death, is characterized by membrane damage due to lipid peroxidation caused by iron overload. Many studies have shown that excessive ferroptosis can affect tumor metastasis and thus inhibit tumor progression. Recently, circular RNA (circRNA), a type of non-coding RNA, has been shown to be associated with the progression of ferroptosis, thus influencing tumor development. However, the specific mechanisms by which circRNAs affect the progression of ferroptosis and their roles in tumor metastasis are not known. In this review, we systematically discuss the role of circRNAs in regulating tumor ferroptosis and their mechanism of action through sponging miRNAS in various tumors, thereby impacting metastasis. This review helps elucidate the relationship and role of ferroptosis-related circRNAs in tumor metastasis and may provide future researchers with new ideas and directions for targeted therapies.
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Affiliation(s)
- Yifei Meng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
- Department of Pathology, Ultrapathology (Biomedical Electron Microscopy) Center, Xiangya Hospital, Central South University, Changsha City, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jingdong Cao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
- Department of Pathology, Ultrapathology (Biomedical Electron Microscopy) Center, Xiangya Hospital, Central South University, Changsha City, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yidan Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
- Department of Pathology, Ultrapathology (Biomedical Electron Microscopy) Center, Xiangya Hospital, Central South University, Changsha City, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Saili Duan
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
- Department of Pathology, Ultrapathology (Biomedical Electron Microscopy) Center, Xiangya Hospital, Central South University, Changsha City, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zongjiang Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Jinghe Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Diabate Ousmane
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Junpu Wang, ; Chunlin Ou,
| | - Junpu Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
- Department of Pathology, Ultrapathology (Biomedical Electron Microscopy) Center, Xiangya Hospital, Central South University, Changsha City, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Junpu Wang, ; Chunlin Ou,
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250
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Cheng Z, Qin W, Li S, Shao S, Liu B. Emerging roles of circular RNAs in cancer therapy-induced cardiotoxicity. Front Cardiovasc Med 2023; 10:1152436. [PMID: 37020518 PMCID: PMC10067915 DOI: 10.3389/fcvm.2023.1152436] [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: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Cancer therapy-induced cardiotoxicity (CTIC) is an important cause of death in cancer survivors which often results in the withdrawal or discontinuation of drugs. The underlying mechanisms of CTIC remain unclear. Circular RNAs (circRNAs) are a class of non-coding regulatory RNA molecules which have emerged in recent years. They are generated by back splicing and have powerful biological functions, including transcription and splicing, isolating or building macromolecular scaffolds to interfere with microRNA activity and signaling pathways, and acting as templates for translation. Moreover, circRNAs demonstrate high abundance and significant stability. CircRNAs can be used as novel biomarkers because they often function in a cell-type and tissue-specific manner. CircRNAs have attracted increasing attention in cardiovascular disease research, and recent studies exploring the role of circRNAs in CTIC have had promising results. This review will summarize the current understanding of circRNAs' biogenesis, regulation and function. Their clinical potential as biomarkers, therapeutic agents and drug targets will also be explored.
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Affiliation(s)
- Ziji Cheng
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wanting Qin
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shaoling Li
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shuijin Shao
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baonian Liu
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Correspondence: Baonian Liu
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