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Li J, Wang X. Functional roles of conserved lncRNAs and circRNAs in eukaryotes. Noncoding RNA Res 2024; 9:1271-1279. [PMID: 39036601 PMCID: PMC11260338 DOI: 10.1016/j.ncrna.2024.06.014] [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: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as critical regulators in essentially all biological processes across eukaryotes. They exert their functions through chromatin remodeling, transcriptional regulation, interacting with RNA-binding proteins (RBPs), serving as microRNA sponges, etc. Although non-coding RNAs are typically more species-specific than coding RNAs, a number of well-characterized lncRNA (such as XIST and NEAT1) and circRNA (such as CDR1as and ciRS-7) are evolutionarily conserved. The studies on conserved lncRNA and circRNAs across multiple species could facilitate a comprehensive understanding of their roles and mechanisms, thereby overcoming the limitations of single-species studies. In this review, we provide an overview of conserved lncRNAs and circRNAs, and summarize their conserved roles and mechanisms.
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Affiliation(s)
- Jingxin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, Anhui, China
| | - Xiaolin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, Anhui, China
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2
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Qiu M, Chen Y, Zeng C. Biological functions of circRNA in regulating the hallmarks of gastrointestinal cancer (Review). Int J Oncol 2024; 64:49. [PMID: 38488023 PMCID: PMC10997371 DOI: 10.3892/ijo.2024.5637] [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: 11/04/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Circular RNA (circRNA) was first observed in the cytoplasm of eukaryotic cells in 1979, but it was not characterized in detail until 2012, when high‑throughput sequencing technology was more advanced and available. Consequently, the mechanism of circRNA formation and its biological function have been progressively elucidated by researchers. circRNA is abundant in eukaryotic cells and exhibits a certain degree of organization, timing and disease‑specificity. Additionally, it is poorly degradable, meeting the characteristics of an ideal clinical biomarker. In the present review, the recent research progress of circRNAs in digestive tract malignant tumors was primarily discussed. This included the roles, biological functions and clinical significance of circRNA, providing references for its research value and clinical potential in gastrointestinal cancer.
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Affiliation(s)
- Mengjun Qiu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chunyan Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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3
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Li Z, Xing J. Potential therapeutic applications of circular RNA in acute kidney injury. Biomed Pharmacother 2024; 174:116502. [PMID: 38569273 DOI: 10.1016/j.biopha.2024.116502] [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: 12/27/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024] Open
Abstract
Acute kidney injury (AKI) is a common clinical syndrome characterized by a rapid deterioration in renal function, manifested by a significant increase in creatinine and a sharp decrease in urine output. The incidence of morbidity and mortality associated with AKI is on the rise, with most patients progressing to chronic kidney disease or end-stage renal disease. Treatment options for patients with AKI remain limited. Circular RNA (circRNA) is a wide and diverse class of non-coding RNAs that are present in a variety of organisms and are involved in gene expression regulation. Studies have shown that circRNA acts as a competing RNA, is involved in disease occurrence and development, and has potential as a disease diagnostic and prognostic marker. CircRNA is involved in the regulation of important biological processes, including apoptosis, oxidative stress, and inflammation. This study reviews the current status and progress of circRNA research in the context of AKI.
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Affiliation(s)
- Zheng Li
- Department of Emergency Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Jihong Xing
- Department of Emergency Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
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Ren Y, Manoharan T, Liu B, Cheng CZM, En Siew B, Cheong WK, Lee KY, Tan IJW, Lieske B, Tan KK, Chia G. Circular RNA as a source of neoantigens for cancer vaccines. J Immunother Cancer 2024; 12:e008402. [PMID: 38508656 PMCID: PMC10952939 DOI: 10.1136/jitc-2023-008402] [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] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effectiveness of somatic neoantigen-based immunotherapy is often hindered by the limited number of mutations in tumors with low to moderate mutation burden. Focusing on microsatellite-stable colorectal cancer (CRC), this study investigates the potential of tumor-associated circular RNAs (circRNAs) as an alternative source of neoepitopes in CRC. METHODS Tumor-associated circRNAs in CRC were identified using the MiOncoCirc database and ribo-depletion RNA sequencing of paired clinical normal and tumor samples. Candidate circRNA expression was validated by quantitative real-time PCR (RT-qPCR) using divergent primers. TransCirc database was used for translation prediction. Human leukocyte antigen binding affinity of open reading frames from potentially translatable circRNA was predicted using pVACtools. Strong binders from messenger RNA-encoded proteins were excluded using BlastP. The immunogenicity of the candidate antigens was functionally validated through stimulation of naïve CD8+ T cells against the predicted neoepitopes and subsequent analysis of the T cells through enzyme-linked immunospot (ELISpot) assay, intracellular cytokine staining (ICS) and granzyme B (GZMB) reporter. The cytotoxicity of T cells trained with antigen peptides was further tested using patient-derived organoids. RESULTS We identified a neoepitope from circRAPGEF5 that is upregulated in CRC tumor samples from MiOncoCirc database, and two neoepitopes from circMYH9, which is upregulated across various tumor samples from our matched clinical samples. The translation potential of candidate peptides was supported by Clinical Proteomic Tumor Analysis Consortium database using PepQuery. The candidate peptides elicited antigen-specific T cells response and expansion, evidenced by various assays including ELISpot, ICS and GZMB reporter. Furthermore, T cells trained with circMYH9 peptides were able to specifically target and eliminate tumor-derived organoids but not match normal organoids. This observation underscores the potential of circRNAs as a source of immunogenic neoantigens. Lastly, circMYH9 was enriched in the liquid biopsies of patients with CRC, thus enabling a detection-to-vaccination treatment strategy for patients with CRC. CONCLUSIONS Our findings underscore the feasibility of tumor-associated circRNAs as an alternative source of neoantigens for cancer vaccines targeting tumors with moderate mutation levels.
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Affiliation(s)
- Yi Ren
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Thamizhanban Manoharan
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Beijia Liu
- Department of Pharmacy, National University of Singapore, Singapore
| | - Cyrus Zai Ming Cheng
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Bei En Siew
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, National University Hospital, Singapore
| | - Kai Yin Lee
- Department of Surgery, National University Hospital, Singapore
| | - Ian Jse-Wei Tan
- Department of Surgery, National University Hospital, Singapore
| | - Bettina Lieske
- Department of Surgery, National University Hospital, Singapore
| | - Ker-Kan Tan
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Gloryn Chia
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
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5
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Wang Y, Chen X, Yang Y. CircRNA-regulated glucose metabolism in ovarian cancer: an emerging landscape for therapeutic intervention. Clin Transl Oncol 2024; 26:584-596. [PMID: 37578652 DOI: 10.1007/s12094-023-03285-4] [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: 05/11/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023]
Abstract
Ovarian cancer (OC) has the highest mortality rate among female reproductive system tumours, with limited efficacy of traditional treatments and 5-year survival rates that rarely exceed 40%. Circular RNA (circRNA) is a stable endogenous circular RNA that typically regulates protein expression by binding to downstream miRNA. It has been demonstrated that circRNAs play an important role in the proliferation, migration, and glucose metabolism (such as the Warburg effect) of OC and can regulate the expression of glucose metabolism-related proteins such as GLUT1 and HK2, promoting anaerobic glycolysis of cancer cells, increasing glucose uptake and ATP production, and affecting energy supply and biosynthetic substances to support tumour growth and invasion. This review summarises the formation and characteristics of circRNAs and focuses on their role in regulating glucose metabolism in OC cells and their potential therapeutic value, providing insights for identifying new therapeutic targets.
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Affiliation(s)
- Yaolong Wang
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Gynecological Oncology of Gansu Province, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Xi Chen
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Gynecological Oncology of Gansu Province, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Yongxiu Yang
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Gynecological Oncology of Gansu Province, Lanzhou, Gansu, China.
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China.
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Zhang Q, Luo Y, Zhang S, Huang Q, Liu G. Development of a necroptosis-related prognostic model for uterine corpus endometrial carcinoma. Sci Rep 2024; 14:4257. [PMID: 38383747 PMCID: PMC10881509 DOI: 10.1038/s41598-024-54651-3] [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: 11/29/2022] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
Necroptosis is a recently identified caspase-independent form of cell death which plays a significant role in the onset and progression of cancer. MicroRNAs (miRNAs) are vital for the development of uterine corpus endometrial carcinoma (UCEC) because they are an important regulatory component in necroptosis. This study developed a new necroptosis-related miRNAs profile to predict the prognosis of patients with UCEC. The TCGA-UCEC cohort's RNA sequencing data, consisting of 534 tumor samples and 33 normal samples, was downloaded. Ten differentially expressed miRNAs related to necroptosis were identified. A prediction model for necroptosis-related miRNAs was then created through COX regression and nomograms analysis. Clinical and pathological parameters were integrated to construct a nomogram and evaluate the model. Prognosis-related miRNAs were further used to predict target genes, and functional analysis was conducted to explore the potential mechanisms of these target genes. Subsequently, immune infiltration analysis was performed using transcriptome data to identify immune genes associated with prognosis, and the expression levels of target gene was validated using UCEC tissues. We identified 7 up-regulated miRNAs (hsa-miR-577, hsa-miR-7-5p, hsa-miR-210-3p, hsa-miR-210-5p, hsa-miR-200a-5p, hsa-miR-141-3p, hsa-miR-425-5p) and 3 down-regulated miRNAs (hsa-miR-7-2-3p, hsa-miR-383-5p, hsa-miR-29a-3p). The risk signature was based on univariate and multivariate COX analyses, constructed using 2 independent prognostic factors and miRNAs (hsa-miR-425-5p, hsa-miR-7-5p) associated with necroptosis. Nomograms demonstrated the prognostic value of risk level, age, FIGO stage, and histological type. Kaplan-Meier analysis revealed significant differences in overall survival (OS) outcomes associated with the expression of hsa-miR-425-5p (P < 0.001) and hsa-miR-7-5p (P = 0.015). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) investigations indicated that these miRNAs play crucial roles in tumor development, metastasis, and prognosis. Immune infiltration analysis showed decreased infiltration of CD8+ T cells, CD8+ T cells, NK cells, and M1 macrophages in normal tissues. Subsequently, a necroptosis-related immune gene significantly associated with prognosis (THRB) was identified, western blot and immunohistochemical staining confirmed the differential expression of THRB in normal endometrial tissues and tumor. Our findings demonstrate a close association between necroptosis and UCEC. The two necroptosis-related miRNAs used in this study may serve as valuable prognostic markers for UCEC patients, and are associated with immune cell infiltration. This suggests that necroptosis may be involved in the development of UCEC through its interaction with immune responses.
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Affiliation(s)
- Qi Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yongfu Luo
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Department of General Surgery, Xintian People's Hospital, Xintian, 425700, Hunan, China
| | - Shiyao Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Qianpeng Huang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Gang Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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Saleem A, Khan MU, Zahid T, Khurram I, Ghani MU, Ullah I, Munir R, Calina D, Sharifi-Rad J. Biological role and regulation of circular RNA as an emerging biomarker and potential therapeutic target for cancer. Mol Biol Rep 2024; 51:296. [PMID: 38340202 DOI: 10.1007/s11033-024-09211-3] [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: 11/15/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
Circular RNAs (circRNAs) are a unique family of endogenous RNAs devoid of 3' poly-A tails and 5' end caps. These single-stranded circRNAs, found in the cytoplasm, are synthesized via back-splicing mechanisms, merging introns, exons, or both, resulting in covalently closed circular loops. They are profusely expressed across the eukaryotic transcriptome and offer heightened stability against exonuclease RNase R compared to linear RNA counterparts. This review endeavors to provide a comprehensive overview of circRNAs' characteristics, biogenesis, and mechanisms of action. Furthermore, aimed to shed light on the potential of circRNAs as significant biomarkers in various cancer types. It has been performed an exhaustive literature review, drawing on recent studies and findings related to circRNA characteristics, synthesis, function, evaluation techniques, and their associations with oncogenesis. CircRNAs are intricately associated with tumor progression and development. Their multifaceted roles encompass gene regulation through the sponging of proteins and microRNAs, controlling transcription and splicing, interacting with RNA binding proteins (RBPs), and facilitating gene translation. Due to these varied roles, circRNAs have become a focal point in tumor pathology investigations, given their promising potential as both biomarkers and therapeutic agents. CircRNAs, due to their unique biogenesis and multifunctionality, hold immense promise in the realm of oncology. Their stability, widespread expression, and intricate involvement in gene regulation underscore their prospective utility as reliable biomarkers and therapeutic targets in cancer. As our understanding of circRNAs deepens, advanced techniques for their detection, evaluation, and manipulation will likely emerge. These advancements might catalyze the translation of circRNA-based diagnostics and therapeutics into clinical practice, potentially revolutionizing cancer care and prognosis.
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Affiliation(s)
- Ayman Saleem
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Tazeen Zahid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Iqra Khurram
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Rakhtasha Munir
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
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Sun ZY, Yang CL, Huang LJ, Mo ZC, Zhang KN, Fan WH, Wang KY, Wu F, Wang JG, Meng FL, Zhao Z, Jiang T. circRNADisease v2.0: an updated resource for high-quality experimentally supported circRNA-disease associations. Nucleic Acids Res 2024; 52:D1193-D1200. [PMID: 37897359 PMCID: PMC10767896 DOI: 10.1093/nar/gkad949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
circRNADisease v2.0 is an enhanced and reliable database that offers experimentally verified relationships between circular RNAs (circRNAs) and various diseases. It is accessible at http://cgga.org.cn/circRNADisease/ or http://cgga.org.cn:9091/circRNADisease/. The database currently includes 6998 circRNA-disease entries across multiple species, representing a remarkable 19.77-fold increase compared to the previous version. This expansion consists of a substantial rise in the number of circRNAs (from 330 to 4246), types of diseases (from 48 to 330) and covered species (from human only to 12 species). Furthermore, a new section has been introduced in the database, which collects information on circRNA-associated factors (genes, proteins and microRNAs), molecular mechanisms (molecular pathways), biological functions (proliferation, migration, invasion, etc.), tumor and/or cell line and/or patient-derived xenograft (PDX) details, and prognostic evidence in diseases. In addition, we identified 7 159 865 relationships between mutations and circRNAs among 30 TCGA cancer types. Due to notable enhancements and extensive data expansions, the circRNADisease 2.0 database has become an invaluable asset for both clinical practice and fundamental research. It enables researchers to develop a more comprehensive understanding of how circRNAs impact complex diseases.
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Affiliation(s)
- Zhi-Yan Sun
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Chang-Lin Yang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Li-Jie Huang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Zong-Chao Mo
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen 518045, China
- Division of Life Science, Department of Chemical and Biological Engineering, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ke-Nan Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Wen-Hua Fan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Kuan-Yu Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Ji-Guang Wang
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen 518045, China
- Division of Life Science, Department of Chemical and Biological Engineering, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fan-Lin Meng
- Marketing and Management Department, CapitalBio Technology, Beijing 101111, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen 518045, China
- Division of Life Science, Department of Chemical and Biological Engineering, and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
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Meng L, Wu H, Wu J, Ding P, He J, Sang M, Liu L. Mechanisms of immune checkpoint inhibitors: insights into the regulation of circular RNAS involved in cancer hallmarks. Cell Death Dis 2024; 15:3. [PMID: 38177102 PMCID: PMC10766988 DOI: 10.1038/s41419-023-06389-5] [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: 09/15/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Current treatment strategies for cancer, especially advanced cancer, are limited and unsatisfactory. One of the most substantial advances in cancer therapy, in the last decades, was the discovery of a new layer of immunotherapy approach, immune checkpoint inhibitors (ICIs), which can specifically activate immune cells by targeting immune checkpoints. Immune checkpoints are a type of immunosuppressive molecules expressed on immune cells, which can regulate the degree of immune activation and avoid autoimmune responses. ICIs, such as anti-PD-1/PD-L1 drugs, has shown inspiring efficacy and broad applicability across various cancers. Unfortunately, not all cancer patients benefit remarkably from ICIs, and the overall response rates to ICIs remain relatively low for most cancer types. Moreover, the primary and acquired resistance to ICIs pose serious challenges to the clinical application of cancer immunotherapy. Thus, a deeper understanding of the molecular biological properties and regulatory mechanisms of immune checkpoints is urgently needed to improve clinical options for current therapies. Recently, circular RNAs (circRNAs) have attracted increasing attention, not only due to their involvement in various aspects of cancer hallmarks, but also for their impact on immune checkpoints in shaping the tumor immune microenvironment. In this review, we systematically summarize the current status of immune checkpoints in cancer and the existing regulatory roles of circRNAs on immune checkpoints. Meanwhile, we also aim to settle the issue in an evidence-oriented manner that circRNAs involved in cancer hallmarks regulate the effects and resistance of ICIs by targeting immune checkpoints.
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Affiliation(s)
- Lingjiao Meng
- Department of Tumor Immunotherapy, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
- Research Center and Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Haotian Wu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Jiaxiang Wu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Ping'an Ding
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Jinchen He
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Meixiang Sang
- Research Center and Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, China.
- Science and Education Department, Shanghai Electric Power Hospital, Shanghai, 20050, China.
| | - Lihua Liu
- Department of Tumor Immunotherapy, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China.
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10
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Tang S, Cai L, Wang Z, Pan D, Wang Q, Shen Y, Zhou Y, Chen Q. Emerging roles of circular RNAs in the invasion and metastasis of head and neck cancer: Possible functions and mechanisms. CANCER INNOVATION 2023; 2:463-487. [PMID: 38125767 PMCID: PMC10730008 DOI: 10.1002/cai2.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2023]
Abstract
Head and neck cancer (HNC) is the seventh most prevalent malignancy worldwide in 2020. Cancer metastasis is the main cause of poor prognosis in HNC patients. Recently, circular RNAs (circRNAs), initially thought to have no biological function, are attracting increasing attention, and their crucial roles in mediating HNC metastasis are being extensively investigated. Existing studies have shown that circRNAs primarily function through miRNA sponges, transcriptional regulation, interacting with RNA-binding proteins (RBPs) and as translation templates. Among these functions, the function of miRNA sponge is the most prominent. In this review, we summarized the reported circRNAs involved in HNC metastasis, aiming to elucidate the regulatory relationship between circRNAs and HNC metastasis. Furthermore, we summarized the latest advances in the epidemiological information of HNC metastasis and the tumor metastasis theories, the biogenesis, characterization and functional mechanisms of circRNAs, and their potential clinical applications. Although the research on circRNAs is still in its infancy, circRNAs are expected to serve as prognostic markers and effective therapeutic targets to inhibit HNC metastasis and significantly improve the prognosis of HNC patients.
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Affiliation(s)
- Shouyi Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Luyao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Zhen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Dan Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Qing Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Yingqiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
- State Institute of Drug/Medical Device Clinical TrialWest China Hospital of StomatologyChengduChina
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
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Dai S, Zhang C, Wei X, Wang X, Wen Y, Gao F, Zhao L, Shan B. RNA sequencing reveals the implication of the circRNA-associated ceRNA network in oesophageal squamous cell carcinoma. Carcinogenesis 2023; 44:596-609. [PMID: 37402652 DOI: 10.1093/carcin/bgad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023] Open
Abstract
Circular RNAs (circRNAs) have attracted increasing attention in cancer research. However, there are few studies about the high-throughput sequencing for clinical cohorts focussing on the expression characteristics and regulatory networks of circRNAs in oesophageal squamous cell carcinoma (ESCC) until now. Present study aim to comprehensively recognize the functional and mechanistic patterns of circRNA through constructing a circRNA-related competing endogenous RNA (ceRNA) network in ESCC. Summarily, RNA high-throughput sequencing was adopted to assess the circRNA, miRNA and mRNA expression profiles in ESCC. Through bioinformatics methods, a circRNA-miRNA-mRNA coexpression network was constructed and hub genes was identified. Finally, cellular function experiments combined with bioinformatics analysis were conducted to verify the identified circRNA was involved in the progression of ESCC through ceRNA mechanism. In this study, we established a ceRNA regulatory network, including 5 circRNAs, 7 miRNAs and 197 target mRNAs, and 20 hub genes were screened and identified to exert important roles in the progression of ESCC. As a verification, hsa_circ_0002470 (circIFI6) was revealed to be highly expressed in ESCC and regulate the expression of hub genes by absorbing miR-497-5p and miR-195-5p through ceRNA mechanism. Our results further indicated that silencing of circIFI6 repressed proliferation and migration of ESCC cells, highlighting the tumour promotion effects of circIFI6 in ESCC. Collectively, our study contributes a new insight into the progression of ESCC from the perspective of the circRNA-miRNA-mRNA network, shedding light on the circRNA research in ESCC.
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Affiliation(s)
- Suli Dai
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Cong Zhang
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Xiaojian Wei
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Xiaohan Wang
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Yang Wen
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Feng Gao
- Thoracic Surgery Department, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Baoen Shan
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
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Rao G, Peng X, Tian Y, Fu X, Zhang Y. Circular RNAs in hepatocellular carcinoma: biogenesis, function, and pathology. Front Genet 2023; 14:1106665. [PMID: 37485335 PMCID: PMC10361733 DOI: 10.3389/fgene.2023.1106665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. Both genetic and environmental factors through a multitude of underlying molecular mechanisms participate in the pathogenesis of HCC. Recently, numerous studies have shown that circular RNAs (circRNAs), an emerging class of non-coding RNAs characterized by the presence of covalent bonds linking 3' and 5' ends, play an important role in the initiation and progression of cancers, including HCC. In this review, we outline the current status of the field of circRNAs, with an emphasis on the functions and mechanisms of circRNAs in HCC and its microenvironment. We also summarize and discuss recent advances of circRNAs as biomarkers and therapeutic targets. These efforts are anticipated to throw new insights into future perspectives about circRNAs in basic, translational and clinical research, eventually advancing the diagnosis, prevention and treatment of HCC.
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Affiliation(s)
- Guocheng Rao
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Xi Peng
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yan Tian
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yuwei Zhang
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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Gu A, Jaijyan DK, Yang S, Zeng M, Pei S, Zhu H. Functions of Circular RNA in Human Diseases and Illnesses. Noncoding RNA 2023; 9:38. [PMID: 37489458 PMCID: PMC10366867 DOI: 10.3390/ncrna9040038] [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: 05/15/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023] Open
Abstract
Circular RNAs (circRNAs) represent single-stranded RNA species that contain covalently closed 3' and 5' ends that provide them more stability than linear RNA, which has free ends. Emerging evidence indicates that circRNAs perform essential functions in many DNA viruses, including coronaviruses, Epstein-Barr viruses, cytomegalovirus, and Kaposi sarcoma viruses. Recent studies have confirmed that circRNAs are present in viruses, including DNA and RNA viruses, and play various important functions such as evading host immune response, disease pathogenesis, protein translation, miRNA sponges, regulating cell proliferation, and virus replication. Studies have confirmed that circRNAs can be biological signatures or pathological markers for autoimmune diseases, neurological diseases, and cancers. However, our understanding of circRNAs in DNA and RNA viruses is still limited, and functional evaluation of viral and host circRNAs is essential to completely understand their biological functions. In the present review, we describe the metabolism and cellular roles of circRNA, including its roles in various diseases and viral and cellular circRNA functions. Circular RNAs are found to interact with RNA, proteins, and DNA, and thus can modulate cellular processes, including translation, transcription, splicing, and other functions. Circular RNAs interfere with various signaling pathways and take part in vital functions in various biological, physiological, cellular, and pathophysiological processes. We also summarize recent evidence demonstrating cellular and viral circRNA's roles in DNA and RNA viruses in this growing field of research.
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Affiliation(s)
- Alison Gu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Mulan Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaokai Pei
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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Gilyazova I, Enikeeva K, Rafikova G, Kagirova E, Sharifyanova Y, Asadullina D, Pavlov V. Epigenetic and Immunological Features of Bladder Cancer. Int J Mol Sci 2023; 24:9854. [PMID: 37373000 DOI: 10.3390/ijms24129854] [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: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Bladder cancer (BLCA) is one of the most common types of malignant tumors of the urogenital system in adults. Globally, the incidence of BLCA is more than 500,000 new cases worldwide annually, and every year, the number of registered cases of BLCA increases noticeably. Currently, the diagnosis of BLCA is based on cystoscopy and cytological examination of urine and additional laboratory and instrumental studies. However, cystoscopy is an invasive study, and voided urine cytology has a low level of sensitivity, so there is a clear need to develop more reliable markers and test systems for detecting the disease with high sensitivity and specificity. Human body fluids (urine, serum, and plasma) are known to contain significant amounts of tumorigenic nucleic acids, circulating immune cells and proinflammatory mediators that can serve as noninvasive biomarkers, particularly useful for early cancer detection, follow-up of patients, and personalization of their treatment. The review describes the most significant advances in epigenetics of BLCA.
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Affiliation(s)
- Irina Gilyazova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Kadriia Enikeeva
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Guzel Rafikova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Evelina Kagirova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Yuliya Sharifyanova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Dilara Asadullina
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
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15
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Zhong G, Zhao Q, Chen Z, Yao T. TGF-β signaling promotes cervical cancer metastasis via CDR1as. Mol Cancer 2023; 22:66. [PMID: 37004067 PMCID: PMC10064584 DOI: 10.1186/s12943-023-01743-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/07/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Due to the lack of effective treatment, metastasis is the main cause of cancer related deaths. TGF-β pathway has been reported related to cervical cancer metastasis. However, mechanism is still unclear. METHODS After agonist of TGF-β treatment, RNA sequencing revealed the expression profiles of circRNA in cervical cancer. In situ hybridization was used to analysis relationship between CDR1as and prognosis. Real-time PCR, Western blot, RNA interference, Transwell assay, Wound healing assay, RNA pulldown assay and RIP assays were performed in vitro. And in vivo cervical cancer model (including foot pad model and subcutaneous tumor formation) was also performed. RESULTS CDR1as was found upregulated obviously following TGF-β activation. In situ hybridization showed CDR1as was positively correlated with lymph node metastasis and shortened survival length. Simultaneously, overexpression of CDR1as promoted cervical cancer metastasis in vitro and in vivo. It was also found that CDR1as could facilitate the orchestration of IGF2BP1 on the mRNA of SLUG and stabilize it from degradation. Silencing IGF2BP1 hampers CDR1as related metastasis in cervical cancer. Additionally, effective CDR1as has been proven to activate TGF-β signaling factors known to promote EMT, including P-Smad2 and P-Smad3. CONCLUSIONS Our study proved TGF-β signaling may promote cervical cancer metastasis via CDR1as.
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Affiliation(s)
- Guanglei Zhong
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yan Jiang West Road, Guangzhou, People's Republic of China, 510120
| | - Qian Zhao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yan Jiang West Road, Guangzhou, People's Republic of China, 510120
| | - Zhiliao Chen
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yan Jiang West Road, Guangzhou, People's Republic of China, 510120
| | - Tingting Yao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yan Jiang West Road, Guangzhou, People's Republic of China, 510120.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
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16
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Ye Z, Jiang Y, Wu J. A novel necroptosis-associated miRNA signature predicting prognosis of endometrial cancer and correlated with immune infiltration. Taiwan J Obstet Gynecol 2023; 62:291-298. [PMID: 36965898 DOI: 10.1016/j.tjog.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2022] [Indexed: 03/27/2023] Open
Abstract
OBJECTIVE Necroptosis is a form of programmed cell death identified irrelevant to caspases, which plays an important role in the tumorigenesis and development of cancer. MicroRNAs (miRNAs) are important regulators of both necroptosis and cancer. MATERIALS AND METHODS Expression of sixteen necroptosis-associated miRNAs were analyzed in 546 endometrial cancer (EC) tissues and 33 paracancerous samples from the Cancer Genome Atlas (TCGA). Cox regression analysis was used to evaluate the correlations between miRNAs and overall survival. MiRNAs risk score (Mrs) and nomogram were established to assess the potential value of necroptosis-related miRNAs on prognosis. Expression of miRNA-148a-3p in endometrial cancer cells and endometrial epithelial cells was detected by quantitative real-time PCR (qRT-PCR). The targets genes of miR-148a-3p were predicted using miRDB, miRTarBase and TargetScan and the prognostic-related genes were screened. Immune infiltration analysis was conducted to explore the potential mechanism of these target genes. RESULTS We identified fourteen differentially expressed miRNAs and selected seven miRNAs (miR-15a-5p, miR148a-3p, miR-7-5p, miR-141-3p, miR-200a-5p, miR-223-3p, miR-16-5p) for prognostic-model construction. The area under the curve (AUC) of receiver operating characteristic (ROC) curve for 1-, 2- and 5-year survival were 0.678, 0.652 and 0.656 respectively. Multivariate analysis revealed that the Mrs was an independent prognostic factor considering other risk factors (HR = 1.928, 95% CI = 1.072-3.467, P = 0.028). Among these miRNAs, miRNA-148a-3p was up-regulated in cancer tissues and cells, and Kaplan-Meier analysis showed its significance in overall survival (OS). The target genes, DNAJB4 and PRNP, were associated with poor prognosis and correlated with tumor immune infiltration. CONCLUSIONS Our study constructed a novel necroptosis-associated miRNAs model for prognosis prediction, and DNAJB4 and PRNP may be therapeutic targets for EC.
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Affiliation(s)
- Zhongxue Ye
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yafen Jiang
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Junlong Wu
- Department of Orthopedics, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.
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17
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Zhao L, Yu L, Wang X, He J, Zhu X, Zhang R, Yang A. Mechanisms of function and clinical potential of exosomes in esophageal squamous cell carcinoma. Cancer Lett 2023; 553:215993. [PMID: 36328162 DOI: 10.1016/j.canlet.2022.215993] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 11/20/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) remains one of the most lethal and widespread malignancies in China. Exosomes, a subset of tiny extracellular vesicles manufactured by all cells and present in all body fluids, contribute to intercellular communication and have become a focus of the search for new therapeutic strategies for cancer. A number of global analyses of exosome-mediated functions and regulatory mechanism in malignant diseases have recently been reported. There is extensive evidence that exosomes can be used as diagnostic and prognostic markers for cancer. However, our understanding of their clinical value and mechanisms of action in ESCC is still limited and has not been systematically reviewed. Here, we review current research specifically focused on the functions and mechanisms of action of ESCC tumor-derived exosomes and non-ESCC-derived exosomes in ESCC progression and describe opportunities and challenges in the clinical translation of exosomes.
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Affiliation(s)
- Lijun Zhao
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Lili Yu
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Xiangpeng Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Jangtao He
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Xiaofei Zhu
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
| | - Rui Zhang
- The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Angang Yang
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, China; The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, China.
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Karami Fath M, Akhavan Masouleh R, Afifi N, Loghmani S, Tamimi P, Fazeli A, Mousavian SA, Falsafi MM, Barati G. PI3K/AKT/mTOR signaling pathway modulation by circular RNAs in breast cancer progression. Pathol Res Pract 2023; 241:154279. [PMID: 36584499 DOI: 10.1016/j.prp.2022.154279] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
The PI3K/Akt/mTOR signaling pathway is responsible for many cellular behaviors, including survival, growth, and proliferation. A newly identified RNA, circular RNA (circRNA), plays a crucial role in the regulation of gene expression. The upregulation of the PI3K/Akt pathway through dysregulated circRNAs promotes breast tumor initiation, growth, and progression. The dysregulation of PI3K/Akt-regulating circRNAs seems to be directly correlated with breast cancer clinical features, including overall survival, tumor size, cancer stage, and lymph node metastasis. In addition, targeting these circRNAs may be a promising option in cancer-targeted therapy. Understanding the molecular pathogenesis of the circRNA-PI3K/AKT axis may give the insight to develop new therapeutic and diagnostic approaches for breast cancer therapy. Here we reviewed the expression and functions of PI3K/AKT-regulating circRNAs, and their correlation with breast cancer clinical features. In addition, the potential of PI3K/AKT-regulating circRNAs as diagnostic/prognostic biomarkers or therapeutic targets was discussed.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Negin Afifi
- School of Medicine, Islamic Azad University, Qeshm Branch, Qeshm, Iran
| | - Shirin Loghmani
- Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Parham Tamimi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Fazeli
- Department of Medical Education, Medical Education Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Ali Mousavian
- Pharmacy Department, EMU(Eastern Mediterranean University), Famagusta, North Cyprus, Republic of Cyprus
| | | | - Ghasem Barati
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran; Stem Cell Technology Research Center, Tehran, Iran.
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circPOLR1C Promotes the Development of Esophageal Cancer by Adsorbing miR-361-3p and Regulating Cancer Cell Apoptosis and Metastasis. JOURNAL OF ONCOLOGY 2022; 2022:9124142. [PMID: 36590309 PMCID: PMC9803566 DOI: 10.1155/2022/9124142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Background The effect of circular RNA-RNA polymerase I and III subunit C (circPOLR1C) on esophageal cancer (EC) has not been reported. Herein, this study is designed to unveil the effect and the regulatory mechanism of circPOLR1C on EC. Methods The expression of circPOLR1C in EC tissues and cells was detected by qRT-PCR. Circular structure, stability, and cell localization of circPOLR1C were confirmed by qRT-PCR, RNase R, actinomycin D, and fluorescence in situ hybridization (FISH) assay. Cell function experiments, nude mouse xenograft, lung transplant model, and HE staining were performed to evaluate the effects of CircPOLR1C on EC in vitro and in vivo. A regulatory relationship between miR-361-3p and circPOLR1C was confirmed by qRT-PCR, circRNA in vivo precipitation, RIP, FISH, CircInteractome database, dual-luciferase reporter assay, and immunohistochemistry. Rescue experiments were applied to assess the effects of miR-361-3p and circPOLR1C on EC cells and tissues. Apoptosis- and epithelial-mesenchymal transformation (EMT)-related gene expressions were quantified by qRT-PCR and Western blot. Results Highly expressed circPOLR1C in EC was related to tumor differentiation and invasion. circPOLR1C, which mainly exists in the cytoplasm, is a stable circular RNA. circPOLR1C silencing inhibited circPOLR1C expression and EC cell malignant function, while circPOLR1C overexpression promoted the growth of transplanted tumors and lung metastasis. The enrichment of miR-361-3p was higher than that of other targeted miRNAs. circPOLR1C adsorbed miR-361-3p to regulate apoptosis- and EMT-related genes and partially reversed the tumor suppressive effect of miR-361-3p, which was lowly expressed in EC tissues. Silencing the target genes of miR-361-3p also inhibited the malignant development of EC cells. Conclusion circPOLR1C adsorbs miR-361-3p and regulates apoptosis- and EMT-related gene expressions to promote the development of EC.
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circRNAs May Be Involved in Dysfunction of Neutrophils of Type 2 Diabetic Mice through Regulation of Specific miRNAs. Biomedicines 2022; 10:biomedicines10123129. [PMID: 36551885 PMCID: PMC9775479 DOI: 10.3390/biomedicines10123129] [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: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Diabetes is known to delay wound healing, and this delay is attributed to prolonged inflammation. We found that microRNAs (miRNAs) might be involved in the dysfunction of diabetic-derived neutrophils, and dynamics of neutrophil and chronic inflammation might be initiated by miRNA-regulated genes. Moreover, studies of miRNA function in nephropathy have suggested that circular RNAs (circRNAs), which function as sponges of miRNA to regulate their expression, are potential biomarkers and new therapeutic targets for the diagnosis of diabetic nephropathy. Accordingly, to investigate the molecular mechanism of the regulation of inflammation in diabetic-derived neutrophils, we identified circRNAs in diabetic-derived neutrophils obtained from BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/db and Leprdb/+) mice using microarrays. Neutrophils from pooled bone marrow of three diabetic and three non-diabetic mice were isolated and total RNA was extracted. Microarray analysis was performed using the Arraystar Mouse Circular RNA Array. The results showed that three circRNAs were significantly increased and six circRNAs were significantly decreased in diabetic-derived neutrophils compared with non-diabetic-derived neutrophils. The expressions of some circRNAs in diabetic-derived neutrophils were more than double those in non-diabetic-derived neutrophils. The circRNAs contain binding sites of miRNAs, which were differentially expressed in diabetic-derived neutrophils. Our results suggest that circRNAs may be involved in the regulation of inflammation in diabetic-derived neutrophils.
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Zhao K, Ye F, Gao P, Zhu X, Hao S, Lou W. Circular RNA ciRS-7 promotes laryngeal squamous cell carcinoma development by inducing TGM3 hypermethylation via miR-432-5p/DNMT3B axis. Pathol Res Pract 2022; 240:154193. [PMID: 36356335 DOI: 10.1016/j.prp.2022.154193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/08/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
OBJECTIVE This work is to explore the mechanism by which circular RNA ciRS-7 affects laryngeal squamous cell carcinoma (LSCC). METHODS ciRS-7 expression in LSCC tissues was detected by qRT-PCR, and the association between ciRS-7 with clinicopathological features of LSCC patients was evaluated. HN-4 and UM-SCC-10A cells were transfected or cotransfected with si-ciRS-7, miR-432-5p inhibitor, LV-DNMT3B or si-TGM3. Then, the viability and aggressive nature of the cells were tested. The binding site between ciRS-7 and miR-432-5p or between miR-432-5p and DNMT3B was predicted and the targeting relationship was identified. The specific binding between ciRS-7 and miR-432-5p was further verified by AGO2 RIP assay. HN-4 cells transfected with si-ciRS-7 was injected into nude mice to induce xenograft tumors. RESULTS Higher ciRS-7 expression in LSCC tissues was closely associated with higher clinical stage, and exacerbated infiltration and lymph node metastasis in LSCC patients. Silencing ciRS-7 inhibited LSCC cell viability, epithelial-mesenchymal transition (EMT), and promoted the apoptosis. When miR-432-5p was inhibited or DNMT3B was overexpressed, the growth and EMT of LSCC cells were stimulated despite ciRS-7 silencing. Downregulation of ciRS-7 restrained the growth of xenograft tumors in vivo. CONCLUSION ciRS-7 promotes the progression of LSCC through increasing TGM3 methylation via miR-432-5p/DNMT3B axis.
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Affiliation(s)
- Kun Zhao
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, PR China
| | - Fanglei Ye
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, PR China
| | - Pei Gao
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, PR China
| | - Xiaodan Zhu
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, PR China
| | - Shaojuan Hao
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, PR China
| | - Weihua Lou
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, PR China.
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22
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Josipovic N, Ebbesen KK, Zirkel A, Danieli-Mackay A, Dieterich C, Kurian L, Hansen TB, Papantonis A. circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner. RNA (NEW YORK, N.Y.) 2022; 28:1481-1495. [PMID: 35973723 PMCID: PMC9745835 DOI: 10.1261/rna.079195.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 05/18/2023]
Abstract
Circular RNAs are an endogenous long-lived and abundant noncoding species. Despite their prevalence, only a few circRNAs have been dissected mechanistically to date. Here, we cataloged nascent RNA-enriched circRNAs from primary human cells and functionally assigned a role to circRAB3IP in sustaining cellular homeostasis. We combined "omics" and functional experiments to show how circRAB3IP depletion deregulates hundreds of genes, suppresses cell cycle progression, and induces senescence-associated gene expression changes. Conversely, excess circRAB3IP delivered to endothelial cells via extracellular vesicles suffices for accelerating their division. We attribute these effects to an interplay between circRAB3IP and the general splicing factor SF3B1, which can affect transcript variant expression levels of cell cycle-related genes. Together, our findings link the maintenance of cell homeostasis to the presence of a single circRNA.
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Affiliation(s)
- Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Karoline K Ebbesen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Adi Danieli-Mackay
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christoph Dieterich
- Bioinformatics and Systems Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, 8000 Aarhus, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
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23
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Yuan P, Zhao Y, Li H, Li S, Fan S, Zhai B, Li Y, Han R, Liu X, Tian Y, Kang X, Zhang Y, Li G. CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken. Genes (Basel) 2022; 13:1974. [PMID: 36360215 PMCID: PMC9689937 DOI: 10.3390/genes13111974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/26/2023] Open
Abstract
Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1-9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.
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Affiliation(s)
- Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hongtai Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Shuaihao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Yanhua Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
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24
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Shi Y, Li J, Tang M, Liu J, Zhong Y, Huang W. CircHADHA-augmented autophagy suppresses tumor growth of colon cancer by regulating autophagy-related gene via miR-361. Front Oncol 2022; 12:937209. [PMID: 36313671 PMCID: PMC9606334 DOI: 10.3389/fonc.2022.937209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
Colon cancer undergoes a traditional pathway from colon polyps to colon cancer. It is of great significance to investigate the key molecules involved in carcinogenesis from polyps to malignancies. Circular RNAs (circRNAs) are stably expressed in human body fluids such as plasma. Here, we demonstrated a differential expression pattern of plasma circRNAs in healthy individuals, colon polyp patients and colon cancer patients using circRNA Arraystar microarray. We explored that circRNA HADHA (circHADHA) was upregulated in plasma from polyp patients, whereas it was downregulated in plasma from colon cancer patients. Overexpression of circHADHA promoted autophagy in colon epithelial cells. Moreover, in colon cancer cells, overexpression of circHADHA promoted autophagy, whereas it inhibited cell proliferation and colony formation. CircHADHA increased the expression of ATG13 via miR-361 in both colon epithelial and cancer cells. ATG13 knockdown reduced autophagy even in the presence of circHADHA in colon cancer cells. Furthermore, the growth of circHADHA-overexpressing colon cancer cell-derived xenograft tumors was significantly decreased compared with control tumors in nude mice. In conclusion, circHADHA was differentially expressed in the plasma of healthy individuals, colon polyp patients and colon cancer patients. CircHADHA promoted autophagy by regulating ATG13 via miR-361 in both colon epithelial and cancer cells. CircHADHA suppressed tumor growth by inducing cell autophagy in colon cancer cells. CircHADHA potentially serves as a biomarker for screening of precursor colon cancer and a therapeutic target for colon cancer treatment.
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Affiliation(s)
- Ying Shi
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Gastroenterology, Hepatology and Infectious Diseases, Internal Medicine I, Tübingen University Hospital, Tübingen, Germany
| | - Jinying Li
- Endoscopy Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Ming Tang
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jingwen Liu
- Endoscopy Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yalu Zhong
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wei Huang
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Endoscopy Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- *Correspondence: Wei Huang,
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25
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Wu Z, Yu X, Zhang S, He Y, Guo W. Mechanism underlying circRNA dysregulation in the TME of digestive system cancer. Front Immunol 2022; 13:951561. [PMID: 36238299 PMCID: PMC9550895 DOI: 10.3389/fimmu.2022.951561] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Circular RNAs (circRNAs) are a new series of noncoding RNAs (ncRNAs) that have been reported to be expressed in eukaryotic cells and have a variety of biological functions in the regulation of cancer pathogenesis and progression. The TME, as a microscopic ecological environment, consists of a variety of cells, including tumor cells, immune cells and other normal cells, ECM and a large number of signaling molecules. The crosstalk between circRNAs and the TME plays a complicated role in affecting the malignant behaviors of digestive system cancers. Herein, we summarize the mechanisms underlying aberrant circRNA expression in the TME of the digestive system cancers, including immune surveillance, angiogenesis, EMT, and ECM remodelling. The regulation of the TME by circRNA is expected to be a new therapeutic method.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
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26
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Lu J, Li R, Fang M, Ke S. Hub Genes and Long Noncoding RNAs That Regulates It Associated with the Prognosis of Esophageal Squamous Cell Carcinoma Based on Bioinformatics Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:6027058. [PMID: 36238478 PMCID: PMC9553368 DOI: 10.1155/2022/6027058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 12/09/2022]
Abstract
Objective Through bioinformatics analysis methods, the public databases GEO and TCGA were used to research mRNA and squamous cell carcinoma of the esophagus, construct a lncRNA-mRNA network, and screen hub genes and lncRNAs related to prognosis. Method Download esophageal squamous cell carcinoma-related mRNA and lncRNA datasets GEO and TCGA public datasets, as well as clinical data, use bioinformatic tools to perform gene differential expression analysis on the datasets to obtain differentially expressing mRNA (DEmRNA) and lncRNA (DElncRNA), and plot volcano plots and cluster heatmaps. The differential intersection of differentially expressed DEmRNA and DElncRNA was extracted by Venn diagram and imported into CytoScape software, a regulatory network visualization software, to construct a lncRNA-mRNA network and use cytoHubba and MCODE plug-ins to screen hub genes and key lncRNAs. The DEmRNA in the network was imported into the Gene and Protein Interaction Retrieval Database (STRING), gene-encoded protein-protein interactions (PPI) network maps were created, and the genes in the PPI network maps were submitted to GO functional annotation and pathway enrichment analysis using Kyoto Encyclopedia of Gene Genomes (KEGG) (KEGG). The link between hub gene and prognosis was studied using the clinical data collected by TCGA. Result Retrieve the datasets GSE23400 and GSE38129 from the GEO database and the esophageal squamous cell carcinoma-related mRNAs from TCGA databases and then obtain intersection. Differentially regulated genes revealed a correlation of 326 (up) with 191 (down) in terms of the differential intersection; for this study, we need to collect the GSE130078 dataset from GEO, as well as the lncRNAs from TCGA databases that are connected to esophageal squamous cell cancer. There were 184 differentially up- and downregulated genes in the differential intersection. A differential intersection network of the differential intersection lncRNA-mRNA network allowed us to identify the hub genes, including COL5A2 (COL3A1), COL1A1 (COL1A1), CTD-2171N6.1 (CTD-2171N6.1), and RP11-863P13.3 (RP11-863P13.3). The extracellular matrix, which is important in protein digestion and absorption, was shown to be the primary site of functional enrichment, as shown by GO/KEGG analysis. Squamous cell carcinoma of the mouth and throat is associated with a poor prognosis because of a change in the extracellular matrix structure caused by specific long noncoding RNA (lncRNA) regulatory upregulation. Conclusion For the purpose of predicting the prognosis of cancer of the esophagus, researchers studied the esophageal squamous cell carcinoma-related hub genes and important noncoding RNAs (ncRNAs).
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Affiliation(s)
- Jun Lu
- Department of Emergency Medicine & Intensive Care Unit, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ruichao Li
- Department of General Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Minghao Fang
- Department of Emergency Medicine & Intensive Care Unit, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shun Ke
- Department of Emergency Medicine & Intensive Care Unit, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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27
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Li J, Li P, Shao J, Liang S, Wan Y, Zhang Q, Li C, Li Y, Wang C. Emerging Role of Noncoding RNAs in EGFR TKI-Resistant Lung Cancer. Cancers (Basel) 2022; 14:cancers14184423. [PMID: 36139582 PMCID: PMC9496789 DOI: 10.3390/cancers14184423] [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: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Lung cancer accounts for the majority of malignancy-related mortalities worldwide. The introduction of epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) has revolutionized the treatment and significantly improved the overall survival (OS) of lung cancer. Nevertheless, almost all EGFR-mutant patients invariably acquire TKI resistance. Accumulating evidence has indicated that noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), have a central role in the tumorigenesis and progression of lung cancer by regulating crucial signaling pathways, providing a new approach for exploring the underlying mechanisms of EGFR-TKI resistance. Therefore, this review comprehensively describes the dysregulation of ncRNAs in EGFR TKI-resistant lung cancer and its underlying mechanisms. We also underscore the clinical application of ncRNAs as prognostic, predictive and therapeutic biomarkers for EGFR TKI-resistant lung cancer. Furthermore, the barriers that need to be overcome to translate the basic findings of ncRNAs into clinical practice are discussed.
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Affiliation(s)
- Jingwei Li
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peiyi Li
- Department of Anesthesiology, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jun Shao
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shufan Liang
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuntian Wan
- West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiran Zhang
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Changshu Li
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (Y.L.); (C.W.)
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, West China Medical School/West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (Y.L.); (C.W.)
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28
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Chen H, Fan X, Zhang W, Ye Y, Cai Z, Zhang K, Zhang K, Fu Z, Chen D, Guo R. Deciphering the CircRNA-Regulated Response of Western Honey Bee ( Apis mellifera) Workers to Microsporidian Invasion. BIOLOGY 2022; 11:biology11091285. [PMID: 36138764 PMCID: PMC9495892 DOI: 10.3390/biology11091285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 05/13/2023]
Abstract
Vairimorpha ceranae is a widespread fungal parasite of adult honey bees that leads to a serious disease called nosemosis. Circular RNAs (circRNAs) are newly discovered non-coding RNAs (ncRNAs) that regulate biological processes such as immune defense and development. Here, 8199 and 8711 circRNAs were predicted from the midguts of Apis mellifera ligustica workers at 7 d (Am7T) and 10 d (Am10T) after inoculation (dpi) with V. ceranae spores. In combination with transcriptome data from corresponding uninoculated midguts (Am7CK and Am10CK), 4464 circRNAs were found to be shared by these four groups. Additionally, 16 circRNAs were highly conserved among A. m. ligustica, Apis cerana cerana, and Homo sapiens. In the Am7CK vs. Am7T (Am10CK vs. Am10T) comparison group, 168 (306) differentially expressed circRNAs (DEcircRNAs) were identified. RT-qPCR results showed that the expression trend of eight DEcircRNAs was consistent with that in the transcriptome datasets. The source genes of DEcircRNAs in Am7CK vs. Am7T (Am10CK vs. Am10T) were engaged in 27 (35) GO functional terms, including 1 (1) immunity-associated terms. Moreover, the aforementioned source genes were involved in three cellular immune-related pathways. Moreover, 86 (178) DEcircRNAs in workers' midguts at 7 (10) dpi could interact with 75 (103) miRNAs, further targeting 215 (305) mRNAs. These targets were associated with cellular renewal, cellular structure, carbohydrate and energy metabolism, and cellular and humoral immunity. Findings in the present study unraveled the mechanism underlying circRNA-mediated immune responses of western honey bee workers to V. ceranae invasion, but also provided new insights into host-microsporidian interaction during nosemosis.
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Affiliation(s)
- Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Xiaoxue Fan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Wende Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Yaping Ye
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Zongbing Cai
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Kaiyao Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Kuihao Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Zhongmin Fu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Correspondence: ; Tel./Fax: +86-0591-8764-0197
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29
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Wang J, Li X, Duan C, Jia Y. CircFNDC3B
knockdown restrains the progression of esophageal squamous cell carcinoma through
miR
‐214‐3p/
CDC25A
axis. Clin Exp Pharmacol Physiol 2022; 49:1209-1220. [DOI: 10.1111/1440-1681.13707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Jiawei Wang
- Department of Thoracic Surgery Affiliated Hospital of Jiangnan University Wuxi China
| | - Xiaolin Li
- Department of Thoracic Surgery Affiliated Hospital of Jiangnan University Wuxi China
| | - Chao Duan
- Department of Thoracic Surgery Affiliated Hospital of Jiangnan University Wuxi China
| | - Yifei Jia
- Department of Thoracic Surgery Affiliated Hospital of Jiangnan University Wuxi China
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30
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Qi X, Chen X, Zhao Y, Chen J, Niu B, Shen B. Prognostic Roles of ceRNA Network-Based Signatures in Gastrointestinal Cancers. Front Oncol 2022; 12:921194. [PMID: 35924172 PMCID: PMC9339642 DOI: 10.3389/fonc.2022.921194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/15/2022] [Indexed: 01/19/2023] Open
Abstract
Gastrointestinal cancers (GICs) are high-incidence malignant tumors that seriously threaten human health around the world. Their complexity and heterogeneity make the classic staging system insufficient to guide patient management. Recently, competing endogenous RNA (ceRNA) interactions that closely link the function of protein-coding RNAs with that of non-coding RNAs, such as long non-coding RNA (lncRNA) and circular RNA (circRNA), has emerged as a novel molecular mechanism influencing miRNA-mediated gene regulation. Especially, ceRNA networks have proven to be powerful tools for deciphering cancer mechanisms and predicting therapeutic responses at the system level. Moreover, abnormal gene expression is one of the critical breaking events that disturb the stability of ceRNA network, highlighting the role of molecular biomarkers in optimizing cancer management and treatment. Therefore, developing prognostic signatures based on cancer-specific ceRNA network is of great significance for predicting clinical outcome or chemotherapy benefits of GIC patients. We herein introduce the current frontiers of ceRNA crosstalk in relation to their pathological implications and translational potentials in GICs, review the current researches on the prognostic signatures based on lncRNA or circRNA-mediated ceRNA networks in GICs, and highlight the translational implications of ceRNA signatures for GICs management. Furthermore, we summarize the computational approaches for establishing ceRNA network-based prognostic signatures, providing important clues for deciphering GIC biomarkers.
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Affiliation(s)
- Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Xingqi Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Yuanchun Zhao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Jiajia Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Bairong Shen,
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31
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circRNA: A New Biomarker and Therapeutic Target for Esophageal Cancer. Biomedicines 2022; 10:biomedicines10071643. [PMID: 35884948 PMCID: PMC9313320 DOI: 10.3390/biomedicines10071643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) comprise a large class of endogenous non-coding RNA with covalently closed loops and have independent functions as linear transcripts transcribed from identical genes. circRNAs are generated by a “back-splicing” process regulated by regulatory elements in cis and associating proteins in trans. Many studies have shown that circRNAs play important roles in multiple processes, including splicing, transcription, chromatin modification, miRNA sponges, and protein decoys. circRNAs are highly stable because of their closed ring structure, which prevents them from degradation by exonucleases, and are more abundant in terminally differentiated cells, such as brains. Recently, it was demonstrated that numerous circRNAs are differentially expressed in cancer cells, and their dysfunction is involved in tumorigenesis and metastasis. However, the crucial functions of these circRNAs and the dysregulation of circRNAs in cancer are still unknown. In this review, we summarize the recent reports on the biogenesis and biology of circRNAs and then catalog the advances in using circRNAs as biomarkers and therapeutic targets for cancer therapy, particularly esophageal cancer.
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Asadi MR, Moslehian MS, Sabaie H, Sharifi-Bonab M, Hakimi P, Hussen BM, Taheri M, Rakhshan A, Rezazadeh M. CircRNA-Associated CeRNAs Regulatory Axes in Retinoblastoma: A Systematic Scoping Review. Front Oncol 2022; 12:910470. [PMID: 35865469 PMCID: PMC9294360 DOI: 10.3389/fonc.2022.910470] [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: 04/01/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022] Open
Abstract
Retinoblastoma (RB) is one of the most common childhood cancers caused by RB gene mutations (tumor suppressor gene in various patients). A better understanding of molecular pathways and the development of new diagnostic approaches may lead to better treatment for RB patients. The number of studies on ceRNA axes is increasing, emphasizing the significance of these axes in RB. Circular RNAs (circRNAs) play a vital role in competing endogenous RNA (ceRNA) regulatory axes by sponging microRNAs and regulating gene expression. Because of the broadness of ceRNA interaction networks, they may assist in investigating treatment targets in RB. This study conducted a systematic scoping review to evaluate verified loops of ceRNA in RB, focusing on the ceRNA axis and its relationship to circRNAs. This scoping review was carried out using a six-step strategy and the Prisma guideline, and it involved systematically searching the publications of seven databases. Out of 363 records, sixteen articles were entirely consistent with the defined inclusion criteria and were summarized in the relevant table. The majority of the studies focused on the circRNAs circ_0000527, circ_0000034, and circTET1, with approximately two-fifths of the studies focusing on a single circRNA. Understanding the many features of this regulatory structure may help elucidate RB’s unknown causative factors and provide novel molecular potential therapeutic targets and medical fields.
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Affiliation(s)
- Mohammad Reza Asadi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Sadat Moslehian
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mirmohsen Sharifi-Bonab
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Hakimi
- Woman’s Reproductive Health Research Center, Tabriz University of medical sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- *Correspondence: Mohammad Taheri, ; Azadeh Rakhshan, ; Maryam Rezazadeh,
| | - Azadeh Rakhshan
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohammad Taheri, ; Azadeh Rakhshan, ; Maryam Rezazadeh,
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Woman’s Reproductive Health Research Center, Tabriz University of medical sciences, Tabriz, Iran
- *Correspondence: Mohammad Taheri, ; Azadeh Rakhshan, ; Maryam Rezazadeh,
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Zhu C, Bi W, Li H, Wang W. CircLONP2 Accelerates Esophageal Squamous Cell Carcinoma Progression via Direct MiR-27b-3p-ZEB1 Axis. Front Oncol 2022; 12:822839. [PMID: 35865464 PMCID: PMC9294169 DOI: 10.3389/fonc.2022.822839] [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: 12/22/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Circular RNAs (circRNAs) are important mediators in esophageal squamous cell carcinoma (ESCC) carcinogenesis. We aim to explore the functions and mechanisms of circLONP2 in ESCC progression. The circLONP2 level was evaluated in ESCC samples and cell lines. The role and mechanisms of circLONP2 in ESCC proliferation and migration were demonstrated in vitro. We found that circLONP2 was upregulated in human ESCC and predicts poor overall survival (OS) and disease-free survival (DFS). CircLONP2 promotes ESCC aggressiveness by directly interacting with miR-27b-3p, thus upregulating the expression levels of its target gene ZEB1 by suppressing miR-27b-3p activity. Therefore, we demonstrated that circLONP2/miR-27b-3p/ZEB1 axis promotes ESCC metastasis via regulating epithelial-to-mesenchymal transition (EMT)-related proteins. CircLONP2 may serve as an oncogenic circRNA and as a prognostic biomarker in ESCC progression.
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Affiliation(s)
- Cailin Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Weiyun Bi
- Department of Clinical Skills Training Center, XiJing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Hongtao Li
- Department of General Surgery, General Hospital of Lanzhou PLA, Lanzhou, China
| | - Wen Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of General Surgery, People’s Hospital of Tongchuan, Tongchuan, China
- *Correspondence: Wen Wang,
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Beilerli A, Begliarzade S, Sufianov A, Ilyasova T, Liang Y, Beylerli O. Circulating ciRS-7 as a potential non-invasive biomarker for epithelial ovarian cancer: An investigative study. Noncoding RNA Res 2022; 7:197-204. [PMID: 35991513 PMCID: PMC9361213 DOI: 10.1016/j.ncrna.2022.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Background Ovarian cancer (OC) is the most common malignant neoplasm of the female reproductive system in developed countries. Early detection, diagnosis and prognosis are particularly important to OC. The potential of circulating circular RNAs (circRNAs) as non-invasive biomarkers of various tumors has been especially described in recent years. The aim of this study was to explore the diagnostic and prognostic value of circulating cirRS-7 in patients with epithelial ovarian cancer (EOC). Methods Pre- and postoperative plasma samples from 111 EOC patients (47 cases with FIGO stage IA-IIB and 64 cases with FIGO stage IIB-IV) and healthy female volunteers was collected. Circulating ciRS-7 and hsa-miR-7-5p was analyzed using reverse transcription polymerase chain reaction (qRT-PCR). The diagnostic and prognostic value of circulating cirRS-7 as biomarker was estimated by the Receiver Operating Characteristic (ROC) curve and the area under the curve (AUC) and Kaplan–Meier analysis. Results The preoperative expression levels of circulating ciRS-7 were increased in plasma of EOC FIGO stage I-IV patients than in the healthy controls (p < 0.001). However, the expression levels of ciRS-7 in the postoperative period were significantly lower in EOC FIGO stage IIA-IIA patients than healthy controls and EOC FIGO stage IIB-IV patients (p < 0.05, p < 0.001). The AUC of ciRS-7 for diagnosing EOC FIGO stage I-IV patients in pre-and postoperative periods was 0.90, 0.92, 0.84, 0.88, 0.58 and 0.86, respectively. Higher circulating ciRS-7 expression is associated with lymph node invasion, FIGO stage, distant metastasis, and worse overall survival (OS) of patients. Moreover, multivariate Cox analysis showed that higher circulating ciRS-7 was an independent predictor of OS in EOC FIGO stage IIB-IV patients. In addition, in plasma of EOC patients, ciRS-7 negatively correlated with has-miR-7-5p in pre-and postoperative periods (p < 0.001). Conclusions Circulating ciRS-7 levels in plasma can be considered a potential candidate biomarker for diagnosing EOC patients. Dysregulation of ciRS-7 may participate in the molecular mechanism of EOC through hsa-miR-7-5p sponging.
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Zhou X, Du J. CircRNAs: novel therapeutic targets in multiple myeloma. Mol Biol Rep 2022; 49:10667-10676. [PMID: 35729478 DOI: 10.1007/s11033-022-07668-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/31/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Circular RNA (circRNA) is a type of non-coding RNA that has recently attracted the attention of researchers. Multiple myeloma (MM) is a hematological malignancy with a dismal prognosis that indicates a pressing need for better treatment alternatives, particularly in terms of biological indicators. According to recent research findings, the presence of circRNA is also closely related to the incidence and progression of malignant hemopathy. There have been, however, only a few investigations of circRNA in MM. MATERIAL AND METHODS This review will be on the biological properties and functions of circRNA in MM and a discussion of the clinical utility of circRNA in the diagnosis, prognosis, and treatment of MM. CONCLUSIONS CircRNA is involved in gene transcription, translation, and epigenetic modification as well as the regulation of cancer cell proliferation, invasion, and metastasis, and hence, promotes or inhibits the occurrence and progression of MM. Therefore, circRNA holds promise as a potential future MM biomarker.
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Affiliation(s)
- Xinyi Zhou
- Department of Hematology, Myeloma and Lymphoma Center, Shanghai Changzheng Hospital, Naval Medical University, No. 415 Fengyang Road, Huangpu Area, Shanghai, 200003, China
| | - Juan Du
- Department of Hematology, Myeloma and Lymphoma Center, Shanghai Changzheng Hospital, Naval Medical University, No. 415 Fengyang Road, Huangpu Area, Shanghai, 200003, China.
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Ju C, He J, Wang C, Sheng J, Jia J, Du D, Li H, Zhou M, He F. Current advances and future perspectives on the functional roles and clinical implications of circular RNAs in esophageal squamous cell carcinoma: more influential than expected. Biomark Res 2022; 10:41. [PMID: 35672804 PMCID: PMC9171998 DOI: 10.1186/s40364-022-00388-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/29/2022] [Indexed: 11/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive gastrointestinal cancers with high incidence and mortality. Therefore, it is necessary to identify novel sensitive and specific biomarkers for ESCC detection and treatment. Circular RNAs (circRNAs) are a type of noncoding RNAs featured by their covalently closed circular structure. This special structure makes circRNAs more stable in mammalian cells, coupled with their great abundance and tissue specificity, suggesting circRNAs may present enormous potential to be explored as valuable prognostic and diagnostic biomarkers for tumor. Mounting studies verified the critical roles of circRNAs in regulating ESCC cells malignant behaviors. Here, we summarized the current progresses in a handful of aberrantly expressed circRNAs, and elucidated their biological function and clinical significance in ESCC, and introduced a series of databases for circRNA research. With the improved advancement in high-throughput sequencing and bioinformatics technique, new frontiers of circRNAs will pave the path for the development of precision treatment in ESCC.
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Affiliation(s)
- Chenxi Ju
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jing He
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chang Wang
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jinxiu Sheng
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jinlin Jia
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Dan Du
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hongle Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China.
| | - Mingxia Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Fucheng He
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Ge L, Sun Y, Shi Y, Liu G, Teng F, Geng Z, Chen X, Xu H, Xu J, Jia X. Plasma circRNA microarray profiling identifies novel circRNA biomarkers for the diagnosis of ovarian cancer. J Ovarian Res 2022; 15:58. [PMID: 35550610 PMCID: PMC9097182 DOI: 10.1186/s13048-022-00988-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/23/2022] [Indexed: 12/14/2022] Open
Abstract
Background Circular RNA (circRNA), a class of RNA with a covalent closed circular structure that widely existed in serum and plasma, has been considered an ideal liquid biopsy marker in many diseases. In this study, we employed microarray and qRT-PCR to evaluate the potential circulating circRNAs with diagnostic efficacy in ovarian cancer. Methods We used microarray to explore the circRNA expression profile in ovarian cancer patients’ plasma and quantitative real-time (qRT)-PCR approach to assessing the candidate circRNA’s expression. Then the receiver operating characteristic (ROC) curve was employed to analyze the diagnostic values of candidate circRNAs. The diagnostic model circCOMBO was a combination of hsa_circ_0003972 and hsa_circ_0007288 built by binary logistic regression. Then bioinformatic tools were used to predict their potential mechanisms. Results Hsa_circ_0003972 and hsa_circ_0007288 were downregulated in ovarian cancer patients’ plasma, tissues, and cell lines, comparing with the controls. Hsa_circ_0003972 and hsa_circ_0007288 exhibited diagnostic values with the Area Under Curve (AUC) of 0.724 and 0.790, respectively. circCOMBO showed a better diagnostic utility (AUC: 0.781), while the combination of circCOMBO and carbohydrate antigen 125 (CA125) showed the highest diagnostic value (AUC: 0.923). Furthermore, the higher expression level of hsa_circ_0007288 in both plasma and ovarian cancer tissues was associated with lower lymph node metastasis potential in ovarian cancer. Conclusions Our results revealed that hsa_circ_0003972 and hsa_circ_0007288 may serve as novel circulating biomarkers for ovarian cancer diagnosis. Supplementary information The online version contains supplementary material available at 10.1186/s13048-022-00988-0.
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Affiliation(s)
- Lili Ge
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Yu Sun
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Yaqian Shi
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Guangquan Liu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Fang Teng
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Zhe Geng
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Xiyi Chen
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Hanzi Xu
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, China.
| | - Juan Xu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China.
| | - Xuemei Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China.
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circHtra1/miR-3960/GRB10 Axis Promotes Neuronal Loss and Immune Deficiency in Traumatic Brain Injury. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3522492. [PMID: 35571247 PMCID: PMC9106453 DOI: 10.1155/2022/3522492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 01/19/2023]
Abstract
Circular RNAs (circRNAs) are abundant in the brain and contribute to central nervous system diseases; however, the exact roles of circRNAs in human traumatic brain injury (TBI) have not been established. In this study, we used a competing endogenous RNA (ceRNA) chipset as well as in vitro and in vivo assays to characterize differentially expressed circRNAs in TBI. We detected 3035 differentially expressed circRNAs in the severe TBI group, 2362 in the moderate group, and 433 in the mild group. A ceRNA network was constructed. The circRNA has_circ_0020269 (circHtra1) was significantly upregulated after brain insults and was correlated with the severity of injury. circHtra1 inhibited cell proliferation and promoted apoptosis, and its knockdown reversed these effects. Further analyses revealed that circHtra1 functions as a miR-3960 sponge and increases the expression of GRB10, which is involved in NK cell infiltration after TBI. circHtra1 was identified as a target of the IGF-1/ADAR1 axis. Reduced expression of ADAR1 (involved in A-to-I editing) after brain insults upregulated circHtra1. Our results show that circHtra1 promotes neuronal loss by sponging miR-3960 and regulating GRB10 and apoptosis during brain insults. In addition, A-to-I editing could regulate circRNA expression profiles after TBI, and circHtra1 is a potential therapeutic target.
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Liang W, Wang C, Wang J, Zhang M. Hsa_circ_0023984 Regulates Cell Proliferation, Migration, and Invasion in Esophageal Squamous Cancer via Regulating miR-1294/PI3K/Akt/c-Myc Pathway. Appl Biochem Biotechnol 2022; 194:1-16. [PMID: 35522362 DOI: 10.1007/s12010-022-03935-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 11/02/2022]
Abstract
Circular RNAs (circRNAs) exert an essential function in the tumorigenesis and progression of esophageal squamous cancer (ESCC). Nonetheless, the role and potential mechanism of circ_0023984 in ESCC are blurred. circRNA expression profile data from Gene Expression Omnibus (GEO) database was applied to analyze circRNAs that were differentially expressed between ESCC tissues and paracancerous tissues. Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze circ_0023984 expression and miR-1294 expression in ESCC tissues and cells. Then a series of functional experiments were executed to validate the role of circ_0023984 and miR-1294 in modulating the proliferation, migration, invasion, and cell cycle progression of ESCC cells. Luciferase reporter experiment was performed to confirm the targeting relationship between circ_0023984 and miR-1294. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were carried out with DAVID database. Western blot assay was utilized to detect phosphorylated-Akt (p-Akt) expression and c-Myc expression. circ_0023984 was remarkably upmodulated in ESCC tumor tissues and cell lines. circ_0023984 overexpression was correlated with advanced clinical stage and lymph node metastasis of ESCC patients. circ_0023984 overexpression remarkably enhanced ESCC cell proliferation, migration, invasion, and cell cycle progression, while knockdown of circ_0023984 showed the opposite effect. circ_0023984 was the molecular sponge of miR-1294. miR-1294 could significantly inhibit ESCC cell proliferation, migration, invasion, and induce cell cycle arrest at G0/G1 phase. circ_0023984 affected ESCC progression through regulating miR-1294 expression. The target genes of miR-1294 were associated with cell cycle arrest and PI3K-Akt signaling pathway. circ_0023984 upregulated the expression of p-Akt and c-Myc by repressing miR-1294. circ_0023984 facilitates the malignant biological behaviors of ESCC cells through inhibiting miR-1294 and activating PI3K/Akt/c-myc pathway.
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Affiliation(s)
- Wenchang Liang
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Jianshedong Road No.1, Zhengzhou, 450000, Henan, China.,Department of Oncology, Anyang Tumor Hospital, the Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Henan Medical Key Laboratory of Precise Prevention and Treatment of Esophageal Cancer, Anyang, 455000, Henan, China
| | - Cailing Wang
- Department of Oncology, Anyang Tumor Hospital, the Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Henan Medical Key Laboratory of Precise Prevention and Treatment of Esophageal Cancer, Anyang, 455000, Henan, China
| | - Junsheng Wang
- Department of Oncology, Anyang Tumor Hospital, the Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Henan Medical Key Laboratory of Precise Prevention and Treatment of Esophageal Cancer, Anyang, 455000, Henan, China
| | - Mingzhi Zhang
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Jianshedong Road No.1, Zhengzhou, 450000, Henan, China.
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Sun Z, Zhang S, Zhang N, Wang J, Wang J, Liu J. Circ_0005231 promotes the progression of esophageal squamous cell carcinoma via sponging miR-383-5p and regulating KIAA0101. Thorac Cancer 2022; 13:1751-1762. [PMID: 35524161 PMCID: PMC9200875 DOI: 10.1111/1759-7714.14450] [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: 02/25/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background Circular RNAs (circRNAs) can act as key regulators in human cancers, including esophageal squamous cell carcinoma (ESCC). However, the role and mechanism of circ_0005231 in ESCC have not previously been reported. Methods RNA levels and protein levels were detected by real‐time quantitative polymerase chain reaction (RT‐qPCR) and Western blot assay, respectively. Cell proliferation was assessed by colony formation assay and 5‐ethynyl‐2'‐deoxyuridine (EdU) assay. Wound healing and transwell assays were used to assess cell migration and invasion, respectively. The intermolecular interaction was predicted by bioinformatic analysis and verified by RNA immunoprecipitation (RIP), RNA pulldown and dual‐luciferase reporter assays. Xenograft tumor model was used for exploring the biological function of circ_0005231 in vivo. Results Circ_0005231 was upregulated in ESCC plasma, tissues and cells. Cell proliferation, migration and invasion were significantly restrained by knockdown of circ_0005231 in ESCC cells. Circ_0005231 acted as a sponge of miR‐383‐5p, and circ_0005231 regulated ESCC cellular behavior by sponging miR‐383‐5p. Moreover, miR‐383‐5p directly targeted KIAA0101, and circ_0005231 positively regulated KIAA0101 expression by sponging miR‐383‐5p. Furthermore, circ_0005231 knockdown suppressed the malignant behavior of ESCC cells by downregulating KIAA0101. Importantly, knockdown of circ_0005231 blocked xenograft tumor growth in vivo. Conclusion Circ_0005231 acted as a sponge of miR‐383‐5p to promote ESCC progression by upregulating KIAA0101, which provided a potential therapeutic strategy for ESCC treatment.
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Affiliation(s)
- Zhiguang Sun
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.,Department of Thoracic Surgery, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Hebei, China
| | - Shaowei Zhang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Nan Zhang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jianxin Wang
- Department of Thoracic Surgery, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Hebei, China
| | - Jindong Wang
- Department of Thoracic Surgery, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Hebei, China
| | - Junfeng Liu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Weidle UH, Sela T, Brinkmann U, Niewoehner J. Circular RNAs With Efficacy in Preclinical In Vitro and In Vivo Models of Esophageal Squamous Cell Carcinoma. Cancer Genomics Proteomics 2022; 19:283-298. [PMID: 35430563 DOI: 10.21873/cgp.20320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
Esophageal cancer is associated with a dismal prognosis. The armamentarium of approved drugs is focused on chemotherapy with modest therapeutic benefit. Recently, checkpoint inhibitory monoclonal antibody Pembrolizumab was approved. In order to identify new targets and modalities for the treatment of esophagus squamous cell carcinoma (ESCC) we searched the literature for circRNAs involved in the pathogenesis of ESCC. We identified two down-regulated and 17 up-regulated circRNAs as well as a synthetic circRNA with efficacy in preclinical in vivo systems. Down-regulated circRNAs sponge microRNAs directed against tumor suppressor genes. Up-regulated circRNAs sponge microRNAs directed against mRNAs, which encode proteins with pro-tumoral functions. We discuss issues such as reconstitution of down-regulated circRNAs and inhibition of up-regulated circRNAs with short interfering RNA (siRNA)- related entities. Also, we address druggability issues of the identified targets.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Tatjana Sela
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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Song H, Tian D, Sun J, Mao X, Kong W, Xu D, Ji Y, Qiu B, Zhan M, Wang J. circFAM120B functions as a tumor suppressor in esophageal squamous cell carcinoma via the miR-661/PPM1L axis and the PKR/p38 MAPK/EMT pathway. Cell Death Dis 2022; 13:361. [PMID: 35436983 PMCID: PMC9016076 DOI: 10.1038/s41419-022-04818-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023]
Abstract
Extensive changes of circRNA expression underscore their essential contributions to multiple hallmarks of cancers; however, their functions and mechanisms of action in esophageal squamous cell carcinoma (ESCC) remain undetermined. Here, we adopted a three-stage approach by first screening for significantly differentially expressed circRNAs in ESCC and performing an external validation study, followed by the functional analyses. The properties of circRNAs were evaluated using Sanger sequencing, RNase R digestion, actinomycin D treatment, subcellular localization analysis, and fluorescence in situ hybridization. Target transcripts were predicted using online tools and verified by dual-luciferase, RNA immunoprecipitation, qRT-PCR, and western blot. Biotin-labeled RNA-protein pull-down, mass spectrometry, and RNA immunoprecipitation were employed to identify proteins interacting with circRNAs. Gain- and loss-of-function experiments were performed to uncover the roles of circRNAs, their target genes, and binding proteins in the proliferation, metastasis, and invasion. We observed that circFAM120B (hsa_circ_0001666) was frequently downregulated in cancer tissues and patient plasma, and its expression level was related to overall survival in ESCC patients. Overexpression of circFAM120B inhibited the proliferation, metastasis, and invasion of ESCC while silencing it enhanced malignant phenotypes. Mechanistically, circFAM120B was predominantly located in the cytoplasm, guarantying its sponging for miR-661 to restore the expression of PPM1L, a tumor suppressor. We observed that circFAM120B could reduce the stability of RNA-dependent protein kinase (PKR) by promoting its ubiquitination-dependent degradation and subsequently regulating the p38 MAPK signaling pathway, resulting in the repression of EMTs in ESCC cells. Our findings suggest that circFAM120B is a promising biomarker of ESCC, which acts as a tumor suppressor via the circFAM120B/miR-661/PPM1L axis and PKR/p38 MAPK/EMT pathway, supporting its significance as a candidate therapeutic target.
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Affiliation(s)
- Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Dan Tian
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jian Sun
- Department of Thoracic Surgery, The First People's Hospital of Yancheng and Yancheng Clinical College of Xuzhou Medical University, Yancheng, 224001, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Weimin Kong
- Department of Thoracic Surgery, The First People's Hospital of Yancheng and Yancheng Clinical College of Xuzhou Medical University, Yancheng, 224001, China
| | - Dian Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Ye Ji
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mengyao Zhan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China. .,Department of Epidemiology, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
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Yang J, Qi M, Fei X, Wang X, Wang K. Hsa_circRNA_0088036 acts as a ceRNA to promote bladder cancer progression by sponging miR-140-3p. Cell Death Dis 2022; 13:322. [PMID: 35396504 PMCID: PMC8993833 DOI: 10.1038/s41419-022-04732-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/17/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs that play vital roles in cancer biology. However, the potential role of hsa_circRNA_0088036 in bladder cancer (BCa) remains unknown. Hsa_circRNA_0088036 was identified by microarray analysis and validated by quantitative real-time polymerase chain reaction. Functional assays were conducted to confirm the effects of hsa_circRNA_0088036 on the growth, migration, invasion, tumorigenesis, and metastasis of BCa cells. The luciferase reporter assay and RNA pull down assay were performed to investigate the interactions between hsa_circRNA_0088036, miR-140-3p, and forkhead box protein Q1 (FOXQ1). Upregulated expression of hsa_circRNA_0088036 in BCa tissues and cell lines was positively correlated with overall survival and clinicopathologic characteristics. Knockdown of hsa_circRNA_0088036 inhibited the growth, migration, and invasion of BCa cells both in vivo and in vitro. Mechanistically, hsa_circRNA_0088036 could directly interact with miR-140-3p and act as a miRNA sponge to modulate FOXQ1 expression. Knockdown of hsa_circRNA_0088036 inhibited the proliferation, migration, and metastasis of BCa cells via miR-140-3p/FOXQ1 signaling, suggesting that hsa_circRNA_0088036 is a potential biomarker and therapeutic target for BCa.
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Affiliation(s)
- Jun Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Manlong Qi
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xiang Fei
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Zhang RM, Pan Y, Zou CX, An Q, Cheng JR, Li PJ, Zheng ZH, Pan Y, Feng WY, Yang SF, Shi DS, Wei YM, Deng YF. CircUBE2Q2 promotes differentiation of cattle muscle stem cells and is a potential regulatory molecule of skeletal muscle development. BMC Genomics 2022; 23:267. [PMID: 35387588 PMCID: PMC8985345 DOI: 10.1186/s12864-022-08518-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Background The growth and development of muscle stem cells (MuSCs) are significant events known to affect muscle plasticity, disease, meat production, and meat quality, which involves the types and functions of mRNA and non-coding RNA. Here, MuSCs were cultured from Guangxi fetal cattle. RNA sequencing was used to analyze the RNA expression of mRNA and non-coding RNAs during the cell proliferation and differentiation phases. Results Two thousand one hundred forty-eight mRNAs and 888 non-coding RNAs were differentially expressed between cell proliferation and differentiation phases, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. RT-qPCR verified the differential expression levels of mRNAs and non-coding RNAs, and the differentially expressed circUBE2Q2 was subsequently characterized. Expression profile analysis revealed that circUBE2Q2 was abundant in muscle tissues and intramuscular fat. The expression of cricUBE2Q2 was also significantly upregulated during MuSCs myogenic differentiation and SVFs adipogenic differentiation and decreased with age in cattle muscle tissue. Finally, the molecular mechanism of circUBE2Q2 regulating MuSCs function that affects skeletal muscle development was investigated. The results showed that circUBE2Q2 could serve as a sponge for miR-133a, significantly promoting differentiation and apoptosis of cultured MuSCs, and inhibiting proliferation of MuSCs. Conclusions CircUBE2Q2 is associated with muscle growth and development and induces MuSCs myogenic differentiation through sponging miR-133a. This study will provide new clues for the mechanisms by which mRNAs and non-coding RNAs regulate skeletal muscle growth and development, affecting muscle quality and diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08518-4.
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Affiliation(s)
- Rui-Men Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yu Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Chao-Xia Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qiang An
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Juan-Ru Cheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Peng-Ju Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Zi-Hua Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yan Pan
- Guangxi Agricultural Vocational University, Nanning, 530007, Guangxi, China
| | - Wan-You Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Su-Fang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.,International Zhuang Medical Hospital Affiliated to Guangxi University Chinese Medicine, Nanning, 530000, Guangxi, China
| | - De-Shun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Ying-Ming Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Yan-Fei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.
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45
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Huang Y, Su D, Ye B, Huang Y, Qin S, Chen C, Zhao Y, Pang Y. Expression and clinical significance of circular RNA hsa_circ_0003416 in pediatric pulmonary arterial hypertension associated with congenital heart disease. J Clin Lab Anal 2022; 36:e24273. [PMID: 35165927 PMCID: PMC8993640 DOI: 10.1002/jcla.24273] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/04/2022] [Accepted: 01/21/2022] [Indexed: 12/27/2022] Open
Abstract
Background Circular RNAs (circRNAs) have been found to be involved in the development of pulmonary arterial hypertension (PAH). However, their diagnostic value in pediatric PAH remains unclear. This study aimed to examine the characteristic expression of the circRNA hsa_circ_0003416 in the plasma of children with PAH caused by congenital heart disease (CHD); the potential of hsa_circ_0003416 as a diagnostic biomarker was also investigated. Methods The plasma expression levels of hsa_circ_0003416 were determined via quantitative reverse transcription–polymerase chain reaction in 50 CHD patients, 50 PAH patients, and 20 healthy subjects; the associations between hsa_circ_0003416 levels and clinical data were analyzed thereafter. Receiver operating characteristic curves were employed to determine the diagnostic capacity of this circRNA. Results Expression levels of hsa_circ_0003416 in plasma were lower in the PAH‐CHD group than in the CHD and healthy control groups (p = 0.009 vs. healthy control group, p = 0.026 vs. CHD group). Moreover, hsa_circ_0003416 was found to be negatively associated with B‐type natriuretic peptide (r = −0.342, p = 0.013). In addition, the area under the curve of hsa_circ_0003416 levels in plasma was 0.721 (95% confidence intervals = 0.585–0.857, p = 0.004), suggesting that it has a promising diagnostic value. Conclusions Overall, hsa_circ_0003416 was found to be significantly downregulated in children with PAH‐CHD and to be potent as a biomarker for PAH‐CHD diagnosis.
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Affiliation(s)
- Yanyun Huang
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Danyan Su
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bingbing Ye
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuqin Huang
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Suyuan Qin
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Cheng Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yijue Zhao
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yusheng Pang
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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46
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Wu S, Chen L, Zhou X. Circular RNAs in the regulation of cardiac hypertrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:484-490. [PMID: 35036059 PMCID: PMC8728521 DOI: 10.1016/j.omtn.2021.12.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cardiac hypertrophy is a physiological adaptation to pressure stress that augments or preserves cardiac function. Prolonged hypertrophy can, however, eventually lead to heart failure. Although some effector molecules and signaling pathways have been associated with myocardial hypertrophy, progress has been limited, and further studies are needed to thoroughly explore the underlying mechanisms and to discover novel and effective therapeutic targets. Recently, non-coding RNAs, which are well-known physiological regulators, have attracted much attention in the field of cardiovascular research. Circular RNA, in particular, has emerged as a key player in cardiac hypertrophy, and increasing numbers of papers are now being devoted to this topic. In this review, we will give a brief introduction to circular RNA and then focus on its role as a potential therapeutic target in cardiac hypertrophy.
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Affiliation(s)
- Siyi Wu
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lili Chen
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiang Zhou
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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47
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Liu Y, Ao X, Yu W, Zhang Y, Wang J. Biogenesis, functions, and clinical implications of circular RNAs in non-small cell lung cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:50-72. [PMID: 34938606 PMCID: PMC8645422 DOI: 10.1016/j.omtn.2021.11.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide, with high morbidity and mortality. Non-small cell lung cancer (NSCLC) is a major pathological type of LC and accounts for more than 80% of all cases. Circular RNAs (circRNAs) are a large class of non-coding RNAs (ncRNAs) with covalently closed-loop structures, a high abundance, and tissue-specific expression patterns. They participate in various pathophysiological processes by regulating complex gene networks involved in proliferation, apoptosis, migration, and epithelial-to-mesenchymal transition (EMT), as well as metastasis. A growing number of studies have revealed that the dysregulation of circRNAs contributes to many aspects of cancer progression, such as its occurrence, metastasis, and recurrence, suggesting their great potential as efficient and specific biomarkers in the diagnosis, prognosis, and therapeutic targeting of NSCLC. In this review, we systematically elucidate the characteristics, biogenesis, and functions of circRNAs and focus on their molecular mechanisms in NSCLC progression. Moreover, we highlight their clinical implications in NSCLC treatment.
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Affiliation(s)
- Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, China.,School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Xiang Ao
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Wanpeng Yu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
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Arora S, Khan S, Zaki A, Tabassum G, Mohsin M, Bhutto HN, Ahmad T, Fatma T, Syed MA. Integration of chemokine signaling with non-coding RNAs in tumor microenvironment and heterogeneity in different cancers. Semin Cancer Biol 2022; 86:720-736. [DOI: 10.1016/j.semcancer.2022.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023]
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49
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Li T, Li S. Circ_0023984 Facilitates Esophageal Squamous Cell Carcinoma Progression by Regulating miR-433-3p/REV3L Axis. Dig Dis Sci 2022; 67:892-903. [PMID: 33725240 DOI: 10.1007/s10620-021-06916-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND It has been revealed that circular RNAs (circRNAs) play an important role in regulating the malignant phenotype of tumor cells, thus involving in the progression of malignancies. However, the role of circ_0023984 in esophageal squamous cell carcinoma (ESCC) remains largely unclear. METHODS The quantitative real-time polymerase chain reaction and Western blot assays were used to detect the expression of circ_0023984, microRNA (miR)-443-3p, and protein reversionless 3-like (REV3L). In vitro and in vivo assays were performed using cell counting kit-8, colony formation, transwell, wound healing, flow cytometry, and xenograft assays. The interaction miR-433-3p and circ_0023984 or REV3L was confirmed by dual-luciferase reporter, pull-down or RIP assays. RESULTS Circ_0023984 was highly expressed in ESCC tissues and cells, knockdown of circ_0023984 suppressed cancer cell proliferation, migration, invasion, and promoted cell apoptosis in vitro. Mechanistic analysis confirmed that circ_0023984 functioned as a sponge for miR-433-3p to positively regulate the expression of REV3L that was verified to be a target of miR-433-3p. Circ_0023984 knockdown repressed the tumorigenesis of ESCC cells via targeting miR-433-3p. Additionally, miR-433-3p performed anti-proliferative, anti-migratory, and anti-invasive abilities in ESCC cells, which were reversed by REV3L overexpression. Pre-clinically, silencing of circ_0023984 suppresses the tumorigenesis and growth of xenografts in nude mice. CONCLUSION Circ_0023984 exerted an oncogenic role in ESCC tumorigenesis and aggressiveness through promoting cell growth, migration, and invasion via miR-433-3p/REV3L axis.
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Affiliation(s)
- Ting Li
- Department of Gastroenterology, The NO.2 People's Hospital of Lanzhou City, No. 388 Jingyuan Road, Chengguan District, Lanzhou, 730046, Gansu Province, China
| | - Suping Li
- Department of Gastroenterology, The NO.2 People's Hospital of Lanzhou City, No. 388 Jingyuan Road, Chengguan District, Lanzhou, 730046, Gansu Province, China.
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50
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Lee B, Mohamad I, Pokhrel R, Murad R, Yuan M, Stapleton S, Bettegowda C, Jallo G, Eberhart CG, Garrett T, Perera RJ. Medulloblastoma cerebrospinal fluid reveals metabolites and lipids indicative of hypoxia and cancer-specific RNAs. Acta Neuropathol Commun 2022; 10:25. [PMID: 35209946 PMCID: PMC8867780 DOI: 10.1186/s40478-022-01326-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/04/2022] [Indexed: 02/07/2023] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children. There remains an unmet need for diagnostics to sensitively detect the disease, particularly recurrences. Cerebrospinal fluid (CSF) provides a window into the central nervous system, and liquid biopsy of CSF could provide a relatively non-invasive means for disease diagnosis. There has yet to be an integrated analysis of the transcriptomic, metabolomic, and lipidomic changes occurring in the CSF of children with MB. CSF samples from patients with (n = 40) or without (n = 11; no cancer) MB were subjected to RNA-sequencing and high-resolution mass spectrometry to identify RNA, metabolite, and lipid profiles. Differentially expressed transcripts, metabolites, and lipids were identified and their biological significance assessed by pathway analysis. The DIABLO multivariate analysis package (R package mixOmics) was used to integrate the molecular changes characterizing the CSF of MB patients. Differentially expressed transcripts, metabolites, and lipids in CSF were discriminatory for the presence of MB but not the exact molecular subtype. One hundred and ten genes and ten circular RNAs were differentially expressed in MB CSF compared with normal, representing TGF-β signaling, TNF-α signaling via NF-kB, and adipogenesis pathways. Tricarboxylic acid cycle and other metabolites (malate, fumarate, succinate, α-ketoglutarate, hydroxypyruvate, N-acetyl-aspartate) and total triacylglycerols were significantly upregulated in MB CSF compared with normal CSF. Although separating MBs into subgroups using transcriptomic, metabolomic, and lipid signatures in CSF was challenging, we were able to identify a group of omics signatures that could separate cancer from normal CSF. Metabolic and lipidomic profiles both contained indicators of tumor hypoxia. Our approach provides several candidate signatures that deserve further validation, including the novel circular RNA circ_463, and insights into the impact of MB on the CSF microenvironment.
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Affiliation(s)
- Bongyong Lee
- grid.21107.350000 0001 2171 9311Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St, Baltimore, MD 21231 USA ,grid.413611.00000 0004 0467 2330Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA
| | - Iqbal Mohamad
- grid.15276.370000 0004 1936 8091Department Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 1395 Center Drive, Gainesville, FL 32610 USA ,grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Rudramani Pokhrel
- grid.21107.350000 0001 2171 9311Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St, Baltimore, MD 21231 USA ,grid.413611.00000 0004 0467 2330Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA
| | - Rabi Murad
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Menglang Yuan
- grid.21107.350000 0001 2171 9311Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St, Baltimore, MD 21231 USA ,grid.413611.00000 0004 0467 2330Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA
| | - Stacie Stapleton
- grid.413611.00000 0004 0467 2330Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA
| | - Chetan Bettegowda
- grid.21107.350000 0001 2171 9311Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St, Baltimore, MD 21231 USA ,grid.21107.350000 0001 2171 9311Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - George Jallo
- grid.413611.00000 0004 0467 2330Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA
| | - Charles G. Eberhart
- grid.21107.350000 0001 2171 9311Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St, Baltimore, MD 21231 USA ,grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, MD 21205 USA
| | - Timothy Garrett
- Department Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 1395 Center Drive, Gainesville, FL, 32610, USA.
| | - Ranjan J. Perera
- grid.21107.350000 0001 2171 9311Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St, Baltimore, MD 21231 USA ,grid.413611.00000 0004 0467 2330Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA
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