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1.
Mol Cancer ; 23(1): 4, 2024 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-38184608

RESUMO

BACKGROUND: Renal cell carcinoma (RCC) is one of the most common malignant tumor worldwide. Metastasis is a leading case of cancer-related deaths of RCC. Circular RNAs (circRNAs), a class of noncoding RNAs, have emerged as important regulators in cancer metastasis. However, the functional effects and regulatory mechanisms of circRNAs on RCC metastasis remain largely unknown. METHODS: High-throughput RNA sequencing techniques were performed to analyze the expression profiles of circRNAs and mRNAs in highly and poorly invasive clear cell renal cell carcinoma (ccRCC) cell lines. Functional experiments were performed to unveil the regulatory role of circPPAP2B in the proliferation and metastatic capabilities of ccRCC cells. RNA pulldown, Mass spectrometry analysis, RNA methylation immunoprecipitation (MeRIP), RNA immunoprecipitation (RIP), co-immunoprecipitation (CoIP), next-generation RNA-sequencing and double luciferase experiments were employed to clarify the molecular mechanisms by which circPPAP2B promotes ccRCC metastasis. RESULTS: In this study, we describe a newly identified circular RNA called circPPAP2B, which is overexpressed in highly invasive ccRCC cells, as determined through advanced high-throughput RNA sequencing techniques. Furthermore, we observed elevated circPPAP2B in ccRCC tissues, particularly in metastatic ccRCC tissues, and found it to be associated with poor prognosis. Functional experiments unveiled that circPPAP2B actively stimulates the proliferation and metastatic capabilities of ccRCC cells. Mechanistically, circPPAP2B interacts with HNRNPC in a m6A-dependent manner to facilitate HNRNPC nuclear translocation. Subcellular relocalization was dependent upon nondegradable ubiquitination of HNRNPC and stabilization of an HNRNPC/Vimentin/Importin α7 ternary complex. Moreover, we found that circPPAP2B modulates the interaction between HNRNPC and splicing factors, PTBP1 and HNPNPK, and regulates pre-mRNA alternative splicing. Finally, our studies demonstrate that circPPAP2B functions as a miRNA sponge to directly bind to miR-182-5p and increase CYP1B1 expression in ccRCC. CONCLUSIONS: Collectively, our study provides comprehensive evidence that circPPAP2B promotes proliferation and metastasis of ccRCC via HNRNPC-dependent alternative splicing and miR-182-5p/CYP1B1 axis and highlights circPPAP2B as a potential therapeutic target for ccRCC intervention.


Assuntos
Carcinoma de Células Renais , Neoplasias Renais , MicroRNAs , Humanos , Carcinoma de Células Renais/genética , Processamento Alternativo , RNA Circular/genética , MicroRNAs/genética , Neoplasias Renais/genética , Ribonucleoproteínas Nucleares Heterogêneas , Proteína de Ligação a Regiões Ricas em Polipirimidinas , Citocromo P-450 CYP1B1 , Ribonucleoproteínas Nucleares Heterogêneas Grupo C/genética
2.
J Transl Med ; 22(1): 207, 2024 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-38414006

RESUMO

With an estimated one million new cases reported annually, gastric cancer (GC) ranks as the fifth most diagnosed malignancy worldwide. The early detection of GC remains a major challenge, and the prognosis worsens either when patients develop resistance to chemotherapy or radiotherapy or when the cancer metastasizes. The precise pathogenesis underlying GC is not well understood, which further complicates its treatment. Circular RNAs (circRNAs), a recently discovered class of noncoding RNAs that originate from parental genes through "back-splicing", have been shown to play a key role in various biological processes in both eukaryotes and prokaryotes. CircRNAs have been linked to cardiovascular diseases, diabetes, hypertension, Alzheimer's disease, and the occurrence and progression of tumors. Prior studies have established that circRNAs play a crucial role in GC, impacting tumorigenesis, diagnosis, progression, and therapy resistance. This review aims to summarize how circRNAs contribute to GC tumorigenesis and progression, examine their roles in the development of drug resistance, discuss their potential as biotechnological drugs, and summarize their response to therapeutic drugs and microorganism in GC.


Assuntos
RNA Circular , Neoplasias Gástricas , Humanos , RNA Circular/genética , Neoplasias Gástricas/genética , Neoplasias Gástricas/terapia , Neoplasias Gástricas/diagnóstico , Prognóstico , Carcinogênese/genética , Transformação Celular Neoplásica
3.
Metab Brain Dis ; 39(3): 361-371, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38091240

RESUMO

Circular RNAs (circRNAs) can play essential roles in tumor development, including glioblastoma (GBM). The current study was performed to explore the function and mechanism of circ_0027446 in GBM progression. Circ_0027446, microRNA-346 (miR-346) and Phosphoglycerate kinase 1 (PGK1) levels were detected using reverse transcription-quantitative polymerase chain reaction assay. Cell behaviors were examined using Cell Counting Kit-8 assay, colony formation assay, EdU assay, flow cytometry, and transwell assay. Glycolytic metabolism was analyzed by commercial kits. The protein level was determined via western blot. The target interaction was analyzed by dual-luciferase reporter assay. Circ_0027446 function in vivo was explored by tumor xenograft assay. Circ_0027446 expression was significantly up-regulated in GBM samples and cells. Circ_0027446 down-regulation suppressed proliferation, invasion, glycolytic metabolism and enhanced apoptosis of GBM cells. MiR-346 was a target of circ_0027446, and circ_0027446 promoted GBM progression by sponging miR-346. PGK1 acted as a target gene of miR-346, and circ_0027446 interacted with miR-346 to regulate PGK1 expression. Overexpression of miR-346 inhibited malignant behaviors of GBM cells through down-regulating PGK1. Circ_0027446 contributed to tumor growth in vivo via miR-346/PGK1 axis. The current evidences demonstrated that circ_0027446 facilitated malignant progression of GBM through binding to miR-346 to up-regulate PGK1.


Assuntos
Glioblastoma , MicroRNAs , Humanos , Glioblastoma/genética , Apoptose , Contagem de Células , Regulação para Baixo , MicroRNAs/genética , Proliferação de Células/genética , Linhagem Celular Tumoral , Fosfoglicerato Quinase/genética
4.
Environ Toxicol ; 39(8): 4249-4260, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38775215

RESUMO

BACKGROUND: Circular RNA (circRNA) plays a crucial role in the pathogenesis and progression of colorectal cancer (CRC). However, the current understanding of the emerging function and mechanism of circ-RAPGEF5 in CRC remains poorly understood. METHODS: We first evaluated the expression level of circ-RAPGEF5 in CRC tissues and cells by quantitative real-time polymerase chain reaction (qRT-PCR). Then, we analyzed cell proliferation (EdU and colony formation assay), migration (cell wound healing assay), invasion (transwell assay), and apoptosis (flow cytometry assay). To further elucidate the mechanism of circ-RAPGEF5 in CRC, bioinformatics tools, Dual-luciferase reporter assay, Ago2 RNA immunoprecipitation assay, and RNA pull-down assay were employed. Moreover, we established a CRC transplantation tumor model to evaluate the effect of circ-RAPGEF5 on tumor growth in vivo. RESULTS: circ-RAPGEF5 was significantly upregulated in CRC tissues and CRC cells. Furthermore, the downregulation of circ-RAPGEF5 restrained CRC cell proliferation, migration, and invasion, and promoted cell apoptosis in vitro. Mechanistically, circ-RAPGEF5 accelerated the malignant behaviors of CRC cells by sponging miR-545-5p, which targeted polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). In addition, we revealed that circ-RAPGEF5 silence curbed tumor growth in vivo. CONCLUSION: These findings revealed that circ-RAPGEF5 played an oncogenic role through the miR-545-5p/GALNT3 axis in CRC progression, providing potential therapeutic targets for the treatment of CRC.


Assuntos
Neoplasias Colorretais , Regulação para Baixo , N-Acetilgalactosaminiltransferases , RNA Circular , Animais , Humanos , Masculino , Camundongos , Apoptose , Linhagem Celular Tumoral , Movimento Celular , Proliferação de Células , Neoplasias Colorretais/patologia , Neoplasias Colorretais/genética , Progressão da Doença , Regulação Neoplásica da Expressão Gênica , Camundongos Endogâmicos BALB C , Camundongos Nus , MicroRNAs/genética , MicroRNAs/metabolismo , N-Acetilgalactosaminiltransferases/genética , N-Acetilgalactosaminiltransferases/metabolismo , Polipeptídeo N-Acetilgalactosaminiltransferase , RNA Circular/genética , RNA Circular/metabolismo
5.
Cancer Cell Int ; 23(1): 45, 2023 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-36899354

RESUMO

BACKGROUND: Breast cancer is a prevalent disease in women, with high prevalence worldwide. The hypoxic microenvironment of solid tumors develops during the progress of carcinogenesis and leads to greater malignancy and treatment resistance. Recently, accumulating evidence indicates that non-coding RNAs, such as circular RNAs (circRNAs), play a pivotal role in altering cellular functions. However, the underlying mechanisms of circRNAs in breast cancer are still unclear. Therefore, the purpose of this study was to investigate the role of a tumor-suppressive circRNA, circAAGAB, in breast cancer by assuming down-regulation of circAAGAB under hypoxia and the properties of a tumor suppressor. METHODS: Firstly, circAAGAB was identified from expression profiling by next generation sequencing. Next, the stability of circAAGAB increased by interacting with the RNA binding protein FUS. Moreover, cellular and nuclear fractionation showed that most circAAGAB resided in the cytoplasm and that it up-regulated KIAA1522, NKX3-1, and JADE3 by sponging miR-378 h. Lastly, the functions of circAAGAB were explored by identifying its down-stream genes using Affymetrix microarrays and validated by in vitro assays. RESULTS: The results showed that circAAGAB reduced cell colony formation, cell migration, and signaling through p38 MAPK pathway, as well as increased radiosensitivity. CONCLUSION: These findings suggest that the oxygen-responsive circAAGAB acts as a tumor suppressor in breast cancer, and may contribute to the development of a more specific therapeutic regimen for breast cancer.

6.
Brain Behav Immun ; 107: 140-151, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36202171

RESUMO

BACKGROUND: Severe pain in patients can be alleviated by morphine treatment. However, long-term morphine treatment induces analgesic tolerance and the molecular mechanism of morphine analgesic intolerance is still not fully elucidated. Therefore, a novel target for improving morphine analgesic tolerance is required. Whole-genome sequencing showed that circNf1 is highly expressed in the dorsal horns of morphine-treated rats. Circular RNAs (circRNAs) are known to be unique and conserved cellular molecules that are mostly present in cytoplasm and participate in various biochemical processes with different functions. Therefore, we focused on exploring the molecular mechanism by which circNf1 contributes to morphine analgesic tolerance. METHODS: CircRNA sequencing revealed differential expression of circRNAs after morphine treatment, and bioinformatics software programs (miRNAda, PicTar, and RNAhybrid) were used to predict possible mRNAs and binding sites. RNA binding protein immunoprecipitation (RIP), chromatin isolation by RNA purification (ChIRP), fluorescence in situ hybridization (FISH), western blotting, biotin-coupled probe pull-down assay, luciferase assay, and quantitative real-time polymerase chain reaction (qRT-PCR) were conducted to detect and measure the expression levels of circRNAs, mRNAs, and proteins. Intrathecal injections of small interfering RNAs (siRNAs), microRNA (miRNA) agomirs, and functional virus microinjections were administered to artificially mediate the expression of molecules. Tail immersion and hotplate tests were performed to evaluate morphine analgesic tolerance. RESULTS: Morphine-induced circNf1 expression was high in the spinal cord. RIP-PCR and luciferase assay data showed that circNf1 could combine with both miR-330-3p and miR-665, and FISH showed that circNf1 co-localized with miR-330-3p and miR-665. qRT-PCR assay showed downregulation of miR-330-3p and miR-665 in morphine-treated rats; western blotting results showed that CXCL12 increased after morphine treatment, however, the upregulation of CXCL12 could be alleviated after the intrathecal injection of miR-330-3p as well as miR-665 agomir. qRT-PCR indicated that circNf1 can bind to CXCL12 promoter, the increased circNf1 can enhance CXCL12 mRNA in naïve rats, and inhibition of circNf1 can alleviate the upregulation of CXCL12 mRNA in morphine-treated rats. Behavioral tests revealed that inhibition of circNf1 and CXCL12 and the enhancement of miR-330-3p and miR-665 can alleviate morphine analgesic tolerance. CONCLUSIONS: Our study indicates a novel pathway that can contribute to morphine analgesic tolerance, the circRNA to cytokine pathway, in which circNf1 functions as a sponge for miR-330-3p and miR-665 and induces the upregulation of CXCL12 at both transcriptional and translational levels in morphine-treated rats.


Assuntos
MicroRNAs , Morfina , Ratos , Animais , Morfina/farmacologia , Hibridização in Situ Fluorescente , Medula Espinal , RNA Mensageiro , Quimiocina CXCL12 , MicroRNAs/genética
7.
Cell Commun Signal ; 21(1): 90, 2023 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-37131173

RESUMO

Organ fibrosis can occur in virtually all major organs with relentlessly progressive and irreversible progress, ultimately resulting in organ dysfunction and potentially death. Unfortunately, current clinical treatments cannot halt or reverse the progression of fibrosis to end-stage organ failure, and thus, advanced antifibrotic therapeutics are urgently needed. In recent years, a growing body of research has revealed that circular RNAs (circRNAs) play pivotal roles in the development and progression of organ fibrosis through highly diverse mechanisms of action. Thus, manipulating circRNAs has emerged as a promising strategy to mitigate fibrosis across different organ types. In this review, we systemically summarize the current state of knowledge about circRNA biological properties and the regulatory mechanisms of circRNAs. A comprehensive overview of major fibrotic signaling pathways and representative circRNAs that are known to modulate fibrotic signals are outlined. Then, we focus on the research progress of the versatile functional roles and underlying molecular mechanisms of circRNAs in various fibrotic diseases in different organs, including the heart, liver, lung, kidney and skin. Finally, we offer a glimpse into the prospects of circRNA-based interference and therapy, as well as their utilization as biomarkers in the diagnosis and prognosis of fibrotic diseases. Video abstract.


Assuntos
RNA Circular , RNA , Humanos , RNA Circular/genética , RNA/genética , RNA/metabolismo , Fibrose , Pele/metabolismo , Transdução de Sinais/genética
8.
Pharmacol Res ; 197: 106946, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37797661

RESUMO

Ocular neovascular disease (OND), characterized by the aberrant formation of immature blood vessels, is the leading cause of vision impairment and blindness. It is important to find effective ways to diagnose and treat these diseases. Circular RNA (circRNA) is a group of endogenous non-coding RNA that play a crucial role in regulating different biological processes. Due to their close association with ocular disease and angiogenesis, circRNAs have become a hotspot in OND research. In this review, we intensively investigate the possibility of using circRNAs in the management of ONDs. In general, angiogenesis is divided into five phases. On the basis of these five steps, we describe the potential of using circRNAs by introducing how they regulate angiogenesis. Subsequently, the interactions between circRNAs and ONDs, including pterygium, corneal neovascularization, age-related macular degeneration, diabetic retinopathy, and retinopathy of prematurity, are analyzed in detail. We also introduce the potential use of circRNAs as OND diagnostic biomarkers. Finally, we summarize the prospects of using circRNAs as a potential strategy in OND management. The gaps in recent research are also pointed out with the purpose of promoting the introduction of circRNAs into clinical applications.


Assuntos
Retinopatia Diabética , Degeneração Macular , Doenças Retinianas , Humanos , Recém-Nascido , RNA Circular/genética , Olho , Retinopatia Diabética/genética
9.
Cell Mol Life Sci ; 79(2): 75, 2022 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-35039944

RESUMO

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA-miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman's correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student's t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman's correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.


Assuntos
COVID-19/genética , COVID-19/metabolismo , RNA Circular/genética , RNA Viral , SARS-CoV-2/genética , Biologia Computacional , Regulação Viral da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Subunidades beta do Canal de Potássio Ativado por Cálcio de Condutância Alta/genética , MicroRNAs/genética , MicroRNAs/metabolismo , Nasofaringe/virologia , Proteínas do Tecido Nervoso/genética , Mapeamento de Interação de Proteínas , Proteína Quinase C-épsilon/genética , Reprodutibilidade dos Testes
10.
Biochem Genet ; 61(1): 279-298, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35857217

RESUMO

GSE137836 and GSE100186 shows that upregulated hsa_circRNA_0000798 (circ_0000798) is associated with the development and progression of renal cell carcinoma (RCC). However, its biological functions in RCC cells remain unclarified. Here, we planned to explore its action and action of mechanism in RCC cells. Real-time quantitative PCR detected RNA expression and western blotting and immunohistochemistry measured protein expression. In vitro assays, including MTT, EdU, Transwell, and plate colony, scratch wound, apoptosis, and cell cycle assays, and in vivo xenograft tumor model were launched to measure cell dysfunctions. Dual-luciferase reporter assay and RNA pull-down were employed to identify target relationship. Circ_0000798 is upregulated in RCC patients' tumors and cells, and high circ_0000798 is associated with shorter overall survival. RNA interference of circ_0000798 impedes cell metabolic viability and abilities of DNA synthesis, colony formation, wound healing, migration, and invasion in RCC cells but also induces cell cycle arrest and apoptosis. Moreover, circ_0000798 interference could delay tumor growth in vivo. Proliferation markers Ki67 and Bcl-2 were depressed by inhibiting circ_0000798, accompanied with promoted levels of apoptosis proteins Bax and cleaved caspase-3. Of note, circ_0000798 functions as microRNA (miR) sponge for miR-589-5p and thus controls the expression of miR-589-5p-targeting Ras-GTPase-activating protein-binding protein 1 (G3BP1), a newly identified tumor-promoting gene in RCC. Their expressions are linearly correlated with each other in these tumor samples. Circ_0000798 might function oncogenic role in RCC and its downregulation could combat RCC cell growth and motility via targeting miR-589-5p/G3BP1 axis.


Assuntos
Carcinoma de Células Renais , Neoplasias Renais , MicroRNAs , Humanos , MicroRNAs/genética , Carcinoma de Células Renais/genética , DNA Helicases , Proteínas de Ligação a Poli-ADP-Ribose , RNA Helicases , Proteínas com Motivo de Reconhecimento de RNA , Ciclo Celular , Proliferação de Células , Neoplasias Renais/genética , Linhagem Celular Tumoral
11.
Int J Mol Sci ; 24(18)2023 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-37762497

RESUMO

CircRNAs are a class of endogenous long non-coding RNAs with a single-stranded circular structure. Most circRNAs are relatively stable, highly conserved, and specifically expressed in tissue during the cell and developmental stages. Many circRNAs have been discovered in OSCC. OSCC is one of the most severe and frequent forms of head and neck cancer today, with a poor prognosis and low overall survival rate. Due to its prevalence, OSCC is a global health concern, characterized by genetic and epigenomic changes. However, the mechanism remains vague. With the advancement of biotechnology, a large number of circRNAs have been discovered in mammalian cells. CircRNAs are dysregulated in OSCC tissues and thus associated with the clinicopathological characteristics and prognosis of OSCC patients. Research studies have demonstrated that circRNAs can serve as biomarkers for OSCC diagnosis and treatment. Here, we summarized the properties, functions, and biogenesis of circRNAs, focusing on the progress of current research on circRNAs in OSCC.

12.
Int J Mol Sci ; 25(1)2023 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-38203348

RESUMO

Ischemic stroke is one of the most significant causes of morbidity and mortality worldwide. However, there is a dearth of effective drugs and treatment methods for ischemic stroke. Significant numbers of circular RNAs (circRNAs) exhibit abnormal expression following ischemic stroke and are considered potential therapeutic targets. CircRNAs have emerged as promising biomarkers due to their stable expression in peripheral blood and their potential significance in ischemic stroke diagnosis and prognosis. This review provides a summary of 31 circRNAs involved in the pathophysiological processes of apoptosis, autophagy, inflammation, oxidative stress, and angiogenesis following ischemic stroke. Furthermore, we discuss the mechanisms of action of said circRNAs and their potential clinical applications. Ultimately, circRNAs exhibit promise as both therapeutic targets and biomarkers for ischemic stroke.


Assuntos
AVC Isquêmico , RNA Circular , Humanos , RNA Circular/genética , AVC Isquêmico/diagnóstico , AVC Isquêmico/tratamento farmacológico , AVC Isquêmico/genética , Apoptose , Autofagia , Biomarcadores
13.
Yale J Biol Med ; 96(4): 495-509, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38161577

RESUMO

Colorectal cancer (CRC) has been recorded amongst the most common cancers in the world, with high morbidity and mortality rates, and relatively low survival rates. With risk factors such as chronic illness, age, and lifestyle associated with the development of CRC, the incidence of CRC is increasing each year. Thus, the discovery of novel biomarkers to improve the diagnosis and prognosis of CRC has become beneficial. Long non-coding RNAs (lncRNAs) have been emerging as potential players in several tumor types, one among them is the lncRNA H19. The paternally imprinted oncofetal gene is expressed in the embryo, downregulated at birth, and reappears in tumors. H19 aids in CRC cell growth, proliferation, invasion, and metastasis via various mechanisms of action, significantly through the lncRNA-microRNA (miRNA)-messenger RNA (mRNA)-competitive endogenous RNA (ceRNA) network, where H19 behaves as a miRNA sponge. The RNA transcript of H19 obtained from the first exon of the H19 gene, miRNA-675 also promotes CRC carcinogenesis. Overexpression of H19 in malignant tissues compared to adjacent non-malignant tissues marks H19 as an independent prognostic marker in CRC. Besides its prognostic value, H19 serves as a promising target for therapy in CRC treatment.


Assuntos
Neoplasias Colorretais , MicroRNAs , RNA Longo não Codificante , Humanos , Biomarcadores , Neoplasias Colorretais/genética , Regulação Neoplásica da Expressão Gênica/genética , MicroRNAs/genética , RNA Longo não Codificante/genética
14.
BMC Bioinformatics ; 23(1): 166, 2022 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-35524174

RESUMO

BACKGROUND: Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions. This methodology has aroused a broad acknowledgment within the scientific community thanks to the encouraging results achieved when applied to breast invasive carcinoma, leading to the identification of PVT1, a long non-coding RNA functioning as ceRNA for the miR-200 family. The main shortcoming of the model is that it is no freely available and implemented in MATLAB®, a proprietary programming platform requiring a paid license for installing, operating, manipulating, and running the software. RESULTS: Breaking through these model limitations demands to distribute it in an open-source, freely accessible environment, such as R, designed for an ordinary audience of users that are not able to afford a proprietary solution. Here, we present SPINNAKER (SPongeINteractionNetworkmAKER), the open-source version of our widely established mathematical model for predicting ceRNAs crosstalk, that is released as an exhaustive collection of R functions. SPINNAKER has been even designed for providing many additional features that facilitate its usability, make it more efficient in terms of further implementation and extension, and less intense in terms of computational execution time. CONCLUSIONS: SPINNAKER source code is freely available at https://github.com/sportingCode/SPINNAKER.git together with a thoroughgoing PPT-based guideline. In order to help users get the key points more conveniently, also a practical R-styled plain-text guideline is provided. Finally, a short movie is available to help the user to set the own directory, properly.


Assuntos
Neoplasias da Mama , MicroRNAs , Modelos Teóricos , RNA Longo não Codificante , Neoplasias da Mama/genética , Feminino , Redes Reguladoras de Genes , Humanos , MicroRNAs/genética , RNA Longo não Codificante/genética , RNA Mensageiro/genética , Software
15.
J Transl Med ; 20(1): 533, 2022 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-36401311

RESUMO

Circular ribonucleic acids (circRNAs) are a class of long non-coding RNA that were once regarded as non-functional transcription byproducts. However, recent studies suggested that circRNAs may exhibit important regulatory roles in many critical biological pathways and disease pathologies. These studies have identified significantly differential expression profiles of circRNAs upon changes in physiological and pathological conditions of eukaryotic cells. Importantly, a substantial number of studies have suggested that circRNAs may play critical roles in organ injuries. This review aims to provide a summary of recent studies on circRNAs in organ injuries with respect to (1) changes in circRNAs expression patterns, (2) main mechanism axi(e)s, (3) therapeutic implications and (4) future study prospective. With the increasing attention to this research area and the advancement in high-throughput nucleic acid sequencing techniques, our knowledge of circRNAs may bring fruitful outcomes from basic and clinical research.


Assuntos
RNA Circular , RNA , RNA Circular/genética , Estudos Prospectivos , RNA/genética , RNA/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala
16.
Cancer Cell Int ; 22(1): 141, 2022 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-35361205

RESUMO

Circular RNA (circRNA), a new type of endogenous non-coding RNA, is abundantly present in eukaryotic cells, and characterized as stable high conservation and tissue specific expression. It has been generated increasing attention because of their close association with the progress of diseases. The liver is the vital organ of humans, while it is prone to acute and chronic diseases due to the influence of multiple pathogenic factors. Moreover, hepatocellular carcinoma (HCC) is the one of most common cancer and the leading cause of cancer death worldwide. Overwhelming evidences indicate that some circRNAs are differentially expressed in liver diseases, such as, HCC, chronic hepatitis B, hepatic steatosis and hepatoblastoma tissues, etc. Additionally, these circRNAs are related to proliferation, invasion, migration, angiogenesis, apoptosis, and metastasis of cell in liver diseases and act as oncogenic agents or suppressors, and linked to clinical manifestations. In this review, we briefly summarize the biogenesis, characterization and biological functions, recent detection and identification technologies of circRNA, and regulation network mechanism of circRNA in liver diseases, and discuss their potential values as biomarkers or therapeutic targets for liver diseases, especially on HCC.

17.
Int J Mol Sci ; 23(22)2022 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-36430607

RESUMO

In recent years, interest in non-coding RNAs as important physiological regulators has grown significantly. Their participation in the pathophysiology of cardiovascular diseases is extremely important. Circular RNA (circRNA) has been shown to be important in the development of heart failure. CircRNA is a closed circular structure of non-coding RNA fragments. They are formed in the nucleus, from where they are transported to the cytoplasm in a still unclear mechanism. They are mainly located in the cytoplasm or contained in exosomes. CircRNA expression varies according to the type of tissue. In the brain, almost 12% of genes produce circRNA, while in the heart it is only 9%. Recent studies indicate a key role of circRNA in cardiomyocyte hypertrophy, fibrosis, autophagy and apoptosis. CircRNAs act mainly by interacting with miRNAs through a "sponge effect" mechanism. The involvement of circRNA in the development of heart failure leads to the suggestion that they may be promising biomarkers and useful targets in the treatment of cardiovascular diseases. In this review, we will provide a brief introduction to circRNA and up-to-date understanding of their role in the mechanisms leading to the development of heart failure.


Assuntos
Insuficiência Cardíaca , RNA Circular , Humanos , Doenças Cardiovasculares/genética , Fibrose/genética , Insuficiência Cardíaca/genética , Insuficiência Cardíaca/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , RNA Circular/genética , RNA Circular/metabolismo
18.
Zhonghua Nan Ke Xue ; 28(7): 649-655, 2022 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-37556225

RESUMO

Prostate cancer (PCa) has become one of the most common malignancies in men, and its incidence is increasing year by year in China. When PCa develops into castration-resistant PCa (CRPC), it deteriorates rapidly. So, it is important to find more sensitive molecular markers and effective therapeutic targets for the diagnosis and treatment of the malignancy. Circular RNA (circRNA) is a covalently closed loop non-coding RNA formed by reverse splicing, playing an important regulatory role in a variety of tumors. In recent years, many studies show that circRNA is involved in the regulation of PCa as miRNA sponge, binding with the RNA binding protein and other molecular sponges, and may be a potential molecular marker and therapeutic target for PCa. This review summarizes the advances in recent studies of circRNA in the development and progression of PCa, CRPC, and radiation-resistant PCa.


Assuntos
MicroRNAs , Neoplasias de Próstata Resistentes à Castração , Masculino , Humanos , RNA Circular , Neoplasias de Próstata Resistentes à Castração/tratamento farmacológico , MicroRNAs/genética , China
19.
IUBMB Life ; 73(2): 408-417, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33372396

RESUMO

Hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC), whether circular RNA (circRNA) is involved in this process remains unknown. In this study, we performed circRNA microarray profile and found an HBV-related circRNA, circ-ARL3 (hsa_circ_0092493). Stable knockdown of circ-ARL3 inhibited the proliferation and invasion of HBV+ HCC cells. High circ-ARL3 was positively correlated with malignant clinical features and poor prognosis. In terms of mechanism, HBx protein upregulated N6 -methyladenosine (m6 A) methyltransferases METTL3 expression, increasing the m6 A modification of circ-ARL3; then, m6 A reader YTHDC1 bound to m6 A-modified of circ-ARL3 and favored its reverse splicing and biogenesis. Furthermore, circ-ARL3 was able to sponge miR-1305, antagonizing the inhibitory effects of miR-1305 on a cohort of target oncogenes, thereby promoting HBV+ HCC progression. Importantly, depletion of circ-ARL3 significantly retarded HBV+ HCC cell growth in vivo, whereas this effect was evidently blocked after silencing of miR-1305. Collectively, our data suggest that circ-ARL3 is a critical regulator in HBV-related HCC, targeting the axis of circ-ARL3/miR-1305 may be a promising treatment for HBV+ HCC patients.


Assuntos
Fatores de Ribosilação do ADP/genética , Adenosina/análogos & derivados , Carcinoma Hepatocelular/patologia , Regulação Neoplásica da Expressão Gênica , Hepatite B/complicações , MicroRNAs/genética , RNA Circular/química , Adenosina/química , Animais , Apoptose , Biomarcadores Tumorais/genética , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/virologia , Proliferação de Células , Feminino , Hepatite B/virologia , Vírus da Hepatite B/isolamento & purificação , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/patologia , Neoplasias Hepáticas/virologia , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Pessoa de Meia-Idade , Prognóstico , RNA Circular/genética , Taxa de Sobrevida , Células Tumorais Cultivadas , Ensaios Antitumorais Modelo de Xenoenxerto
20.
Cancer Cell Int ; 21(1): 11, 2021 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-33407501

RESUMO

Noncoding RNAs, including long noncoding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs), are involved in regulating biological functions. In recent decades, miRNAs and lncRNAs have both inspired a wave of research, but the study of circRNA functions is still in its infancy. Studies have found that circRNAs actively participate in the occurrence and development of various diseases, which emphasizes the importance of circRNAs. Here, we review the features and classification of circRNAs and summarize their functions. Then, we briefly describe how to analyze circRNAs by bioinformatics procedures. In addition, the relationship between circRNAs and cancers is discussed with an emphasis on proving whether circRNAs can be potential biomarkers for the prognosis and diagnosis of cancer.

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