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Liao Y, Qiu X, Liu J, Zhang Z, Liu B, Jin C. The role of m6A-modified CircEPHB4 in glioma pathogenesis: Insights into cancer stemness metastasis. Ann Clin Transl Neurol 2023; 10:1749-1767. [PMID: 37614011 PMCID: PMC10578901 DOI: 10.1002/acn3.51864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023] Open
Abstract
OBJECTIVE While existing literature has provided insights into involvement of circEPHB4, SOX2 in glioma, their precise molecular mechanisms and synergistic implications in glioma pathogenesis still dim. This study aims to investigate significance and underlying mechanism of m6A-modified circEPHB4 in regulating SOX2/PHLDB2 axis in gliomas. METHODS The mRNA and protein expression were tested by qRT-PCR and Western blot, respectively. ChIP assay was performed to detect SOX2 enrichment on the PHLDB2 promoter. Cell sphere-forming assay to detect self-renewal ability, flow cytometry to determine positivity of CD133 expressions, Malignant behavior of glioma cells were detected by CCK-8, plate colony formation, scratch, and transwell assays. Glioma xenograft models were constructed to investigate effects of CircEPHB4 in tumor development in vivo. RESULTS Methyltransferase MELLT3 upregulated m6A modification of CircEPHB4, and YTHDC1 promoted cytoplasmic localization of m6A-modified CircEPHB4. Overexpression of wild-type CircEPHB4 enhanced glioma cells' stemness, metastasis, and proliferation. Cytoplasmic CircEPHB4 increased SOX2 mRNA stability by binding to IGF2BP2, and the effects observed by SOX2 knockdown were reversed by CircEPHB4 in glioma cells. SOX2 promoted transcriptional expression of PHLDB2 by enriching the PHLDB2 promoter region. SOX2 reversed the inhibition of PHLDB2 knockdown on stemness of glioma, cell proliferation, and metastasis. In vivo experiments also revealed that CircEPHB4 upregulated PHLDB2 expression by stabilizing SOX2 mRNA, which promoted in vivo tumor growth and accelerated stemness of glioma cells and metastasis. CONCLUSION This study reveals functional interaction and molecular mechanisms of m6A-modified circEPHB4 in regulating SOX2/PHLDB2 axis, highlighting their importance in glioma pathogenesis and potential as therapeutic targets.
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Affiliation(s)
- Yuxiang Liao
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Xiaohui Qiu
- Department of Plastic Surgery, The Third Xiangya HospitalCentral South UniversityChangsha410013HunanP.R. China
| | - Jingping Liu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Zhiping Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Bo Liu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Chen Jin
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
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Levacher C, Viennot M, Drouet A, Beaussire L, Coutant S, Théry JC, Baert-Desurmont S, Laé M, Ruminy P, Houdayer C. Disequilibrium between BRCA1 and BRCA2 Circular and Messenger RNAs Plays a Role in Breast Cancer. Cancers (Basel) 2023; 15:cancers15072176. [PMID: 37046838 PMCID: PMC10093293 DOI: 10.3390/cancers15072176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Breast cancer is a frequent disease for which the discovery of markers that enable early detection or prognostic assessment remains challenging. Circular RNAs (circRNAs) are single-stranded structures in closed loops that are produced by backsplicing. CircRNA and messenger RNA (mRNA) are generated co-transcriptionally, and backsplicing and linear splicing compete against each other. As mRNAs are key players in tumorigenesis, we hypothesize that a disruption of the balance between circRNAs and mRNAs could promote breast cancer. Hence, we developed an assay for a simultaneous study of circRNAs and mRNAs, which we have called splice and expression analyses by exon ligation and high-throughput sequencing (SEALigHTS). Following SEALigHTS validation for BRCA1 and BRCA2, our hypothesis was tested using an independent research set of 95 pairs from tumor and adjacent normal breast tissues. In this research set, ratios of BRCA1 and BRCA2 circRNAs/mRNAs were significantly lower in the tumor breast tissue compared to normal tissue (p = 1.6 × 10-9 and p = 4.4 × 10-5 for BRCA1 and BRCA2, respectively). Overall, we developed an innovative method to study linear splicing and backsplicing, described the repertoire of BRCA1 and BRCA2 circRNAs, including 15 novel ones, and showed for the first time that a disequilibrium between BRCA1 and BRCA2 circRNAs and mRNAs plays a role in breast cancer.
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Affiliation(s)
- Corentin Levacher
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
| | - Mathieu Viennot
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France
| | - Aurélie Drouet
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
| | - Ludivine Beaussire
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
- Department of Pathology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038 Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
| | - Jean-Christophe Théry
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038 Rouen, France
| | - Stéphanie Baert-Desurmont
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, Department of Genetics, 76000 Rouen, France
| | - Marick Laé
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France
- Department of Pathology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038 Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France
| | - Claude Houdayer
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, Department of Genetics, 76000 Rouen, France
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Zhang Q, Song X, Song X. Contents in tumor-educated platelets as the novel biosource for cancer diagnostics. Front Oncol 2023; 13:1165600. [PMID: 37139159 PMCID: PMC10151018 DOI: 10.3389/fonc.2023.1165600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Liquid biopsy, a powerful non-invasive test, has been widely used in cancer diagnosis and treatment. Platelets, the second most abundant cells in peripheral blood, are becoming one of the richest sources of liquid biopsy with the capacity to systematically and locally respond to the presence of cancer and absorb and store circulating proteins and different types of nucleic acids, thus called "tumor-educated platelets (TEPs)". The contents of TEPs are significantly and specifically altered, empowering them with the potential as cancer biomarkers. The current review focuses on the alternation of TEP content, including coding and non-coding RNA and proteins, and their role in cancer diagnostics.
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Affiliation(s)
- Qianru Zhang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- *Correspondence: Xingguo Song,
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4
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Gianni C, Palleschi M, Merloni F, Bleve S, Casadei C, Sirico M, Di Menna G, Sarti S, Cecconetto L, Mariotti M, De Giorgi U. Potential Impact of Preoperative Circulating Biomarkers on Individual Escalating/de-Escalating Strategies in Early Breast Cancer. Cancers (Basel) 2022; 15:96. [PMID: 36612091 PMCID: PMC9817806 DOI: 10.3390/cancers15010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The research on non-invasive circulating biomarkers to guide clinical decision is in wide expansion, including the earliest disease settings. Several new intensification/de-intensification strategies are approaching clinical practice, personalizing the treatment for each patient. Moreover, liquid biopsy is revealing its potential with multiple techniques and studies available on circulating biomarkers in the preoperative phase. Inflammatory circulating cells, circulating tumor cells (CTCs), cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), and other biological biomarkers are improving the armamentarium for treatment selection. Defining the escalation and de-escalation of treatments is a mainstay of personalized medicine in early breast cancer. In this review, we delineate the studies investigating the possible application of these non-invasive tools to give a more enlightened approach to escalating/de-escalating strategies in early breast cancer.
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Affiliation(s)
- Caterina Gianni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
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De Palma FDE, Carbonnier V, Salvatore F, Kroemer G, Pol JG, Maiuri MC. Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers. Cancers (Basel) 2022; 14:cancers14235980. [PMID: 36497462 PMCID: PMC9738797 DOI: 10.3390/cancers14235980] [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: 09/27/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Long non-coding RNAs may constitute epigenetic biomarkers for the diagnosis, prognosis, and therapeutic response of a variety of tumors. In this context, we aimed at assessing the diagnostic and prognostic value of the recently described long intergenic non-coding RNA 01087 (LINC01087) in human cancers. (2) Methods: We studied the expression of LINC01087 across 30 oncological indications by interrogating public resources. Data extracted from the TCGA and GTEx databases were exploited to plot receiver operating characteristic curves (ROC) and determine the diagnostic performance of LINC01087. Survival data from TCGA and KM-Plotter directories allowed us to graph Kaplan-Meier curves and evaluate the prognostic value of LINC01087. To investigate the function of LINC01087, gene ontology (GO) annotation and Kyoto Encyclopedia of Gene and Genomes (KEGG) enrichment analyses were performed. Furthermore, interactions between LINC01087 and both miRNA and mRNA were studied by means of bioinformatics tools. (3) Results: LINC01087 was significantly deregulated in 7 out of 30 cancers, showing a predominant upregulation. Notably, it was overexpressed in breast (BC), esophageal (ESCA), and ovarian (OV) cancers, as well as lung squamous cell carcinoma (LUSC), stomach adenocarcinoma (STAD), and uterine carcinosarcoma (UCS). By contrast, LINC01087 displayed downregulation in testicular germ cell tumors (TGCT). ROC curve analyses identified LINC01087 as a potential diagnostic indicator in BC, ESCA, OV, STAD, and TGCT. Moreover, high and low expression of LINC01087 predicted a favorable prognosis in BC and papillary cell carcinoma, respectively. In silico analyses indicated that deregulation of LINC01087 in cancer was associated with a modulation of genes related to ion channel, transporter, and peptide receptor activity. (4) Conclusions: the quantification of an altered abundance of LINC01087 in tissue specimens might be clinically useful for the diagnosis and prognosis of some hormone-related tumors, including BC, OV, and TGCT, as well as other cancer types such as ESCA and STAD. Moreover, our study revealed the potential of LINC01087 (and perhaps other lncRNAs) to regulate neuroactive molecules in cancer.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Napoli, Italy
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Vincent Carbonnier
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Napoli, Italy
- Centro Interuniversitario per Malattie Multigeniche e Multifattoriali e Loro Modelli Animali (Federico II, 80131, Napoli, Tor Vergata, Rome and “G. D’Annunzio”, Chieti-Pescara), 80131 Napoli, Italy
| | - Guido Kroemer
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, 75004 Paris, France
| | - Jonathan G. Pol
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Correspondence: (J.G.P.); (M.C.M.)
| | - Maria Chiara Maiuri
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, 80131 Napoli, Italy
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Correspondence: (J.G.P.); (M.C.M.)
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6
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Niu ZS, Wang WH. Circular RNAs in hepatocellular carcinoma: Recent advances. World J Gastrointest Oncol 2022; 14:1067-1085. [PMID: 35949213 PMCID: PMC9244981 DOI: 10.4251/wjgo.v14.i6.1067] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/22/2021] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) have covalently closed loop structures at both ends, exhibiting characteristics dissimilar to those of linear RNAs. Emerging evidence suggests that aberrantly expressed circRNAs play crucial roles in hepatocellular carcinoma (HCC) by affecting the proliferation, apoptosis and invasive capacity of HCC cells. Certain circRNAs may be used as biomarkers to diagnose and predict the prognosis of HCC. Therefore, circRNAs are expected to become novel biomarkers and therapeutic targets for HCC. Herein, we briefly review the characteristics and biological functions of circRNAs, focusing on their roles in HCC to provide new insights for the early diagnosis and targeted therapy of HCC.
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Affiliation(s)
- Zhao-Shan Niu
- Laboratory of Micromorphology, School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Wen-Hong Wang
- Department of Pathology, School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong Province, China
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Guria A, Sharma P, Srikakulam N, Baby A, Natesan S, Pandi G. Cost-Effective Transcriptome-Wide Profiling of Circular RNAs by the Improved-tdMDA-NGS Method. Front Mol Biosci 2022; 9:886366. [PMID: 35647023 PMCID: PMC9136142 DOI: 10.3389/fmolb.2022.886366] [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: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Covalently closed circular RNAs are neoteric to the eukaryotic family of long non-coding RNAs emerging as a result of 5′–3′ backsplicing from exonic, intronic, or intergenic regions spanning the parental gene. Owing to their unique structure and stability, circular RNAs have a multitude of functional properties such as micro-RNA and protein sponges, direct and indirect modulators of gene expression, protein translation, and many unproven activities apart from being potential biomarkers. However, due to their low abundance, most of the global circular RNA identification is carried out by high-throughput NGS-based approaches requiring millions of sequencing reads. This lag in methodological advancements demands for newer, more refined, and efficient identification techniques. Here, we aim to show an improved version of our previously reported template-dependent multiple displacement amplification (tdMDA)-NGS method by superimposing the ribosomal depletion step and use of H minus reverse transcriptase and RNase H. Implication of tdMDA using highly replicative Phi29 DNA polymerase after minimizing the linear and ribosomal RNA content further intensifies its detection limit toward even the abysmally expressing circular RNA at a low NGS depth, thereby decreasing the cost of identifying a single circular RNA. A >11-fold and >6-fold increase in total circular RNA was identified from the improved-tdMDA-NGS method over the traditional method of circRNA sequencing using DCC and CIRI2 pipelines, respectively, from Oryza sativa subsp. Indica. Furthermore, the reliability of the improved-tdMDA-NGS method was also asserted in HeLa cell lines, showing a significant fold difference in comparison with the existing traditional method of circRNA sequencing. Among the identified circular RNAs, a significant percentage from both rice (∼58%) and HeLa cell lines (∼84%) is found to be matched with the previously reported circular RNAs, suggesting that the improved-tdMDA-NGS method can be adapted to detect and characterize the circular RNAs from different biological systems.
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Affiliation(s)
- Ashirbad Guria
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Priyanka Sharma
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Nagesh Srikakulam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Akhil Baby
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Sankar Natesan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
- *Correspondence: Gopal Pandi,
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Morovat P, Morovat S, Ashrafi AM, Teimourian S. Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis. Sci Rep 2022; 12:4933. [PMID: 35322101 PMCID: PMC8943026 DOI: 10.1038/s41598-022-08867-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent cancers worldwide, which has a high mortality rate and poor treatment outcomes with yet unknown molecular basis. It seems that gene expression plays a pivotal role in the pathogenesis of the disease. Circular RNAs (circRNAs) can interact with microRNAs (miRNAs) to regulate gene expression in various malignancies by acting as competitive endogenous RNAs (ceRNAs). However, the potential pathogenesis roles of the ceRNA network among circRNA/miRNA/mRNA in HCC are unclear. In this study, first, the HCC circRNA expression data were obtained from three Gene Expression Omnibus microarray datasets (GSE164803, GSE94508, GSE97332), and the differentially expressed circRNAs (DECs) were identified using R limma package. Also, the liver hepatocellular carcinoma (LIHC) miRNA and mRNA sequence data were retrieved from TCGA and differentially expressed miRNAs (DEMIs) and mRNAs (DEGs) were determined using the R DESeq2 package. Second, CSCD website was used to uncover the binding sites of miRNAs on DECs. The DECs' potential target miRNAs were revealed by conducting an intersection between predicted miRNAs from CSCD and downregulated DEMIs. Third, candidate genes were uncovered by intersecting targeted genes predicted by miRWalk and targetscan online tools with upregulated DEGs. The ceRNA network was then built using the Cytoscape software. The functional enrichment and the overall survival time of these potential targeted genes were analyzed, and a PPI network was constructed in the STRING database. Network visualization was performed by Cytoscape, and ten hub genes were detected using the CytoHubba plugin tool. Four DECs (hsa_circ_0000520, hsa_circ_0008616, hsa_circ_0070934, hsa_circ_0004315) were obtained and six miRNAs (hsa-miR-542-5p, hsa-miR-326, hsa-miR-511-5p, hsa-miR-195-5p, hsa-miR-214-3p, and hsa-miR-424-5p) which are regulated by the above DECs were identified. Then 543 overlapped genes regulated by six miRNAs mentioned above were predicted. Functional enrichment analysis showed that these genes are mostly associated with regulatory pathways in cancer. Ten hub genes (TTK, AURKB, KIF20A, KIF23, CEP55, CDC6, DTL, NCAPG, CENPF, PLK4) have been screened from the PPI network of the 204 survival-related genes. KIF20A, NCAPG, TTK, PLK4, and CDC6 were selected for the highest significance p-values. At the end, a circRNA-miRNA-mRNA regulatory axis was established for five final selected hub genes. This study implies the potential pathogenesis of the obtained network and proposes that the two DECs (has_circ_0070934 and has_circ_0004315) may be important prognostic markers for HCC.
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Affiliation(s)
- Pejman Morovat
- Department of Medical Biotechnology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Science, Babol, Iran
| | - Saman Morovat
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Arash M Ashrafi
- Neuroscience Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Shahram Teimourian
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.
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De Palma FDE, Salvatore F, Pol JG, Kroemer G, Maiuri MC. Circular RNAs as Potential Biomarkers in Breast Cancer. Biomedicines 2022; 10:biomedicines10030725. [PMID: 35327527 PMCID: PMC8945016 DOI: 10.3390/biomedicines10030725] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Due to the high heterogeneity and initially asymptomatic nature of breast cancer (BC), the management of this disease depends on imaging together with immunohistochemical and molecular evaluations. These tests allow early detection of BC and patient stratification as they guide clinicians in prognostication and treatment decision-making. Circular RNAs (circRNAs) represent a class of newly identified long non-coding RNAs. These molecules have been described as key regulators of breast carcinogenesis and progression. Moreover, circRNAs play a role in drug resistance and are associated with clinicopathological features in BC. Accumulating evidence reveals a clinical interest in deregulated circRNAs as diagnostic, prognostic and predictive biomarkers. Furthermore, due to their covalently closed structure, circRNAs are highly stable and easily detectable in body fluids, making them ideal candidates for use as non-invasive biomarkers. Herein, we provide an overview of the biogenesis and pleiotropic functions of circRNAs, and report on their clinical relevance in BC.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy;
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
- Correspondence: (F.D.E.D.P.); (M.C.M.); Tel.: +39-3348176281 (F.D.E.D.P.)
| | - Francesco Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy;
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
- Inter-University Center for multifactorial and multi genetic chronic human diseases, “Federico II”-Naples, Tor Vergata-Roma II, and Chieti-Pescara Universities, 80131 Naples, Italy
| | - Jonathan G. Pol
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Guido Kroemer
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Maria Chiara Maiuri
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy
- Correspondence: (F.D.E.D.P.); (M.C.M.); Tel.: +39-3348176281 (F.D.E.D.P.)
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Afzal S, Hassan M, Ullah S, Abbas H, Tawakkal F, Khan MA. Breast Cancer; Discovery of Novel Diagnostic Biomarkers, Drug Resistance, and Therapeutic Implications. Front Mol Biosci 2022; 9:783450. [PMID: 35265667 PMCID: PMC8899313 DOI: 10.3389/fmolb.2022.783450] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the second most reported cancer in women with high mortality causing millions of cancer-related deaths annually. Early detection of breast cancer intensifies the struggle towards discovering, developing, and optimizing diagnostic biomarkers that can improve its prognosis and therapeutic outcomes. Breast cancer-associated biomarkers comprise macromolecules, such as nucleic acid (DNA/RNA), proteins, and intact cells. Advancements in molecular technologies have identified all types of biomarkers that are exclusively studied for diagnostic, prognostic, drug resistance, and therapeutic implications. Identifying biomarkers may solve the problem of drug resistance which is a challenging obstacle in breast cancer treatment. Dysregulation of non-coding RNAs including circular RNAs (circRNAs) and microRNAs (miRNAs) initiates and progresses breast cancer. The circulating multiple miRNA profiles promise better diagnostic and prognostic performance and sensitivity than individual miRNAs. The high stability and existence of circRNAs in body fluids make them a promising new diagnostic biomarker. Many therapeutic-based novels targeting agents have been identified, including ESR1 mutation (DNA mutations), Oligonucleotide analogs and antagonists (miRNA), poly (ADP-ribose) polymerase (PARP) in BRCA mutations, CDK4/6 (cell cycle regulating factor initiates tumor progression), Androgen receptor (a steroid hormone receptor), that have entered clinical validation procedure. In this review, we summarize the role of novel breast cancer diagnostic biomarkers, drug resistance, and therapeutic implications for breast cancer.
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Affiliation(s)
- Samia Afzal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- *Correspondence: Samia Afzal,
| | - Muhammad Hassan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Safi Ullah
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Hazrat Abbas
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Farah Tawakkal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mohsin Ahmad Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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11
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Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, Plavec J, Egli M, Manoharan M, Zlatev I. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Res 2021; 49:10250-10264. [PMID: 34508350 PMCID: PMC8501968 DOI: 10.1093/nar/gkab724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
In order to achieve efficient therapeutic post-transcriptional gene-silencing mediated by the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be chemically modified. Several supra-RNA structures, with the potential to stabilize siRNAs metabolically have been evaluated for their ability to induce gene silencing, but all have limitations or have not been explored in therapeutically relevant contexts. Covalently closed circular RNA transcripts are prevalent in eukaryotes and have potential as biomarkers and disease targets, and circular RNA mimics are being explored for use as therapies. Here we report the synthesis and evaluation of small circular interfering RNAs (sciRNAs). To synthesize sciRNAs, a sense strand functionalized with the trivalent N-acetylgalactosamine (GalNAc) ligand and cyclized using ‘click’ chemistry was annealed to an antisense strand. This strategy was used for synthesis of small circles, but could also be used for synthesis of larger circular RNA mimics. We evaluated various sciRNA designs in vitro and in vivo. We observed improved metabolic stability of the sense strand upon circularization and off-target effects were eliminated. The 5′-(E)-vinylphosphonate modification of the antisense strand resulted in GalNAc-sciRNAs that are potent in vivo at therapeutically relevant doses. Physicochemical studies and NMR-based structural analysis, together with molecular modeling studies, shed light on the interactions of this novel class of siRNAs, which have a partial duplex character, with the RNAi machinery.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Peter Podbevsek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Krishna Aluri
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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12
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D’Ambrosi S, Visser A, Antunes-Ferreira M, Poutsma A, Giannoukakos S, Sol N, Sabrkhany S, Bahce I, Kuijpers MJE, Oude Egbrink MGA, Griffioen AW, Best MG, Koppers-Lalic D, Oudejans C, Würdinger T. The Analysis of Platelet-Derived circRNA Repertoire as Potential Diagnostic Biomarker for Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:4644. [PMID: 34572871 PMCID: PMC8468408 DOI: 10.3390/cancers13184644] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor-educated Platelets (TEPs) have emerged as rich biosources of cancer-related RNA profiles in liquid biopsies applicable for cancer detection. Although human blood platelets have been found to be enriched in circular RNA (circRNA), no studies have investigated the potential of circRNA as platelet-derived biomarkers for cancer. In this proof-of-concept study, we examine whether the circRNA signature of blood platelets can be used as a liquid biopsy biomarker for the detection of non-small cell lung cancer (NSCLC). We analyzed the total RNA, extracted from the platelet samples collected from NSCLC patients and asymptomatic individuals, using RNA sequencing (RNA-Seq). Identification and quantification of known and novel circRNAs were performed using the accurate CircRNA finder suite (ACFS), followed by the differential transcript expression analysis using a modified version of our thromboSeq software. Out of 4732 detected circRNAs, we identified 411 circRNAs that are significantly (p-value < 0.05) differentially expressed between asymptomatic individuals and NSCLC patients. Using the false discovery rate (FDR) of 0.05 as cutoff, we selected the nuclear receptor-interacting protein 1 (NRIP1) circRNA (circNRIP1) as a potential biomarker candidate for further validation by reverse transcription-quantitative PCR (RT-qPCR). This analysis was performed on an independent cohort of platelet samples. The RT-qPCR results confirmed the RNA-Seq data analysis, with significant downregulation of circNRIP1 in platelets derived from NSCLC patients. Our findings suggest that circRNAs found in blood platelets may hold diagnostic biomarkers potential for the detection of NSCLC using liquid biopsies.
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Affiliation(s)
- Silvia D’Ambrosi
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (S.D.); (M.A.-F.); (M.G.B.); (D.K.-L.)
| | - Allerdien Visser
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (A.V.); (A.P.); (C.O.)
| | - Mafalda Antunes-Ferreira
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (S.D.); (M.A.-F.); (M.G.B.); (D.K.-L.)
| | - Ankie Poutsma
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (A.V.); (A.P.); (C.O.)
| | - Stavros Giannoukakos
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain;
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, 18100 Granada, Spain
| | - Nik Sol
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Siamack Sabrkhany
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, 6229 ER Maastricht, The Netherlands; (S.S.); (M.G.A.O.E.)
| | - Idris Bahce
- Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Marijke J. E. Kuijpers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Mirjam G. A. Oude Egbrink
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, 6229 ER Maastricht, The Netherlands; (S.S.); (M.G.A.O.E.)
| | - Arjan W. Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Myron G. Best
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (S.D.); (M.A.-F.); (M.G.B.); (D.K.-L.)
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Danijela Koppers-Lalic
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (S.D.); (M.A.-F.); (M.G.B.); (D.K.-L.)
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Cees Oudejans
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (A.V.); (A.P.); (C.O.)
| | - Thomas Würdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (S.D.); (M.A.-F.); (M.G.B.); (D.K.-L.)
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
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