1
|
Li Z, Zhao Z, Zhang G, Liu Y, Zheng S. LncRNA MEG3 inhibits the proliferation and migration abilities of colorectal cancer cells by competitively suppressing MiR-31 and reducing the binding of MiR-31 to target gene SFRP1. Aging (Albany NY) 2023; 16:2061-2076. [PMID: 38309281 PMCID: PMC10911365 DOI: 10.18632/aging.205274] [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: 04/12/2023] [Accepted: 10/04/2023] [Indexed: 02/05/2024]
Abstract
To explore the potential mechanism of long-chain non-coding ribonucleic acid (lncRNA) maternal expression gene 3 (MEG3) in colorectal cancer (CRC). The relationship between MEG3 and miR-31 was detected by dual-luciferase assay. Quantitative polymerase chain reaction was utilized to determine the expression of MEG3 in CRC cell lines. Cell Counting Kit-8 assay was performed to detect cell proliferation. Transwell, cell scratch wound assay, and monoclonal proliferation assay were used to detect the proliferation, migration, and invasion of cells. In addition, cell motility was evaluated by detecting the expression of cellular pseudopodia protein α-actinin via immunofluorescence assay, and cell proliferation and motility were judged by determining the expressions of Ki-67, MMP2 and MMP9 via Western blotting. The effect of MEG3 and miR-31 on the development of colorectal cancer was verified by nude mouse tumor-bearing assay and HE staining. Transient transfection with MEG3 overexpression plasmid revealed that MEG3 inhibited the proliferation and motility of cells. The results of dual-luciferase assay showed that MEG3 could specifically inhibit the expression of miR-31, which inhibits the development of colorectal cancer. Transwell, cell scratch wound assay, and monoclonal proliferation experiment showed that miR-31 enhanced cell proliferation, migration and invasion. MEG3 overexpression plasmid was capable of reversing the proliferation and motility of CRC cells enhanced by miR-31. MEG3 can inhibit the proliferation and motility of CRC cells by competitively suppressing the binding of miR-31 to the target gene SFRP1, thus playing an inhibitory role in the pathogenesis of CRC.
Collapse
Affiliation(s)
- Zheli Li
- Department of Gastroenterology, Dingzhou City People’s Hospital, Baoding, China
| | - Zhi Zhao
- Department of Gastroenterology, Dingzhou City People’s Hospital, Baoding, China
| | - Gang Zhang
- Department of Gastroenterology, Dingzhou City People’s Hospital, Baoding, China
| | - Yufeng Liu
- Department of Gastroenterology, Dingzhou City People’s Hospital, Baoding, China
| | - Shaohua Zheng
- Department of Gastroenterology, Dingzhou City People’s Hospital, Baoding, China
| |
Collapse
|
2
|
Barbagallo C, Stella M, Ferrara C, Caponnetto A, Battaglia R, Barbagallo D, Di Pietro C, Ragusa M. RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases. EXPLORATION OF MEDICINE 2023:504-540. [DOI: 10.37349/emed.2023.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Angela Caponnetto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| |
Collapse
|
3
|
Khalafiyan A, Emadi-Baygi M, Wolfien M, Salehzadeh-Yazdi A, Nikpour P. Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer. J Cell Biochem 2023; 124:396-408. [PMID: 36748954 DOI: 10.1002/jcb.30373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Altered expression and functional roles of the transcribed ultraconserved regions (T-UCRs), as genomic sequences with 100% conservation between the genomes of human, mouse, and rat, in the pathophysiology of neoplasms has already been investigated. Nevertheless, the relevance of the functions for T-UCRs in gastric cancer (GC) is still the subject of inquiry. In the current study, we first used a genome-wide profiling approach to analyze the expression of T-UCRs in GC patients. Then, we constructed a three-component regulatory network and investigated potential diagnostic and prognostic values of the T-UCRs. The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset was used as a resource for the RNA-sequencing data. FeatureCounts was utilized to quantify the number of reads mapped to each T-UCR. Differential expression analysis was then conducted using DESeq2. In the following, interactions between T-UCRs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were combined into a three-component network. Enrichment analyses were performed and a protein-protein interaction (PPI) network was constructed. The R Survival package was utilized to identify survival-related significantly differentially expressed T-UCRs (DET-UCRs). Using an in-house cohort of GC tissues, expression of two DET-UCRs was furthermore experimentally verified. Our results showed that several T-UCRs were dysregulated in TCGA-STAD tumoral samples compared to nontumoral counterparts. The three-component network was constructed which composed of DET-UCRs, miRNAs, and mRNAs nodes. Functional enrichment and PPI network analyses revealed important enriched signaling pathways and gene ontologies such as "pathway in cancer" and regulation of cell proliferation and apoptosis. Five T-UCRs were significantly correlated with the overall survival of GC patients. While no expression of uc.232 was observed in our in-house cohort of GC tissues, uc.343 showed an increased expression, although not statistically significant, in gastric tumoral tissues. The constructed three-component regulatory network of T-UCRs in GC presents a comprehensive understanding of the underlying gene expression regulation processes involved in tumor development and can serve as a basis to investigate potential prognostic biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Anis Khalafiyan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Markus Wolfien
- Department of System Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Center for Medical Informatics, Dresden, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
4
|
Abkenar BR, Mohammadi A, Amoli HA, Soleimani AA, Korani M, Mahmoodi H, Najafi M. Non-coding RNAs are correlated to TGF-β receptor type 2 in patients with colorectal cancer. J Gene Med 2023; 25:e3472. [PMID: 36579810 DOI: 10.1002/jgm.3472] [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: 07/30/2022] [Revised: 11/14/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Multiple molecular expression alterations, particularly in non-coding RNAs, play fundamental roles in the regulations of cellular processes and may relate to the occurrence and progression of colorectal cancer (CRC). In the present study, we investigated the associations between TGFBR2, miR20a-5p and long non-coding RNA (lncRNA) LAMTOR5-AS1 in CRC patients. METHODS Colorectal cancer and adjacent normal tissue samples (n = 34) were prepared from CRC patients. The associations between TGFBR2, miR20a-5p and lncRNA LAMTOR5-AS1 were predicted using bioinformatics tools. The expression levels of TGFBR2, miR20a-5p and lncRNA LAMTOR5-AS1 were measured using a quantitative real-time polymerase chain reaction technique. The TGFBR2 protein values were measured by western blotting. The clinical importance of lncRNA LAMTOR5-AS1 was assessed using receiver operating characteristic curve. RESULTS The up-regulated levels of TGFBR2 (p = 0.02), TGFBR2 protein (p = 0.008) and lncRNA LAMTOR5-AS1 (p = 0.02) were significantly observed in CRC tissues compared to the adjacent normal tissues. The miR20a-5p expression level (p = 0.009) was downregulated in CRC tissues. In addition, the miR20a-5p expression level was inversely correlated to the TGFBR2 gene (r2 = 0.88, p < 0.0001), protein (r2 = 0.95, p < 0.0001) and lncRNA LAMTOR5-AS1 gene (r2 = 0.93, p < 0.0001) expression levels. Based on the area under curve, the increase of lncRNA LAMTOR5-AS1 expression level with a sensitivity of 64.52% and specificity of 65.52% was considered in CRC patients. CONCLUSIONS We propose that miR20a-5p is inversely related to long non-coding RNA (lncRNA) LAMTOR5-AS, such that it may be involved in the regulation of TGFBR2 expression level in CRC patients.
Collapse
Affiliation(s)
| | - Asghar Mohammadi
- Shohada Hospital of Tarom, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hadi Ahmadi Amoli
- Sina Trauma and Surgery Research Center, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohsen Korani
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hassan Mahmoodi
- Biochemistry Department, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Najafi
- Biochemistry Department, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Center, Biochemistry Department, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
5
|
circSMARCA5 Is an Upstream Regulator of the Expression of miR-126-3p, miR-515-5p, and Their mRNA Targets, Insulin-like Growth Factor Binding Protein 2 ( IGFBP2) and NRAS Proto-Oncogene, GTPase ( NRAS) in Glioblastoma. Int J Mol Sci 2022; 23:ijms232213676. [PMID: 36430152 PMCID: PMC9690846 DOI: 10.3390/ijms232213676] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022] Open
Abstract
The involvement of non-coding RNAs (ncRNAs) in glioblastoma multiforme (GBM) pathogenesis and progression has been ascertained but their cross-talk within GBM cells remains elusive. We previously demonstrated the role of circSMARCA5 as a tumor suppressor (TS) in GBM. In this paper, we explore the involvement of circSMARCA5 in the control of microRNA (miRNA) expression in GBM. By using TaqMan® low-density arrays, the expression of 748 miRNAs was assayed in U87MG overexpressing circSMARCA5. Differentially expressed (DE) miRNAs were validated through single TaqMan® assays in: (i) U87MG overexpressing circSMARCA5; (ii) four additional GBM cell lines (A172; CAS-1; SNB-19; U251MG); (iii) thirty-eight GBM biopsies; (iv) twenty biopsies of unaffected brain parenchyma (UC). Validated targets of DE miRNAs were selected from the databases TarBase and miRTarbase, and the literature; their expression was inferred from the GBM TCGA dataset. Expression was assayed in U87MG overexpressing circSMARCA5, GBM cell lines, and biopsies through real-time PCR. TS miRNAs 126-3p and 515-5p were upregulated following circSMARCA5 overexpression in U87MG and their expression was positively correlated with that of circSMARCA5 (r-values = 0.49 and 0.50, p-values = 9 × 10-5 and 7 × 10-5, respectively) in GBM biopsies. Among targets, IGFBP2 (target of miR-126-3p) and NRAS (target of miR-515-5p) mRNAs were positively correlated (r-value = 0.46, p-value = 0.00027), while their expression was negatively correlated with that of circSMARCA5 (r-values = -0.58 and -0.30, p-values = 0 and 0.019, respectively), miR-126-3p (r-value = -0.36, p-value = 0.0066), and miR-515-5p (r-value = -0.34, p-value = 0.010), respectively. Our data identified a new GBM subnetwork controlled by circSMARCA5, which regulates downstream miRNAs 126-3p and 515-5p, and their mRNA targets IGFBP2 and NRAS.
Collapse
|
6
|
De Martino M, Esposito F, Capone M, Pallante P, Fusco A. Noncoding RNAs in Thyroid-Follicular-Cell-Derived Carcinomas. Cancers (Basel) 2022; 14:cancers14133079. [PMID: 35804851 PMCID: PMC9264824 DOI: 10.3390/cancers14133079] [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: 04/21/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Thyroid tumors represent the most common neoplastic pathology of the endocrine system. Mutations occurring in oncogenes and tumor suppressor genes are responsible for thyroid carcinogenesis; however, the complete mutational landscape characterizing these neoplasias has not been completely unveiled. It has been established that only the 2% of the human genome codes for proteins, suggesting that the vast majority of the genome has regulatory capabilities, which, if altered, could account for the onset of cancer. Hence, many scientific efforts are currently focused on the characterization of the heterogeneous class of noncoding RNAs, which represent an abundant part of the transcribed noncoding genome. In this review, we mainly focus on the involvement of microRNAs, long noncoding RNAs, and pseudogenes in thyroid cancer. The determination of the diagnosis, prognosis, and treatment of thyroid cancers based on the evaluation of the noncoding RNA network could allow the implementation of a more personalized approach to fighting these pathologies. Abstract Among the thyroid neoplasias originating from follicular cells, we can include well-differentiated carcinomas, papillary (PTC) and follicular (FTC) thyroid carcinomas, and the undifferentiated anaplastic (ATC) carcinomas. Several mutations in oncogenes and tumor suppressor genes have already been observed in these malignancies; however, we are still far from the comprehension of their full regulation-altered landscape. Even if only 2% of the human genome has the ability to code for proteins, most of the noncoding genome is transcribed, constituting the heterogeneous class of noncoding RNAs (ncRNAs), whose alterations are associated with the development of several human diseases, including cancer. Hence, many scientific efforts are currently focused on the elucidation of their biological role. In this review, we analyze the scientific literature regarding the involvement of microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and pseudogenes in FTC, PTC, and ATC. Recent findings emphasized the role of lncRNAs in all steps of cancer progression. In particular, lncRNAs may control progression steps by regulating the expression of genes and miRNAs involved in cell proliferation, apoptosis, epithelial–mesenchymal transition, and metastatization. In conclusion, the determination of the diagnosis, prognosis, and treatment of cancer based on the evaluation of the ncRNA network could allow the implementation of a more personalized approach to fighting thyroid tumors.
Collapse
Affiliation(s)
- Marco De Martino
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
| | - Francesco Esposito
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
| | - Maria Capone
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli “Federico II”, Via S. Pansini 5, 80131 Napoli, Italy
| | - Pierlorenzo Pallante
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
- Correspondence: (P.P.); (A.F.)
| | - Alfredo Fusco
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli “Federico II”, Via S. Pansini 5, 80131 Napoli, Italy
- Correspondence: (P.P.); (A.F.)
| |
Collapse
|
7
|
Chen Z, Cao X, Lu Q, Zhou J, Wang Y, Wu Y, Mao Y, Xu H, Yang Z. circ01592 regulates unsaturated fatty acid metabolism through adsorbing miR-218 in bovine mammary epithelial cells. Food Funct 2021; 12:12047-12058. [PMID: 34761771 DOI: 10.1039/d1fo02797b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The composition of fatty acids plays a key role in regulating milk flavor and quality. Therefore, to improve the quality of milk, it is particularly important to study the regulatory mechanism of fatty acid metabolism in dairy cows. In this study, the expression profiles at non-lactation, peak-lactation, mid-lactation and late-lactation were constructed by high-throughput sequencing. Considering non-lactation as the control group and the other points as the experimental groups, the differentially expressed genes were screened. ELOVL5 was significantly upregulated and was selected for subsequent analyses. Bioinformatics prediction, a dual-luciferase assay, qPCR analysis and western blot analysis were used for verification. The results showed that ELOVL5 was a downstream target gene of miR-218 that regulated milk fat metabolism. A dual-luciferase assay and expression level analysis showed that circ01592 can directly bind to miR-218 and that overexpression of circ01592 (pcDNA-circ01592) significantly reduced the expression of miR-218 and enhanced the expression of ELOVL5, the target gene of miR-218 in BMECs. A functional study of BMECs showed that circ01592 promoted the synthesis of TAG and increased the content of UFA. The function of miR-218 was opposite to that of circ01592. Overall, the data showed that circ01592 promoted TAG synthesis and fatty acid composition by binding miR-218, alleviating the inhibitory effect of miR-218 on ELOVL5 expression. These mechanisms provide a new research approach and theoretical basis for improving milk quality.
Collapse
Affiliation(s)
- Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xiang Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qinyue Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jingpeng Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yuhao Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yanni Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Huifen Xu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| |
Collapse
|
8
|
Barbagallo C, Platania CBM, Drago F, Barbagallo D, Di Pietro C, Purrello M, Bucolo C, Ragusa M. Do Extracellular RNAs Provide Insight into Uveal Melanoma Biology? Cancers (Basel) 2021; 13:5919. [PMID: 34885029 PMCID: PMC8657116 DOI: 10.3390/cancers13235919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults, showing a high mortality due to metastasis. Although it is considered a rare disease, a growing number of papers have reported altered levels of RNAs (i.e., coding and non-coding RNAs) in cancerous tissues and biological fluids from UM patients. The presence of circulating RNAs, whose dysregulation is associated with UM, paved the way to the possibility of exploiting it for diagnostic and prognostic purposes. However, the biological meaning and the origin of such RNAs in blood and ocular fluids of UM patients remain unexplored. In this review, we report the state of the art of circulating RNAs in UM and debate whether the amount and types of RNAs measured in bodily fluids mirror the RNA alterations from source cancer cells. Based on literature data, extracellular RNAs in UM patients do not represent, with rare exceptions, a snapshot of RNA dysregulations occurring in cancerous tissues, but rather the complex and heterogeneous outcome of a systemic dysfunction, including immune system activity, that modifies the mechanisms of RNA delivery from several cell types.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Chiara Bianca Maria Platania
- Department of Biomedical and Biotechnological Sciences—Section of Pharmacology, University of Catania, 95123 Catania, Italy; (C.B.M.P.); (F.D.)
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences—Section of Pharmacology, University of Catania, 95123 Catania, Italy; (C.B.M.P.); (F.D.)
- Center of Research in Ocular Pharmacology—CERFO, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Claudio Bucolo
- Department of Biomedical and Biotechnological Sciences—Section of Pharmacology, University of Catania, 95123 Catania, Italy; (C.B.M.P.); (F.D.)
- Center of Research in Ocular Pharmacology—CERFO, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| |
Collapse
|
9
|
Zhong Y, Qin K, Li L, Liu H, Xie Z, Zeng K. Identification of Immunological Biomarkers of Atopic Dermatitis by Integrated Analysis to Determine Molecular Targets for Diagnosis and Therapy. Int J Gen Med 2021; 14:8193-8209. [PMID: 34815693 PMCID: PMC8605491 DOI: 10.2147/ijgm.s331119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose Atopic dermatitis (AD) is a common chronic inflammatory skin disorder associated with immune dysregulation and barrier dysfunction. In this study, we investigated immunological biomarkers for AD diagnosis and treatment using CIBERSORT to identify immune cell infiltration characteristics. Patients and Methods Common differentially expressed genes (DEGs) of lesioned (LS) vs non-lesioned (NL) groups were obtained from public datasets (GSE140684 and GSE99802). We performed functional enrichment analysis and selected hub genes from the protein-protein interaction (PPI) network. The hub genes were then subjected to transcription factor (TF), microRNA (miRNA), long non-coding RNA (lncRNA), drug interaction, and protein subcellular localization analyses. We also performed correlation analysis on differentially expressed immune cells, TFs, and hub genes. Receiver operating characteristic (ROC) curve analysis and binomial least absolute shrinkage and selection operator (LASSO) regression analysis were employed to assess the expression of hub genes in the GSE99802, GSE140684, GSE58558, GSE120721, and GSE36842 datasets. Results We identified 238 common DEGs and 25 hub genes. Additionally, we predicted TFs, miRNAs, lncRNA, drugs, and protein subcellular localizations. The proportions of activated dendritic cells (DCs) and CD4+ memory T cells were relatively high in the LS skin. Expression levels of the TF FOXC1 were negatively correlated with target genes and the abundance of two immune cell types. The LASSO model showed that GZMB, CXCL1, and CD274 are candidate diagnostic biomarkers. Conclusion Our study suggests that downregulated expression of FOXC1 expression may enhance the levels of chemokines, chemokine receptors, T cell receptor signaling molecules, activating CD4+ memory T cells and DCs in AD.
Collapse
Affiliation(s)
- Yixiu Zhong
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Kaiwen Qin
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Leqian Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Huiye Liu
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Zhiyue Xie
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Kang Zeng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| |
Collapse
|
10
|
Wozniak M, Czyz M. The Functional Role of Long Non-Coding RNAs in Melanoma. Cancers (Basel) 2021; 13:cancers13194848. [PMID: 34638331 PMCID: PMC8508152 DOI: 10.3390/cancers13194848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022] Open
Abstract
Melanoma is the most lethal skin cancer, with increasing incidence worldwide. The molecular events that drive melanoma development and progression have been extensively studied, resulting in significant improvements in diagnostics and therapeutic approaches. However, a high drug resistance to targeted therapies and adverse effects of immunotherapies are still a major challenge in melanoma treatment. Therefore, the elucidation of molecular mechanisms of melanomagenesis and cancer response to treatment is of great importance. Recently, many studies have revealed the close association of long noncoding RNAs (lncRNAs) with the development of many cancers, including melanoma. These RNA molecules are able to regulate a plethora of crucial cellular processes including proliferation, differentiation, migration, invasion and apoptosis through diverse mechanisms, and even slight dysregulation of their expression may lead to tumorigenesis. lncRNAs are able to bind to protein complexes, DNA and RNAs, affecting their stability, activity, and localization. They can also regulate gene expression in the nucleus. Several functions of lncRNAs are context-dependent. This review summarizes current knowledge regarding the involvement of lncRNAs in melanoma. Their possible role as prognostic markers of melanoma response to treatment and in resistance to therapy is also discussed.
Collapse
|
11
|
Barbagallo C, Di Maria A, Alecci A, Barbagallo D, Alaimo S, Colarossi L, Ferro A, Di Pietro C, Purrello M, Pulvirenti A, Ragusa M. VECTOR: An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma. Genes (Basel) 2021; 12:genes12071004. [PMID: 34210067 PMCID: PMC8305227 DOI: 10.3390/genes12071004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults and, although its genetic background has been extensively studied, little is known about the contribution of non-coding RNAs (ncRNAs) to its pathogenesis. Indeed, its competitive endogenous RNA (ceRNA) regulatory network comprising microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and mRNAs has been insufficiently explored. Thanks to UM findings from The Cancer Genome Atlas (TCGA), it is now possible to statistically elaborate these data to identify the expression relationships among RNAs and correlative interaction data. In the present work, we propose the VECTOR (uVeal mElanoma Correlation NeTwORk) database, an interactive tool that identifies and visualizes the relationships among RNA molecules, based on the ceRNA model. The VECTOR database contains: (i) the TCGA-derived expression correlation values of miRNA-mRNA, miRNA-lncRNA and lncRNA-mRNA pairs combined with predicted or validated RNA-RNA interactions; (ii) data of sense-antisense sequence overlapping; (iii) correlation values of Transcription Factor (TF)-miRNA, TF-lncRNA, and TF-mRNA pairs associated with ChiPseq data; (iv) expression data of miRNAs, lncRNAs and mRNAs both in UM and physiological tissues. The VECTOR web interface can be queried, by inputting the gene name, to retrieve all the information about RNA signaling and visualize this as a graph. Finally, VECTOR provides a very detailed picture of ceRNA networks in UM and could be a very useful tool for researchers studying RNA signaling in UM. The web version of Vector is freely available at the URL reported at the end of the Introduction.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Antonio Di Maria
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Adriana Alecci
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Lorenzo Colarossi
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), 95029 Catania, Italy;
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
- Correspondence:
| | - Marco Ragusa
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| |
Collapse
|
12
|
Pandey M, Mukhopadhyay A, Sharawat SK, Kumar S. Role of microRNAs in regulating cell proliferation, metastasis and chemoresistance and their applications as cancer biomarkers in small cell lung cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188552. [PMID: 33892053 DOI: 10.1016/j.bbcan.2021.188552] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 12/22/2022]
Abstract
Small cell lung cancer (SCLC), a smoking-related highly aggressive neuroendocrine cancer, is characterized by rapid cell proliferation, early metastatic dissemination, and early relapse due to chemoresistance to first-line platinum-doublet chemotherapy. Genomically, SCLC tumors show nearly universal loss of TP53 and RB1 tumor suppressor genes, while gene expression signature classifies them into 4 distinct subgroups based on the expression patterns of lineage transcription factors - ASCL1/ASH1, NEUROD1, YAP-1, and POU2F3. Due to the lack of targetable molecular alterations and clinically useful diagnostic, prognostic and predictive biomarker, there is insignificant progress in the therapeutic management of SCLC patients. Numerous studies have shown a significant involvement of non-coding RNAs in the regulation of cell proliferation, invasion and migration, apoptosis, metastasis, and chemoresistance in various human cancers. In this review, we comprehensively discuss the role of microRNAs (miRNAs) in regulating the aforementioned biological process in SCLC. For this, we searched the scientific literature and selected studies that have evaluated the role of miRNAs in the disease pathogenesis or as a cancer biomarker in SCLC. Our review suggests that several miRNAs are involved in the pathogenesis of SCLC mainly by regulating cell proliferation, metastasis, and chemoresistance. Few studies have also demonstrated the clinical utility of miRNAs in monitoring response to chemotherapy as well as in predicting survival outcomes. However, more in-depth mechanistic studies utilizing in vivo models and multicentric studies with larger patient cohorts are needed before the applications of miRNAs as therapeutic targets or as biomarkers are translated from the laboratory into clinics.
Collapse
Affiliation(s)
- Monu Pandey
- Dept. of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Abhirup Mukhopadhyay
- Dept. of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Surender K Sharawat
- Dept. of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sachin Kumar
- Dept. of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India.
| |
Collapse
|
13
|
Altieri R, Barbagallo D, Certo F, Broggi G, Ragusa M, Di Pietro C, Caltabiano R, Magro G, Peschillo S, Purrello M, Barbagallo G. Peritumoral Microenvironment in High-Grade Gliomas: From FLAIRectomy to Microglia-Glioma Cross-Talk. Brain Sci 2021; 11:200. [PMID: 33561993 PMCID: PMC7915863 DOI: 10.3390/brainsci11020200] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Cellular composition and molecular signatures of the glioma core compared with infiltrative margins are different, and it is well known that the tumor edge is enriched in microglia. In this review of the literature, we summarize the role of the peritumoral area in high-grade gliomas (HGGs) from surgical and biological points of view. There is evidence on the dual role of microglia in HGGs-a scavenger-tumoricidal role when microglia are activated in an M1 phenotype and a role favoring tumor growth and infiltration/migration when microglia are activated in an M2 phenotype. Microglia polarization is mediated by complex pathways involving cross-talk with glioma cells. In this scenario, extracellular vesicles and their miRNA cargo seem to play a central role. The switch to a specific phenotype correlates with prognosis and the pathological assessment of a specific microglial setting can predict a patient's outcome. Some authors have designed an engineered microglial cell as a biologically active vehicle for the delivery of intraoperative near-infrared fluorescent dye with the aim of helping surgeons detect peritumoral infiltrated areas during resection. Furthermore, the pharmacological modulation of microglia-glioma cross-talk paves the way to more effective therapies.
Collapse
Affiliation(s)
- Roberto Altieri
- Department of Neurological Surgery, Policlinico “G. Rodolico-S. Marco” University Hospital, 95121 Catania, Italy; (F.C.); (S.P.); (G.B.)
- Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, 95123 Catania, Italy; (D.B.); (M.R.); (M.P.)
| | - Davide Barbagallo
- Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, 95123 Catania, Italy; (D.B.); (M.R.); (M.P.)
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123 Catania, Italy;
| | - Francesco Certo
- Department of Neurological Surgery, Policlinico “G. Rodolico-S. Marco” University Hospital, 95121 Catania, Italy; (F.C.); (S.P.); (G.B.)
- Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, 95123 Catania, Italy; (D.B.); (M.R.); (M.P.)
| | - Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies “G. F. Ingrassia”, Anatomic Pathology, University of Catania, 95123 Catania, Italy; (G.B.); (R.C.); (G.M.)
| | - Marco Ragusa
- Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, 95123 Catania, Italy; (D.B.); (M.R.); (M.P.)
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123 Catania, Italy;
- Oasi Research Institute—IRCCS, 94018 Troina, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123 Catania, Italy;
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies “G. F. Ingrassia”, Anatomic Pathology, University of Catania, 95123 Catania, Italy; (G.B.); (R.C.); (G.M.)
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technologies “G. F. Ingrassia”, Anatomic Pathology, University of Catania, 95123 Catania, Italy; (G.B.); (R.C.); (G.M.)
| | - Simone Peschillo
- Department of Neurological Surgery, Policlinico “G. Rodolico-S. Marco” University Hospital, 95121 Catania, Italy; (F.C.); (S.P.); (G.B.)
| | - Michele Purrello
- Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, 95123 Catania, Italy; (D.B.); (M.R.); (M.P.)
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123 Catania, Italy;
| | - Giuseppe Barbagallo
- Department of Neurological Surgery, Policlinico “G. Rodolico-S. Marco” University Hospital, 95121 Catania, Italy; (F.C.); (S.P.); (G.B.)
- Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, 95123 Catania, Italy; (D.B.); (M.R.); (M.P.)
| |
Collapse
|
14
|
Brex D, Barbagallo C, Mirabella F, Caponnetto A, Battaglia R, Barbagallo D, Caltabiano R, Broggi G, Memeo L, Di Pietro C, Purrello M, Ragusa M. LINC00483 Has a Potential Tumor-Suppressor Role in Colorectal Cancer Through Multiple Molecular Axes. Front Oncol 2021; 10:614455. [PMID: 33552987 PMCID: PMC7855711 DOI: 10.3389/fonc.2020.614455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are the most heterogeneous class of non-protein-coding RNAs involved in a broad spectrum of molecular mechanisms controlling genome function, including the generation of complex networks of RNA-RNA competitive interactions. Accordingly, their dysregulation contributes to the onset of many tumors, including colorectal cancer (CRC). Through a combination of in silico approaches (statistical screening of expression datasets) and in vitro analyses (enforced expression, artificial inhibition, or activation of pathways), we identified LINC00483 as a potential tumor suppressor lncRNA in CRC. LINC00483 was downregulated in CRC biopsies and metastases and its decreased levels were associated with severe clinical features. Inhibition of the MAPK pathway and cell cycle arrest by starvation induced an upregulation of LINC00483, while the epithelial to mesenchymal transition activation by TGFβ-1 and IL-6 caused its down-modulation. Moreover, enforced expression of LINC00483 provoked a slowing down of cell migration rate without affecting cell proliferation. Since LINC00483 was predominantly cytoplasmic, we hypothesized a “miRNA sponge” role for it. Accordingly, we computationally reconstructed the LINC00483/miRNA/mRNA axes and evaluated the expression of mRNAs in different experimental conditions inducing LINC00483 alteration. By this approach, we identified a set of mRNAs sharing the miRNA response elements with LINC00483 and modulated in accordance with it. Moreover, we found that LINC00483 is potentially under negative control of transcription factor HNF4α. In conclusion, we propose that LINC00483 is a tumor suppressor in CRC that, through an RNA-RNA network, may control cell migration and participate in proliferation signaling.
Collapse
Affiliation(s)
- Duilia Brex
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Federica Mirabella
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania, Italy
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| |
Collapse
|
15
|
Cardoso AM, Morais CM, Rebelo O, Tão H, Barbosa M, Pedroso de Lima MC, Jurado AS. Downregulation of long non-protein coding RNA MVIH impairs glioblastoma cell proliferation and invasion through an miR-302a-dependent mechanism. Hum Mol Genet 2021; 30:46-64. [PMID: 33438023 DOI: 10.1093/hmg/ddab009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma (GB) is the most frequent and malignant type of brain tumor, for which no effective therapy exists. The high proliferative and invasive nature of GB, as well as its acquired resistance to chemotherapy, makes this type of cancer extremely lethal shortly after diagnosis. Long non-protein coding RNAs (lncRNA) are a class of regulatory RNAs whose levels can be dysregulated in the context of diseases, unbalancing several physiological processes. The lncRNA associated with microvascular invasion in hepatocellular carcinoma (lncRNA-MVIH), overexpressed in several cancers, was described to co-precipitate with phosphoglycerate kinase 1 (PGK1), preventing secretion of this enzyme to the extracellular environment and promoting cell migration and invasion. We hypothesized that, by silencing the expression of lncRNA-MVIH, the secretion of PGK1 would increase, reducing GB cell migration and invasion capabilities. We observed that lncRNA-MVIH silencing in human GB cells significantly decreased glycolysis, cell growth, migration, and invasion and sensitized GB cells to cediranib. However, no increase in extracellular PGK1 was observed as a consequence of lncRNA-MVIH silencing, and therefore, we investigated the possibility of a mechanism of miRNA sponge of lncRNA-MVIH being in place. We found that the levels of miR-302a loaded onto RISC increased in GB cells after lncRNA-MVIH silencing, with the consequent downregulation of several miR-302a molecular targets. Our findings suggest a new mechanism of action of lncRNA-MVIH as a sponge of miR-302a. We suggest that lncRNA-MVIH knockdown may be a promising strategy to address GB invasiveness and chemoresistance, holding potential towards its future application in a clinical context.
Collapse
Affiliation(s)
- Ana M Cardoso
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, IIIUC - Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Catarina M Morais
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Olinda Rebelo
- Neuropathology Laboratory, Neurology Service, University Hospital of Coimbra, 3004-561 Coimbra, Portugal
| | - Hermínio Tão
- Neurosurgery Service, University Hospital of Coimbra, 33004-561 Coimbra, Portugal
| | - Marcos Barbosa
- Neurosurgery Service, University Hospital of Coimbra, 33004-561 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria C Pedroso de Lima
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, IIIUC - Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Amália S Jurado
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, IIIUC - Institute for Interdisciplinary Research, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| |
Collapse
|
16
|
Mirabella F, Gulisano M, Capelli M, Lauretta G, Cirnigliaro M, Palmucci S, Stella M, Barbagallo D, Di Pietro C, Purrello M, Ragusa M, Rizzo R. Enrichment and Correlation Analysis of Serum miRNAs in Comorbidity Between Arnold-Chiari and Tourette Syndrome Contribute to Clarify Their Molecular Bases. Front Mol Neurosci 2021; 13:608355. [PMID: 33469418 PMCID: PMC7813987 DOI: 10.3389/fnmol.2020.608355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022] Open
Abstract
Due to its rarity, coupled to a multifactorial and very heterogeneous nature, the molecular etiology of Arnold-Chiari (AC) syndrome remains almost totally unknown. Its relationship with other neuropsychiatric disorders such as Tourette syndrome (TS) is also undetermined. The rare comorbid status between both disorders (ACTS) complicates the framework of diagnosis and negatively affects the patients' quality of life. In this exploratory study, we aimed to identify serum microRNA expression profiles as molecular fingerprints for AC, TS, and ACTS, by using a high-throughput approach. For this aim, 10 AC patients, 11 ACTS patients, 6 TS patients, and 8 unaffected controls (NC) were recruited. Nine miRNAs resulted significantly differentially expressed (DE): let-7b-5p (upregulated in ACTS vs. TS); miR-21-5p (upregulated in ACTS vs. AC; downregulated in AC vs. TS); miR-23a-3p (upregulated in TS vs. NCs; downregulated in AC vs. TS); miR-25-3p (upregulated in AC vs. TS and NCs; downregulated in ACTS vs. AC); miR-93-5p (upregulated in AC vs. TS); miR-130a-3p (downregulated in ACTS and TS vs. NCs); miR-144-3p (downregulated in ACTS vs. AC; upregulated in AC vs. TS); miR-222-3p (upregulated in ACTS vs. NCs); miR-451a (upregulated in AC vs. TS and NCs; in ACTS vs. NCs). Altered expression of miRNAs was statistically correlated to neuroimaging and neuropsychological anomalies. Furthermore, computational analyses indicated that DE miRNAs are involved in AC and TS pathomechanisms. Finally, we propose the dysregulation of the miRNA set as a potential molecular tool for supporting the current diagnosis of AC, TS, and ACTS by using liquid biopsies, in an unbiased and non-invasive way.
Collapse
Affiliation(s)
- Federica Mirabella
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Mariangela Gulisano
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Mara Capelli
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Lauretta
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Stefano Palmucci
- Radiology Unit 1, Department of Medical Surgical Sciences and Advanced Technologies, University Hospital “Policlinico-Vittorio Emanuele”, University of Catania, Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Oasi Research Institute–IRCCS, Troina, Italy
| | - Renata Rizzo
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| |
Collapse
|
17
|
LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network. Cancers (Basel) 2020; 12:cancers12123867. [PMID: 33371395 PMCID: PMC7767460 DOI: 10.3390/cancers12123867] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Uveal melanoma (UM) is the most frequent primary tumor of the eye in adults. Although molecular alterations on protein-coding genes have been associated with the development of UM, the role of non-coding RNAs and their competitive endogenous networks remain poorly investigated. Starting from a computational analysis on UM expression dataset deposited in The Cancer Genome Atlas, we identified the long non-coding RNA LINC00518 as a potential oncogene. We then experimentally evaluated LINC00518 and its supposed RNA signaling in human biopsies and in vitro functional assays. The results obtained suggest that LINC00518, under potential transcriptional control by MITF, regulates an RNA–RNA network promoting cancer-related processes (i.e., cell proliferation and migration). These findings open the way to the characterization of the unknown RNA signaling associated with UM and pave the way to the exploitation of a potential target for RNA-based therapeutics. Abstract Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults; little is known about the contribution of non-coding RNAs (ncRNAs) to UM pathogenesis. Competitive endogenous RNA (ceRNA) networks based on RNA–RNA interactions regulate physiological and pathological processes. Through a combined approach of in silico and experimental biology, we investigated the expression of a set of long non-coding RNAs (lncRNAs) in patient biopsies, identifying LINC00518 as a potential oncogene in UM. The detection of LINC00518 dysregulation associated with several in vitro functional assays allowed us to investigate its ceRNA regulatory network and shed light on its potential involvement in cancer-related processes, such as epithelial to mesenchymal transition (EMT) and CoCl2-induced hypoxia-like response. In vitro transient silencing of LINC00518 impaired cell proliferation and migration, and affected mRNA expression of LINGO2, NFIA, OTUD7B, SEC22C, and VAMP3. A “miRNA sponge” and “miRNA protector” model have been hypothesized for LINC00518-induced regulation of mRNAs. In vitro inhibition of MITF suggested its role as a potential activator of LINC00518 expression. Comprehensively, LINC00518 may be considered a new oncogene in UM and a potential target for RNA-based therapeutic approaches.
Collapse
|
18
|
Barbagallo C, Di Martino MT, Grasso M, Salluzzo MG, Scionti F, Cosentino FII, Caruso G, Barbagallo D, Di Pietro C, Ferri R, Caraci F, Purrello M, Ragusa M. Uncharacterized RNAs in Plasma of Alzheimer's Patients Are Associated with Cognitive Impairment and Show a Potential Diagnostic Power. Int J Mol Sci 2020; 21:ijms21207644. [PMID: 33076555 PMCID: PMC7588983 DOI: 10.3390/ijms21207644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
Alzheimer’s disease (AD) diagnosis is actually based on clinical evaluation and brain-imaging tests, and it can often be confirmed only post-mortem. Therefore, new non-invasive molecular biomarkers are necessary to improve AD diagnosis. As circulating microRNA biomarkers have been proposed for many diseases, including AD, we aimed to identify new diagnostic non-small RNAs in AD. Whole transcriptome analysis was performed on plasma samples of five AD and five unaffected individuals (CTRL) using the Clariom D Pico Assay, followed by validation in real-time PCR on 37 AD patients and 37 CTRL. Six differentially expressed (DE) transcripts were identified: GS1-304P7.3 (upregulated), NONHSAT090268, TC0100011037, TC0400008478, TC1400008125, and UBE2V1 (downregulated). Peripheral blood mononuclear cells (PBMCs) may influence the expression of circulating RNAs and their analysis has been proposed to improve AD clinical management. Accordingly, DE transcript expression was also evaluated in PBMCs, showing no difference between AD and CTRL. ROC (receiver operating characteristic) curve analysis was performed to evaluate the diagnostic accuracy of each DE transcript and a signature including all of them. A correlation between cognitive impairment and GS1-304P7.3, NONHSAT090268, TC0100011037, and TC0400008478 was detected, suggesting a potential association between their extracellular abundance and AD clinical phenotype. Finally, this study identified six transcripts showing altered expression in the plasma of AD patients. Given the need for new, accurate blood biomarkers for AD diagnosis, these transcripts may be considered for further analyses in larger cohorts, also in combination with other biomarkers, aiming to identify specific RNA-based biomarkers to be eventually applied to clinical practice.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (M.T.D.M.); (F.S.)
| | - Margherita Grasso
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (M.G.); (M.G.S.); (F.I.I.C.); (G.C.); (R.F.)
- Department of Drug Sciences, University of Catania, 95125 Catania, Italy
| | - Maria Grazia Salluzzo
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (M.G.); (M.G.S.); (F.I.I.C.); (G.C.); (R.F.)
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (M.T.D.M.); (F.S.)
| | | | - Giuseppe Caruso
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (M.G.); (M.G.S.); (F.I.I.C.); (G.C.); (R.F.)
- Department of Drug Sciences, University of Catania, 95125 Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Raffaele Ferri
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (M.G.); (M.G.S.); (F.I.I.C.); (G.C.); (R.F.)
| | - Filippo Caraci
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (M.G.); (M.G.S.); (F.I.I.C.); (G.C.); (R.F.)
- Department of Drug Sciences, University of Catania, 95125 Catania, Italy
- Correspondence:
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (M.G.); (M.G.S.); (F.I.I.C.); (G.C.); (R.F.)
| |
Collapse
|
19
|
Zare Chavoshy H, Ghasemi R. Fabrication of a novel fluorescent polyacrylonitrile electrospun nanofiber for DNA-based optical biosensing of microRNA-21. NANO EXPRESS 2020. [DOI: 10.1088/2632-959x/ab96b5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
In this study, an optical platform based on fluorescent nanofiber was developed for detection of microRNA-21 as a biomarker of cancerous cells. The fluorescent polyacrylonitrile nanofiber was fabricated using electrospinning method. The surfaces of nanofiber were treated by NaOH to convert nitrile groups to carboxyl moieties. Activation of these carboxyl groups by EDC-sulfo NHS coupling agents was done and then the covalent bonding between COOH groups of nanofiber and –NH2 groups of amino-probe was formed. The results of SEM, XRD, FTIR, and fluorescence microscopy confirmed that the process of fluorescent nanofiber synthesis was successfully performed. Hybridization of probe and microRNA-21 showed that the capture efficiency of this fluorescent nanofiber was 1 pmol μl−1 and these nanofibers have the potential to be used as optical sensors for detection of microRNA-21.
Collapse
|
20
|
Wang Q, Cang Z, Shen L, Peng W, Xi L, Jiang X, Ge X, Xu B, Huang S. circ_0037128/miR-17-3p/AKT3 axis promotes the development of diabetic nephropathy. Gene 2020; 765:145076. [PMID: 32860899 DOI: 10.1016/j.gene.2020.145076] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/01/2020] [Accepted: 08/19/2020] [Indexed: 12/26/2022]
Abstract
Circular RNAs (circRNAs) play vital roles in the development of diabetic nephropathy (DN). In this study, we investigated the function of circ_0037128 and molecular mechanism via which it regulates diabetic nephropathy development. It was found that expression of circ_0037128 was significantly increased in mouse DN model and high glucose treated mesangial cells (MCs), and circ_0037128 loss-of-function led to reduced cell proliferation and fibrosis in vitro. Moreover, miR-17-3p acts as competitive endogenous RNA (ceRNA) that directly interacts with circ_0037128 through its miRNA response elements (MREs). Consistently, expression of miR-17-3p was remarkably down-regulated in DN model, and negatively regulated cell proliferation and fibrosis. Further investigations revealed that AKT3 was the putative target of miR-17-3p, whose expression was elevated in DN model. In conclusion, we have characterized the function of a novel circ_0037128 and illustrated the significance of circ_0037128-miR-17-3p-AKT3 axis in DN pathogenesis.
Collapse
Affiliation(s)
- Qianqian Wang
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Zheng Cang
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Lisha Shen
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Wenfang Peng
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Liuqing Xi
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Xiaohong Jiang
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Xiaoxu Ge
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Bojin Xu
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Shan Huang
- Department of Endocrinology, Shanghai Tongren Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China.
| |
Collapse
|
21
|
Fawzy MS, Toraih EA, Ageeli EA, Al-Qahtanie SA, Hussein MH, Kandil E. Noncoding RNAs orchestrate cell growth, death and drug resistance in renal cell carcinoma. Epigenomics 2020; 12:199-219. [PMID: 32011160 DOI: 10.2217/epi-2019-0120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: We aimed to explore the roles of noncoding RNAs (ncRNAs) in renal cell carcinoma. Materials & methods: The altered expressions of miR-196a2, miR-499a, H19, MALAT1 and GAS5, as well as some target transcripts were identified by quantitative real-time reverse transcription polymerase chain reaction. Results: Up-regulation of miR-196a2, E2F3, HSPA4 and MALAT1 (median fold change: 5.69, 25.6, 4.15 and 19.6, respectively) and down-regulation of miR-499a, GAS5, PDCD4, ANXA1 and DFFA (median fold change: 0.28, 0.25, 0.12, 0.09 and 0.08, respectively) were reported compared with paired non-cancer tissue. PDCD4, DFFA and GAS5 down-regulation was associated with poor prognosis in terms of high grade, larger tumor, nodal invasion, capsular and pelvic infiltration. Conclusion: The identified ncRNAs could represent potential theranostic biomarkers for renal cell carcinoma.
Collapse
Affiliation(s)
- Manal S Fawzy
- Department of Medical Biochemistry & Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt.,Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
| | - Eman A Toraih
- Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana 70112, USA.,Genetics Unit, Department of Histology & Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Essam Al Ageeli
- Department of Clinical Biochemistry (Medical Genetics), Faculty of Medicine, University, Jazan 45142, Saudi Arabia
| | - Saeed Awad Al-Qahtanie
- Department of Physiology, Faculty of Medicine, Taibah University, Almadinah Almunawwarah 344, Saudi Arabia
| | - Mohamed H Hussein
- Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana 70112, USA
| | - Emad Kandil
- Division of Endocrine & Oncologic Surgery, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
| |
Collapse
|
22
|
Wang H, Huang C, Yao X. The functions of long non-coding RNAs in colorectal cancer. Transl Cancer Res 2019; 8:2192-2204. [PMID: 35116969 PMCID: PMC8797667 DOI: 10.21037/tcr.2019.08.23] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/25/2019] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the third most prevalent malignant neoplasm worldwide. Recently, in terms of the mechanism of CRC, most studies have focused on protein-coding genes. However, studies have increasingly shown that long non-coding RNAs (lncRNAs) play crucial roles in the proliferation and metastasis of CRC. Investigating this molecular mechanism may provide potential diagnostic tools and therapeutic targets for CRC. This review closely examines the dysregulation of lncRNAs in CRC. On account of different mechanisms being involved in the occurrence and development of CRC, there are several categories of lncRNAs, including lncRNAs related to the Wnt/β-catenin pathway, epithelial mesenchymal transition, epigenetic regulation, angiopoiesis, and chemoresistance. This review summarizes lncRNAs related to the progression of CRC, which may provide insight into the mechanisms and potential markers for prognostic prediction and monitoring relapse of CRC.
Collapse
Affiliation(s)
- Huaiming Wang
- Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
- Department of Gastrointestinal Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Chengzhi Huang
- Department of Gastrointestinal Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Medical College, Shantou University, Shantou 515063, China
| | - Xueqing Yao
- Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Department of Gastrointestinal Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| |
Collapse
|
23
|
López-Urrutia E, Bustamante Montes LP, Ladrón de Guevara Cervantes D, Pérez-Plasencia C, Campos-Parra AD. Crosstalk Between Long Non-coding RNAs, Micro-RNAs and mRNAs: Deciphering Molecular Mechanisms of Master Regulators in Cancer. Front Oncol 2019; 9:669. [PMID: 31404273 PMCID: PMC6670781 DOI: 10.3389/fonc.2019.00669] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Cancer is a complex disease, and its study requires deep understanding of several biological processes and their regulation. It is an accepted fact that non-coding RNAs are vital components of the regulation and cross-talk among cancer-related signaling pathways that favor tumor aggressiveness and metastasis, such as neovascularization, angiogenesis, and vasculogenic mimicry. Both long non-coding RNAs (lncRNAs) and micro-RNAs (miRNAs) have been described as master regulators of cancer on their own; yet there is accumulating evidence that, besides regulating mRNA expression through independent mechanisms, these classes of non-coding RNAs interact with each other directly, fine-tuning the effects of their regulation. While still relatively scant, research on the lncRNA-miRNA-mRNA axis regulation is growing at a fast rate, it is only in the last 5 years, that lncRNA-miRNA interactions have been identified in tumor-related vascular processes. In this review, we summarize the current progress of research on the cross-talk between lncRNAs and miRNAs in the regulation of neovascularization, angiogenesis and vasculogenic mimicry.
Collapse
Affiliation(s)
- Eduardo López-Urrutia
- Unidad de Biomedicina, FES-IZTACALA, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | | | | | - Carlos Pérez-Plasencia
- Unidad de Biomedicina, FES-IZTACALA, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico.,Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Alma D Campos-Parra
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| |
Collapse
|
24
|
Zhu M, Li M, Zhou W, Yang Y, Li F, Zhang L, Ji G. Qianggan extract improved nonalcoholic steatohepatitis by modulating lncRNA/circRNA immune ceRNA networks. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:156. [PMID: 31269941 PMCID: PMC6609373 DOI: 10.1186/s12906-019-2577-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/25/2019] [Indexed: 01/01/2023]
Abstract
Background The traditional Chinese medicine prescription, Qianggan formula have been confirmed to be effective on non-alcoholic steatohepatitis (NASH), however, the underlying molecular mechanisms remain obscure. Methods Thirty-six male C57BL/6 mice were randomly divided into three groups: normal chow diet group; methionine-and-choline-deficient diet (MCD) group, and Qianggan extract (QG) intervention group (0.4 g/kg daily) that fed with MCD. The efficacy of QG was biochemically and histologically evaluated. The expression profiles of messenger ribonucleic acids (mRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) were examined using microarray and verified by RT-qPCR. Results QG significantly improved the phenotypic characteristics of NASH, as serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and lactate dehydrogenase (LDH) levels and liver inflammatory cytokines were significantly decreased. By the cutoff of a 1.5-fold change and P < 0.05, 6193 mRNAs, 5692 lncRNAs and 4843 circRNAs were identified as differentially expressed between the MCD and normal groups, and 514 mRNAs, 1182 lncRNAs and 443 circRNAs were identified as differentially expressed between the QG and MCD groups. The intersections (244 mRNAs, 259 lncRNAs and 98 circRNAs) among the three groups were chosen for analysis. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that most overlapping mRNAs were related to immune functions such as natural-killer-cell-mediated cytotoxicity, intestinal immune network for IgA production, and T cell receptor signaling pathway. Pathway interactions, protein-protein interactions and molecular complex detection (MCODE) analysis identified numerous immune-related hub genes e.g. natural cytotoxicity triggering receptor 1(Ncr1), C-X-C motif chemokine ligand 9 (Cxcl9), Klra1, and Cd28. Finally, two lncRNAs (Sngh1 and Slc36a3os) and four circRNAs (circ_0009029, circ_0004572, circ_0009212 and circ_0009453) in competing endogenous RNA (ceRNA) networks were constructed by Cytoscape, and immune-related mRNAs (e.g., Cd28, Cd8a, Il15, and Klrk1) were involved in the ceRNA networks. Conclusions LncRNA and circRNA-associated immune ceRNA networks might be the targets of QG in alleviating NASH, and our work may provide valuable clues for exploring the mechanisms underlying the effect of QG. Electronic supplementary material The online version of this article (10.1186/s12906-019-2577-6) contains supplementary material, which is available to authorized users.
Collapse
|
25
|
Barbagallo C, Passanisi R, Mirabella F, Cirnigliaro M, Costanzo A, Lauretta G, Barbagallo D, Bianchi C, Pagni F, Castorina S, Granata A, Di Pietro C, Ragusa M, Malatino LS, Purrello M. Upregulated microRNAs in membranous glomerulonephropathy are associated with significant downregulation of IL6 and MYC mRNAs. J Cell Physiol 2018; 234:12625-12636. [PMID: 30515781 DOI: 10.1002/jcp.27851] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022]
Abstract
Membranous glomerulonephropathy (MGN) is a glomerulopathy characterized by subepithelial deposits of immune complexes on the extracapillary side of the glomerular basement membrane. Insertion of C5b-9 (complement membrane-attack complex) into the membrane leads to functional impairment of the glomerular capillary wall. Knowledge of the molecular pathogenesis of MGN is actually scanty. MicroRNA (miRNA) profiling in MGN and unaffected tissues was performed by TaqMan Low-Density Arrays. Expression of miRNAs and miRNA targets was evaluated in Real-Time polymerase chain reaction (PCR). In vitro transient silencing of miRNAs was achieved through transfection with miRNA inhibitors. Ten miRNAs (let-7a-5p, let-7b-5p, let-7c-5p, let-7d-5p, miR-107, miR-129-3p, miR-423-5p, miR-516-3p, miR-532-3p, and miR-1275) were differentially expressed (DE) in MGN biopsies compared to unaffected controls. Interleukin 6 (IL6) and MYC messenger RNAs (mRNAs; targets of DE miRNAs) were significantly downregulated in biopsies from MGN patients, and upregulated in A498 cells following let-7a-5p or let-7c-5p transient silencing. Gene ontology analysis showed that DE miRNAs regulate pathways associated with MGN pathogenesis, including cell cycle, proliferation, and apoptosis. A significant correlation between DE miRNAs and mRNAs and clinical parameters (i.e., antiphospholipid antibodies, serum creatinine, estimated glomerular filtration, proteinuria, and serum cholesterol) has been detected. Based on our data, we propose that DE miRNAs and their downstream network may be involved in MGN pathogenesis and could be considered as potential diagnostic biomarkers of MGN.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Roberta Passanisi
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Department of Thoracic Surgery, Centro Clinico e Diagnostico Morgagni, Catania, Italy
| | - Federica Mirabella
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Arianna Costanzo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Lauretta
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cristina Bianchi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Section of Pathology, University of Milano-Bicocca, Monza, Italy
| | - Sergio Castorina
- Department of Thoracic Surgery, Centro Clinico e Diagnostico Morgagni, Catania, Italy.,Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, Catania, Italy
| | - Antonio Granata
- Unit of Nephrology, Ospedale S. Giovanni di Dio, Agrigento, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Oasi Research Institute - IRCCS, Troina, Italy
| | - Lorenzo S Malatino
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| |
Collapse
|
26
|
A novel feedback loop between high MALAT-1 and low miR-200c-3p promotes cell migration and invasion in pancreatic ductal adenocarcinoma and is predictive of poor prognosis. BMC Cancer 2018; 18:1032. [PMID: 30352575 PMCID: PMC6199802 DOI: 10.1186/s12885-018-4954-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background It was demonstrated that long non-coding RNAs occupied an important position in tumor pathogenesis and progression. We have previously found that the metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) promotes cell proliferation and metastases in pancreatic ductal adenocarcinoma (PDAC). The present study was aimed to discuss the underlying mechanisms. Methods Bioinformatics method was used to identify the miRNA target of MALAT-1. Expressions of relative genes were assessed by quantitative real-time PCR and western blotting, respectively. Sulforhodamine B assay and Transwell assay were employed to detect cell proliferation, migration and invasion, respectively. Moreover, RNA immunoprecipitation was performed to determine whether RNA-induced silencing complex contained MALAT-1 and its potential binding miRNA. Luciferase assays was used to confirm potential binding site. Results Bioinformatics search predicted that miR-200c-3p was a direct target of MALAT-1. Further, we found a reciprocal suppression between MALAT-1 and miR-200c-3p expression. In terms of mechanisms, high MALAT-1 and low miR-200c-3p may form a novel feedback loop. On the one hand, MALAT-1 functioned as a competing endogenous RNA to suppress miR-200c-3p expression, leading to upregulation of ZEB1 expression. On the other hand, miR-200c-3p inhibited the level of MALAT-1 expression was in a way similar to miRNA-mediated downregulation of target genes. Clinical data further indicated that MALAT-1 and ZEB1 expression was negatively correlated with miR-200c-3p transcript level of PDAC tissues. There was a positive correlation between MALAT-1 and ZEB1 level. MALAT-1 (high)/miR-200c-3p (low) correlated with shorter overall survival of PDAC patients. Multivariate analysis revealed that both MALAT-1 and miR-200c-3p levels were independent prognostic factors. Conclusion Our findings firstly revealed a novel feedback loop between high MALAT-1 and low miR-200c-3p. Targeting the feedback loop between high MALAT-1 and low miR-200c-3p will be a therapeutic strategy for PDAC. Electronic supplementary material The online version of this article (10.1186/s12885-018-4954-9) contains supplementary material, which is available to authorized users.
Collapse
|
27
|
Di Pietro V, Porto E, Ragusa M, Barbagallo C, Davies D, Forcione M, Logan A, Di Pietro C, Purrello M, Grey M, Hammond D, Sawlani V, Barbey AK, Belli A. Salivary MicroRNAs: Diagnostic Markers of Mild Traumatic Brain Injury in Contact-Sport. Front Mol Neurosci 2018; 11:290. [PMID: 30177873 PMCID: PMC6109773 DOI: 10.3389/fnmol.2018.00290] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/02/2018] [Indexed: 12/31/2022] Open
Abstract
Concussion is difficult to diagnose, particularly when symptoms are atypical or late in presenting. An accurate and timely initial assessment is crucial for clinical management. Cerebral spinal fluid (CSF) and blood markers of traumatic brain injury show promising results but their clinical applicability in concussion has significant limitations. In the study, we explored saliva as a new source of biomarkers of concussion. Saliva samples of concussed players were collected after 48-72 h from concussion and analyzed by high-throughput technologies. A discovery group of 10 concussed rugby professional and semiprofessional athletes and 10 non-concussed matched controls was used for the analysis of 92 inflammatory proteins by the Proseek-Multiplex-Inflammation technology. In addition, saliva samples of 6 concussed and 6 non-concussed athletes were used to screen 800 human microRNAs (miRNAs) by the Nanostring Technology. The results were then validated by RT-qPCR in an enlarged cohort (validation group) comprising 22 concussed athletes. Results showed, no significant variations of the 65 inflammatory proteins detected in saliva between groups but 5 microRNAs, miR-27b-3p (p = 0.016), let-7i-5p (p = 0.001), miR-142-3p (p = 0.008), miR-107 (p = 0.028), miR-135b-5p (p = 0.017) significantly upregulated in concussed athletes. Univariate ROC curve analysis showed that the differentially expressed miRNAs could be considered good classifiers of concussion. Further analyses showed significant correlation between these microRNAs and Reaction Time component of the ImPACT concussion assessment tool. In addition, biocomputation analysis predicted the involvement of these microRNAs in important biological processes that might be related to trauma, such as response to hypoxia, cell death, neurogenesis, axon repair and myelination. Ease of access and non-invasiveness of saliva samples make these biomarkers particularly suitable for concussion assessment.
Collapse
Affiliation(s)
- Valentina Di Pietro
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Edoardo Porto
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Marco Ragusa
- BioMolecular, Genome and Complex Systems BioMedicine Unit (BMGS), Section of Biology and Genetics G Sichel, Department of Biomedical Sciences and Biotechnology, University of Catania, Catania, Italy.,IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Italy
| | - Cristina Barbagallo
- BioMolecular, Genome and Complex Systems BioMedicine Unit (BMGS), Section of Biology and Genetics G Sichel, Department of Biomedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - David Davies
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Mario Forcione
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Ann Logan
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Cinzia Di Pietro
- BioMolecular, Genome and Complex Systems BioMedicine Unit (BMGS), Section of Biology and Genetics G Sichel, Department of Biomedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Michele Purrello
- BioMolecular, Genome and Complex Systems BioMedicine Unit (BMGS), Section of Biology and Genetics G Sichel, Department of Biomedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Michael Grey
- School of Sport and Exercise, University of East Anglia, Norwich, United Kingdom
| | - Douglas Hammond
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Vijay Sawlani
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Aron K Barbey
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Antonio Belli
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, United Kingdom
| |
Collapse
|
28
|
Roy S, Trautwein C, Luedde T, Roderburg C. A General Overview on Non-coding RNA-Based Diagnostic and Therapeutic Approaches for Liver Diseases. Front Pharmacol 2018; 9:805. [PMID: 30158867 PMCID: PMC6104154 DOI: 10.3389/fphar.2018.00805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022] Open
Abstract
Liver diseases contribute to the global mortality and morbidity and still represent a major health problem leading to the death of people worldwide. Although there are several treatment options available for Hepatitis C infections, for most liver disease the pharmacological options are still limited. Therefore, the development of new targets against liver diseases is of high interest. Non-coding RNA (ncRNA) such as microRNA (miRNA) or long ncRNA (lncRNA) have been shown to be deeply involved in the pathophysiology of almost all acute and chronic liver diseases. The emerging evidence showed the potential therapeutic use of miRNA associated with different steps of hepatic pathophysiology. In the present review, we summarize emerging insights of ncRNA in liver diseases. We also highlight example of ncRNAs participating in the pathogenesis of different forms of liver disease and how they can be used as potential therapeutic targets for novel treatment paradigms. Furthermore, we describe an overview of up-to-date clinical trials and discuss about its future in clinical applications. Finally, we highlight the role of circulating ncRNAs in diagnosis of liver diseases and discuss the challenges and drawbacks of the usage of ncRNAs in clinical setting.
Collapse
Affiliation(s)
- Sanchari Roy
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Tom Luedde
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Roderburg
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| |
Collapse
|
29
|
Fawzy MS, Ellawindy A, Hussein MH, Khashana MS, Darwish MK, Abdel-Daim MM, Toraih EA. Long noncoding RNA H19, and not microRNA miR-326, is over-expressed and predicts survival in glioblastoma. Biochem Cell Biol 2018; 96:832-839. [PMID: 30096248 DOI: 10.1139/bcb-2018-0122] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Glioblastoma (GB) represents the most common malignant brain tumor, which, despite extensive research, remains of poor prognosis. The focus of recent studies of GB pathogenesis has shifted to the study of the role of noncoding RNAs (ncRNAs). In this study, we examined the expression levels of the microRNA miR-326 and the long ncRNA H19 (on which a miR-326 putative binding site was found by in-silico analysis) in brain tumor tissue from GB patients as compared to cancer-free brain tissue. Relative expression levels of miR-326 were not found to be significantly altered in GB patients. By comparison, H19 was consistently over-expressed in all GB patients (p < 0.001), and correlated with poorer overall survival (OS) and progression-free survival (PFS) (p = 0.026 and p = 0.045, respectively). At a cutoff value of 5.27, H19 up-regulation could predict OS in GB patients, with a 71.4% sensitivity and 59.6% specificity (p = 0.026). The current GB patients were clustered by the multivariate analysis into 4 groups based on miR-326 and H19 expression profiles, age at diagnosis, and PFS. Our data suggest a role for H19 in the pathogenesis of GB and could be a potential prognostic biomarker for GB.
Collapse
Affiliation(s)
- Manal S Fawzy
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.,Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
| | - Alia Ellawindy
- Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | | | | | - Marwa K Darwish
- Department of Chemistry, Biochemistry Branch, Faculty of Science, Suez University, Suez, Egypt
| | - Mohamed M Abdel-Daim
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Eman A Toraih
- Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.,Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
30
|
Emerging roles of non-coding RNAs in the pathogenesis, diagnosis and prognosis of osteosarcoma. Invest New Drugs 2018; 36:1116-1132. [DOI: 10.1007/s10637-018-0624-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/18/2018] [Indexed: 12/13/2022]
|
31
|
Ferlita AL, Battaglia R, Andronico F, Caruso S, Cianci A, Purrello M, Pietro CD. Non-Coding RNAs in Endometrial Physiopathology. Int J Mol Sci 2018; 19:ijms19072120. [PMID: 30037059 PMCID: PMC6073439 DOI: 10.3390/ijms19072120] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/12/2018] [Accepted: 07/14/2018] [Indexed: 12/18/2022] Open
Abstract
The Human Genome Project led to the discovery that about 80% of our DNA is transcribed in RNA molecules. Only 2% of the human genome is translated into proteins, the rest mostly produces molecules called non-coding RNAs, which are a heterogeneous class of RNAs involved in different steps of gene regulation. They have been classified, according to their length, into small non-coding RNAs and long non-coding RNAs, or to their function, into housekeeping non-coding RNAs and regulatory non-coding RNAs. Their involvement has been widely demonstrated in all cellular processes, as well as their dysregulation in human pathologies. In this review, we discuss the function of non-coding RNAs in endometrial physiology, analysing their involvement in embryo implantation. Moreover, we explore their role in endometrial pathologies such as endometrial cancer, endometriosis and chronic endometritis.
Collapse
Affiliation(s)
- Alessandro La Ferlita
- Department of Biomedical and Biotechnological Sciences, Biology and Genetics Section G. Sichel, University of Catania, 95123 Catania, Italy.
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Biology and Genetics Section G. Sichel, University of Catania, 95123 Catania, Italy.
| | - Francesca Andronico
- Department of Biomedical and Biotechnological Sciences, Biology and Genetics Section G. Sichel, University of Catania, 95123 Catania, Italy.
| | - Salvatore Caruso
- Department of General Surgery and Medical Surgical Specialties, University of Catania, 95123 Catania, Italy.
| | - Antonio Cianci
- Department of General Surgery and Medical Surgical Specialties, University of Catania, 95123 Catania, Italy.
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Biology and Genetics Section G. Sichel, University of Catania, 95123 Catania, Italy.
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Biology and Genetics Section G. Sichel, University of Catania, 95123 Catania, Italy.
| |
Collapse
|
32
|
Barbagallo C, Brex D, Caponnetto A, Cirnigliaro M, Scalia M, Magnano A, Caltabiano R, Barbagallo D, Biondi A, Cappellani A, Basile F, Di Pietro C, Purrello M, Ragusa M. LncRNA UCA1, Upregulated in CRC Biopsies and Downregulated in Serum Exosomes, Controls mRNA Expression by RNA-RNA Interactions. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:229-241. [PMID: 30195762 PMCID: PMC6023947 DOI: 10.1016/j.omtn.2018.05.009] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) contribute to the onset of many neoplasias through RNA-RNA competitive interactions; in addition, they could be secreted by cancer cells into biological fluids, suggesting their potential diagnostic application. By analyzing the expression of 17 lncRNAs and 31 circRNAs in biopsies and serum exosomes from colorectal cancer (CRC) patients through qRT-PCR, we detected CCAT1, CCAT2, HOTAIR, and UCA1 upregulation and CDR1AS, MALAT1, and TUG1 downregulation in biopsies. In serum exosomes, UCA1 was downregulated, while circHIPK3 and TUG1 were upregulated. Combined receiver operating characteristic (ROC) curves of TUG1:UCA1 and circHIPK3:UCA1 showed high values of sensitivity and specificity. Through in vitro (i.e., RNA silencing and mitogen-activated protein kinase [MAPK] inhibition) and in silico analyses (i.e., expression correlation and RNA-RNA-binding prediction), we found that UCA1 could (1) be controlled by MAPKs through CEBPB; (2) sequester miR-135a, miR-143, miR-214, and miR-1271, protecting ANLN, BIRC5, IPO7, KIF2A, and KIF23 from microRNA (miRNA)-induced degradation; and (3) interact with mRNA 3'-UTRs, preventing miRNA binding. UCA1 and its co-regulated antisense LINC01764 could interact and reciprocally mask their own miRNA-binding sites. Functional enrichment analysis of the RNA-RNA network controlled by UCA1 suggested its potential involvement in cellular migration. The UCA1 regulatory axis would represent a promising target to develop innovative RNA-based therapeutics against CRC.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Duilia Brex
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Matilde Cirnigliaro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Marina Scalia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Antonio Magnano
- Digestive Endoscopy Service, Vittorio Emanuele Hospital, Catania 95124, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania 95123, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Antonio Biondi
- Department of Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
| | - Alessandro Cappellani
- Department of Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
| | - Francesco Basile
- Department of Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina (EN) 94018, Italy.
| |
Collapse
|
33
|
Shao Y, Li H, Du R, Meng J, Yang G. Involvement of non-coding RNAs in chemotherapy resistance of ovarian cancer. J Cancer 2018; 9:1966-1972. [PMID: 29896281 PMCID: PMC5995945 DOI: 10.7150/jca.24550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/25/2018] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecological malignancy, with a low 5-year survival rate. Most patients with ovarian cancer are diagnosed in late-stages. A rising number of non-coding RNAs (ncRNAs) have been found to act as key regulators of gene expression by applying novel high-thought methods, such as next generation sequencing (NGS). Non-coding RNAs not only play important roles in carcinogenesis, but also affect the clinical treatment strategies. One of the biggest challenge in OC treatment was chemoresistance, which causes poor prognosis and high recurrence rate after applying traditional remedies. Of note, it has been proved that ncRNAs were deeply correlated with chemoresistance in several cancers, which made ncRNAs considered to be potential therapeutic targets in ovarian cancer. Among of all ncRNAs, the studies of miRNAs and lncRNAs in ovarian cancer chemoresistance were much clearer. In this study, we reviewed the most relevant researches in this field, and described the relationships between ncRNAs and chemoresistance in ovarian cancer.
Collapse
Affiliation(s)
- Yang Shao
- Cancer Institute, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hui Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Central Laboratory, The Fifth People's Hospital of Shanghai Fudan University, Shanghai 200240, China
| | - Ran Du
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Central Laboratory, The Fifth People's Hospital of Shanghai Fudan University, Shanghai 200240, China
| | - Jiao Meng
- Cancer Institute, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Gong Yang
- Cancer Institute, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Central Laboratory, The Fifth People's Hospital of Shanghai Fudan University, Shanghai 200240, China
| |
Collapse
|