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Bocchini M, Tazzari M, Ravaioli S, Piccinini F, Foca F, Tebaldi M, Nicolini F, Grassi I, Severi S, Calogero RA, Arigoni M, Schrader J, Mazza M, Paganelli G. Circulating hsa-miR-5096 predicts 18F-FDG PET/CT positivity and modulates somatostatin receptor 2 expression: a novel miR-based assay for pancreatic neuroendocrine tumors. Front Oncol 2023; 13:1136331. [PMID: 37287922 PMCID: PMC10242108 DOI: 10.3389/fonc.2023.1136331] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/25/2023] [Indexed: 06/09/2023] Open
Abstract
Gastro-entero-pancreatic neuroendocrine tumors (GEP-NETs) are rare diseases encompassing pancreatic (PanNETs) and ileal NETs (SINETs), characterized by heterogeneous somatostatin receptors (SSTRs) expression. Treatments for inoperable GEP-NETs are limited, and SSTR-targeted Peptide Receptor Radionuclide Therapy (PRRT) achieves variable responses. Prognostic biomarkers for the management of GEP-NET patients are required. 18F-FDG uptake is a prognostic indicator of aggressiveness in GEP-NETs. This study aims to identify circulating and measurable prognostic miRNAs associated with 18F-FDG-PET/CT status, higher risk and lower response to PRRT. Methods Whole miRNOme NGS profiling was conducted on plasma samples obtained from well-differentiated advanced, metastatic, inoperable G1, G2 and G3 GEP-NET patients enrolled in the non-randomized LUX (NCT02736500) and LUNET (NCT02489604) clinical trials prior to PRRT (screening set, n= 24). Differential expression analysis was performed between 18F-FDG positive (n=12) and negative (n=12) patients. Validation was conducted by Real Time quantitative PCR in two distinct well-differentiated GEP-NET validation cohorts, considering the primary site of origin (PanNETs n=38 and SINETs n=30). The Cox regression was applied to assess independent clinical parameters and imaging for progression-free survival (PFS) in PanNETs. In situ RNA hybridization combined with immunohistochemistry was performed to simultaneously detect miR and protein expression in the same tissue specimens. This novel semi-automated miR-protein protocol was applied in PanNET FFPE specimens (n=9). In vitro functional experiments were performed in PanNET models. Results While no miRNAs emerged to be deregulated in SINETs, hsa-miR-5096, hsa-let-7i-3p and hsa-miR-4311 were found to correlate with 18F-FDG-PET/CT in PanNETs (p-value:<0.005). Statistical analysis has shown that, hsa-miR-5096 can predict 6-month PFS (p-value:<0.001) and 12-month Overall Survival upon PRRT treatment (p-value:<0.05), as well as identify 18F-FDG-PET/CT positive PanNETs with worse prognosis after PRRT (p-value:<0.005). In addition, hsa-miR-5096 inversely correlated with both SSTR2 expression in PanNET tissue and with the 68Gallium-DOTATOC captation values (p-value:<0.05), and accordingly it was able to decrease SSTR2 when ectopically expressed in PanNET cells (p-value:<0.01). Conclusions hsa-miR-5096 well performs as a biomarker for 18F-FDG-PET/CT and as independent predictor of PFS. Moreover, exosome-mediated delivery of hsa-miR-5096 may promote SSTR2 heterogeneity and thus resistance to PRRT.
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Affiliation(s)
- Martine Bocchini
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Marcella Tazzari
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Sara Ravaioli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Filippo Piccinini
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Flavia Foca
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Michela Tebaldi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Fabio Nicolini
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Ilaria Grassi
- Nuclear Medicine and Radiometabolic Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Stefano Severi
- Nuclear Medicine and Radiometabolic Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Raffaele Adolfo Calogero
- Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Maddalena Arigoni
- Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Joerg Schrader
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Giovanni Paganelli
- Nuclear Medicine and Radiometabolic Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
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Kamenova S, Aralbayeva A, Kondybayeva A, Akimniyazova A, Pyrkova A, Ivashchenko A. Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson's Disease. Front Genet 2021; 12:647288. [PMID: 33859673 PMCID: PMC8042338 DOI: 10.3389/fgene.2021.647288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
Parkinson’s disease (PD) exhibits the second-highest rate of mortality among neurodegenerative diseases. PD is difficult to diagnose and treat due to its polygenic nature. In recent years, numerous studies have established a correlation between this disease and miRNA expression; however, it remains necessary to determine the quantitative characteristics of the interactions between miRNAs and their target genes. In this study, using novel bioinformatics approaches, the quantitative characteristics of the interactions between miRNAs and the mRNAs of candidate PD genes were established. Of the 6,756 miRNAs studied, more than one hundred efficiently bound to mRNA of 61 candidate PD genes. The miRNA binding sites (BS) were located in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR) of the mRNAs. In the mRNAs of many genes, the locations of miRNA BS with overlapping nucleotide sequences (clusters) were identified. Such clusters substantially reduced the proportion of nucleotide sequences of miRNA BS in the 5′UTRs, CDSs, and 3′UTRs. The organization of miRNA BS into clusters leads to competition among miRNAs to bind mRNAs. Differences in the binding characteristics of miRNAs to the mRNAs of genes expressed at different rates were identified. Single miRNA BS, polysites for the binding for one miRNA, and multiple BS for two or more miRNAs in one mRNA were identified. Evolutionary changes in the BS of miRNAs and their clusters in 5′UTRs, CDSs and 3′UTRs of mRNA of orthologous candidate PD genes were established. Based on the quantitative characteristics of the interactions between miRNAs and mRNAs candidate PD genes, several associations recommended as markers for the diagnosis of PD.
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Affiliation(s)
- Saltanat Kamenova
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Assel Aralbayeva
- Department of Neurology, Kazakh Medical University, Almaty, Kazakhstan
| | - Aida Kondybayeva
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigul Akimniyazova
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anatoliy Ivashchenko
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Predicting Associations of miRNAs and Candidate Gastric Cancer Genes for Nanomedicine. NANOMATERIALS 2021; 11:nano11030691. [PMID: 33801990 PMCID: PMC8000878 DOI: 10.3390/nano11030691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/17/2022]
Abstract
Nanoscale miRNAs regulate the synthesis of most human proteins involved in differentiation, proliferation, cell cycle, apoptosis, and other processes associated with the growth and the development of an organism. miRNAs also play a number of important roles in the development of gastric cancer. In this work, we studied the quantitative characteristics of miRNA interactions with 69 candidate gastric cancer genes using bioinformatics approaches. To this end, the MirTarget program was used, which determines the characteristics of miRNA binding to mRNA in the 5′UTR, CDS, and 3′UTR. Associations of miRNAs with alternative target genes and associations of genes with alternative miRNAs were established. The cluster organization of miRNA binding sites (BSs) in mRNA was revealed, leading to the emergence of miRNA competition for binding to the mRNA of a target gene. Groups of target genes with clusters of overlapping BSs include miR-5095, miR-619-5p, miR-1273 family, miR-466, ID01030.3p-miR, ID00436.3p-miR, miR-574-5p, and ID00470.5p-miR. In the defined associations of target genes and miRNAs, miRNA BSs are organized into clusters of multiple BSs, which facilitate the design and the development of a system of chips that can be used to control the state of miRNA and target genes associations in gastric cancer.
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Mukushkina D, Aisina D, Pyrkova A, Ryskulova A, Labeit S, Ivashchenko A. In silico Prediction of miRNA Interactions With Candidate Atherosclerosis Gene mRNAs. Front Genet 2020; 11:605054. [PMID: 33329752 PMCID: PMC7672156 DOI: 10.3389/fgene.2020.605054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
The involvement of genes and miRNAs in the development of atherosclerosis is a challenging problem discussed in recent publications. It is necessary to establish which miRNAs affect the expression of candidate genes. We used known candidate atherosclerosis genes to predict associations. The quantitative characteristics of interactions of miRNAs with mRNA candidate genes were determined using the program, which identifies the localization of miRNA binding sites in mRNA, the free energy interaction of miRNA with mRNA. In mRNAs of GAS6 and NFE2L2 candidate genes, binding sites of 21 miRNAs and of 15 miRNAs, respectively, were identified. In IRS2 mRNA binding sites of 25 miRNAs were located in a cluster of 41 nt. In ADRB3, CD36, FASLG, FLT1, PLA2G7, and PPARGC1A mRNAs, clusters of miR-466, ID00436.3p-miR, and ID01030.3p-miR BS were identified. The organization of overlapping miRNA binding sites in clusters led to their compaction and caused competition among the miRNAs. The binding of 53 miRNAs to the mRNAs of 14 candidate genes with free energy interactions greater than -130 kJ/mole was determined. The miR-619-5p was fully complementary to ADAM17 and CD36 mRNAs, ID01593.5p-miR to ANGPTL4 mRNA, ID01935.5p-miR to NFE2L2, and miR-5096 to IL18 mRNA. Associations of miRNAs and candidate atherosclerosis genes are proposed for the early diagnosis of this disease.
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Affiliation(s)
- Dina Mukushkina
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dana Aisina
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Alma Ryskulova
- Department of microbiology, Kazakh Medical University of Continuing Education, Almaty, Kazakhstan
| | - Siegfried Labeit
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Anatoliy Ivashchenko
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Kondybayeva А, Akimniyazova A, Kamenova S, Duchshanova G, Aisina D, Goncharova A, Ivashchenko А. Prediction of miRNA interaction with mRNA of stroke candidate genes. Neurol Sci 2019; 41:799-808. [PMID: 31784845 DOI: 10.1007/s10072-019-04158-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The role of miRNA in tissue affected by stroke is actively studied, but it remains unclear which miRNAs and target genes are involved in the development of stroke. METHODS The MirTarget program defines the following features of a miRNA binding to a mRNA: the binding start site, the location of the binding site in mRNA, the free energy of a miRNA binding with a mRNA, and the interaction schemes of miRNA and mRNA. RESULTS The interaction of 6565 miRNAs with mRNAs of stroke candidate genes was determined. The association of the mRNAs of stroke candidate genes with miRNAs depends on the level of gene expression. Some highly expressed candidate genes are targets of miR-619-5p and miR-5095, which have binding sites located on overlapping mRNA nucleotide sequences (clusters). miR-619-5p and miR-5095 bind to mRNA of 15 genes. Clusters for the binding of miR-1273f,d,e are in mRNAs of highly expressed genes. The start sites of miR-1273d and miR-1273e binding in all clusters are in sequences with one and ten nucleotides, respectively. The clusters of multiple miR-574-5p and ID00470.5p-miR binding sites and the clusters of the miR-466, ID01030.3p-miR, and ID00436.3p-miR binding sites are in mRNAs of some genes expressed at low levels. CONCLUSION The organization of miRNA binding sites into clusters reduces the length of mRNA and creates competition between miRNAs for binding to mRNA of a target gene. The characteristics of miRNA associations with target genes can be used to recommend markers for a diagnosis of stroke.
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Affiliation(s)
- Аida Kondybayeva
- Join-Stock Company "National Medical University", Almaty, Kazakhstan, 050012
| | - Aigul Akimniyazova
- SRI of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Saltanat Kamenova
- Join-Stock Company "National Medical University", Almaty, Kazakhstan, 050012
| | - Gulsum Duchshanova
- Join-Stock Company "South Kazakhstan Medical Academy", Shymkent, Kazakhstan, 160019
| | - Dana Aisina
- SRI of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Alla Goncharova
- SRI of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Аnatoliy Ivashchenko
- SRI of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.
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Aisina D, Niyazova R, Atambayeva S, Ivashchenko A. Prediction of clusters of miRNA binding sites in mRNA candidate genes of breast cancer subtypes. PeerJ 2019; 7:e8049. [PMID: 31741798 PMCID: PMC6858813 DOI: 10.7717/peerj.8049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022] Open
Abstract
The development of breast cancer (BC) subtypes is controlled by distinct sets of candidate genes, and the expression of these genes is regulated by the binding of their mRNAs with miRNAs. Predicting miRNA associations and target genes is thus essential when studying breast cancer. The MirTarget program identifies the initiation of miRNA binding to mRNA, the localization of miRNA binding sites in mRNA regions, and the free energy from the binding of all miRNA nucleotides with mRNA. Candidate gene mRNAs have clusters (miRNA binding sites with overlapping nucleotide sequences). mRNAs of EPOR, MAZ and NISCH candidate genes of the HER2 subtype have clusters, and there are four clusters in mRNAs of MAZ, BRCA2 and CDK6 genes. Candidate genes of the triple-negative subtype are targets for multiple miRNAs. There are 11 sites in CBL mRNA, five sites in MMP2 mRNA, and RAB5A mRNA contains two clusters in each of the three sites. In SFN mRNA, there are two clusters in three sites, and one cluster in 21 sites. Candidate genes of luminal A and B subtypes are targets for miRNAs: there are 21 sites in FOXA1 mRNA and 15 sites in HMGA2 mRNA. There are clusters of five sites in mRNAs of ITGB1 and SOX4 genes. Clusters of eight sites and 10 sites are identified in mRNAs of SMAD3 and TGFB1 genes, respectively. Organizing miRNA binding sites into clusters reduces the proportion of nucleotide binding sites in mRNAs. This overlapping of miRNA binding sites creates a competition among miRNAs for a binding site. From 6,272 miRNAs studied, only 29 miRNAs from miRBase and 88 novel miRNAs had binding sites in clusters of target gene mRNA in breast cancer. We propose using associations of miRNAs and their target genes as markers in breast cancer subtype diagnosis.
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Affiliation(s)
- Dana Aisina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Raigul Niyazova
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Shara Atambayeva
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anatoliy Ivashchenko
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients. Int J Mol Sci 2019; 20:ijms20040937. [PMID: 30795533 PMCID: PMC6412294 DOI: 10.3390/ijms20040937] [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: 01/23/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/19/2022] Open
Abstract
Background: Skin cancer represents the most common human malignancy, and it includes BCC, SCC, and melanoma. Since melanoma is one of the most aggressive types of cancer, we have herein attempted to develop a gene-specific intron retention signature that can distinguish BCC and SCC from melanoma biopsy tumors. Methods: Intron retention events were examined through RT-sqPCR protocols, using total RNA preparations derived from BCC, SCC, and melanoma Greek biopsy specimens. Intron-hosted miRNA species and their target transcripts were predicted via the miRbase and miRDB bioinformatics platforms, respectively. Ιntronic ORFs were recognized through the ORF Finder application. Generation and visualization of protein interactomes were achieved by the IntAct and Cytoscape softwares, while tertiary protein structures were produced by using the I-TASSER online server. Results: c-MYC and Sestrin-1 genes proved to undergo intron retention specifically in melanoma. Interaction maps of proteins encoded by genes being potentially targeted by retained intron-accommodated miRNAs were generated and SRPX2 was additionally delivered to our melanoma-specific signature. Novel ORFs were identified in MCT4 and Sestrin-1 introns, with potentially critical roles in melanoma development. Conclusions: The property of c-MYC, Sestrin-1, and SRPX2 genes to retain specific introns could be clinically used to molecularly differentiate non-melanoma from melanoma tumors.
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Guerrero Flórez M, Guerrero Gómez OA, Mena Huertas J, Yépez Chamorro MC. Mapping of microRNAs related to cervical cancer in Latin American human genomic variants. F1000Res 2018; 6:946. [PMID: 37766816 PMCID: PMC10521080 DOI: 10.12688/f1000research.10138.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 09/29/2023] Open
Abstract
Background: MicroRNAs are related to human cancers, including cervical cancer (CC) caused by HPV. In 2018, approximately 56.075 cases and 28.252 deaths from this cancer were registered in Latin America and the Caribbean according to GLOBOCAN reports. The main molecular mechanism of HPV in CC is related to integration of viral DNA into the hosts' genome. However, the different variants in the human genome can result in different integration mechanisms, specifically involving microRNAs (miRNAs). Methods: The miRNAs associated with CC were obtained from literature, the miRNA sequences and four human genome variants (HGV) from Latin American populations were obtained from miRBase and 1000 Genomes Browser, respectively. HPV integration sites near cell cycle regulatory genes were identified. miRNAs were mapped on HGV. miRSNPs were identified in the miRNA sequences located at HPV integration sites on the Latin American HGV. Results: Two hundred seventy-two miRNAs associated with CC were identified in 139 reports from different geographic locations. By mapping with Blast-Like Alignment Tool (BLAT), 2028 binding sites were identified from these miRNAs on the human genome (version GRCh38/hg38); 42 miRNAs were located on unique integration sites; and miR-5095, miR-548c-5p and miR-548d-5p were involved with multiple genes related to the cell cycle. Thirty-seven miRNAs were mapped on the Latin American HGV (PUR, MXL, CLM and PEL), but only miR-11-3p, miR-31-3p, miR-107, miR-133a-3p, miR-133a-5p, miR-133b, miR-215-5p, miR-491-3p, miR-548d-5p and miR-944 were conserved. Conclusions: Ten miRNAs were conserved in the four HGV. In the remaining 27 miRNAs, substitutions, deletions or insertions were observed. These variation patterns can imply differentiated mechanisms towards each genomic variant in human populations because of specific genomic patterns and geographic features. These findings may help in determining susceptibility for CC development. Further identification of cellular genes and signalling pathways involved in CC progression could lead new therapeutic strategies based on miRNAs.
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Affiliation(s)
- Milena Guerrero Flórez
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - Olivia Alexandra Guerrero Gómez
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - Jaqueline Mena Huertas
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - María Clara Yépez Chamorro
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
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Thuringer D, Boucher J, Jego G, Pernet N, Cronier L, Hammann A, Solary E, Garrido C. Transfer of functional microRNAs between glioblastoma and microvascular endothelial cells through gap junctions. Oncotarget 2018; 7:73925-73934. [PMID: 27661112 PMCID: PMC5342024 DOI: 10.18632/oncotarget.12136] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/04/2016] [Indexed: 12/29/2022] Open
Abstract
Extensive invasion and angiogenesis are hallmark features of malignant glioblastomas. Here, we co-cultured U87 human glioblastoma cells and human microvascular endothelial cells (HMEC) to demonstrate the exchange of microRNAs that initially involve the formation of gap junction communications between the two cell types. The functional inhibition of gap junctions by carbenoxolone blocks the transfer of the anti-tumor miR-145-5p from HMEC to U87, and the transfer of the pro-invasive miR-5096 from U87 to HMEC. These two microRNAs exert opposite effects on angiogenesis in vitro. MiR-5096 was observed to promote HMEC tubulogenesis, initially by increasing Cx43 expression and the formation of heterocellular gap junctions, and secondarily through a gap-junction independent pathway. Our results highlight the importance of microRNA exchanges between tumor and endothelial cells that in part involves the formation of functional gap junctions between the two cell types.
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Affiliation(s)
| | | | - Gaetan Jego
- INSERM, U866, Faculty of Medecine, 21000 Dijon, France.,University of Bourgogne-Franche-Comté, 21000 Dijon, France
| | - Nicolas Pernet
- INSERM, U866, Faculty of Medecine, 21000 Dijon, France.,University of Bourgogne-Franche-Comté, 21000 Dijon, France
| | | | | | - Eric Solary
- INSERM, U1170, Institut Gustave Roussy, 94508 Villejuif, France
| | - Carmen Garrido
- INSERM, U866, Faculty of Medecine, 21000 Dijon, France.,University of Bourgogne-Franche-Comté, 21000 Dijon, France.,CGFL, 21000 Dijon, France
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10
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Balachander GM, Rajashekar B, M Sarashetti P, Rangarajan A, Chatterjee K. MiRNomics Reveals Breast Cancer Cells Cultured on 3D Scaffolds Better Mimic Tumors in Vivo than Conventional 2D Culture. ACS Biomater Sci Eng 2017; 4:116-127. [DOI: 10.1021/acsbiomaterials.7b00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Balaji Rajashekar
- Genotypic Technology Pvt. Ltd., 259, Apurva, Fourth Cross, 80 Feet Road, RMV Second Stage, Bangalore 560094, India
| | - Prasad M Sarashetti
- Genotypic Technology Pvt. Ltd., 259, Apurva, Fourth Cross, 80 Feet Road, RMV Second Stage, Bangalore 560094, India
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11
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Chen D, Liu L, Luo X, Mu A, Yan L, Chen X, Wang L, Wang N, He H, Zhou H, Zhang T. Effect of SMYD3 on the microRNA expression profile of MCF-7 breast cancer cells. Oncol Lett 2017; 14:1831-1840. [PMID: 28789418 DOI: 10.3892/ol.2017.6320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 03/28/2017] [Indexed: 01/02/2023] Open
Abstract
SET and MYND domain containing 3 (SMYD3) is a histone methyltransferase (HMT) and transcription factor, which serves important roles in carcinogenesis. Numerous downstream target genes of SMYD3 have been identified in previous studies. However, the downstream microRNA (miRNA) s regulated by SMYD3 are yet to be elucidated. In the present study, the results of miRNA microarray demonstrated that 30 miRNA expression profiles were upregulated, whilst 24 miRNAs were downregulated by >2.0-fold in the SMYD3-overexpressed MCF-7 breast cancer cells. The HMT activity was demonstrated to be essential for SMYD3-mediated transactivation of miR-200c-3p and the overexpression of miR-200c-3p inhibited the transactivation effects of SMYD3 on myocardin-related transcription factor-A-dependent migration-associated genes. To our best knowledge, the current study is the first to report on the transcriptional regulation of SMYD3 on miRNAs, and miR-200c may be a downstream negative regulator of the SMYD3-mediated pathway in the migration of breast cancer cells. These results may provide a novel theoretical basis to understand the mechanisms underlying the initiation, progression, diagnosis, prevention and therapy of breast cancer.
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Affiliation(s)
- Dongju Chen
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Lei Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Xuegang Luo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Ai Mu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Lihua Yan
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Xiaoying Chen
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Lei Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Hongpeng He
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Hao Zhou
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, P.R. China.,Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
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Atambayeva S, Niyazova R, Ivashchenko A, Pyrkova A, Pinsky I, Akimniyazova A, Labeit S. The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes. BMC Genomics 2017; 18:428. [PMID: 28569192 PMCID: PMC5452331 DOI: 10.1186/s12864-017-3811-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/22/2017] [Indexed: 01/13/2023] Open
Abstract
Background Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the properties of miRNAs and their diagnostic and medical applications. Results The search of 2,750 human microRNAs (miRNAs) binding sites in 12,175 mRNAs of human genes using the MirTarget program has been completed. For the binding sites of the miR-619-5p the hybridization free energy of the bonds was equal to 100% of the maximum potential free energy. The mRNAs of 201 human genes have complete complementary binding sites of miR-619-5p in the 3’UTR (214 sites), CDS (3 sites), and 5’UTR (4 sites). The mRNAs of CATAD1, ICA1L, GK5, POLH, and PRR11 genes have six miR-619-5p binding sites, and the mRNAs of OPA3 and CYP20A1 genes have eight and ten binding sites, respectively. All of these miR-619-5p binding sites are located in the 3’UTRs. The miR-619-5p binding site in the 5’UTR of mRNA of human USP29 gene is found in the mRNAs of orthologous genes of primates. Binding sites of miR-619-5p in the coding regions of mRNAs of C8H8orf44, C8orf44, and ISY1 genes encode the WLMPVIP oligopeptide, which is present in the orthologous proteins. Binding sites of miR-619-5p in the mRNAs of transcription factor genes ZNF429 and ZNF429 encode the AHACNP oligopeptide in another reading frame. Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes. Conclusions The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3811-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shara Atambayeva
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan.
| | - Raigul Niyazova
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anatoliy Ivashchenko
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ilya Pinsky
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigul Akimniyazova
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Siegfried Labeit
- Institute for Anaesthesiology and Intensive Operative Care Medical Faculty Mannheim, Mannheim, Germany
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Qiu G, Zhang XB, Zhang SQ, Liu PL, Wu W, Zhang JY, Dai SR. Dysregulation of MALAT1 and miR-619-5p as a prognostic indicator in advanced colorectal carcinoma. Oncol Lett 2016; 12:5036-5042. [PMID: 28101234 DOI: 10.3892/ol.2016.5312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/24/2016] [Indexed: 12/12/2022] Open
Abstract
The present study aimed to detect the expression of metastasis associated lung adenocarcinoma transcript 1 (MALAT1) and microRNA (miR)-619-5p in colorectal carcinoma (CRC), and to evaluate the significance of MALAT1 and miR-619-5p expression in the clinical diagnosis and prognosis of CRC. Quantitative polymerase chain reaction was used to detect MALAT1 and miR-619-5p expression in 120 colorectal carcinoma and 120 adjacent normal tissue samples. The expression levels of MALAT1 and miR-619-5p were significantly different between colorectal carcinoma and adjacent normal tissues (P<0.05). MALAT1 exhibited an average 2.52-fold increase in colorectal adenoma when compared with adjacent normal tissues, while miR-619-5p exhibited an average 5.79-fold decrease in colorectal adenoma when compared with adjacent normal tissues. There was a significant difference between the MALAT1 expression in CRC tissues obtained from men and women (P=0.027), and in tumor-node-metastasis (TNM) stage II and stage III lesions (P=0.019). MALAT1 expression was associated with lymphovascular invasion (P=0.047) and perineural invasion (P=0.012). In addition, miR-619-5p expression was also significantly different between men and women (P=0.032), and between TNM stage II and stage III lesions (P=0.012). miR-619-5p expression was also associated with lymphovascular invasion (P=0.023) and perineural invasion (P=0.009). Patients with high expression of MALAT1 and low expression of miR-619-5p demonstrated significantly shorter disease-free survival (DFS) (P=0.002) and overall survival (OS) times (P=0.004) compared with patients with low MALAT1 expression and high miR-619-5p expression. Patients with perineural invasion demonstrated significantly shorter DFS (P=0.001) and OS times (P=0.003) compared with patients without perineural invasion. In addition, there was a negative correlation between MALAT1 expression and miR-619-5p expression (r=-0.415, P=0.004) in CRC tissues. In conclusion, MALAT1 and miR-619-5p have potential for the molecular diagnosis of CRC patients, and combined assaying of MALAT1 and miR-619-5p may improve the accuracy of the diagnosis of CRC and act as a good prognostic indicator in CRC patients.
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Affiliation(s)
- Gu Qiu
- Department of Clinical Laboratories, Nantong Second People's Hospital, Nantong, Jiangsu 226002, P.R. China
| | - Xiu-Bing Zhang
- Department of Internal Medicine-Oncology, Nantong Second People's Hospital, Nantong, Jiangsu 226002, P.R. China
| | - Shu-Qing Zhang
- Department of Clinical Laboratories, Nantong Second People's Hospital, Nantong, Jiangsu 226002, P.R. China
| | - Pei-Long Liu
- Department of Clinical Laboratories, Nantong Second People's Hospital, Nantong, Jiangsu 226002, P.R. China
| | - Wei Wu
- Department of Experimental Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jin-Ye Zhang
- Department of Clinical Laboratories, Nantong Tumor Hospital, Nantong, Jiangsu 226018, P.R. China
| | - Shi-Rong Dai
- Department of Clinical Laboratories, Nantong Second People's Hospital, Nantong, Jiangsu 226002, P.R. China
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Tang Y, Ji H, Liu H, Gu W, Li X, Peng T. Identification and functional analysis of microRNA in myometrium tissue from spontaneous preterm labor. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:12811-12819. [PMID: 26722471 PMCID: PMC4680416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 09/25/2015] [Indexed: 06/05/2023]
Abstract
Spontaneous preterm labor is an important complication in perinatology characterized by early onset myometrium contractions leading to labor at preterm. However, the exact mechanism that maintain uterine quiescence and promote increased uterine contractility during labor were incompletely defined. MicroRNAs is a class of short non-coding RNAs that regulate gene expression at the post-transcriptional level by binding the 3' untranslated region of target mRNAs and play an important role in biological process and cellular functions. We hypothesized we could find differentially expressed microRNAs in the myometrium of women in spontaneous preterm labor. Thus, a microarray analysis of miRNAs of preterm myometrium was performed. 18 out of the 2006 detected microRNAs were found to be significantly dysregulated in myometrium in labor verse not in labor at preterm. Biological validation by quantitative real-time polymerase chain reaction confirms us a consistence rate of 83.3% (5 out of 6) with microarray analysis. The target genes for validated microRNAs were predicted by three algorithms (PicTar, TargetScan, and miRanda). Most of the potential targets of the miRNAs were relevant to positive regulation of cardiac muscle hypertrophy, reduction of cytosolic calcium ion concentration and relaxation of cardiac muscle as well as prostate cancer, adherents junction, regulation of actin cytoskeleton and regulation and other factor-regulated calcium reabsorption. Our result illustrates a characteristic microRNA profile in myometrium tissues and provides a new understanding of the process involved in spontaneous preterm labor.
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Affiliation(s)
- Yao Tang
- The Department of Obstetrics, Shanghai Obstetrics and Gynecology Hospital of Fudan UniversityShanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related DiseasesShanghai, China
| | - Hongjing Ji
- The Department of Obstetrics, Shanghai Obstetrics and Gynecology Hospital of Fudan UniversityShanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related DiseasesShanghai, China
| | - Haiyan Liu
- The Department of Obstetrics, Shanghai Obstetrics and Gynecology Hospital of Fudan UniversityShanghai, China
| | - Weirong Gu
- The Department of Obstetrics, Shanghai Obstetrics and Gynecology Hospital of Fudan UniversityShanghai, China
| | - Xiaotian Li
- The Department of Obstetrics, Shanghai Obstetrics and Gynecology Hospital of Fudan UniversityShanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related DiseasesShanghai, China
| | - Ting Peng
- The Department of Obstetrics, Shanghai Obstetrics and Gynecology Hospital of Fudan UniversityShanghai, China
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