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Stefanou IK, Dovrolis N, Gazouli M, Theodorou D, Zografos GK, Toutouzas KG. miRNAs expression pattern and machine learning models elucidate risk for gastric GIST. Cancer Biomark 2022; 33:237-247. [PMID: 35213356 DOI: 10.3233/cbm-210173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Gatrointestinal stromal tumors (GISTs) are the main mesenchymal tumors found in the gastrointestinal system. GISTs clinical phenotypes differ significantly and their molecular basis is not yet completely known. microRNAs (miRNAs) have been involved in carcinogenesis pathways by regulating gene expression at post-transcriptional level. OBJECTIVE The aim of the present study was to elucidate the expression profiles of miRNAs relevant to gastric GIST carcinogenesis, and to identify miRNA signatures that can discriminate the GIST from normal cases. METHODS miRNA expression was tested by miScript™miRNA PCR Array Human Cancer PathwayFinder kit and then we used machine learning in order to find a miRNA profile that can predict the risk for GIST development. RESULTS A number of miRNAs were found to be differentially expressed in GIST cases compared to healthy controls. Among them the hsa-miR-218-5p was found to be the best predictor for GIST development in our cohort. Additionally, hsa-miR-146a-5p, hsa-miR-222-3p, and hsa-miR-126-3p exhibit significantly lower expression in GIST cases compared to controls and were among the top predictors in all our predictive models. CONCLUSIONS A machine learning classification approach may be accurate in determining the risk for GIST development in patients. Our findings indicate that a small number of miRNAs, with hsa-miR218-5p as a focus, may strongly affect the prognosis of GISTs.
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Affiliation(s)
- Ioannis K Stefanou
- 1st Propaedeutic Department of Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece.,1st Propaedeutic Department of Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece.,1st Propaedeutic Department of Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, National and Kapodistrian University of Athens, Athens, Greece.,School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Dimitrios Theodorou
- 1st Propaedeutic Department of Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios K Zografos
- 1st Propaedeutic Department of Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos G Toutouzas
- 1st Propaedeutic Department of Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
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Ravegnini G, Serrano C, Simeon V, Sammarini G, Nannini M, Roversi E, Urbini M, Ferrè F, Ricci R, Tarantino G, Pantaleo MA, Hrelia P, Angelini S. The rs17084733 variant in the KIT 3' UTR disrupts a miR-221/222 binding site in gastrointestinal stromal tumour: a sponge-like mechanism conferring disease susceptibility. Epigenetics 2019; 14:545-557. [PMID: 30983504 PMCID: PMC6557610 DOI: 10.1080/15592294.2019.1595997] [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] [Indexed: 12/26/2022] Open
Abstract
Several miRNAs are dysregulated in gastrointestinal stromal tumours (GIST), and miR-221/222 appear to have a prominent role in GIST biology. Therefore, we investigated the role of DNA variants located in miR-221/222 precursor sequences and their target KIT 3'UTR. Ninety-five polymorphisms were analysed in 115 GIST cases and 88 healthy controls. KIT 3'UTR rs17084733 and pri-miR-222 rs75246947 were found significantly associated with GIST susceptibility. Specifically, KIT rs17084733 A allele was more common in GIST, particularly in KIT wild-type (WT) patients (Padj = 0.017). rs17084733 variant is located within one of the three miR-221/222 binding sites in the KIT 3'UTR, resulting in a mismatch in this seed region. Conversely, KIT mRNA levels were lower in patients carrying the variant allele, except for KIT mutant GIST. Luciferase assay data in GIST cells, generated using a construct containing all the three miR-221/222 binding sites, are consistent with KIT mRNA levels in GIST patients. Reporter assay data, generated using a construct containing only the site encompassing rs17084733, confirmed that this is a functional variant disrupting the miR-221/222 binding site. In conclusion, this is the first study investigating the role of SNPs on miR-221/222 precursor sequences and their binding region on KIT 3'UTR in GIST. We identified the KIT variant rs17084733 as a possible novel genetic biomarker for risk of developing KIT-WT GIST. Moreover, our findings suggest the role of one of the three miR-221/222 binding sites on KIT 3'UTR as endogenous sponge, soaking up and subtracting miR-221/222 to the other two sites characterized by a higher affinity.
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Affiliation(s)
- Gloria Ravegnini
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - César Serrano
- b Medical Oncology Department , Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital , Barcelona , Spain
| | - Vittorio Simeon
- c Medical Statistics Unit , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Giulia Sammarini
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Margherita Nannini
- d Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy
| | - Erica Roversi
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Milena Urbini
- e "Giorgio Prodi" Cancer Research Center , University of Bologna , Bologna , Italy
| | - Fabrizio Ferrè
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Riccardo Ricci
- f UOC di Anatomia Patologica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy.,g Department of Pathology , Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Tarantino
- e "Giorgio Prodi" Cancer Research Center , University of Bologna , Bologna , Italy
| | - Maria A Pantaleo
- d Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy.,e "Giorgio Prodi" Cancer Research Center , University of Bologna , Bologna , Italy
| | - Patrizia Hrelia
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Sabrina Angelini
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
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Settas N, Faucz FR, Stratakis CA. Succinate dehydrogenase (SDH) deficiency, Carney triad and the epigenome. Mol Cell Endocrinol 2018; 469:107-111. [PMID: 28739378 PMCID: PMC5776069 DOI: 10.1016/j.mce.2017.07.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 07/13/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
In this report, we review the relationship between succinate dehydrogenase (SDH) deficiency and the epigenome, especially with regards to two clinical conditions. Carney triad (CT) is a very rare disease with synchronous or metachronous occurrence of at least three different tumor entities; gastric gastrointestinal stromal tumor (GIST), paraganglioma (PGL), and pulmonary chondroma. This condition affects mostly females and it is never inherited. Another disease that shares two of the tumor components of CT, namely GIST and PGL is the Carney-Stratakis syndrome (CSS) or dyad. CSS affects both genders during childhood and adolescence. We review herein the main clinical features and molecular mechanisms behind those two syndromes that share quite a bit of similarities, but one is non-hereditary (CT) whereas the other shows an autosomal-dominant, with incomplete penetrance, inheritance pattern (CSS). Both CT and CSS are caused by the deficiency of the succinate dehydrogenase (SDH) enzyme. The key difference between the two syndromes is the molecular mechanism that causes the SDH deficiency. Most cases of CT show down-regulation of SDH through site-specific hyper-methylation of the SDHC gene, whereas CSS cases carry inactivating germline mutations within one of the genes coding for the SDH subunits A, B, C, or D (SDHA, SDHB, SDHC, and SDHD). There is only partial overlap between the two conditions (there are a few patients with CT that have SDH subunit mutations) but both lead to increased methylation of the entire genome in the tumors associated with them. Other tumors (outside CT and CSS) that have SDH deficiency are associated with increased methylation of the entire genome, but only in CT there is site-specific methylation of the SDHC gene. These findings have implications for diagnostics and the treatment of patients with these, often metastatic tumors.
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Affiliation(s)
- Nikolaos Settas
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, USA.
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, USA
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Brahmi M, Alberti L, Dufresne A, Ray-Coquard I, Cassier P, Meeus P, Decouvelaere AV, Ranchère-Vince D, Blay JY. KIT exon 10 variant (c.1621 A > C) single nucleotide polymorphism as predictor of GIST patient outcome. BMC Cancer 2015; 15:780. [PMID: 26498480 PMCID: PMC4619434 DOI: 10.1186/s12885-015-1817-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022] Open
Abstract
Background Tumor genotype plays a crucial role in clinical management of GIST. Whether genetic polymorphism of KIT may influence GIST patient outcome is unclear. Methods We investigated the biological and clinical significance of the presence of KIT exon 10 variant (c.1621 A > C), KITL541, in a transfected cell line (3 T3 L541) and in two retrospectively collected series of 109 GIST patients in total. The control group consisted of 60 healthy donors collected at the French department of blood transfusion. Results In the 3 T3 L541 cell line, KITL541 protein exhibited a spontaneous phosphorylation status comparable to that of wild-type KIT but displayed a phosphorylation pattern of AKT and ERK1/2 that was found similar to that of the classical mutated forms of the KIT receptor. Of 109 patients enrolled in this retrospective translational research study, 24 (22 %) harboured KITL541, similarly to the control group of healthy donors (n = 10 of 60, 17 %). A higher prevalence of the variant KITL541 was observed in patients with metastatic status at diagnosis (KITL541 correlated nine of 22 versus 15 of 87, p = 0.02). In addition, patients with KITL541 and localized GIST had a higher rate of relapse at 5 years and lower relapse free survival at 5 years in univariate, as well as in multivariate analysis. Response rate and duration of response to imatinib was similar in KITL541 and KITM541 patients. Conclusion KITL541 genotype is associated with a higher risk of metastasis at diagnosis and a higher risk of relapse in GIST patients. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1817-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mehdi Brahmi
- Department of medical oncology, Centre Leon Berard, 28 rue Laennec, Lyon, France.
| | - Laurent Alberti
- Cancer Research Center of Lyon, INSERM UMR 1052, CNRS UMR 5286, Centre Leon Berard, 28 rue Laennec, Lyon, France.
| | - Armelle Dufresne
- Cancer Research Center of Lyon, INSERM UMR 1052, CNRS UMR 5286, Centre Leon Berard, 28 rue Laennec, Lyon, France.
| | - Isabelle Ray-Coquard
- Department of medical oncology, Centre Leon Berard, 28 rue Laennec, Lyon, France.
| | - Philippe Cassier
- Department of medical oncology, Centre Leon Berard, 28 rue Laennec, Lyon, France.
| | - Pierre Meeus
- Department of medical oncology, Centre Leon Berard, 28 rue Laennec, Lyon, France.
| | | | | | - Jean-Yves Blay
- Department of medical oncology, Centre Leon Berard, 28 rue Laennec, Lyon, France.
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Nannini M, Ravegnini G, Angelini S, Astolfi A, Biasco G, Pantaleo MA. miRNA profiling in gastrointestinal stromal tumors: implication as diagnostic and prognostic markers. Epigenomics 2015; 7:1033-49. [PMID: 26447534 DOI: 10.2217/epi.15.52] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are a class of short noncoding RNAs, that play a relevant role in multiple biological processes, such as differentiation, proliferation and apoptosis. Gastrointestinal stromal tumors (GIST) are considered as a paradigm of molecular biology in solid tumors worldwide, and after the discovery of specific alterations in the KIT and PDGFRA genes, they have emerged from anonymity to become a model for targeted therapy. Epigenetics have an emerging and relevant role in different steps of GIST biology such as tumorigenesis, disease progression, prognosis and drug resistance. The aim of the present review was to summarize the current evidence about the role of microRNAs in GIST, including their potential application as well as their limits.
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Affiliation(s)
- Margherita Nannini
- Department of Specialized, Experimental & Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Gloria Ravegnini
- Department of Pharmacy & Biotechnology, FaBit; University of Bologna, Italy
| | - Sabrina Angelini
- Department of Pharmacy & Biotechnology, FaBit; University of Bologna, Italy
| | - Annalisa Astolfi
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Guido Biasco
- Department of Specialized, Experimental & Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.,"Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Maria A Pantaleo
- Department of Specialized, Experimental & Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.,"Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
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Haller F, Zhang JD, Moskalev EA, Braun A, Otto C, Geddert H, Riazalhosseini Y, Ward A, Balwierz A, Schaefer IM, Cameron S, Ghadimi BM, Agaimy A, Fletcher JA, Hoheisel J, Hartmann A, Werner M, Wiemann S, Sahin Ö. Combined DNA methylation and gene expression profiling in gastrointestinal stromal tumors reveals hypomethylation ofSPP1as an independent prognostic factor. Int J Cancer 2014; 136:1013-23. [DOI: 10.1002/ijc.29088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/03/2014] [Indexed: 02/05/2023]
Affiliation(s)
- Florian Haller
- Institute of Pathology; Friedrich Alexander University; Erlangen-Nuremberg Germany
| | - Jitao David Zhang
- Division of Molecular Genome Analysis; German Cancer Research Center; Heidelberg Germany
| | - Evgeny A. Moskalev
- Institute of Pathology; Friedrich Alexander University; Erlangen-Nuremberg Germany
| | - Alexander Braun
- Institute of Pathology; Albert Ludwigs University; Freiburg Germany
| | - Claudia Otto
- Institute of Pathology; Albert Ludwigs University; Freiburg Germany
| | - Helene Geddert
- Institute of Pathology; St. Vincentius Hospital; Karlsruhe Germany
| | - Yasser Riazalhosseini
- Division of Functional Genome Analysis; German Cancer Research Center; Heidelberg Germany
| | - Aoife Ward
- Division of Molecular Genome Analysis; German Cancer Research Center; Heidelberg Germany
| | - Aleksandra Balwierz
- Division of Molecular Genome Analysis; German Cancer Research Center; Heidelberg Germany
| | | | - Silke Cameron
- Department of Gastroenterology and Endocrinology; Georg August University; Göttingen Germany
| | - B. Michael Ghadimi
- Department of General and Visceral Surgery; Georg August University; Göttingen Germany
| | - Abbas Agaimy
- Institute of Pathology; Friedrich Alexander University; Erlangen-Nuremberg Germany
| | | | - Jörg Hoheisel
- Division of Functional Genome Analysis; German Cancer Research Center; Heidelberg Germany
| | - Arndt Hartmann
- Institute of Pathology; Friedrich Alexander University; Erlangen-Nuremberg Germany
| | - Martin Werner
- Institute of Pathology; Albert Ludwigs University; Freiburg Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis; German Cancer Research Center; Heidelberg Germany
- Genomics and Proteomics Core Facility; German Cancer Research Center; Heidelberg Germany
| | - Özgür Sahin
- Division of Molecular Genome Analysis; German Cancer Research Center; Heidelberg Germany
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