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Tomasello L, Holub SM, Nigita G, Distefano R, Croce CM. Poly(A)-specific RNase (PARN) generates and regulates miR-125a-5p 3'-isoforms, displaying an altered expression in breast cancer. Signal Transduct Target Ther 2024; 9:90. [PMID: 38616203 PMCID: PMC11016533 DOI: 10.1038/s41392-024-01795-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/12/2024] [Accepted: 03/10/2024] [Indexed: 04/16/2024] Open
Affiliation(s)
- Luisa Tomasello
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.
| | - Shoshanah M Holub
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.
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2
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La Ferlita A, Alaimo S, Nigita G, Distefano R, Beane JD, Tsichlis PN, Ferro A, Croce CM, Pulvirenti A. tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer. iScience 2024; 27:108810. [PMID: 38303722 PMCID: PMC10831894 DOI: 10.1016/j.isci.2024.108810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/02/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
tRNA-derived ncRNAs are a heterogeneous class of non-coding RNAs recently proposed to be active regulators of gene expression and be involved in many diseases, including cancer. Consequently, several online resources on tRNA-derived ncRNAs have been released. Although interesting, such resources present only basic features and do not adequately exploit the wealth of knowledge available about tRNA-derived ncRNAs. Therefore, we introduce tRFUniverse, a novel online resource for the analysis of tRNA-derived ncRNAs in human cancer. tRFUniverse presents an extensive collection of classes of tRNA-derived ncRNAs analyzed across all the TCGA and TARGET tumor cohorts, NCI-60 cell lines, and biological fluids. Moreover, public AGO CLASH/CLIP-Seq data were analyzed to identify the molecular interactions between tRNA-derived ncRNAs and other transcripts. Importantly, tRFUniverse combines in a single resource a comprehensive set of features that we believe may be helpful to investigate the involvement of tRNA-derived ncRNAs in cancer biology.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Joal D. Beane
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
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3
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Rampioni Vinciguerra GL, Capece M, Reggiani Bonetti L, Nigita G, Calore F, Rentsch S, Magistri P, Ballarin R, Di Benedetto F, Distefano R, Cirombella R, Vecchione A, Belletti B, Baldassarre G, Lovat F, Croce CM. Nutrient restriction-activated Fra-2 promotes tumor progression via IGF1R in miR-15a downmodulated pancreatic ductal adenocarcinoma. Signal Transduct Target Ther 2024; 9:31. [PMID: 38342897 PMCID: PMC10859382 DOI: 10.1038/s41392-024-01740-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/07/2023] [Accepted: 01/03/2024] [Indexed: 02/13/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease, characterized by an intense desmoplastic reaction that compresses blood vessels and limits nutrient supplies. PDAC aggressiveness largely relies on its extraordinary capability to thrive and progress in a challenging tumor microenvironment. Dysregulation of the onco-suppressor miR-15a has been extensively documented in PDAC. Here, we identified the transcription factor Fos-related antigen-2 (Fra-2) as a miR-15a target mediating the adaptive mechanism of PDAC to nutrient deprivation. We report that the IGF1 signaling pathway was enhanced in nutrient deprived PDAC cells and that Fra-2 and IGF1R were significantly overexpressed in miR-15a downmodulated PDAC patients. Mechanistically, we discovered that miR-15a repressed IGF1R expression via Fra-2 targeting. In miR-15a-low context, IGF1R hyperactivated mTOR, modulated the autophagic flux and sustained PDAC growth in nutrient deprivation. In a genetic mouse model, Mir15aKO PDAC showed Fra-2 and Igf1r upregulation and mTOR activation in response to diet restriction. Consistently, nutrient restriction improved the efficacy of IGF1R inhibition in a Fra-2 dependent manner. Overall, our results point to a crucial role of Fra-2 in the cellular stress response due to nutrient restriction typical of pancreatic cancer and support IGF1R as a promising and vulnerable target in miR-15a downmodulated PDAC.
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Affiliation(s)
- Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant'Andrea Hospital, University of Rome "Sapienza", Rome, 00189, Italy
| | - Marina Capece
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
| | - Luca Reggiani Bonetti
- Department of Diagnostic, Clinic and Public Health Medicine, University of Modena and Reggio Emilia, Modena, 41100, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
| | - Federica Calore
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
| | - Sydney Rentsch
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
| | - Paolo Magistri
- Hepato-pancreato-biliary Surgery and Liver Transplantation Unit, University of Modena and Reggio Emilia, Modena, 41100, Italy
| | - Roberto Ballarin
- Hepato-pancreato-biliary Surgery and Liver Transplantation Unit, University of Modena and Reggio Emilia, Modena, 41100, Italy
| | - Fabrizio Di Benedetto
- Hepato-pancreato-biliary Surgery and Liver Transplantation Unit, University of Modena and Reggio Emilia, Modena, 41100, Italy
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
| | - Roberto Cirombella
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant'Andrea Hospital, University of Rome "Sapienza", Rome, 00189, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant'Andrea Hospital, University of Rome "Sapienza", Rome, 00189, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, 33081, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, 33081, Italy
| | - Francesca Lovat
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.
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Saviana M, Romano G, McElroy J, Nigita G, Distefano R, Toft R, Calore F, Le P, Morales DDV, Atmajoana S, Deppen S, Wang K, Lee LJ, Acunzo M, Nana-Sinkam P. A plasma miRNA-based classifier for small cell lung cancer diagnosis. Front Oncol 2023; 13:1255527. [PMID: 37869089 PMCID: PMC10585112 DOI: 10.3389/fonc.2023.1255527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Small cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based classifier to assist in SCLC diagnoses. Methods We profiled deregulated circulating cell-free miRNAs in the plasma of SCLC patients. We tested selected miRNAs on a training cohort and created a classifier by integrating miRNA expression and patients' clinical data. Finally, we applied the classifier on a validation dataset. Results We determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients. Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group. Discussion This study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis.
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Affiliation(s)
- Michela Saviana
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Giulia Romano
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Joseph McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH, United States
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Robin Toft
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Federica Calore
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Patricia Le
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Daniel Del Valle Morales
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah Atmajoana
- Vanderbilt University Medical Center and Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Stephen Deppen
- Vanderbilt University Medical Center and Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Kai Wang
- Institute for System Biology, Seattle, WA, United States
| | - L. James Lee
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Mario Acunzo
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Patrick Nana-Sinkam
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, United States
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5
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Vinciguerra GLR, Capece M, Bonetti LR, Magistri P, Calore F, Nigita G, Distefano R, Ballarin R, Benedetto FD, Vecchione A, Belletti B, Baldassarre G, Lovat F, Croce CM. Abstract 4823: The novel miR-15a/Fra-2/IGF1R axis drives response to starvation-induced cell stress in pancreatic ductal adenocarcinoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a relatively uncommon malignancy; however, its incidence is rising worldwide, and it is expected to become the second-leading cause of cancer-related death by 2030. From a histological point of view, PDAC is characterized by a prominent desmoplastic reaction that compresses blood vessels, limiting oxygen and nutrient availability in the tumor microenvironment. Despite that, PDAC cells are capable to adapt dynamically to these stress conditions, adopting different strategies that includes the strict regulation of the autophagic flux. Thus, studying these adaptive mechanisms is crucial to understand PDAC progression and to establish new therapeutic modalities to tackle it. Here, we explore the role of the tumor suppressor miR-15a in the regulation of its putative target Fra-2, a transcription factor, commonly activated by cell stress. By employing IPA on PDAC tumors from TCGA dataset, we found that both miR-15a and its target Fra-2 are predicted to regulate the IGF-1 signaling pathway. In an independent cohort of 44 PDAC samples, miR-15a levels inversely correlated with both Fra-2 and IGF1R expression; conversely, Fra-2 significantly correlated with IGF1R. By chromatin immunoprecipitation and luciferase assay, we assessed that miR-15a directly targeted Fra-2 and IGF1R that, in turn, is transcriptionally regulated by Fra-2 activity. Then, we investigated the role of miR-15a/Fra-2 regulation of IGF1R in the response to starvation-induced cell stress. In starved PDAC cell lines, Fra-2 transcriptional activity triggered IGF1R promoter, causing IGF1R overexpression in control cells but not in miR-15a-overexpressing cells. Consistently, the IGF1 release after starvation induced phosphorylation of IGF1R and activation of the downstream mTOR pathway in control cells but not in miR-15a-overexpressing cells. Therefore, TEM and western blot analysis demonstrated that activation of mTOR via IGF1 release reduced the autophagic flux of PDAC control cell lines compared to miR-15a overexpressing cells under starvation. To assess our results in vivo, we injected PDAC cells wild type or Fra-2 knockout into the flank of nude mice. At tumor onset, mice were randomly divided in two groups and fed with control or hypoproteic diet for three weeks. Hypoproteic diet did not interfere with the growth of wild-type tumors, by contrast, significantly impaired Fra-2KO tumors growth rate. Tumor analysis revealed that hypoproteic diet potently induced IGF1R overexpression and mTOR pathway activation in wild-type tumors but not in Fra-2KO tumors. Our findings demonstrate that IGF1R expression is regulated by miR-15a directly and indirectly via Fra-2 in PDAC. This novel miR-15a/Fra-2/IGF1R axis, triggered by starvation, regulates the autophagic flux and growth of PDAC cells in stress condition, and could be targeted by specific small inhibitors.
Citation Format: Gian Luca Rampioni Vinciguerra, Marina Capece, Luca Reggiani Bonetti, Paolo Magistri, Federica Calore, Giovanni Nigita, Rosario Distefano, Roberto Ballarin, Fabrizio Di Benedetto, Andrea Vecchione, Barbara Belletti, Gustavo Baldassarre, Francesca Lovat, Carlo M. Croce. The novel miR-15a/Fra-2/IGF1R axis drives response to starvation-induced cell stress in pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4823.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Barbara Belletti
- 4Centro di Riferimento Oncologico di Aviano (CRO), Aviano, Italy
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Lovat F, Vinciguerra GLR, Capece M, Distefano R, Nigita G, Vecchione A, Croce CM. Abstract 3903: Role of the miR-301a/Fra-2/GLIPR1 axis in lung cancer cisplatin resistance. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Lung cancer is the leading cause of cancer-related mortality in both men and women worldwide. Despite the administration of platinum compounds represents the main treatment, the majority of tumors remains intrinsically resistant. In lung cancer, miR-301a exerts a main role by modulating the activity of transcription factors like NF-kB and Stat3. Here, we dissected the contribution of miR-301a in the regulation of its new identified target Fos-related antigen-2 (Fra-2), a transcription factor that belongs to the Fos/AP-1 family. By microarray analysis, we discovered that Fra-2 overexpression increased glioma pathogenesis-related protein 1 (GLIPR1) levels, a mediator of cisplatin resistance in lung cancer. Its mechanism of regulation is still unclear. We demonstrated that GLIPR1 is also a miR-301a target. In vitro, modulation of miR-301a reduced Fra-2 and GLIPR1 levels; conversely, Fra-2 overexpression significantly increased GLIPR1 and miR-301a. Then, by chromatin immunoprecipitation assay, we confirmed that Fra-2 interacts with the promoter regions of both GLIPR1 and MIR301A genes, supporting that miR-301a/Fra-2/GLIPR1 axis could be autoregulated by feedback loop in which Fra-2 promotes the transcription of MIR301A gene. Investigating the effect of this new axis on the response to cisplatin, we observed that both Fra-2/GLIPR1 overexpression and miR-301a silencing induced cisplatin resistance in lung cancer cells. By contrast, silencing of GLIPR1 and combined administration of low doses of Fos/AP-1 inhibitor restored the cisplatin sensitivity in Fra-2 overexpressing cells. In the lung adenocarcinoma samples from the TCGA dataset, miR-301a overexpression inversely correlated with Fra-2 and GLIPR1 expression. Consistently, the overexpression of miR-301a identified a fraction of tumors with low expression of Fra-2 and GLIPR1 in an internal cohort of lung cancer samples. Altogether, our findings identify the miR-301a/Fra-2/GLIPR1 axis that contributes to cisplatin resistance in lung cancer cells and could serve as biomarker to stratify patients who may benefit from cisplatin administration, alone or in combination with Fos/AP-1 inhibitors.
Citation Format: Francesca Lovat, Gian Luca Rampioni Vinciguerra, Marina Capece, Rosario Distefano, Giovanni Nigita, Andrea Vecchione, Carlo M. Croce. Role of the miR-301a/Fra-2/GLIPR1 axis in lung cancer cisplatin resistance. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3903.
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Rajendran S, Hu Y, Canella A, Peterson C, Gross A, Cam M, Nazzaro M, Haffey A, Serin-Harmanci A, Distefano R, Nigita G, Wang W, Kreatsoulas D, Li Z, Sepeda JA, Sas A, Hester ME, Miller KE, Elemento O, Roberts RD, Holland EC, Rao G, Mardis ER, Rajappa P. Single-cell RNA sequencing reveals immunosuppressive myeloid cell diversity during malignant progression in a murine model of glioma. Cell Rep 2023; 42:112197. [PMID: 36871221 DOI: 10.1016/j.celrep.2023.112197] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/22/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Recent studies have shown the importance of the dynamic tumor microenvironment (TME) in high-grade gliomas (HGGs). In particular, myeloid cells are known to mediate immunosuppression in glioma; however, it is still unclear if myeloid cells play a role in low-grade glioma (LGG) malignant progression. Here, we investigate the cellular heterogeneity of the TME using single-cell RNA sequencing in a murine glioma model that recapitulates the malignant progression of LGG to HGG. LGGs show increased infiltrating CD4+ and CD8+ T cells and natural killer (NK) cells in the TME, whereas HGGs abrogate this infiltration. Our study identifies distinct macrophage clusters in the TME that show an immune-activated phenotype in LGG but then evolve to an immunosuppressive state in HGG. We identify CD74 and macrophage migration inhibition factor (MIF) as potential targets for these distinct macrophage populations. Targeting these intra-tumoral macrophages in the LGG stage may attenuate their immunosuppressive properties and impair malignant progression.
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Affiliation(s)
- Sakthi Rajendran
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alessandro Canella
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Clayton Peterson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Gross
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Maren Cam
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Matthew Nazzaro
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Abigail Haffey
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Rosario Distefano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Wesley Wang
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Daniel Kreatsoulas
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Zihai Li
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jesse A Sepeda
- Department of Neurology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Neuroscience Research Institute, The Ohio State University, Columbus, OH, USA
| | - Andrew Sas
- Department of Neurology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Neuroscience Research Institute, The Ohio State University, Columbus, OH, USA
| | - Mark E Hester
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neurology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ryan D Roberts
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Eric C Holland
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ganesh Rao
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Prajwal Rajappa
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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8
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Rampioni Vinciguerra GL, Capece M, Distefano R, Nigita G, Vecchione A, Lovat F, Croce CM. Role of the miR-301a/Fra-2/GLIPR1 axis in lung cancer cisplatin resistance. Signal Transduct Target Ther 2023; 8:37. [PMID: 36702817 PMCID: PMC9879967 DOI: 10.1038/s41392-022-01228-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Marina Capece
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome 'Sapienza', Sant'Andrea Hospital, Rome, 00189, Italy
| | - Francesca Lovat
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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9
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Distefano R, Tomasello L, Rampioni Vinciguerra GL, Gasparini P, Xiang Y, Bagnoli M, Marceca GP, Fadda P, Laganà A, Acunzo M, Ma Q, Nigita G, Croce CM. Pan-Cancer Analysis of Canonical and Modified miRNAs Enhances the Resolution of the Functional miRNAome in Cancer. Cancer Res 2022; 82:3687-3700. [PMID: 36040379 PMCID: PMC9574374 DOI: 10.1158/0008-5472.can-22-0240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/24/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Epitranscriptomic studies of miRNAs have added a new layer of complexity to the cancer field. Although there is fast-growing interest in adenosine-to-inosine (A-to-I) miRNA editing and alternative cleavage that shifts miRNA isoforms, simultaneous evaluation of both modifications in cancer is still missing. Here, we concurrently profiled multiple miRNA modification types, including A-to-I miRNA editing and shifted miRNA isoforms, in >13,000 adult and pediatric tumor samples across 38 distinct cancer cohorts from The Cancer Genome Atlas and The Therapeutically Applicable Research to Generate Effective Treatments data sets. The differences between canonical miRNAs and the wider miRNAome in terms of expression, clustering, dysregulation, and prognostic standpoint were investigated. The combination of canonical miRNAs and modified miRNAs boosted the quality of clustering results, outlining unique clinicopathologic features among cohorts. Certain modified miRNAs showed opposite expression from their canonical counterparts in cancer, potentially impacting their targets and function. Finally, a shifted and edited miRNA isoform was experimentally validated to directly bind and suppress a unique target. These findings outline the importance of going beyond the well-established paradigm of one mature miRNA per miRNA arm to elucidate novel mechanisms related to cancer progression. SIGNIFICANCE Modified miRNAs may act as cancer biomarkers and function as allies or antagonists of their canonical counterparts in gene regulation, suggesting the concurrent consideration of canonical and modified miRNAs can boost patient stratification.
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Affiliation(s)
- Rosario Distefano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome “Sapienza,” Santo Andrea Hospital, Rome, Italy
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Yujia Xiang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Marina Bagnoli
- Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
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10
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Rajendran S, Peterson C, Canella A, Hu Y, Gross A, Cam M, Serin-Harmanci A, Distefano R, Nigita G, Wang W, Hester M, Miller K, Elemento O, Roberts R, Holland E, Rao G, Mardis E, Rajappa P. LGG-47. Single-cell RNA Sequencing Reveals Immunosuppressive Myeloid Cell Diversity During Malignant Progression in Glioma. Neuro Oncol 2022. [PMCID: PMC9164692 DOI: 10.1093/neuonc/noac079.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Myeloid cells and macrophages have been shown to promote immunosuppression in high-grade gliomas (HGG), however their roles in malignant progression of low-grade glioma (LGG) are poorly understood. Here, we investigated the heterogeneity of the immune microenvironment during glioma progression using a murine model that recapitulates the malignant progression of low to high-grade glioma. To that end, we performed single-cell RNA sequencing on CD45+ immune cells isolated from animals bearing no tumor (NT), LGG, and HGG. We observed an increased infiltration of CD4+ T cells, CD8+ T cells, B cells, and natural killer cells in the tumor microenvironment of LGG, whereas this infiltration was abrogated in HGG. Our study identified two distinct macrophage clusters across all 3 samples, with signatures of bone marrow derived and resident macrophages, respectively. These macrophages showed an immune-activated phenotype (Stat1, Tnf, Cxcl9 and Cxcl10) in LGG, but then evolved to a more immunosuppressive state (Lgals3, Apoc1 and Id2) in HGG, restricting T cell recruitment and activation. In addition, we identified CD74 and macrophage migration inhibition factor (MIF) as potential targets for both these distinct macrophage populations, based on their increased expression in LGG and HGG compared to NT. Targeting these factors during the LGG therapeutic window may inhibit myeloid cells and intra-tumoral macrophages and attenuate their immunosuppressive properties and impair malignant progression.
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Affiliation(s)
- Sakthi Rajendran
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
| | - Clayton Peterson
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
| | - Alessandro Canella
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
| | - Yang Hu
- Weill Cornell Medicine, New York , NY , USA
| | - Amy Gross
- Nationwide Children's Hospital , Columbus, OH , USA
| | - Maren Cam
- Nationwide Children's Hospital , Columbus, OH , USA
| | | | - Rosario Distefano
- The Ohio State University Wexner Medical Center , Columbus, OH , USA
| | - Giovanni Nigita
- The Ohio State University Wexner Medical Center , Columbus, OH , USA
| | - Wesley Wang
- The Ohio State University Wexner Medical Center , Columbus, OH , USA
| | - Mark Hester
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
| | - Katherine Miller
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
| | | | - Ryan Roberts
- Nationwide Children's Hospital , Columbus, OH , USA
| | - Eric Holland
- Fred Hutchinson Cancer Research Center , Seattle, WA , USA
| | - Ganesh Rao
- Baylor College of Medicine , Houston, TX , USA
| | - Elaine Mardis
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
| | - Prajwal Rajappa
- Nationwide Children's Hospital , Columbus, OH , USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine , Columbus, OH , USA
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11
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Distefano R, Nigita G, Le P, Romano G, Acunzo M, Nana-Sinkam P. Disparities in Lung Cancer: miRNA Isoform Characterization in Lung Adenocarcinoma. Cancers (Basel) 2022; 14:cancers14030773. [PMID: 35159038 PMCID: PMC8833952 DOI: 10.3390/cancers14030773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/04/2023] Open
Abstract
Despite the development of targeted therapeutics, immunotherapy, and strategies for early detection, lung cancer carries a high mortality. Further, significant racial disparities in outcomes exist for which the molecular drivers have yet to be fully elucidated. The growing field of Epitranscriptomics has introduced a new layer of complexity to the molecular pathogenesis of cancer. RNA modifications can occur in coding and non-coding RNAs, such as miRNAs, possibly altering their gene regulatory function. The potential role for such modifications as clinically informative biomarkers remains largely unknown. Here, we concurrently profiled canonical miRNAs, shifted isomiRs (templated and non-templated), and miRNAs with single-point modification events (RNA and DNA) in White American (W) and Black or African American (B/AA) lung adenocarcinoma (LUAD) patients. We found that while most deregulated miRNA isoforms were similar in W and B/AA LUAD tissues compared to normal adjacent tissues, there was a subgroup of isoforms with deregulation according to race. We specifically investigated an edited miRNA, miR-151a-3p with an A-to-I editing event at position 3, to determine how its altered expression may be associated with activation of divergent biological pathways between W and B/AA LUAD patients. Finally, we identified distinct race-specific miRNA isoforms that correlated with prognosis for both Ws and B/AAs. Our results suggested that concurrently profiling canonical and non-canonical miRNAs may have potential as a strategy for identifying additional distinct biological pathways and biomarkers in lung cancer.
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Affiliation(s)
- Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (R.D.); (G.N.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (R.D.); (G.N.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
- Correspondence: (M.A.); (P.N.-S.)
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
- Correspondence: (M.A.); (P.N.-S.)
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12
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Kudo M, Zalles N, Distefano R, Nigita G, Veneziano D, Gasparini P, Croce CM. Synergistic apoptotic effect of miR-183-5p and Polo-Like kinase 1 inhibitor NMS-P937 in breast cancer cells. Cell Death Differ 2022; 29:407-419. [PMID: 34561554 PMCID: PMC8816952 DOI: 10.1038/s41418-021-00864-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as endogenous regulatory molecules targeting specific mRNAs for translational repression. Studies of breast cancer genomics indicate that breast cancer subtypes are distinguished and regulated by specific sets of miRNAs which affect activities such as tumor initiation, progression, and even drug response. Polo-like Kinase 1 (PLK1) is widely considered to be a proto-oncogene due to its increased expression in multiple tumor types, as well as its crucial role in regulating mitosis. Pharmacological inhibition of PLK1 can reduce tumor volume and induce tumor cell death in solid and hematologic malignancies. This prompted us to investigate how PLK1 inhibition with the target-specific inhibitor NMS-P937 would impact breast cancer cells, and how miRNAs may influence the overall response of these cells to this inhibition. We found that miR-183-5p targets PLK1 gene, effectively reducing its protein expression. Such miRNA-driven regulation of PLK1 expression sensitizes breast cancer cells to NMS-P937, resulting in synergistically increased apoptosis. We also show that the miRNA-regulated reduction of PLK1 influences the expression of apoptosis-related key proteins and possibly inducing further indirect PLK1 downmodulation through a DNMT1-p53 axis. These results suggest a potential biologically significant link between the expression of miR-183-5p and the efficacy of PLK1-specific inhibitors in breast cancer cells. Our work further elucidates how miR-183-5p regulates PLK1 gene while also enhancing NMS-P937 effect in breast cancer. Future studies assessing the role of miR-183-5p as a novel biomarker for anti-PLK1 chemotherapy agents are warranted.
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Affiliation(s)
- Masahisa Kudo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA
| | - Nicole Zalles
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA
| | - Dario Veneziano
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA.
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia.
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Comprehensive Cancer Center, Columbus, OH, USA.
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13
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Marceca GP, Distefano R, Tomasello L, Lagana A, Russo F, Calore F, Romano G, Bagnoli M, Gasparini P, Ferro A, Acunzo M, Ma Q, Croce CM, Nigita G. MiREDiBase, a manually curated database of validated and putative editing events in microRNAs. Sci Data 2021; 8:199. [PMID: 34349127 PMCID: PMC8338996 DOI: 10.1038/s41597-021-00979-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/10/2021] [Indexed: 11/08/2022] Open
Abstract
MicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase .
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Affiliation(s)
- Gioacchino P Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alessandro Lagana
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Russo
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Federica Calore
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Marina Bagnoli
- Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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14
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Tomasello L, Distefano R, Nigita G, Croce CM. The MicroRNA Family Gets Wider: The IsomiRs Classification and Role. Front Cell Dev Biol 2021; 9:668648. [PMID: 34178993 PMCID: PMC8220208 DOI: 10.3389/fcell.2021.668648] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are the most characterized class of non-coding RNAs and are engaged in many cellular processes, including cell differentiation, development, and homeostasis. MicroRNA dysregulation was observed in several diseases, cancer included. Epitranscriptomics is a branch of epigenomics that embraces all RNA modifications occurring after DNA transcription and RNA synthesis and involving coding and non-coding RNAs. The development of new high-throughput technologies, especially deep RNA sequencing, has facilitated the discovery of miRNA isoforms (named isomiRs) resulting from RNA modifications mediated by enzymes, such as deaminases and exonucleases, and differing from the canonical ones in length, sequence, or both. In this review, we summarize the distinct classes of isomiRs, their regulation and biogenesis, and the active role of these newly discovered molecules in cancer and other diseases.
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Affiliation(s)
- Luisa Tomasello
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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15
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Marceca GP, Tomasello L, Distefano R, Acunzo M, Croce CM, Nigita G. Detecting and Characterizing A-To-I microRNA Editing in Cancer. Cancers (Basel) 2021; 13:1699. [PMID: 33916692 PMCID: PMC8038323 DOI: 10.3390/cancers13071699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.
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Affiliation(s)
- Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, 95125 Catania, Italy
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
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16
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Distefano R, Tomasello L, Marceca GP, Bagnoli M, Lagana' A, Acunzo M, Song C, Gasparini P, Nigita G, Croce CM. Abstract 2543: Concurrent profiling of canonical and modified miRNAomes from TCGA and TARGET cohorts leads to enhanced resolution in cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
MicroRNAs (miRs), a class of regulatory single-stranded small non-coding RNAs, are frequently deregulated in cancer and have been proposed as diagnostic and prognostic biomarkers in this fatal disease. Recent improvements in high-throughput sequencing (HTS) technologies have allowed the discovery of post-transcriptional modification phenomena involving miRs (e.g., isomiRs, A-to-I editing sites) able to alter the miR canonical sequence and thus their function. However, albeit earlier studies have proposed the exploitation of modified miRs as potential cancer biomarkers, their comprehensive and concurrent profiling, in cancer, still lacks. In light of this, we have applied the miRge2 pipeline (PubmedID:30153801) to more than 12K samples across 38 different cancer types from TCGA and TARGET, aiming at profiling the expression of all detectable canonical and modified miR isoforms in cancer. We identified over 29K unique miR isoforms (21 novel ones) expressed in at least one tumor type, whereby about 85% contains at least one modification (e.g., SNPs, RNA editing). According to our results, taking into account both canonical and modified miR isoforms throughout the analysis leads to an increase of about 20-fold in the identification of potential diagnostic and prognostic miRs with respect to conventional methods, which exclusively consider canonical miRs (miRBase v22). Then, leveraging on an independent cohort of 38 colorectal cancers and 21 adjacent healthy tissues (EGAS00001001127), we found that ~600 significantly deregulated miR isoforms were in common with the ones derived from the TCGA COAD dataset. Focusing on two miR isoforms, the canonical miR-151a-3p and its isoform (miR-151a-3p_-2|-2) with two left-shifted residues in both 5' and 3' end, which we found to be up-regulated in both cohorts, we performed a target prediction coupled with a miR/protein anti-correlation analysis. Interestingly, we found that the two miRs have a distinct set of targets. Finally, employing an Ingenuity(R) Pathway Analysis on their predicted targets, we observed that miR-151a-3p_-2|-2, in contrast to the canonical counterpart, is significantly involved in oncogenic pathways, such as PAK and CXCR4 signaling. This suggests that the final tumor phenotype could be substantially affected by modified miR isoforms. Here, we present one of the most in-depth and extensive miRNome profiling in cancer performed to date, revealing one magnitude of novel potential diagnostic and prognostic cancer biomarkers and enlightening the contribution of miR isoforms to the wider miRNome in cancer pathogenesis.
Citation Format: Rosario Distefano, Luisa Tomasello, Gioacchino P. Marceca, Marina Bagnoli, Alessandro Lagana', Mario Acunzo, Chi Song, Pierluigi Gasparini, Giovanni Nigita, Carlo M. Croce. Concurrent profiling of canonical and modified miRNAomes from TCGA and TARGET cohorts leads to enhanced resolution in cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2543.
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Affiliation(s)
| | | | | | - Marina Bagnoli
- 3Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | | | | | - Chi Song
- 1The Ohio State University, Columbus, OH
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17
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Khawaled S, Nigita G, Distefano R, Oster S, Suh SS, Smith Y, Khalaileh A, Peng Y, Croce CM, Geiger T, Seewaldt VL, Aqeilan RI. Pleiotropic tumor suppressor functions of WWOX antagonize metastasis. Signal Transduct Target Ther 2020; 5:43. [PMID: 32300104 PMCID: PMC7162874 DOI: 10.1038/s41392-020-0136-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 02/05/2023] Open
Abstract
Tumor progression and metastasis are the major causes of death among cancer associated mortality. Metastatic cells acquire features of migration and invasion and usually undergo epithelia-mesenchymal transition (EMT). Acquirement of these various hallmarks rely on different cellular pathways, including TGF-β and Wnt signaling. Recently, we reported that WW domain-containing oxidoreductase (WWOX) acts as a tumor suppressor and has anti-metastatic activities involving regulation of several key microRNAs (miRNAs) in triple-negative breast cancer (TNBC). Here, we report that WWOX restoration in highly metastatic MDA-MB435S cancer cells alters mRNA expression profiles; further, WWOX interacts with various proteins to exert its tumor suppressor function. Careful alignment and analysis of gene and miRNA expression in these cells revealed profound changes in cellular pathways mediating adhesion, invasion and motility. We further demonstrate that WWOX, through regulation of miR-146a levels, regulates SMAD3, which is a member of the TGF-β signaling pathway. Moreover, proteomic analysis of WWOX partners revealed regulation of the Wnt-signaling activation through physical interaction with Disheveled. Altogether, these findings underscore a significant role for WWOX in antagonizing metastasis, further highlighting its role and therapeutic potential in suppressing tumor progression.
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Affiliation(s)
- Saleh Khawaled
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Sara Oster
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel
| | - Sung-Suk Suh
- Department of Bioscience, Mokpo National University, Muan, Republic of Korea
| | - Yoav Smith
- Genomic Data Analysis Unit, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Abed Khalaileh
- Department of Surgery, Hadassah Medical Center, Jerusalem, Israel
| | - Yong Peng
- Department of Thoracic Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, China
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Victoria L Seewaldt
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Rami I Aqeilan
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel. .,Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
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18
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Khawaled S, Suh SS, Abdeen SK, Monin J, Distefano R, Nigita G, Croce CM, Aqeilan RI. WWOX Inhibits Metastasis of Triple-Negative Breast Cancer Cells via Modulation of miRNAs. Cancer Res 2019; 79:1784-1798. [PMID: 30622118 DOI: 10.1158/0008-5472.can-18-0614] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/30/2018] [Accepted: 01/03/2019] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous, highly aggressive, and difficult to treat tumor type. The tumor suppressor WWOX spans FRA16D, a common fragile site that is commonly altered in breast cancer. Despite recent progress, the role of WWOX in TNBC metastasis is unknown. Here we report that WWOX inactivation correlates with advanced stages of TNBC and that its levels are frequently altered in TNBC cells. Ectopic restoration of WWOX in WWOX-negative TNBC cells inhibited metastasis while its depletion in WWOX-positive TNBC cells promoted metastasis. WWOX was a negative regulator of c-MYC, which regulated miR-146a expression and consequently fibronectin levels, contributing to an epithelial status of the cell. Treatment of TNBC cells with anti-miR-146a rescued the WWOX antimetastatic phenotype. Moreover, overexpression of MYC in WWOX-expressing TNBC cells overrode WWOX effects on miR-146a and fibronectin levels. Altogether, our data uncover an essential role for WWOX in antagonizing TNBC progression and highlight its potential use as a biomarker for metastasis. SIGNIFICANCE: These findings highlight the mechanism by which the tumor suppressor WWOX regulates metastasis of triple-negative breast cancer.See related commentary by Sharma, p. 1746.
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Affiliation(s)
- Saleh Khawaled
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel
| | - Sung Suk Suh
- Department of Bioscience, Mokpo National University, Muan, Republic of Korea
| | - Suhaib K Abdeen
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel
| | - Jonathan Monin
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Rami I Aqeilan
- Lautenberg Center for Immunology and Cancer Research, Hebrew University-Hadassah Medical School, IMRIC, Jerusalem, Israel. .,Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, Ohio
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Abstract
In the last two decades noncoding RNAs have been the recipients of increasing scientific interest. In particular, miRNAs, short (~22 nts) noncoding transcripts, have been thoroughly investigated since their essential role in posttranscriptional gene expression regulation had been established in the early 2000s. With the advent and the advancements of high-throughput sequencing technologies in recent years, long noncoding RNAs have also started to emerge as important actors in cellular functions and processes. Such transcripts, on average longer than 200 nt, whose functions have yet to be fully characterized, have recently been identified as regulatory elements of the RNAi pathway, harboring several miRNA response elements, uncovering the phenomena of competing endogenous RNAs (ceRNAs), or "sponge RNAs." The present chapter aims to provide a brief update on the actual biomedical relevance of ceRNAs, together with a summary of resources, tools, and practical examples of their application to aid researchers in the discovery and further elucidation of lncRNA-miRNA interactions.
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Affiliation(s)
- Dario Veneziano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Gioacchino P Marceca
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
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20
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Nigita G, Distefano R, Veneziano D, Romano G, Rahman M, Wang K, Pass H, Croce CM, Acunzo M, Nana-Sinkam P. Tissue and exosomal miRNA editing in Non-Small Cell Lung Cancer. Sci Rep 2018; 8:10222. [PMID: 29976955 PMCID: PMC6033928 DOI: 10.1038/s41598-018-28528-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/15/2018] [Indexed: 01/11/2023] Open
Abstract
RNA editing in microRNAs has been recently proposed as a novel biomarker in cancer. Here, we investigated RNA editing by leveraging small-RNA sequencing data from 87 NSCLC (Non-Small Cell Lung Cancer) samples paired with normal lung tissues from The Cancer Genome Atlas (TCGA) combined with 26 plasma-derived exosome samples from an independent cohort. Using both the editing levels and microRNA editing expression, we detected deregulated microRNA editing events between NSCLC tumor and normal tissues. Interestingly, and for the first time, we also detected editing sites in the microRNA cargo of circulating exosomes, providing the potential to non-invasively discriminate between normal and tumor samples. Of note, miR-411-5p edited in position 5 was significantly dysregulated in tissues as well as in exosomes of NSCLC patients, suggesting a potential targetome shift relevant to lung cancer biology.
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Affiliation(s)
- Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Dario Veneziano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammad Rahman
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Kai Wang
- Institute for System Biology, Seattle, WA, USA
| | - Harvey Pass
- Department of Cardiothoracic Surgery, New York University Cancer Center, New York, NY, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA.
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA.
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21
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Busato M, Distefano R, Bates F, Karim K, Bossi AM, López Vilariño JM, Piletsky S, Bombieri N, Giorgetti A. MIRATE: MIps RATional dEsign Science Gateway. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2017-0075/jib-2017-0075.xml. [PMID: 29897885 PMCID: PMC6348745 DOI: 10.1515/jib-2017-0075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/09/2018] [Indexed: 11/15/2022] Open
Abstract
Molecularly imprinted polymers (MIPs) are high affinity robust synthetic receptors, which can be optimally synthesized and manufactured more economically than their biological equivalents (i.e. antibody). In MIPs production, rational design based on molecular modeling is a commonly employed technique. This mostly aids in (i) virtual screening of functional monomers (FMs), (ii) optimization of monomer-template ratio, and (iii) selectivity analysis. We present MIRATE, an integrated science gateway for the intelligent design of MIPs. By combining and adapting multiple state-of-the-art bioinformatics tools into automated and innovative pipelines, MIRATE guides the user through the entire process of MIPs' design. The platform allows the user to fully customize each stage involved in the MIPs' design, with the main goal to support the synthesis in the wet-laboratory. Availability: MIRATE is freely accessible with no login requirement at http://mirate.di.univr.it/. All major browsers are supported.
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Affiliation(s)
- Mirko Busato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Mirko Busato and Rosario Distefano contributed equally to this work
| | - Rosario Distefano
- Department Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Mirko Busato and Rosario Distefano contributed equally to this work
| | - Ferdia Bates
- Institute of Technological Investigations, University of Coruña (UDC), Campus Esteiro, Ferrol 15402, Spain
| | - Kal Karim
- Leicester Biotechnology Group, Department of Chemistry, University of Leicester, LE1 7RH, Leicester, UK
| | - Alessandra Maria Bossi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - José Manuel López Vilariño
- Institute of Technological Investigations, University of Coruña (UDC), Campus Esteiro, Ferrol 15402, Spain
| | - Sergey Piletsky
- Leicester Biotechnology Group, Department of Chemistry, University of Leicester, LE1 7RH, Leicester, UK
| | - Nicola Bombieri
- Department Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
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22
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Privitera AP, Distefano R, Wefer HA, Ferro A, Pulvirenti A, Giugno R. OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder. Database (Oxford) 2015; 2015:bav069. [PMID: 26228432 PMCID: PMC4519680 DOI: 10.1093/database/bav069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 06/23/2015] [Indexed: 12/20/2022]
Abstract
Obsessive-compulsive disorder (OCD) is a psychiatric condition characterized by intrusive and unwilling thoughts (obsessions) giving rise to anxiety. The patients feel obliged to perform a behavior (compulsions) induced by the obsessions. The World Health Organization ranks OCD as one of the 10 most disabling medical conditions. In the class of Anxiety Disorders, OCD is a pathology that shows an hereditary component. Consequently, an online resource collecting and integrating scientific discoveries and genetic evidence about OCD would be helpful to improve the current knowledge on this disorder. We have developed a manually curated database, OCD Database (OCDB), collecting the relations between candidate genes in OCD, microRNAs (miRNAs) involved in the pathophysiology of OCD and drugs used in its treatments. We have screened articles from PubMed and MEDLINE. For each gene, the bibliographic references with a brief description of the gene and the experimental conditions are shown. The database also lists the polymorphisms within genes and its chromosomal regions. OCDB data is enriched with both validated and predicted miRNA-target and drug-target information. The transcription factors regulations, which are also included, are taken from David and TransmiR. Moreover, a scoring function ranks the relevance of data in the OCDB context. The database is also integrated with the main online resources (PubMed, Entrez-gene, HGNC, dbSNP, DrugBank, miRBase, PubChem, Kegg, Disease-ontology and ChEBI). The web interface has been developed using phpMyAdmin and Bootstrap software. This allows (i) to browse data by category and (ii) to navigate in the database by searching genes, miRNAs, drugs, SNPs, regions, drug targets and articles. The data can be exported in textual format as well as the whole database in.sql or tabular format. OCDB is an essential resource to support genome-wide analysis, genetic and pharmacological studies. It also facilitates the evaluation of genetic data in OCD and the detection of alternative treatments.
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Affiliation(s)
- Anna P Privitera
- Department of Clinical and Experimental Medicine, University of Catania, Viale A. Doria 6, Catania, Italy, Istituto di Scienze Neurologiche, CNR, Via Paolo Gaifami, 18, 95125 Catania, Italy
| | - Rosario Distefano
- Department of Computer Science, University of Verona, Strada le Grazie 15, Verona, Italy and
| | - Hugo A Wefer
- KarolinskaInstitutet, Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Stockholm, Sweden
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Viale A. Doria 6, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, Viale A. Doria 6, Catania, Italy
| | - Rosalba Giugno
- Department of Clinical and Experimental Medicine, University of Catania, Viale A. Doria 6, Catania, Italy,
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23
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Pulvirenti A, Giugno R, Distefano R, Pigola G, Mongiovi M, Giudice G, Vendramin V, Lombardo A, Cattonaro F, Ferro A. A knowledge base for Vitis vinifera functional analysis. BMC Syst Biol 2015; 9 Suppl 3:S5. [PMID: 26050794 PMCID: PMC4464603 DOI: 10.1186/1752-0509-9-s3-s5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern quality and safety. In order to significantly improve the achievement of these objectives and to gain biological knowledge about cultivars, a genomic approach is the most reliable strategy. The recent grapevine genome sequencing offers the opportunity to study the potential roles of genes and microRNAs in fruit maturation and other physiological and pathological processes. Although several systems allowing the analysis of plant genomes have been reported, none of them has been designed specifically for the functional analysis of grapevine genomes of cultivars under environmental stress in connection with microRNA data. Description Here we introduce a novel knowledge base, called BIOWINE, designed for the functional analysis of Vitis vinifera genomes of cultivars present in Sicily. The system allows the analysis of RNA-seq experiments of two different cultivars, namely Nero d'Avola and Nerello Mascalese. Samples were taken under different climatic conditions of phenological phases, diseases, and geographic locations. The BIOWINE web interface is equipped with data analysis modules for grapevine genomes. In particular users may analyze the current genome assembly together with the RNA-seq data through a customized version of GBrowse. The web interface allows users to perform gene set enrichment by exploiting third-party databases. Conclusions BIOWINE is a knowledge base implementing a set of bioinformatics tools for the analysis of grapevine genomes. The system aims to increase our understanding of the grapevine varieties and species of Sicilian products focusing on adaptability to different climatic conditions, phenological phases, diseases, and geographic locations.
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Distefano R, Nigita G, Macca V, Laganà A, Giugno R, Pulvirenti A, Ferro A. VIRGO: visualization of A-to-I RNA editing sites in genomic sequences. BMC Bioinformatics 2013; 14 Suppl 7:S5. [PMID: 23815474 PMCID: PMC3837470 DOI: 10.1186/1471-2105-14-s7-s5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Background RNA Editing is a type of post-transcriptional modification that takes place in the eukaryotes. It alters the sequence of primary RNA transcripts by deleting, inserting or modifying residues. Several forms of RNA editing have been discovered including A-to-I, C-to-U, U-to-C and G-to-A. In recent years, the application of global approaches to the study of A-to-I editing, including high throughput sequencing, has led to important advances. However, in spite of enormous efforts, the real biological mechanism underlying this phenomenon remains unknown. Description In this work, we present VIRGO (http://atlas.dmi.unict.it/virgo/), a web-based tool that maps Ato-G mismatches between genomic and EST sequences as candidate A-to-I editing sites. VIRGO is built on top of a knowledge-base integrating information of genes from UCSC, EST of NCBI, SNPs, DARNED, and Next Generations Sequencing data. The tool is equipped with a user-friendly interface allowing users to analyze genomic sequences in order to identify candidate A-to-I editing sites. Conclusions VIRGO is a powerful tool allowing a systematic identification of putative A-to-I editing sites in genomic sequences. The integration of NGS data allows the computation of p-values and adjusted p-values to measure the mapped editing sites confidence. The whole knowledge base is available for download and will be continuously updated as new NGS data becomes available.
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Affiliation(s)
- Rosario Distefano
- Department of Mathematics and Computer Science - University of Catania, Catania, Italy
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25
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Garozzo G, Distefano R, Miceli A, Bonomo P. Detection of ICAM-1, ICAM-2, ICAM-3, PECAM-1 and VCAM-1, evaluation of hypercoagulable state and platelet aggregation in hemoglobinopathy patients with erythroblasts. Haematologica 2001; 86:778-9. [PMID: 11454542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
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26
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Distefano R, Bonomo P, Favacchio PR. Evaluation of a new 5-log filter or packed red cells leucodepletion. Transfus Sci 1997; 18:405-6. [PMID: 10175154 DOI: 10.1016/s0955-3886(97)00038-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- R Distefano
- Immunohematology Service, OMPA Hospital, Ragusa, Italy
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Garozzo G, Bonomo P, Distefano R, Rizzone P. Hepatitis C virus transmission. Eur J Med 1993; 2:316. [PMID: 8252171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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