1
|
Tretti Parenzan C, Molin AD, Longo G, Gaffo E, Buratin A, Cani A, Boldrin E, Serafin V, Guglielmelli P, Vannucchi AM, Cazzaniga G, Biondi A, Locatelli F, Meyer LH, Buldini B, te Kronnie G, Bresolin S, Bortoluzzi S. Functional relevance of circRNA aberrant expression in pediatric acute leukemia with KMT2A::AFF1 fusion. Blood Adv 2024; 8:1305-1319. [PMID: 38029383 PMCID: PMC10918493 DOI: 10.1182/bloodadvances.2023011291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
ABSTRACT Circular RNAs (circRNAs) are emerging molecular players in leukemogenesis and promising therapeutic targets. In KMT2A::AFF1 (MLL::AF4)-rearranged leukemia, an aggressive disease compared with other pediatric B-cell precursor (BCP) acute lymphoblastic leukemia (ALL), data about circRNAs are limited. Here, we disclose the circRNA landscape of infant patients with KMT2A::AFF1 translocated BCP-ALL showing dysregulated, mostly ectopically expressed, circRNAs in leukemia cells. Most of these circRNAs, apart from circHIPK3 and circZNF609, previously associated with oncogenic behavior in ALL, are still uncharacterized. An in vitro loss-of-function screening identified an oncogenic role of circFKBP5, circKLHL2, circNR3C1, and circPAN3 in KMT2A::AFF1 ALL, whose silencing affected cell proliferation and apoptosis. Further study in an extended cohort disclosed a significantly correlated expression of these oncogenic circRNAs and their putative involvement in common regulatory networks. Moreover, it showed that circAFF1 upregulation occurs in a subset of cases with HOXA KMT2A::AFF1 ALL. Collectively, functional analyses and patient data reveal oncogenic circRNA upregulation as a relevant mechanism that sustains the malignant cell phenotype in KMT2A::AFF1 ALL.
Collapse
Affiliation(s)
- Caterina Tretti Parenzan
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University and Hospital, Padua, Italy
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgia Longo
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University and Hospital, Padua, Italy
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Alice Cani
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University and Hospital, Padua, Italy
| | - Elena Boldrin
- Department of Biology, University of Padova, Padova, Italy
- Ulm University Medical Center, Department of Pediatric and Adolescent Medicine, Ulm, Germany
| | - Valentina Serafin
- Onco-Hematology, Stem Cell Transplant and Gene Therapy, Istituto di Ricerca Pediatrica Foundation - Città della Speranza, Padua, Italy
| | - Paola Guglielmelli
- Azienda Ospedaliero Universitaria Careggi, University of Florence, Florence, Italy
| | | | - Giovanni Cazzaniga
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italia
- School of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
| | - Andrea Biondi
- School of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
- Department of Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Catholic University of the Sacred Heart, Rome, Italy
| | - Lueder H. Meyer
- Ulm University Medical Center, Department of Pediatric and Adolescent Medicine, Ulm, Germany
| | - Barbara Buldini
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University and Hospital, Padua, Italy
- Onco-Hematology, Stem Cell Transplant and Gene Therapy, Istituto di Ricerca Pediatrica Foundation - Città della Speranza, Padua, Italy
| | | | - Silvia Bresolin
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University and Hospital, Padua, Italy
- Onco-Hematology, Stem Cell Transplant and Gene Therapy, Istituto di Ricerca Pediatrica Foundation - Città della Speranza, Padua, Italy
| | | |
Collapse
|
2
|
Maltby CJ, Krans A, Grudzien SJ, Palacios Y, Muiños J, Suárez A, Asher M, Khurana V, Barmada SJ, Dijkstra AA, Todd PK. AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571345. [PMID: 38168171 PMCID: PMC10760133 DOI: 10.1101/2023.12.13.571345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by biallelic, non-reference pentameric AAGGG(CCCTT) repeat expansions within the second intron of replication factor complex subunit 1 (RFC1). To investigate how these repeats cause disease, we generated CANVAS patient induced pluripotent stem cell (iPSC) derived neurons (iNeurons) and utilized calcium imaging and transcriptomic analysis to define repeat-elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in CANVAS patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons, and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. These phenotypic deficits were not replicated by knockdown of RFC1 in control neurons and were not rescued by ectopic expression of RFC1. These findings support a repeat-dependent but RFC1-independent cause of neuronal dysfunction in CANVAS, with important implications for therapeutic development in this currently untreatable condition.
Collapse
Affiliation(s)
- Connor J. Maltby
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
| | - Samantha J. Grudzien
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yomira Palacios
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Muiños
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- UM SMART Undergraduate Summer Program, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Suárez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Asher
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Vikram Khurana
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sami J. Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Anke A. Dijkstra
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter K. Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
| |
Collapse
|
3
|
Dal Molin A, Tretti Parenzan C, Gaffo E, Borin C, Boldrin E, Meyer LH, te Kronnie G, Bresolin S, Bortoluzzi S. Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion. Brief Bioinform 2022; 24:6965906. [PMID: 36585787 PMCID: PMC9851293 DOI: 10.1093/bib/bbac589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/12/2022] [Accepted: 12/02/2022] [Indexed: 01/01/2023] Open
Abstract
Chromosomal translocations in cancer genomes, key players in many types of cancers, generate chimeric proteins that drive oncogenesis. Genomes with chromosomal rearrangements can also produce fusion circular RNAs (f-circRNAs) by backsplicing of chimeric transcripts, as first shown in leukemias with PML::RARα and KMT2A::MLLT3 translocations and later in solid cancers. F-circRNAs contribute to the oncogenic processes and reinforce the oncogenic activity of chimeric proteins. In leukemia with KMT2A::AFF1 (MLL::AF4) fusions, we previously reported specific alterations of circRNA expression, but nothing was known about f-circRNAs. Due to the presence of two chimeric sequences, fusion and backsplice junctions, the identification of f-circRNAs with available tools is challenging, possibly resulting in the underestimation of this RNA species, especially when the breakpoint is not known. We developed CircFusion, a new software tool to detect linear fusion transcripts and f-circRNAs from RNA-seq data, both in samples for which the breakpoints are known and when the information about the joined exons is missing. CircFusion can detect linear and circular chimeric transcripts deriving from the main and reciprocal translocations also in the presence of multiple breakpoints, which are common in malignant cells. Benchmarking tests on simulated and real datasets of cancer samples with previously experimentally determined f-circRNAs showed that CircFusion provides reliable predictions and outperforms available methods for f-circRNA detection. We discovered and validated novel f-circRNAs in acute leukemia harboring KMT2A::AFF1 rearrangements, leading the way to future functional studies aimed to unveil their role in this malignancy.
Collapse
Affiliation(s)
- Anna Dal Molin
- Corresponding authors: Anna Dal Molin, Department of Molecular Medicine, University of Padova, Via G. Colombo, 3 - 35131, Padova, Italy. Tel.: +39 049 827 6502; Fax: +39 049 827 6209. ; Stefania Bortoluzzi, Associate Professor of Applied Biology.Department of Molecular Medicine, University of Padova, Via G. Colombo, 3 - 35131, Padova, Italy. Tel.: +39 049 827 6502; Fax: +39 049 827 6209.
| | | | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Cristina Borin
- Department of Molecular Medicine, University of Padova, Padova, Italy,Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, IRP-Istituto di Ricerca Pediatrica, Padova, Italy
| | - Elena Boldrin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany,Department of Molecular Medicine, University of Padova, Padova, Italy,Department of Biology, University of Padova, Padova, Italy
| | - Lueder H Meyer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | | | | | - Stefania Bortoluzzi
- Corresponding authors: Anna Dal Molin, Department of Molecular Medicine, University of Padova, Via G. Colombo, 3 - 35131, Padova, Italy. Tel.: +39 049 827 6502; Fax: +39 049 827 6209. ; Stefania Bortoluzzi, Associate Professor of Applied Biology.Department of Molecular Medicine, University of Padova, Via G. Colombo, 3 - 35131, Padova, Italy. Tel.: +39 049 827 6502; Fax: +39 049 827 6209.
| |
Collapse
|
4
|
Galardi A, Colletti M, Palma A, Di Giannatale A. An Update on Circular RNA in Pediatric Cancers. Biomedicines 2022; 11:biomedicines11010036. [PMID: 36672544 PMCID: PMC9856195 DOI: 10.3390/biomedicines11010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded closed noncoding RNA molecules which are formed as a result of reverse splicing of mRNAs. Despite their relative abundance, only recently there appeared an increased interest in the understanding of their regulatory importance. Among their most relevant characteristics are high stability, abundance and evolutionary conservation among species. CircRNAs are implicated in several cellular functions, ranging from miRNA and protein sponges to transcriptional modulation and splicing. Additionally, circRNAs' aberrant expression in pathological conditions is bringing to light their possible use as diagnostic and prognostic biomarkers. Their use as indicator molecules of pathological changes is also supported by their peculiar covalent closed cyclic structure which bestows resistance to RNases. Their regulatory role in cancer pathogenesis and metastasis is supported by studies involving human tumors that have investigated different expression profiles of these molecules. As endogenous competitive RNA, circRNAs can regulate tumor proliferation and invasion and they arouse great consideration as potential therapeutic biomarkers and targets for cancer. In this review, we describe the most recent findings on circRNAs in the most common pediatric solid cancers (such as brain tumors, neuroblastomas, and sarcomas) and in more rare ones (such as Wilms tumors, hepatoblastomas, and retinoblastomas).
Collapse
Affiliation(s)
- Angela Galardi
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
| | - Marta Colletti
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
| | - Alessandro Palma
- Translational Cytogenomics Research Unit, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
| | - Angela Di Giannatale
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children’s Hospital, Viale San Paolo 15, 00146 Rome, Italy
- Correspondence:
| |
Collapse
|
5
|
De Vos N, Hofmans M, Lammens T, De Wilde B, Van Roy N, De Moerloose B. Targeted therapy in juvenile myelomonocytic leukemia: Where are we now? Pediatr Blood Cancer 2022; 69:e29930. [PMID: 36094370 DOI: 10.1002/pbc.29930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/07/2022]
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare and aggressive clonal neoplasm of early childhood, classified as an overlap myeloproliferative/myelodysplastic neoplasm by the World Health Organization. In 90% of the patients with JMML, typical initiating mutations in the canonical Ras pathway genes NF1, PTPN11, NRAS, KRAS, and CBL can be identified. Hematopoietic stem cell transplantation (HSCT) currently is the established standard of care in most patients, although long-term survival is still only 50-60%. Given the limited therapeutic options and the important morbidity and mortality associated with HSCT, new therapeutic approaches are urgently needed. Hyperactivation of the Ras pathway as disease mechanism in JMML lends itself to the use of targeted therapy. Targeted therapy could play an important role in the future treatment of patients with JMML. This review presents a comprehensive overview of targeted therapies already developed and evaluated in vitro and in vivo in patients with JMML.
Collapse
Affiliation(s)
- Nele De Vos
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University, Ghent, Belgium
| | - Mattias Hofmans
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Cancer Research Institute Ghent, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| |
Collapse
|
6
|
Dal Molin A, Gaffo E, Difilippo V, Buratin A, Tretti Parenzan C, Bresolin S, Bortoluzzi S. CRAFT: a bioinformatics software for custom prediction of circular RNA functions. Brief Bioinform 2022; 23:6518047. [PMID: 35106564 PMCID: PMC8921651 DOI: 10.1093/bib/bbab601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/10/2021] [Accepted: 12/26/2021] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs), transcripts generated by backsplicing, are particularly stable and pleiotropic molecules, whose dysregulation drives human diseases and cancer by modulating gene expression and signaling pathways. CircRNAs can regulate cellular processes by different mechanisms, including interaction with microRNAs (miRNAs) and RNA-binding proteins (RBP), and encoding specific peptides. The prediction of circRNA functions is instrumental to interpret their impact in diseases, and to prioritize circRNAs for functional investigation. Currently, circRNA functional predictions are provided by web databases that do not allow custom analyses, while self-standing circRNA prediction tools are mostly limited to predict only one type of function, mainly focusing on the miRNA sponge activity of circRNAs. To solve these issues, we developed CRAFT (CircRNA Function prediction Tool), a freely available computational pipeline that predicts circRNA sequence and molecular interactions with miRNAs and RBP, along with their coding potential. Analysis of a set of circRNAs with known functions has been used to appraise CRAFT predictions and to optimize its setting. CRAFT provides a comprehensive graphical visualization of the results, links to several knowledge databases, and extensive functional enrichment analysis. Moreover, it originally combines the predictions for different circRNAs. CRAFT is a useful tool to help the user explore the potential regulatory networks involving the circRNAs of interest and generate hypotheses about the cooperation of circRNAs into the modulation of biological processes.
Collapse
Affiliation(s)
- Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy.,Department of Biology, University of Padova, Padova, Italy
| | - Caterina Tretti Parenzan
- Onco-hematology, stem cell transplant and gene therapy laboratory, IRP-Istituto di Ricerca Pediatrica, Padova, Italy.,Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University Hospital
| | - Silvia Bresolin
- Onco-hematology, stem cell transplant and gene therapy laboratory, IRP-Istituto di Ricerca Pediatrica, Padova, Italy.,Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University Hospital
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy.,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, Padova, Italy
| |
Collapse
|
7
|
Gaffo E, Buratin A, Dal Molin A, Bortoluzzi S. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. Brief Bioinform 2021; 23:6409697. [PMID: 34698333 PMCID: PMC8769706 DOI: 10.1093/bib/bbab418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules originating by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments are characterized by low discovery rates and performance dependent on the analysed data set. We developed CirComPara2 (https://github.com/egaffo/CirComPara2), a new automated computational pipeline for circRNA discovery and quantification, which consistently achieves high recall rates without losing precision by combining multiple circRNA detection methods. In our benchmark analysis, CirComPara2 outperformed state-of-the-art circRNA discovery tools and proved to be a reliable and robust method for comprehensive transcriptome characterization.
Collapse
Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy; Department of Biology, University of Padova, Padova, Italy
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy; Interdepartmental Center For Innovative Biotechnologies, University of Padova, Padova, Italy
| |
Collapse
|
8
|
Buratin A, Gaffo E, Dal Molin A, Bortoluzzi S. CircIMPACT: An R Package to Explore Circular RNA Impact on Gene Expression and Pathways. Genes (Basel) 2021; 12:genes12071044. [PMID: 34356060 PMCID: PMC8308052 DOI: 10.3390/genes12071044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are transcripts generated by back-splicing. CircRNAs might regulate cellular processes by different mechanisms, including interaction with miRNAs and RNA-binding proteins. CircRNAs are pleiotropic molecules whose dysregulation has been linked to human diseases and can drive cancer by impacting gene expression and signaling pathways. The detection of circRNAs aberrantly expressed in disease conditions calls for the investigation of their functions. Here, we propose CircIMPACT, a bioinformatics tool for the integrative analysis of circRNA and gene expression data to facilitate the identification and visualization of the genes whose expression varies according to circRNA expression changes. This tool can highlight regulatory axes potentially governed by circRNAs, which can be prioritized for further experimental study. The usefulness of CircIMPACT is exemplified by a case study analysis of bladder cancer RNA-seq data. The link between circHIPK3 and heparanase (HPSE) expression, due to the circHIPK3-miR558-HPSE regulatory axis previously determined by experimental studies on cell lines, was successfully detected. CircIMPACT is freely available at GitHub.
Collapse
Affiliation(s)
- Alessia Buratin
- Department of Biology, University of Padova, 35131 Padova, Italy;
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (E.G.); (A.D.M.)
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (E.G.); (A.D.M.)
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (E.G.); (A.D.M.)
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (E.G.); (A.D.M.)
- Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35131 Padova, Italy
- Correspondence:
| |
Collapse
|