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Fonzino A, Manzari C, Spadavecchia P, Munagala U, Torrini S, Conticello S, Pesole G, Picardi E. Unraveling C-to-U RNA editing events from direct RNA sequencing. RNA Biol 2024; 21:1-14. [PMID: 38090878 PMCID: PMC10732634 DOI: 10.1080/15476286.2023.2290843] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2023] [Indexed: 12/18/2023] Open
Abstract
In mammals, RNA editing events involve the conversion of adenosine (A) in inosine (I) by ADAR enzymes or the hydrolytic deamination of cytosine (C) in uracil (U) by the APOBEC family of enzymes, mostly APOBEC1. RNA editing has a plethora of biological functions, and its deregulation has been associated with various human disorders. While the large-scale detection of A-to-I is quite straightforward using the Illumina RNAseq technology, the identification of C-to-U events is a non-trivial task. This difficulty arises from the rarity of such events in eukaryotic genomes and the challenge of distinguishing them from background noise. Direct RNA sequencing by Oxford Nanopore Technology (ONT) permits the direct detection of Us on sequenced RNA reads. Surprisingly, using ONT reads from wild-type (WT) and APOBEC1-knock-out (KO) murine cell lines as well as in vitro synthesized RNA without any modification, we identified a systematic error affecting the accuracy of the Cs call, thereby leading to incorrect identifications of C-to-U events. To overcome this issue in direct RNA reads, here we introduce a novel machine learning strategy based on the isolation Forest (iForest) algorithm in which C-to-U editing events are considered as sequencing anomalies. Using in vitro synthesized and human ONT reads, our model optimizes the signal-to-noise ratio improving the detection of C-to-U editing sites with high accuracy, over 90% in all samples tested. Our results suggest that iForest, known for its rapid implementation and minimal memory requirements, is a promising tool to denoise ONT reads and reliably identify RNA modifications.
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Affiliation(s)
- Adriano Fonzino
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Paola Spadavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | | | | | - Silvestro Conticello
- Core Research Laboratory, ISPRO, Florence, Italy
- National Research Council, Institute of Clinical Physiology, Pisa, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- National Institute of Biostructures and Biosystems (INBB), Roma, Italy
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2
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De Paolo R, Munagala U, Cucco F, Sarti S, Pitto L, Martignano F, Conticello SG, Poliseno L. Modified Cas9-Guided Oxford Nanopore Technology Sequencing Uncovers Single and Multiple Transgene Insertion Sites in a Zebrafish Melanoma Model. CRISPR J 2023; 6:489-492. [PMID: 38108521 DOI: 10.1089/crispr.2023.0062] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Affiliation(s)
- Raffaella De Paolo
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Uday Munagala
- Molecular Mechanisms of Oncogenesis Unit, Core Research Laboratory, ISPRO, Florence, Italy
| | - Francesco Cucco
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Samanta Sarti
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | | | - Filippo Martignano
- Molecular Mechanisms of Oncogenesis Unit, Core Research Laboratory, ISPRO, Florence, Italy
| | - Silvestro G Conticello
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Molecular Mechanisms of Oncogenesis Unit, Core Research Laboratory, ISPRO, Florence, Italy
| | - Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
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3
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Cosi I, Moccia A, Pescucci C, Munagala U, Di Giorgio S, Sineo I, Conticello SG, Notaro R, De Angioletti M. Identification and characterization of novel ETV4 splice variants in prostate cancer. Sci Rep 2023; 13:5267. [PMID: 37002241 PMCID: PMC10066307 DOI: 10.1038/s41598-023-29484-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/06/2023] [Indexed: 04/03/2023] Open
Abstract
ETV4, one of ETS proteins overexpressed in prostate cancer, promotes migration, invasion, and proliferation in prostate cells. This study identifies a series of previously unknown ETV4 alternatively spliced transcripts in human prostate cell lines. Their expression has been validated using several unbiased techniques, including Nanopore sequencing. Most of these transcripts originate from an in-frame exon skipping and, thus, are expected to be translated into ETV4 protein isoforms. Functional analysis of the most abundant among these isoforms shows that they still bear an activity, namely a reduced ability to promote proliferation and a residual ability to regulate the transcription of ETV4 target genes. Alternatively spliced genes are common in cancer cells: an analysis of the TCGA dataset confirms the abundance of these novel ETV4 transcripts in prostate tumors, in contrast to peritumoral tissues. Since none of their translated isoforms have acquired a higher oncogenic potential, such abundance is likely to reflect the tumor deranged splicing machinery. However, it is also possible that their interaction with the canonical variants may contribute to the biology and the clinics of prostate cancer. Further investigations are needed to elucidate the biological role of these ETV4 transcripts and of their putative isoforms.
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Affiliation(s)
- Irene Cosi
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
- ICCOM - National Research Council, Sesto Fiorentino, Florence, Italy
| | - Annalisa Moccia
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Chiara Pescucci
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Uday Munagala
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Salvatore Di Giorgio
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Irene Sineo
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
- IFC - National Research Council, Pisa, Italy
| | - Rosario Notaro
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
- IFC - National Research Council, Pisa, Italy
| | - Maria De Angioletti
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy.
- ICCOM - National Research Council, Sesto Fiorentino, Florence, Italy.
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4
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Credi C, Balducci V, Munagala U, Cianca C, Bigiarini S, de Vries AAF, Loew LM, Pavone FS, Cerbai E, Sartiani L, Sacconi L. Fast Optical Investigation of Cardiac Electrophysiology by Parallel Detection in Multiwell Plates. Front Physiol 2021; 12:692496. [PMID: 34539428 PMCID: PMC8446431 DOI: 10.3389/fphys.2021.692496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Current techniques for fast characterization of cardiac electrophysiology employ optical technologies to control and monitor action potential features of single cells or cellular monolayers placed in multiwell plates. High-speed investigation capacities are commonly achieved by serially analyzing well after well employing fully automated fluorescence microscopes. Here, we describe an alternative cost-effective optical approach (MULTIPLE) that exploits high-power LED arrays to globally illuminate a culture plate and an sCMOS sensor for parallel detection of the fluorescence coming from multiple wells. MULTIPLE combines optical detection of action potentials using a red-shifted voltage-sensitive fluorescent dye (di-4-ANBDQPQ) with optical stimulation, employing optogenetic actuators, to ensure excitation of cardiomyocytes at constant rates. MULTIPLE was first characterized in terms of interwell uniformity of the illumination intensity and optical detection performance. Then, it was applied for probing action potential features in HL-1 cells (i.e., mouse atrial myocyte-like cells) stably expressing the blue light-activatable cation channel CheRiff. Under proper stimulation conditions, we were able to accurately measure action potential dynamics across a 24-well plate with variability across the whole plate of the order of 10%. The capability of MULTIPLE to detect action potential changes across a 24-well plate was demonstrated employing the selective K v 11.1 channel blocker (E-4031), in a dose titration experiment. Finally, action potential recordings were performed in spontaneous beating human induced pluripotent stem cell derived cardiomyocytes following pharmacological manipulation of their beating frequency. We believe that the simplicity of the presented optical scheme represents a valid complement to sophisticated and expensive state-of-the-art optical systems for high-throughput cardiac electrophysiological investigations.
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Affiliation(s)
- Caterina Credi
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Florence, Italy
| | - Valentina Balducci
- Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Florence, Italy
| | - U Munagala
- Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Florence, Italy.,Core Research Laboratory, ISPRO, Florence, Italy
| | - C Cianca
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy
| | - S Bigiarini
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy
| | - Antoine A F de Vries
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Leslie M Loew
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Francesco S Pavone
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Elisabetta Cerbai
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy.,Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Florence, Italy
| | - Laura Sartiani
- Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Florence, Italy
| | - Leonardo Sacconi
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Florence, Italy
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5
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Martignano F, Munagala U, Crucitta S, Mingrino A, Semeraro R, Del Re M, Petrini I, Magi A, Conticello SG. Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients. Mol Cancer 2021; 20:32. [PMID: 33579306 PMCID: PMC7881593 DOI: 10.1186/s12943-021-01327-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/27/2021] [Indexed: 12/11/2022] Open
Abstract
In the "precision oncology" era the characterization of tumor genetic features is a pivotal step in cancer patients' management. Liquid biopsy approaches, such as analysis of cell-free DNA from plasma, represent a powerful and noninvasive strategy to obtain information about the genomic status of the tumor. Sequencing-based analyses of cell-free DNA, currently performed with second generation sequencers, are extremely powerful but poorly scalable and not always accessible also due to instrumentation costs. Third generation sequencing platforms, such as Nanopore sequencers, aim at overcoming these obstacles but, unfortunately, are not designed for cell-free DNA analysis.Here we present a customized workflow to exploit low-coverage Nanopore sequencing for the detection of copy number variations from plasma of cancer patients. Whole genome molecular karyotypes of 6 lung cancer patients and 4 healthy subjects were successfully produced with as few as 2 million reads, and common lung-related copy number alterations were readily detected.This is the first successful use of Nanopore sequencing for copy number profiling from plasma DNA. In this context, Nanopore represents a reliable alternative to Illumina sequencing, with the advantages of minute instrumentation costs and extremely short analysis time.The availability of protocols for Nanopore-based cell-free DNA analysis will make this analysis finally accessible, exploiting the full potential of liquid biopsy both for research and clinical purposes.
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Affiliation(s)
- Filippo Martignano
- Core Research Laboratory, ISPRO, Florence, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Uday Munagala
- Core Research Laboratory, ISPRO, Florence, Italy.,Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessandra Mingrino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Roberto Semeraro
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Unit of Respiratory Medicine, Department of Critical Area and Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa, Italy
| | - Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Silvestro G Conticello
- Core Research Laboratory, ISPRO, Florence, Italy. .,Institute of Clinical Physiology, National Research Council, Pisa, Italy.
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6
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St. Martin A, Salamango D, Serebrenik A, Shaban N, Brown WL, Donati F, Munagala U, Conticello SG, Harris RS. A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC-Cas9 or cleavage by Cas9 in living cells. Nucleic Acids Res 2018; 46:e84. [PMID: 29746667 PMCID: PMC6101615 DOI: 10.1093/nar/gky332] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 08/14/2017] [Revised: 03/26/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
Base editing is an exciting new genome engineering technology. C-to-T mutations in genomic DNA have been achieved using ribonucleoprotein complexes comprised of rat APOBEC1 single-stranded DNA deaminase, Cas9 nickase (Cas9n), uracil DNA glycosylase inhibitor (UGI), and guide (g)RNA. Here, we report the first real-time reporter system for quantification of APOBEC-mediated base editing activity in living mammalian cells. The reporter expresses eGFP constitutively as a marker for transfection or transduction, and editing restores functionality of an upstream mCherry cassette through the simultaneous processing of two gRNA binding regions that each contain an APOBEC-preferred 5'TCA target site. Using this system as both an episomal and a chromosomal editing reporter, we show that human APOBEC3A-Cas9n-UGI and APOBEC3B-Cas9n-UGI base editing complexes are more efficient than the original rat APOBEC1-Cas9n-UGI construct. We also demonstrate coincident enrichment of editing events at a heterologous chromosomal locus in reporter-edited, mCherry-positive cells. The mCherry reporter also quantifies the double-stranded DNA cleavage activity of Cas9, and may therefore be adaptable for use with many different CRISPR systems. The combination of a rapid, fluorescence-based editing reporter system and more efficient, structurally defined DNA editing enzymes broadens the versatility of the rapidly expanding toolbox of genome editing and engineering technologies.
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Affiliation(s)
- Amber St. Martin
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - Daniel Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - Artur Serebrenik
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - Nadine Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | | | | | | | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
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