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Champroux A, Tang Y, Dickson DA, Meng A, Harrington A, Liaw L, Marzi M, Nicassio F, Schlaeger TM, Feig LA. Transmission of reduced levels of miR-34/449 from sperm to preimplantation embryos is a key step in the transgenerational epigenetic inheritance of the effects of paternal chronic social instability stress. Epigenetics 2024; 19:2346694. [PMID: 38739481 DOI: 10.1080/15592294.2024.2346694] [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] [Received: 01/20/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
The transgenerational effects of exposing male mice to chronic social instability (CSI) stress are associated with decreased sperm levels of multiple members of the miR-34/449 family that persist after their mating through preimplantation embryo (PIE) development. Here we demonstrate the importance of these miRNA changes by showing that restoring miR-34c levels in PIEs derived from CSI stressed males prevents elevated anxiety and defective sociability normally found specifically in their adult female offspring. It also restores, at least partially, levels of sperm miR-34/449 normally reduced in their male offspring who transmit these sex-specific traits to their offspring. Strikingly, these experiments also revealed that inducing miR-34c levels in PIEs enhances the expression of its own gene and that of miR-449 in these cells. The same induction of embryo miR-34/449 gene expression likely occurs after sperm-derived miR-34c is introduced into oocytes upon fertilization. Thus, suppression of this miRNA amplification system when sperm miR-34c levels are reduced in CSI stressed mice can explain how a comparable fold-suppression of miR-34/449 levels can be found in PIEs derived from them, despite sperm containing ~50-fold lower levels of these miRNAs than those already present in PIEs. We previously found that men exposed to early life trauma also display reduced sperm levels of miR-34/449. And here we show that miR-34c can also increase the expression of its own gene, and that of miR-449 in human embryonic stem cells, suggesting that human PIEs derived from men with low sperm miR-34/449 levels may also contain this potentially harmful defect.
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Affiliation(s)
- Alexandre Champroux
- Development, Molecular & Chemical Biology/Medical, Tufts University, Boston, MA, USA
| | - Yang Tang
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - David A Dickson
- Tufts Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Alice Meng
- Tufts Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Anne Harrington
- Center for Molecular Medicine, MaineHealth Institute for Research, Scarborough, ME, USA
| | - Lucy Liaw
- Center for Genomic Studies, Instituto Italiano di Tecnologia Institution, Milan, Italy
| | - Matteo Marzi
- Center for Genomic Studies, Instituto Italiano di Tecnologia Institution, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Studies, Instituto Italiano di Tecnologia Institution, Milan, Italy
| | | | - Larry A Feig
- Development, Molecular & Chemical Biology/Medical, Tufts University, Boston, MA, USA
- Tufts Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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Maestri S, Furlan M, Mulroney L, Coscujuela Tarrero L, Ugolini C, Dalla Pozza F, Leonardi T, Birney E, Nicassio F, Pelizzola M. Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing. Brief Bioinform 2024; 25:bbae001. [PMID: 38279646 PMCID: PMC10818168 DOI: 10.1093/bib/bbae001] [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: 07/31/2023] [Revised: 10/27/2023] [Accepted: 12/28/2023] [Indexed: 01/28/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal eukaryotic mRNA modification, and is involved in the regulation of various biological processes. Direct Nanopore sequencing of native RNA (dRNA-seq) emerged as a leading approach for its identification. Several software were published for m6A detection and there is a strong need for independent studies benchmarking their performance on data from different species, and against various reference datasets. Moreover, a computational workflow is needed to streamline the execution of tools whose installation and execution remains complicated. We developed NanOlympicsMod, a Nextflow pipeline exploiting containerized technology for comparing 14 tools for m6A detection on dRNA-seq data. NanOlympicsMod was tested on dRNA-seq data generated from in vitro (un)modified synthetic oligos. The m6A hits returned by each tool were compared to the m6A position known by design of the oligos. In addition, NanOlympicsMod was used on dRNA-seq datasets from wild-type and m6A-depleted yeast, mouse and human, and each tool's hits were compared to reference m6A sets generated by leading orthogonal methods. The performance of the tools markedly differed across datasets, and methods adopting different approaches showed different preferences in terms of precision and recall. Changing the stringency cut-offs allowed for tuning the precision-recall trade-off towards user preferences. Finally, we determined that precision and recall of tools are markedly influenced by sequencing depth, and that additional sequencing would likely reveal additional m6A sites. Thanks to the possibility of including novel tools, NanOlympicsMod will streamline the benchmarking of m6A detection tools on dRNA-seq data, improving future RNA modification characterization.
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Affiliation(s)
- Simone Maestri
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, U.K
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Lucia Coscujuela Tarrero
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Fabio Dalla Pozza
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, U.K
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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3
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Giambruno R, Zacco E, Ugolini C, Vandelli A, Mulroney L, D’Onghia M, Giuliani B, Criscuolo E, Castelli M, Clementi N, Clementi M, Mancini N, Bonaldi T, Gustincich S, Leonardi T, Tartaglia GG, Nicassio F. Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome. Mol Ther Nucleic Acids 2023; 34:102052. [PMID: 38028201 PMCID: PMC10630655 DOI: 10.1016/j.omtn.2023.102052] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral processes such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 5' and 3' terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nanopore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modified consensus regions for PUS7 were identified at both terminal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our findings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modifications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies.
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Affiliation(s)
- Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy
| | - Elsa Zacco
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, Italy
| | - Andrea Vandelli
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, RM 00015, Italy
| | - Manfredi D’Onghia
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Bianca Giuliani
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milano, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, Italy
| | - Stefano Gustincich
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Gian Gaetano Tartaglia
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Catalan Institution for Research and Advanced Studies, ICREA, 08010 Barcelona, Spain
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
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Champroux A, Yang T, Dickson DA, Meng A, Harrington A, Liaw L, Marzi M, Nicassio F, Schlaeger TM, Feig LA. Preimplantation Embryos Amplify Stress-Induced Changes in Sperm-Derived miRNA Content to Mediate Transgenerational Epigenetic Inheritance. bioRxiv 2023:2023.04.21.537854. [PMID: 37786715 PMCID: PMC10541588 DOI: 10.1101/2023.04.21.537854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Chronically stressing male mice can alter the behavior of their offspring across generations. This effect is thought to be mediated by stress-induced changes in the content of specific sperm miRNAs that modify embryo development after their delivery to oocytes at fertilization. A major problem with this hypothesis is that the levels of mouse sperm miRNAs are much lower than those present in preimplantation embryos. This makes it unclear how embryos could be significantly impacted without an amplification system to magnify changes in sperm miRNA content, like those present in lower organisms where transgenerational epigenetic inheritance is well established. Here, we describe such a system for Chronic Social Instability (CSI) stress that can explain how it reduces the levels of the miR-34b,c/449a,b family of miRNAs not only in sperm of exposed males but also in preimplantation embryos ( PIEs ) derived from their mating, as well as in sperm of male offspring. Sperm-derived miR-34c normally positively regulates expression of its own gene and that of miR-449 in PIEs. This feed forward, auto-amplification process is suppressed when CSI stress reduces sperm miR-34c levels. Its suppression is important for the transmission of traits to offspring because restoring miR-34c levels in PIEs from CSI stressed males, which also restores levels of miR-449 in them, suppresses elements of elevated anxiety and defective sociability normally found specifically in their female offspring, as well as reduced sperm miR-34 and miR-449 levels normally found in male offspring, who pass on these traits to their offspring. We previously published that the content of sperm miR-34/449 is also reduced in men raised in highly abusive and/or dysfunctional families. We show here that a similar miRNA auto-amplification system functions in human embryonic stem cells. This raises the possibility that PIEs in offspring of these men also display reduced levels of miR-34/449, enhancing the potential translational significance of these studies.
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Lattanzi G, Strati F, Díaz-Basabe A, Perillo F, Amoroso C, Protti G, Rita Giuffrè M, Iachini L, Baeri A, Baldari L, Cassinotti E, Ghidini M, Galassi B, Lopez G, Noviello D, Porretti L, Trombetta E, Messuti E, Mazzarella L, Iezzi G, Nicassio F, Granucci F, Vecchi M, Caprioli F, Facciotti F. iNKT cell-neutrophil crosstalk promotes colorectal cancer pathogenesis. Mucosal Immunol 2023; 16:326-340. [PMID: 37004750 DOI: 10.1016/j.mucimm.2023.03.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
iNKT cells account for a relevant fraction of effector T-cells in the intestine and are considered an attractive platform for cancer immunotherapy. Although iNKT cells are cytotoxic lymphocytes, their functional role in colorectal cancer (CRC) is still controversial, limiting their therapeutic use. Thus, we examined the immune cell composition and iNKT cell phenotype of CRC lesions in patients (n = 118) and different murine models. High-dimensional single-cell flow-cytometry, metagenomics, and RNA sequencing experiments revealed that iNKT cells are enriched in tumor lesions. The tumor-associated pathobiont Fusobacterium nucleatum induces IL-17 and Granulocyte-macrophage colony-stimulating factor (GM-CSF) expression in iNKT cells without affecting their cytotoxic capability but promoting iNKT-mediated recruitment of neutrophils with polymorphonuclear myeloid-derived suppressor cells-like phenotype and functions. The lack of iNKT cells reduced the tumor burden and recruitment of immune suppressive neutrophils. iNKT cells in-vivo activation with α-galactosylceramide restored their anti-tumor function, suggesting that iNKT cells can be modulated to overcome CRC-associated immune evasion. Tumor co-infiltration by iNKT cells and neutrophils correlates with negative clinical outcomes, highlighting the importance of iNKT cells in the pathophysiology of CRC. Our results reveal a functional plasticity of iNKT cells in CRC, suggesting a pivotal role of iNKT cells in shaping the tumor microenvironment, with relevant implications for treatment.
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Affiliation(s)
- Georgia Lattanzi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-oncology, Università degli Studi di Milano, Milan, Italy
| | - Francesco Strati
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Angélica Díaz-Basabe
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-oncology, Università degli Studi di Milano, Milan, Italy
| | - Federica Perillo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-oncology, Università degli Studi di Milano, Milan, Italy
| | - Chiara Amoroso
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giulia Protti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Rita Giuffrè
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Iachini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Alberto Baeri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Ludovica Baldari
- General and Emergency Surgery Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Cassinotti
- General and Emergency Surgery Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Michele Ghidini
- Medical Oncology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Barbara Galassi
- Medical Oncology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Gianluca Lopez
- Pathology Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Noviello
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Laura Porretti
- Clinical Chemistry and Microbiology Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elena Trombetta
- Clinical Chemistry and Microbiology Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Eleonora Messuti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Giandomenica Iezzi
- Department of Visceral Surgery, EOC Translational Research Laboratory, Bellinzona, Switzerland
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Flavio Caprioli
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Federica Facciotti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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Mulroney L, Birney E, Leonardi T, Nicassio F. Using Nanocompore to Identify RNA Modifications from Direct RNA Nanopore Sequencing Data. Curr Protoc 2023; 3:e683. [PMID: 36840709 DOI: 10.1002/cpz1.683] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
RNA modifications can alter the behavior of RNA molecules depending on where they are located on the strands. Traditionally, RNA modifications have been detected and characterized by biophysical assays, mass spectrometry, or specific next-generation sequencing techniques, but are limited to specific modifications or are low throughput. Nanopore is a platform capable of sequencing RNA strands directly, which permits transcriptome-wide detection of RNA modifications. RNA modifications alter the nanopore raw signal relative to the canonical form of the nucleotide, and several software tools detect these signal alterations. One such tool is Nanocompore, which compares the ionic current features between two different experimental conditions (i.e., with and without RNA modifications) to detect RNA modifications. Nanocompore is not limited to a single type of RNA modification, has a high specificity for detecting RNA modifications, and does not require model training. To use Nanocompore, the following steps are needed: (i) the data must be basecalled and aligned to the reference transcriptome, then the raw ionic current signals are aligned to the sequences and transformed into a Nanocompore-compatible format; (ii) finally, the statistical testing is conducted on the transformed data and produces a table of p-value predictions for the positions of the RNA modifications. These steps can be executed with several different methods, and thus we have also included two alternative protocols for running Nanocompore. Once the positions of RNA modifications are determined by Nanocompore, users can investigate their function in various metabolic pathways. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: RNA modification detection by Nanocompore Alternate Protocol 1: RNA modification detection by Nanocompore with f5c Alternate Protocol 2: RNA modification detection by Nanocompore using Nextflow.
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Affiliation(s)
- Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, U.K.,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, U.K
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
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Giambruno R, Nicassio F. Proximity-dependent biotinylation technologies for mapping RNA-protein interactions in live cells. Front Mol Biosci 2022; 9:1062448. [PMID: 36452457 PMCID: PMC9702341 DOI: 10.3389/fmolb.2022.1062448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/25/2022] [Indexed: 12/01/2023] Open
Abstract
Proximity ligation technologies are extremely powerful tools for unveiling RNA-protein interactions occurring at different stages in living cells. These approaches mainly rely on the inducible activity of enzymes (biotin ligases or peroxidases) that promiscuously biotinylate macromolecules within a 20 nm range. These enzymes can be either fused to an RNA binding protein or tethered to any RNA of interest and expressed in living cells to biotinylate the amino acids and nucleic acids of binding partners in proximity. The biotinylated molecules can then be easily affinity purified under denaturing conditions and analyzed by mass spectrometry or next generation sequencing. These approaches have been widely used in recent years, providing a potent instrument to map the molecular interactions of specific RNA-binding proteins as well as RNA transcripts occurring in mammalian cells. In addition, they permit the identification of transient interactions as well as interactions among low expressed molecules that are often missed by standard affinity purification strategies. This review will provide a brief overview of the currently available proximity ligation methods, highlighting both their strengths and shortcomings. Furthermore, it will bring further insights to the way these technologies could be further used to characterize post-transcriptional modifications that are known to regulate RNA-protein interactions.
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Affiliation(s)
- Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
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Brancato V, Brentari I, Coscujuela Tarrero L, Furlan M, Nicassio F, Denti MA. News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting. Biol Open 2022; 11:277240. [PMID: 36239357 PMCID: PMC9581514 DOI: 10.1242/bio.059597] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the formalization of the Central Dogma of molecular biology, the relevance of RNA in modulating the flow of information from DNA to proteins has been clear. More recently, the discovery of a vast set of non-coding transcripts involved in crucial aspects of cellular biology has renewed the enthusiasm of the RNA community. Moreover, the remarkable impact of RNA therapies in facing the COVID19 pandemics has bolstered interest in the translational opportunities provided by this incredible molecule. For all these reasons, the Italian Society of Biophysics and Molecular Biology (SIBBM) decided to dedicate its 17th yearly meeting, held in June 2022 in Rome, to the many fascinating aspects of RNA biology. More than thirty national and international speakers covered the properties, modes of action and applications of RNA, from its role in the control of development and cell differentiation to its involvement in disease. Here, we summarize the scientific content of the conference, highlighting the take-home message of each presentation, and we stress the directions the community is currently exploring to push forward our comprehension of the RNA World 3.0.
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Affiliation(s)
- Virginia Brancato
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Ilaria Brentari
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | | | - Mattia Furlan
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Francesco Nicassio
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
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9
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Carvelli A, Setti A, Desideri F, Galfrè SG, Biscarini S, Santini T, Colantoni A, Peruzzi G, Marzi MJ, Capauto D, Di Angelantonio S, Ballarino M, Nicassio F, Laneve P, Bozzoni I. A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. EMBO J 2022; 41:e108918. [PMID: 35698802 PMCID: PMC9251839 DOI: 10.15252/embj.2021108918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 06/08/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The transition from dividing progenitors to postmitotic motor neurons (MNs) is orchestrated by a series of events, which are mainly studied at the transcriptional level by analyzing the activity of specific programming transcription factors. Here, we identify a post‐transcriptional role of a MN‐specific transcriptional unit (MN2) harboring a lncRNA (lncMN2‐203) and two miRNAs (miR‐325‐3p and miR‐384‐5p) in this transition. Through the use of in vitro mESC differentiation and single‐cell sequencing of CRISPR/Cas9 mutants, we demonstrate that lncMN2‐203 affects MN differentiation by sponging miR‐466i‐5p and upregulating its targets, including several factors involved in neuronal differentiation and function. In parallel, miR‐325‐3p and miR‐384‐5p, co‐transcribed with lncMN2‐203, act by repressing proliferation‐related factors. These findings indicate the functional relevance of the MN2 locus and exemplify additional layers of specificity regulation in MN differentiation.
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Affiliation(s)
- Andrea Carvelli
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Silvia Giulia Galfrè
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Capauto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Monica Ballarino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Nicassio
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
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10
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Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frigè G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, Corrêa IR, Ettwiller L, Clementi N, Clementi M, Mancini N, Birney E, Akeson M, Nicassio F, Matthews D, Leonardi T. Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs. Nucleic Acids Res 2022; 50:3475-3489. [PMID: 35244721 PMCID: PMC8989550 DOI: 10.1093/nar/gkac144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/25/2021] [Revised: 02/05/2022] [Accepted: 02/16/2022] [Indexed: 01/09/2023] Open
Abstract
The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
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Affiliation(s)
- Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Abdulaziz Almuqrin
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
- Department of Clinical Laboratory Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Miten Jain
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milano, Italy
| | - Hugh Olsen
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | | | | | | | | | | | - Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mark Akeson
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
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11
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Simeone I, Rubolino C, Noviello T, Farinello D, Cerulo L, Marzi M, Nicassio F. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2019-2035. [PMID: 35137158 PMCID: PMC8887481 DOI: 10.1093/nar/gkac057] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 04/12/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
It is currently unknown how many RNA transcripts are able to induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD). We developed TDMDfinder, a computational pipeline that identifies ‘high confidence’ TDMD interactions in the Human and Mouse transcriptomes by combining sequence alignment and feature selection approaches. Our predictions suggested that TDMD is widespread, with potentially every miRNA controlled by endogenous targets. We experimentally tested 37 TDMDfinder predictions, of which 17 showed TDMD effects as measured by RT-qPCR and small RNA sequencing, linking the miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families to novel endogenous TDMDs. In some cases, TDMD was found to affect different members of the same miRNA family selectively. Features like complementarity to the miRNA 3′ region, bulge size and hybridization energy appeared to be the main factors determining sensitivity. Computational analyses performed using the multiomic TCGA platform substantiated the involvement of many TDMD transcripts in human cancer and highlighted 36 highly significant interactions, suggesting TDMD as a new potential oncogenic mechanism. In conclusion, TDMDfinder provides the first inventory of bona fide human and mouse TDMDs. Available as a free webtool, TDMDfinder allows users to search for any TDMD interaction of interest by customizing its selection criteria.
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Affiliation(s)
| | | | - Teresa Maria Rosaria Noviello
- Department of Electrical Engineering and Information Technology, University of Naples “Federico II”, Via Claudio 21, Naples 80128, Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Via Camporeale, Ariano Irpino (AV) 83031, Italy
| | - Diego Farinello
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
| | - Luigi Cerulo
- Dep. of Science and Technology, University of Sannio, via de Sanctis, 11, Benevento 82100, Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Via Camporeale, Ariano Irpino (AV) 83031, Italy
| | - Matteo Jacopo Marzi
- Correspondence may also be addressed to Matteo Jacopo Marzi. Tel: +39 0294375192;
| | - Francesco Nicassio
- To whom correspondence should be addressed. Tel: +39 0294375174; Fax +39 0294375991;
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12
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Tordonato C, Marzi MJ, Di Fiore PP, Nicassio F. microRNAs transcriptional profiling of mammary stem cells isolated by PKH26 staining and FACS sorting. Methods Cell Biol 2022; 170:59-79. [DOI: 10.1016/bs.mcb.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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Bido S, Muggeo S, Massimino L, Marzi MJ, Giannelli SG, Melacini E, Nannoni M, Gambarè D, Bellini E, Ordazzo G, Rossi G, Maffezzini C, Iannelli A, Luoni M, Bacigaluppi M, Gregori S, Nicassio F, Broccoli V. Microglia-specific overexpression of α-synuclein leads to severe dopaminergic neurodegeneration by phagocytic exhaustion and oxidative toxicity. Nat Commun 2021; 12:6237. [PMID: 34716339 PMCID: PMC8556263 DOI: 10.1038/s41467-021-26519-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [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: 11/11/2020] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Recent findings in human samples and animal models support the involvement of inflammation in the development of Parkinson's disease. Nevertheless, it is currently unknown whether microglial activation constitutes a primary event in neurodegeneration. We generated a new mouse model by lentiviral-mediated selective α-synuclein (αSYN) accumulation in microglial cells. Surprisingly, these mice developed progressive degeneration of dopaminergic (DA) neurons without endogenous αSYN aggregation. Transcriptomics and functional assessment revealed that αSYN-accumulating microglial cells developed a strong reactive state with phagocytic exhaustion and excessive production of oxidative and proinflammatory molecules. This inflammatory state created a molecular feed-forward vicious cycle between microglia and IFNγ-secreting immune cells infiltrating the brain parenchyma. Pharmacological inhibition of oxidative and nitrosative molecule production was sufficient to attenuate neurodegeneration. These results suggest that αSYN accumulation in microglia induces selective DA neuronal degeneration by promoting phagocytic exhaustion, an excessively toxic environment and the selective recruitment of peripheral immune cells.
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Affiliation(s)
- Simone Bido
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Sharon Muggeo
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Luca Massimino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Serena Gea Giannelli
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Elena Melacini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy
| | - Melania Nannoni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Diana Gambarè
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Edoardo Bellini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Gabriele Ordazzo
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Greta Rossi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Camilla Maffezzini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Angelo Iannelli
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy
| | - Mirko Luoni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Marco Bacigaluppi
- Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Gregori
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Vania Broccoli
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy.
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy.
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14
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Tordonato C, Marzi MJ, Giangreco G, Freddi S, Bonetti P, Tosoni D, Di Fiore PP, Nicassio F. miR-146 connects stem cell identity with metabolism and pharmacological resistance in breast cancer. J Cell Biol 2021; 220:211945. [PMID: 33819341 PMCID: PMC8025236 DOI: 10.1083/jcb.202009053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/10/2020] [Revised: 01/26/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Although ectopic overexpression of miRNAs can influence mammary normal and cancer stem cells (SCs/CSCs), their physiological relevance remains uncertain. Here, we show that miR-146 is relevant for SC/CSC activity. MiR-146a/b expression is high in SCs/CSCs from human/mouse primary mammary tissues, correlates with the basal-like breast cancer subtype, which typically has a high CSC content, and specifically distinguishes cells with SC/CSC identity. Loss of miR-146 reduces SC/CSC self-renewal in vitro and compromises patient-derived xenograft tumor growth in vivo, decreasing the number of tumor-initiating cells, thus supporting its pro-oncogenic function. Transcriptional analysis in mammary SC-like cells revealed that miR-146 has pleiotropic effects, reducing adaptive response mechanisms and activating the exit from quiescent state, through a complex network of finely regulated miRNA targets related to quiescence, transcription, and one-carbon pool metabolism. Consistent with these findings, SCs/CSCs display innate resistance to anti-folate chemotherapies either in vitro or in vivo that can be reversed by miR-146 depletion, unmasking a “hidden vulnerability” exploitable for the development of anti-CSC therapies.
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Affiliation(s)
- Chiara Tordonato
- European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università Degli Studi di Milano, Milano, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy
| | - Giovanni Giangreco
- European Institute of Oncology IRCCS, Milan, Italy.,Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Paola Bonetti
- Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy
| | | | - Pier Paolo Di Fiore
- European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università Degli Studi di Milano, Milano, Italy
| | - Francesco Nicassio
- Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy
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15
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Mazzara PG, Muggeo S, Luoni M, Massimino L, Zaghi M, Valverde PTT, Brusco S, Marzi MJ, Palma C, Colasante G, Iannielli A, Paulis M, Cordiglieri C, Giannelli SG, Podini P, Gellera C, Taroni F, Nicassio F, Rasponi M, Broccoli V. Frataxin gene editing rescues Friedreich's ataxia pathology in dorsal root ganglia organoid-derived sensory neurons. Nat Commun 2020; 11:4178. [PMID: 32826895 PMCID: PMC7442818 DOI: 10.1038/s41467-020-17954-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/30/2019] [Accepted: 07/28/2020] [Indexed: 12/31/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal-recessive neurodegenerative and cardiac disorder which occurs when transcription of the FXN gene is silenced due to an excessive expansion of GAA repeats into its first intron. Herein, we generate dorsal root ganglia organoids (DRG organoids) by in vitro differentiation of human iPSCs. Bulk and single-cell RNA sequencing show that DRG organoids present a transcriptional signature similar to native DRGs and display the main peripheral sensory neuronal and glial cell subtypes. Furthermore, when co-cultured with human intrafusal muscle fibers, DRG organoid sensory neurons contact their peripheral targets and reconstitute the muscle spindle proprioceptive receptors. FRDA DRG organoids model some molecular and cellular deficits of the disease that are rescued when the entire FXN intron 1 is removed, and not with the excision of the expanded GAA tract. These results strongly suggest that removal of the repressed chromatin flanking the GAA tract might contribute to rescue FXN total expression and fully revert the pathological hallmarks of FRDA DRG neurons.
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Affiliation(s)
- Pietro Giuseppe Mazzara
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- Department of Neuroscience, The Scripps Research Institute, 92037, La Jolla, CA, USA
| | - Sharon Muggeo
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Mirko Luoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Luca Massimino
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Mattia Zaghi
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | | | - Simone Brusco
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Cecilia Palma
- Department of Electronics, Information & Bioengineering, Politecnico di Milano, 20133, Milan, Italy
| | - Gaia Colasante
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Angelo Iannielli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy
| | - Marianna Paulis
- Humanitas Clinical and Research Center, 20089, Rozzano, Milano, Italy
| | - Chiara Cordiglieri
- National Institute of Molecular Genetics "Romeo e Enrica Invernizzi" - INGM, 20122, Milan, Italy
| | - Serena Gea Giannelli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Paola Podini
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Marco Rasponi
- Department of Electronics, Information & Bioengineering, Politecnico di Milano, 20133, Milan, Italy
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy.
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy.
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16
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Santoro A, Vlachou T, Luzi L, Melloni G, Mazzarella L, D'Elia E, Aobuli X, Pasi CE, Reavie L, Bonetti P, Punzi S, Casoli L, Sabò A, Moroni MC, Dellino GI, Amati B, Nicassio F, Lanfrancone L, Pelicci PG. p53 Loss in Breast Cancer Leads to Myc Activation, Increased Cell Plasticity, and Expression of a Mitotic Signature with Prognostic Value. Cell Rep 2020; 26:624-638.e8. [PMID: 30650356 PMCID: PMC6334229 DOI: 10.1016/j.celrep.2018.12.071] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/26/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022] Open
Abstract
Loss of p53 function is invariably associated with cancer. Its role in tumor growth was recently linked to its effects on cancer stem cells (CSCs), although the underlying molecular mechanisms remain unknown. Here, we show that c-myc is a transcriptional target of p53 in mammary stem cells (MaSCs) and is activated in breast tumors as a consequence of p53 loss. Constitutive Myc expression in normal mammary cells leads to increased frequency of MaSC symmetric divisions, extended MaSC replicative-potential, and MaSC-reprogramming of progenitors, whereas Myc activation in breast cancer is necessary and sufficient to maintain the expanding pool of CSCs. Concomitant p53 loss and Myc activation trigger the expression of 189 mitotic genes, which identify patients at high risk of mortality and relapse, independently of other risk factors. Altogether, deregulation of the p53:Myc axis in mammary tumors increases CSC content and plasticity and is a critical determinant of tumor growth and clinical aggressiveness. Myc is overexpressed and deregulated in breast tumors because of p53 signaling attenuation Myc activation favors SC symmetric divisions and SC reprogramming of progenitors Myc activation is necessary and sufficient to sustain the cancer SC phenotype Expression of 189 mitotic p53:Myc targets identifies high-risk breast cancer patients
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Affiliation(s)
- Angela Santoro
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Thalia Vlachou
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Lucilla Luzi
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giorgio Melloni
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy; Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Luca Mazzarella
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Errico D'Elia
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Xieraili Aobuli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Cristina Elisabetta Pasi
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Linsey Reavie
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; BioPharma Excellence, Agnes-Pockels-Bogen 1, 80922 Munich, Germany
| | - Paola Bonetti
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Simona Punzi
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Lucia Casoli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Arianna Sabò
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Maria Cristina Moroni
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Gaetano Ivan Dellino
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142 Milan, Italy
| | - Bruno Amati
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Luisa Lanfrancone
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142 Milan, Italy.
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17
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Spadotto V, Giambruno R, Massignani E, Mihailovich M, Maniaci M, Patuzzo F, Ghini F, Nicassio F, Bonaldi T. PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic Acids Res 2020; 48:96-115. [PMID: 31777917 PMCID: PMC6943135 DOI: 10.1093/nar/gkz1051] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 10/04/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNA (miRNA) biogenesis is a tightly controlled multi-step process operated in the nucleus by the activity of the Microprocessor and its associated proteins. Through high resolution mass spectrometry (MS)- proteomics we discovered that this complex is extensively methylated, with 84 methylated sites associated to 19 out of its 24 subunits. The majority of the modifications occurs on arginine (R) residues (61), leading to 81 methylation events, while 30 lysine (K)-methylation events occurs on 23 sites of the complex. Interestingly, both depletion and pharmacological inhibition of the Type-I Protein Arginine Methyltransferases (PRMTs) lead to a widespread change in the methylation state of the complex and induce global decrease of miRNA expression, as a consequence of the impairment of the pri-to-pre-miRNA processing step. In particular, we show that the reduced methylation of the Microprocessor subunit ILF3 is linked to its diminished binding to the pri-miRNAs miR-15a/16, miR-17-92, miR-301a and miR-331. Our study uncovers a previously uncharacterized role of R-methylation in the regulation of miRNA biogenesis in mammalian cells.
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Affiliation(s)
- Valeria Spadotto
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Giambruno
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesca Patuzzo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Ghini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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18
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Bonetti P, Climent M, Panebianco F, Tordonato C, Santoro A, Marzi MJ, Pelicci PG, Ventura A, Nicassio F. Correction: Dual role for miR-34a in the control of early progenitor proliferation and commitment in the mammary gland and in breast cancer. Oncogene 2019; 39:2228. [PMID: 31705063 PMCID: PMC7056634 DOI: 10.1038/s41388-019-1094-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Paola Bonetti
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy.
| | - Montserrat Climent
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Fabiana Panebianco
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Chiara Tordonato
- IFOM, The FIRC Institute for Molecular Oncology Foundation, 20139, Milan, Italy
| | - Angela Santoro
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Pier Giuseppe Pelicci
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139, Milan, Italy.,Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20100, Milan, Italy
| | - Andrea Ventura
- Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy.
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19
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Pons-Espinal M, Gasperini C, Marzi MJ, Braccia C, Armirotti A, Pötzsch A, Walker TL, Fabel K, Nicassio F, Kempermann G, De Pietri Tonelli D. MiR-135a-5p Is Critical for Exercise-Induced Adult Neurogenesis. Stem Cell Reports 2019; 12:1298-1312. [PMID: 31130358 PMCID: PMC6565832 DOI: 10.1016/j.stemcr.2019.04.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 06/05/2018] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022] Open
Abstract
Physical exercise stimulates adult hippocampal neurogenesis and is considered a relevant strategy for preventing age-related cognitive decline in humans. The underlying mechanisms remains controversial. Here, we show that exercise increases proliferation of neural precursor cells (NPCs) of the mouse dentate gyrus (DG) via downregulation of microRNA 135a-5p (miR-135a). MiR-135a inhibition stimulates NPC proliferation leading to increased neurogenesis, but not astrogliogenesis, in DG of resting mice, and intriguingly it re-activates NPC proliferation in aged mice. We identify 17 proteins (11 putative targets) modulated by miR-135 in NPCs. Of note, inositol 1,4,5-trisphosphate (IP3) receptor 1 and inositol polyphosphate-4-phosphatase type I are among the modulated proteins, suggesting that IP3 signaling may act downstream miR-135. miR-135 is the first noncoding RNA essential modulator of the brain's response to physical exercise. Prospectively, the miR-135-IP3 axis might represent a novel target of therapeutic intervention to prevent pathological brain aging.
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Affiliation(s)
| | - Caterina Gasperini
- Neurobiology of miRNA, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Clarissa Braccia
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Alexandra Pötzsch
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Tara L Walker
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Klaus Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
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20
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Rossi M, Bucci G, Rizzotto D, Bordo D, Marzi MJ, Puppo M, Flinois A, Spadaro D, Citi S, Emionite L, Cilli M, Nicassio F, Inga A, Briata P, Gherzi R. LncRNA EPR controls epithelial proliferation by coordinating Cdkn1a transcription and mRNA decay response to TGF-β. Nat Commun 2019; 10:1969. [PMID: 31036808 PMCID: PMC6488594 DOI: 10.1038/s41467-019-09754-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [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: 05/19/2018] [Accepted: 03/27/2019] [Indexed: 12/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as regulators of fundamental biological processes. Here we report on the characterization of an intergenic lncRNA expressed in epithelial tissues which we termed EPR (Epithelial cell Program Regulator). EPR is rapidly downregulated by TGF-β and its sustained expression largely reshapes the transcriptome, favors the acquisition of epithelial traits, and reduces cell proliferation in cultured mammary gland cells as well as in an animal model of orthotopic transplantation. EPR generates a small peptide that localizes at epithelial cell junctions but the RNA molecule per se accounts for the vast majority of EPR-induced gene expression changes. Mechanistically, EPR interacts with chromatin and regulates Cdkn1a gene expression by affecting both its transcription and mRNA decay through its association with SMAD3 and the mRNA decay-promoting factor KHSRP, respectively. We propose that EPR enables epithelial cells to control proliferation by modulating waves of gene expression in response to TGF-β. Several lncRNAs are regulated by TGF-β. Here the authors report that an intergenic lncRNA —EPR— is a component of the TGF-β signaling pathway and controls epithelial cell proliferation by altering transcription and mRNA decay of Cdkn1a. EPR overexpression restrains tumor growth of orthotopically transplanted mice.
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Affiliation(s)
- Martina Rossi
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy.,DIMES Sezione Biochimica-Università di Genova, 16132, Genova, Italy
| | - Gabriele Bucci
- Center of Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, 20132, Milano, Italy
| | - Dario Rizzotto
- Laboratory of Transcriptional Networks, Center for Integrative Biology, CIBIO, University of Trento, 38123, Trento, Italy
| | - Domenico Bordo
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy
| | - Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy
| | - Margherita Puppo
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy.,DIMES Sezione Biochimica-Università di Genova, 16132, Genova, Italy
| | - Arielle Flinois
- Department of Cell Biology, University of Geneve, 1211, Geneve, Switzerland
| | - Domenica Spadaro
- Department of Cell Biology, University of Geneve, 1211, Geneve, Switzerland
| | - Sandra Citi
- Department of Cell Biology, University of Geneve, 1211, Geneve, Switzerland
| | - Laura Emionite
- Animal Facility, IRCCS Policlinico San Martino, 16132, Genova, Italy
| | - Michele Cilli
- Animal Facility, IRCCS Policlinico San Martino, 16132, Genova, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Center for Integrative Biology, CIBIO, University of Trento, 38123, Trento, Italy.
| | - Paola Briata
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy.
| | - Roberto Gherzi
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy.
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21
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Panebianco F, Climent M, Malvindi MA, Pompa PP, Bonetti P, Nicassio F. Delivery of biologically active miR-34a in normal and cancer mammary epithelial cells by synthetic nanoparticles. Nanomedicine 2019; 19:95-105. [PMID: 31028887 DOI: 10.1016/j.nano.2019.03.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/20/2019] [Indexed: 02/06/2023]
Abstract
Functional RNAs, such as microRNAs, are emerging as innovative tools in the treatment of aggressive and incurable cancers. In this study, we explore the potential of silica dioxide nanoparticles (SiO2NPs) in the delivery of biologically active miRNAs. Focusing on the tumor-suppressor miR-34a, we evaluated miRNAs delivery by SiO2NPs into the mammary gland, using in vitro as well as in vivo model systems. We showed that silica nanoparticles can efficiently deliver miR-34a into normal and cancer epithelial cells grown in culture without major signs of toxicity. Delivered miRNA retained the ability to silence artificial as well endogenous targets and can reduce the growth of mammospheres in 3D culture. Finally, miR-34a delivery through intra-tumor administration of SiO2NPs leads to a reduced mammary tumor growth. In conclusion, our studies suggest that silica nanoparticles can mediate the delivery of miR-34a directly into mammary tumors while preserving its molecular and biological activity.
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Affiliation(s)
- Fabiana Panebianco
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Montserrat Climent
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mari Ada Malvindi
- Nanobiointeractions & Nanodiagnostics, Center for Biomolecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Arnesano (Lecce), Italy
| | - Pier Paolo Pompa
- Nanobiointeractions & Nanodiagnostics, Center for Biomolecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Arnesano (Lecce), Italy; Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Paola Bonetti
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
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22
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Climent M, Bonetti P, Nicassio F. Abstract 4410: miRNA-34a sensitizes triple-negative breast cancer cells to paclitaxel reducing cancer stem cell population and lung colonization. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4410] [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
Background: Cancer stem cells (CSCs) have inherent or developed drug resistance for which chemotherapy fails to eliminate all tumor cells, a property that is critically contributing to recurrence and metastasis. Here, we combine miR-34a, a well-known tumor suppressor miRNA that controls proliferation, apoptosis and self-renewal, with Paclitaxel (PTX), a commonly used first-line chemotherapy drug. Based on our preliminary observations (Bonetti et al., manuscript under revision), we hypothesized a combinatorial approach, coupling miRNA- and chemo- treatment, aimed at reducing CSCs in vitro and recurrence in vivo using triple-negative breast cancer (TNBC) as a model. Methodology: As a model, we exploited SUM159pt cells (TNBC mesenchymal-like, with CSC features) to mimic aggressive breast cancer, which harbor a vector for pLUC, which is induced by luciferin in vivo, to monitor tumor growth in real time. Furthermore, we used i) pSlik34a, with tunable expression of miR-34a by doxycycline; ii) treatment with PTX to select for resistant cells (RC); and combined the two, by treating RC with doxycycline. CSC content was evaluated by ALDH (Aldehyde Dehydrogenase) activity, sphere-forming efficiency (SFE) and qRT-PCR of known markers. A similar approach was followed for in vivo studies, with NSG female injected through tail vein injection with 500,000 SUM159/pLUC/pSlik34a cells, and separated into three groups: not treated (NT), PTX alone, and PTX+34a. Results: As observed for aggressive breast cancer, treatment of SUM159 with PTX generated resistant cells (RC) with increased CSC content (ALDH activity and spheres forming ability). When miR-34a was induced in the RC, cells changed morphology, slowed proliferation rate, and decreased CSC content (ALDH activity and spheres). Moreover, a second PTX treatment almost completely abolished the ALDH activity and SFE. The combined effect was evaluated in vivo, following by luminescence the growth of metastases after lung colonization, with PTX+34a mice reducing lung colonization than the PTX treatment or miR-34a treatment alone. Conclusions: Overall, these results indicate that miR-34a sensitize PTX-resistant cells reducing cancer stem-cell capacities, and in this preclinical setting limited the aggressive phenotype of breast cancer, including proliferation, drug resistance, relapse and metastasis causing in delay of lung colonization in vivo.
Citation Format: Montserrat Climent, Paola Bonetti, Francesco Nicassio. miRNA-34a sensitizes triple-negative breast cancer cells to paclitaxel reducing cancer stem cell population and lung colonization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4410.
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23
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Matteucci E, Maroni P, Nicassio F, Ghini F, Bendinelli P, Desiderio MA. Microenvironment Stimuli HGF and Hypoxia Differently Affected miR-125b and Ets-1 Function with Opposite Effects on the Invasiveness of Bone Metastatic Cells: A Comparison with Breast Carcinoma Cells. Int J Mol Sci 2018; 19:ijms19010258. [PMID: 29337876 PMCID: PMC5796204 DOI: 10.3390/ijms19010258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 12/04/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 12/14/2022] Open
Abstract
We examined the influence of microenvironment stimuli on molecular events relevant to the biological functions of 1833-bone metastatic clone and the parental MDA-MB231 cells. (i) In both the cell lines, hepatocyte growth factor (HGF) and the osteoblasts' biological products down regulated nuclear Ets-1-protein level in concomitance with endogenous miR-125b accumulation. In contrast, under hypoxia nuclear Ets-1 was unchanged, notwithstanding the miR-125b increase. (ii) Also, the 1833-cell invasiveness and the expression of Endothelin-1, the target gene of Ets-1/HIF-1, showed opposite patterns under HGF and hypoxia. We clarified the molecular mechanism(s) reproducing the high miR-125b levels with the mimic in 1833 cells. Under hypoxia, the miR-125b mimic maintained a basal level and functional Ets-1 protein, as testified by the elevated cell invasiveness. However, under HGF ectopic miR-125b downregulated Ets-1 protein and cell motility, likely involving an Ets-1-dominant negative form sensible to serum conditions; Ets-1-activity inhibition by HGF implicated HIF-1α accumulation, which drugged Ets-1 in the complex bound to the Endothelin-1 promoter. Altogether, 1833-cell exposure to HGF would decrease Endothelin-1 transactivation and protein expression, with the possible impairment of Endothelin-1-dependent induction of E-cadherin, and the reversion towards an invasive phenotype: this was favoured by Ets-1 overexpression, which inhibited HIF-1α expression and HIF-1 activity. (iii) In MDA-MB231 cells, HGF strongly and rapidly decreased Ets-1, hampering invasiveness and reducing Ets-1-binding to Endothelin-1 promoter; HIF-1α did not form a complex with Ets-1 and Endothelin-1-luciferase activity was unchanged. Overall, depending on the microenvironment conditions and endogenous miR-125b levels, bone-metastatic cells might switch from Ets-1-dependent motility towards colonization/growth, regulated by the balance between Ets-1 and HIF-1.
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Affiliation(s)
- Emanuela Matteucci
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy.
| | - Paola Maroni
- Istituto Ortopedico Galeazzi, Scientific Institute for Research, Hospitalization and Health Care (IRCCS), Milano 20161, Italy.
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano 20139, Italy.
| | - Francesco Ghini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano 20139, Italy.
| | - Paola Bendinelli
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy.
| | - Maria Alfonsina Desiderio
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy.
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24
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Abstract
MicroRNAs (miRNAs) are an evolutionary conserved class of short, single-stranded noncoding RNAs (<18-22 nt in length) that act in posttranscriptional regulation of gene expression in higher eukaryotes. The abundance of a miRNA is a key feature in control of its activity and, therefore, a number of mechanisms finely regulate miRNA levels, acting at both transcriptional and posttranscriptional level. Recent evidences, including our research, highlighted the role of miRNA decay as a mechanism controlling the miRNA pool. We describe in this chapter an optimized methodology to determine miRNA degradation rates in mammalian cells. Our approach is based on metabolic pulse labeling with 4-thiouridine (4sU), a uridine analog that is incorporated in nascent RNA and allows thiol-specific biotinylation and selective pull-down of labeled RNA. In particular, given the long average half-life and the complex biogenetic process of miRNAs, we developed a "pulse-chase" protocol where 4sU is removed from the medium after a long labeling period (2-3 h pulse), and labeled RNA is purified at different time points to measure the decay of labeled molecules. By combining the 4sU-based "pulse-chase" approach with high-throughput small RNA sequencing (sRNAseq), it is possible to quantify at genome-wide level miRNA degradation rates.
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Affiliation(s)
- Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
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25
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Pons-Espinal M, de Luca E, Marzi MJ, Beckervordersandforth R, Armirotti A, Nicassio F, Fabel K, Kempermann G, De Pietri Tonelli D. Synergic Functions of miRNAs Determine Neuronal Fate of Adult Neural Stem Cells. Stem Cell Reports 2017; 8:1046-1061. [PMID: 28330621 PMCID: PMC5390108 DOI: 10.1016/j.stemcr.2017.02.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 07/12/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 02/04/2023] Open
Abstract
Adult neurogenesis requires the precise control of neuronal versus astrocyte lineage determination in neural stem cells. While microRNAs (miRNAs) are critically involved in this step during development, their actions in adult hippocampal neural stem cells (aNSCs) has been unclear. As entry point to address that question we chose DICER, an endoribonuclease essential for miRNA biogenesis and other RNAi-related processes. By specific ablation of Dicer in aNSCs in vivo and in vitro, we demonstrate that miRNAs are required for the generation of new neurons, but not astrocytes, in the adult murine hippocampus. Moreover, we identify 11 miRNAs, of which 9 have not been previously characterized in neurogenesis, that determine neurogenic lineage fate choice of aNSCs at the expense of astrogliogenesis. Finally, we propose that the 11 miRNAs sustain adult hippocampal neurogenesis through synergistic modulation of 26 putative targets from different pathways. Dicer depletion in aNSCs impairs neurogenesis and stimulates astrogliogenesis Synergy of 11 miRNAs sustains neuronal fate of aNSCs miRNA converge on multiple targets in different pathways to induce neurogenesis
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Affiliation(s)
- Meritxell Pons-Espinal
- Neurobiology of miRNA Lab, Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Emanuela de Luca
- Neurobiology of miRNA Lab, Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science, Istituto Italiano di Tecnologia, IFOM-IEO CAMPUS, Via Adamello 16, 20139 Milan, Italy
| | - Ruth Beckervordersandforth
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Andrea Armirotti
- D3 PharmaChemistry, Department of Drug Discovery and Development, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Francesco Nicassio
- Center for Genomic Science, Istituto Italiano di Tecnologia, IFOM-IEO CAMPUS, Via Adamello 16, 20139 Milan, Italy
| | - Klaus Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Arnoldstraße 18/18b, 01307 Dresden, Germany; CRTD - Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Arnoldstraße 18/18b, 01307 Dresden, Germany; CRTD - Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Davide De Pietri Tonelli
- Neurobiology of miRNA Lab, Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.
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26
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Marinaro F, Marzi MJ, Hoffmann N, Amin H, Pelizzoli R, Niola F, Nicassio F, De Pietri Tonelli D. MicroRNA-independent functions of DGCR8 are essential for neocortical development and TBR1 expression. EMBO Rep 2017; 18:603-618. [PMID: 28232627 DOI: 10.15252/embr.201642800] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 12/31/2022] Open
Abstract
Recent evidence indicates that the miRNA biogenesis factors DROSHA, DGCR8, and DICER exert non-overlapping functions, and have also roles in miRNA-independent regulatory mechanisms. However, it is currently unknown whether miRNA-independent functions of DGCR8 play any role in the maintenance of neuronal progenitors and during corticogenesis. Here, by phenotypic comparison of cortices from conditional Dgcr8 and Dicer knockout mice, we show that Dgcr8 deletion, in contrast to Dicer depletion, leads to premature differentiation of neural progenitor cells and overproduction of TBR1-positive neurons. Remarkably, depletion of miRNAs upon DCGR8 loss is reduced compared to DICER loss, indicating that these phenotypic differences are mediated by miRNA-independent functions of DGCR8. We show that Dgcr8 mutations induce an earlier and stronger phenotype in the developing nervous system compared to Dicer mutants and that miRNA-independent functions of DGCR8 are critical for corticogenesis. Finally, our data also suggest that the Microprocessor complex, with DROSHA and DGCR8 as core components, directly regulates the Tbr1 transcript, containing evolutionarily conserved hairpins that resemble miRNA precursors, independently of miRNAs.
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Affiliation(s)
- Federica Marinaro
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Nadin Hoffmann
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Hayder Amin
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Roberta Pelizzoli
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Niola
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
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Marzi MJ, Montani F, Carletti RM, Dezi F, Dama E, Bonizzi G, Sandri MT, Rampinelli C, Bellomi M, Maisonneuve P, Spaggiari L, Veronesi G, Bianchi F, Di Fiore PP, Nicassio F. Optimization and Standardization of Circulating MicroRNA Detection for Clinical Application: The miR-Test Case. Clin Chem 2016; 62:743-54. [DOI: 10.1373/clinchem.2015.251942] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/19/2016] [Indexed: 01/05/2023]
Abstract
Abstract
BACKGROUND
The identification of circulating microRNAs (miRNAs) in the blood has been recently exploited for the development of minimally invasive tests for the early detection of cancer. Nevertheless, the clinical transferability of such tests is uncertain due to still-insufficient standardization and optimization of methods to detect circulating miRNAs in the clinical setting.
METHODS
We performed a series of tests to optimize the quantification of serum miRNAs that compose the miR-Test, a signature for lung cancer early detection, and systematically analyzed variables that could affect the performance of the test. We took advantage of a large-scale (>1000 samples) validation study of the miR-Test that we recently published, to evaluate, in clinical samples, the effects of analytical and preanalytical variables on the quantification of circulating miRNAs and the clinical output of the signature (risk score).
RESULTS
We developed a streamlined and standardized pipeline for the processing of clinical serum samples that allows the isolation and analysis of circulating miRNAs by quantitative reverse-transcription PCR, with a throughput compatible with screening trials. The major source of analytical variation came from RNA isolation from serum, which could be corrected by use of external (spike-in) or endogenous miRNAs as a reference for normalization. We also introduced standard operating procedures and QC steps to check for unspecific fluctuations that arise from the lack of standardized criteria in the collection or handling of the samples (preanalytical factors).
CONCLUSIONS
We propose our methodology as a reference for the development of clinical-grade blood tests on the basis of miRNA detection.
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Affiliation(s)
- Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Francesca Montani
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
| | - Rose Mary Carletti
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
- The FIRC Institute for Molecular Oncology Foundation (IFOM), Milan, Italy
| | - Fabio Dezi
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
| | - Elisa Dama
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
- Division of Epidemiology and Biostatistics
| | - Giuseppina Bonizzi
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
| | | | | | | | | | - Lorenzo Spaggiari
- Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy
| | - Giulia Veronesi
- Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy
- Humanitas Research Hospital, Thoracic Surgery, Rozzano, Milan, Italy
| | - Fabrizio Bianchi
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
| | - Pier Paolo Di Fiore
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
- The FIRC Institute for Molecular Oncology Foundation (IFOM), Milan, Italy
- Dipartimento di Scienze della Salute, University of Milan, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
- Molecular Medicine Program, European Institute of Oncology, Milan, Italy
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Marzi MJ, Ghini F, Cerruti B, de Pretis S, Bonetti P, Giacomelli C, Gorski MM, Kress T, Pelizzola M, Muller H, Amati B, Nicassio F. Degradation dynamics of microRNAs revealed by a novel pulse-chase approach. Genome Res 2016; 26:554-65. [PMID: 26821571 PMCID: PMC4817778 DOI: 10.1101/gr.198788.115] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/19/2016] [Indexed: 12/22/2022]
Abstract
The regulation of miRNAs is critical to the definition of cell identity and behavior in normal physiology and disease. To date, the dynamics of miRNA degradation and the mechanisms involved in remain largely obscure, in particular, in higher organisms. Here, we developed a pulse-chase approach based on metabolic RNA labeling to calculate miRNA decay rates at genome-wide scale in mammalian cells. Our analysis revealed heterogeneous miRNA half-lives, with many species behaving as stable molecules (T1/2 > 24 h), while others, including passenger miRNAs and a number (25/129) of guide miRNAs, are quickly turned over (T1/2 = 4–14 h). Decay rates were coupled with other features, including genomic organization, transcription rates, structural heterogeneity (isomiRs), and target abundance, measured through quantitative experimental approaches. This comprehensive analysis highlighted functional mechanisms that mediate miRNA degradation, as well as the importance of decay dynamics in the regulation of the miRNA pool under both steady-state conditions and during cell transitions.
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Affiliation(s)
- Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Francesco Ghini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Benedetta Cerruti
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Stefano de Pretis
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Paola Bonetti
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Chiara Giacomelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Marcin M Gorski
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Heiko Muller
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Bruno Amati
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
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Montani F, Marzi M, Dezi F, Dama E, Carletti RM, Veronesi G, Nicassio F, Di Fiore PP, Bianchi F. Abstract 1575: Serum circulating miR–Test application: Standardized protocol for miR–Test clinical application. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1575] [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
Lung cancer is leading cause of cancer death worldwide. Being lung cancer asymptomatic in its early stages, the majority of patients are diagnosed with advanced disease. Therefore, it is vital that screening programs and novel diagnostic tools are developed to increase lung cancer early detection. The development of a minimally invasive blood-based diagnostic tool would be ideal as a first-line screening procedure. An increasing number of studies are demonstrating that fluctuations of circulating miRNAs are associated to lung cancer. Recently, we described a serum circulating miRNA signature (miR-Test) diagnostic for asymptomatic, early stage, lung cancer, that was validated in a large cohort of individuals (N = 1115) enrolled in the lung cancer screening program COSMOS (Continuous Observation of SMOking Subjects). However, the transfer to the clinic of a blood test based on circ-miRNAs requires the establishment of standardized operating procedures (SOPs), working instructions and guidelines for all pre-analytical and analytical procedures.
We identified possible sources of variability affecting circulating miRNAs, analyzed their impact on the miR-Test performance, and defined a standardized protocol to optimize miR-Test application. Analysis of all possible technical and biological variation affecting circ-miRNAs level, revealed two main sources of variability: one related to analytical procedures for miRNAs extraction and quantification, and the other due to pre-analytical conditions, on how samples are prepared. The extraction causes the main source of analytical imprecision.
In conclusion, we identified an optimal protocol for the application of miR-Test for lung cancer early diagnosis.
Citation Format: Francesca Montani, Matteo Marzi, Fabio Dezi, Elisa Dama, Rose Mary Carletti, Giulia Veronesi, Francesco Nicassio, Pier Paolo Di Fiore, Fabrizio Bianchi. Serum circulating miR–Test application: Standardized protocol for miR–Test clinical application. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1575. doi:10.1158/1538-7445.AM2015-1575
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Affiliation(s)
| | - Matteo Marzi
- 2IIT-Istituto Italiano di Tecnologia, Milan, Italy
| | - Fabio Dezi
- 1IEO - European Institue of Oncology, Milan, Italy
| | - Elisa Dama
- 1IEO - European Institue of Oncology, Milan, Italy
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30
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Montani F, Marzi MJ, Dezi F, Dama E, Carletti RM, Bonizzi G, Bertolotti R, Bellomi M, Rampinelli C, Maisonneuve P, Spaggiari L, Veronesi G, Nicassio F, Di Fiore PP, Bianchi F. Abstract 1573: miR-Test: a blood test for lung cancer early detection. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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
Background:
Lung cancer is the leading cause of cancer death worldwide. As lung cancer is asymptomatic in its early stages, the majority of patients are diagnosed with advanced disease, when the tumor is unresectable. Consequently, the survival rate is very low: 15% at 5 years. It is vital, therefore, that screening programs and novel diagnostic tools are developed, which will increase the detection of lung cancer in its early stages (stage I-II), when the tumor is still curable, to reduce lung cancer mortality. Recently, we described a serum microRNA signature diagnostic for asymptomatic, early stage, lung cancer. The availability of reliable biomarkers to identify high-risk individuals might help to reduce the size of the target population for LDCT-based programs, thereby reducing costs and probably increasing compliance
Methods:
We performed a large-scale validation study of a miRNA blood test based on our signature (the miR-Test) in a population of high-risk individuals (N = 1115) enrolled in the lung cancer screening program COSMOS (Continuous Observation of SMOking Subjects), and other 74 lung cancer patients diagnosed outside of screening.
Results:
The miR-Test showed overall accuracy, specificity and sensitivity of 75%, 78%, and 75%, respectively, with an AUC of 0.85. The test appears to have a dual origin: the first from epithelial cells (the epithelial-like component); the second from cells of hematopoietic origin (the inflammatory-like component). Of note, we found that both components are needed to maintain a good performance of the miR-Test.
Conclusions:
The relatively high sensitivity of the miR-Test in detecting asymptomatic lung cancer and its high negative predictive value (NPV > 99%), confirm the effectiveness of the test, both interms of its ability to identify asymptomatic lung cancer patients and to reduce significantly unnecessary CTs on healthy individuals.
Citation Format: Francesca Montani, Matteo Jacopo Marzi, Fabio Dezi, Elisa Dama, Rose Mary Carletti, Giuseppina Bonizzi, Raffaella Bertolotti, Massimo Bellomi, Cristiano Rampinelli, Patrick Maisonneuve, Lorenzo Spaggiari, Giulia Veronesi, Francesco Nicassio, Pier Paolo Di Fiore, Fabrizio Bianchi. miR-Test: a blood test for lung cancer early detection. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1573. doi:10.1158/1538-7445.AM2015-1573
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Affiliation(s)
| | | | - Fabio Dezi
- 1European Institute of Oncology, Milan, Italy
| | - Elisa Dama
- 1European Institute of Oncology, Milan, Italy
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31
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Montani F, Marzi MJ, Dezi F, Dama E, Carletti RM, Bonizzi G, Bertolotti R, Bellomi M, Rampinelli C, Maisonneuve P, Spaggiari L, Veronesi G, Nicassio F, Di Fiore PP, Bianchi F. miR-Test: a blood test for lung cancer early detection. J Natl Cancer Inst 2015; 107:djv063. [PMID: 25794889 DOI: 10.1093/jnci/djv063] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Low-dose computed tomography screening (LDCT) was recently shown to anticipate the time of diagnosis, thus reducing lung cancer mortality. However, concerns persist about the feasibility and costs of large-scale LDCT programs. Such concerns may be addressed by clearly defining the target "high-risk" population that needs to be screened by LDCT. We recently identified a serum microRNA signature (the miR-Test) that could identify the optimal target population. Here, we performed a large-scale validation study of the miR-Test in high-risk individuals (n = 1115) enrolled in the Continuous Observation of Smoking Subjects (COSMOS) lung cancer screening program. The overall accuracy, sensitivity, and specificity of the miR-Test are 74.9% (95% confidence interval [CI] = 72.2% to 77.6%), 77.8% (95% CI = 64.2% to 91.4%), and 74.8% (95% CI = 72.1% to 77.5%), respectively; the area under the curve is 0.85 (95% CI = 0.78 to 0.92). These results argue that the miR-Test might represent a useful tool for lung cancer screening in high-risk individuals.
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Affiliation(s)
- Francesca Montani
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Matteo Jacopo Marzi
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Fabio Dezi
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Elisa Dama
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Rose Mary Carletti
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Giuseppina Bonizzi
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Raffaella Bertolotti
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Massimo Bellomi
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Cristiano Rampinelli
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Patrick Maisonneuve
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Lorenzo Spaggiari
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Giulia Veronesi
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Francesco Nicassio
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Pier Paolo Di Fiore
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
| | - Fabrizio Bianchi
- Molecular Medicine Program, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (FM, FD, ED, RMC, GB, PPDF, FB); Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy (MJM, FN); Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy (ED, PM); IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy (RMC, PPDF); Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy (RB, LS, GV); Division of Radiology, European Institute of Oncology, Milan, Italy (MB, CR); Department of Scienze della Salute, University of Milan, Milan, Italy (MB, LS, PPDF)
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Tordonato C, Di Fiore PP, Nicassio F. The role of non-coding RNAs in the regulation of stem cells and progenitors in the normal mammary gland and in breast tumors. Front Genet 2015; 6:72. [PMID: 25774169 PMCID: PMC4343025 DOI: 10.3389/fgene.2015.00072] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 12/01/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022] Open
Abstract
The outlook on stem cell (SC) biology is shifting from a rigid hierarchical to a more flexible model in which the identity and the behavior of adult SCs, far from being fixed, are determined by the dynamic integration of cell autonomous and non-autonomous mechanisms. Within this framework, the recent discovery of thousands of non-coding RNAs (ncRNAs) with regulatory function is redefining the landscape of transcriptome regulation, highlighting the interplay of epigenetic, transcriptional, and post-transcriptional mechanisms in the specification of cell fate and in the regulation of developmental processes. Furthermore, the expression of ncRNAs is often tissue- or even cell type-specific, emphasizing their involvement in defining space, time and developmental stages in gene regulation. Such a role of ncRNAs has been investigated in embryonic and induced pluripotent SCs, and in numerous types of adult SCs and progenitors, including those of the breast, which will be the topic of this review. We will focus on ncRNAs with an important role in breast cancer, in particular in mammary cancer SCs and progenitors, and highlight the ncRNA-based circuitries whose subversion alters a number of the epigenetic, transcriptional, and post-transcriptional events that control “stemness” in the physiological setting.
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Affiliation(s)
- Chiara Tordonato
- Department of Experimental Oncology, European Institute of Oncology, Milan Italy
| | - Pier Paolo Di Fiore
- Department of Experimental Oncology, European Institute of Oncology, Milan Italy ; Fondazione Istituto FIRC di Oncologia Molecolare, Milan Italy ; Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan Italy
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Marchesi S, Montani F, Deflorian G, D'Antuono R, Cuomo A, Bologna S, Mazzoccoli C, Bonaldi T, Di Fiore PP, Nicassio F. DEPDC1B coordinates de-adhesion events and cell-cycle progression at mitosis. Dev Cell 2014; 31:420-33. [PMID: 25458010 PMCID: PMC4250264 DOI: 10.1016/j.devcel.2014.09.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/05/2014] [Accepted: 09/15/2014] [Indexed: 11/25/2022]
Abstract
Cells entering mitosis become rounded, lose attachment to the substrate, and increase their cortical rigidity. Pivotal to these events is the dismantling of focal adhesions (FAs). How mitotic reshaping is linked to commitment to divide is unclear. Here, we show that DEPDC1B, a protein that accumulates in G2, coordinates de-adhesion events and cell-cycle progression at mitosis. DEPDC1B functions as an inhibitor of a RhoA-based signaling complex, which assembles on the FA-associated protein tyrosine phosphatase, receptor type, F (PTPRF) and mediates the integrity of FAs. By competing with RhoA for the interaction with PTPRF, DEPDC1B promotes the dismantling of FAs, which is necessary for the morphological changes preceding mitosis. The circuitry is relevant in whole organisms, as shown by the control exerted by the DEPDC1B/RhoA/PTPRF axis on mitotic dynamics during zebrafish development. Our results uncover an adhesion-dependent signaling mechanism that coordinates adhesion events with the control of cell-cycle progression. DEPDC1B is a cell-cycle gene involved in the transition from G2 phase to mitosis Persistent adhesion at G2 phase delays CycB/CDK1 activation and G2/M transition DEPDC1B controls RhoA/ROCK-dependent adhesion dynamics at G2 phase DEPDC1B inhibits RhoA activation by displacing it from the PTPRF/GEF-H1 complex
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Affiliation(s)
- Stefano Marchesi
- Istituto Europeo di Oncologia (IEO), 20141 Milan, Italy; Fondazione IFOM-Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | | | - Gianluca Deflorian
- Fondazione IFOM-Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | - Rocco D'Antuono
- Fondazione IFOM-Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | | | - Serena Bologna
- Fondazione IFOM-Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | - Carmela Mazzoccoli
- Laboratory of Preclinical and Translational Research, IRCCS, Centro di Riferimento Oncologico della Basilicata, 85028 Rionero in Vulture (PZ), Italy
| | | | - Pier Paolo Di Fiore
- Istituto Europeo di Oncologia (IEO), 20141 Milan, Italy; Fondazione IFOM-Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy; Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy.
| | - Francesco Nicassio
- Istituto Europeo di Oncologia (IEO), 20141 Milan, Italy; Fondazione IFOM-Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
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Montani F, Marzi M, Carletti RM, Fiore PPD, Nicassio F. Abstract 522: Revealing the complexity of cancer associated small non-coding RNAs by next generation sequencing (NGS) and low-density array. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-522] [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
Background. The recent development of high-throughput sequencing technologies (Next Generation Sequencing - NGS) provided instruments to reveal the complexity of nucleic acids, highlighting the existence of numerous species of non-coding RNAs (ncRNAs) that play a significant regulatory role in complex organisms, impacting on both physiology and disease. In particular, microRNAs (miRNAs) have been proposed as “next-generation” markers for their ability to unambiguously distinguish cellular states, including SCs, progenitors and differentiated cells, as well as tumour types, even among closely related cancers or in different biological fluids. However, a comprehensive approach for the identification and characterization of small non-coding RNAs from pathological samples (blood, FFPE, primary cultures) has not been established nor compared with current available methodologies (i.e. QPCR).
Aim: Our aim is to develop a simultaneous and comparative protocol for the analysis of small non-coding RNAs from pathological samples, which encompasses both high-throughput QPCR and sequencing analysis in order to reveal the complexity of cancer associated small ncRNAs.
Results: An optimized protocol to analyse small ncRNAs from different pathological samples has been developed and compared with high-throughput QPCR. Both platforms resulted as highly efficient and quantitative, although NGS manages to score many molecules and RNA species that could not be analysed by current QPCR platforms, thus revealing a major complexity of cancer associated non-coding RNAs.
Conclusion: We propose that the combined use of NGS and QPCR platforms would allow a wider and more detailed analysis of ncRNAs, expanding our ability to fish out robust and efficient molecular markers for diagnostic (early detection), prognostic or therapeutic use.
Note: This abstract was not presented at the meeting.
Citation Format: Francesca Montani, Matteo Marzi, Rose Mary Carletti, Pier Paolo Di Fiore, Francesco Nicassio. Revealing the complexity of cancer associated small non-coding RNAs by next generation sequencing (NGS) and low-density array. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 522. doi:10.1158/1538-7445.AM2014-522
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Affiliation(s)
| | - Matteo Marzi
- 2IIT - Italian Institute of Technology, Milan, Italy
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Muller H, Marzi MJ, Nicassio F. IsomiRage: From Functional Classification to Differential Expression of miRNA Isoforms. Front Bioeng Biotechnol 2014; 2:38. [PMID: 25325056 PMCID: PMC4179619 DOI: 10.3389/fbioe.2014.00038] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [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: 08/07/2014] [Accepted: 09/12/2014] [Indexed: 01/29/2023] Open
Abstract
As more small RNA sequencing libraries are becoming available, it clearly emerges that microRNAs (miRNAs) are highly heterogeneous both in length and sequence. In comparison to canonical miRNAs, miRNA isoforms (termed as “isomiRs”) might exhibit different biological properties, such as a different target repertoire, or enhanced/reduced stability. Nonetheless, this layer of information has remained largely unexplored due to the scarcity of small RNA NGS-datasets and the absence of proper analytical tools. Here, we present a workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRs can originate from an alternative dicing event (“templated” forms) or from the addition of nucleotides through an enzymatic activity or target-dependent mechanisms (“non-templated” forms). Our pipeline allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3′-, 5′-, and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g., uridylation, adenylation, trimming …) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants. Most modifications were compatible with templated IsomiRs, as a consequence of imprecise Drosha or Dicer cleavage. However, some non-templated variants were consistently found either in the normal or in the cancer cells, with the 3′-end adenylation and uridylation as the most frequent events, suggesting that miRNA post-transcriptional modification frequently occurs. In conclusion, our analytical tool permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms.
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Affiliation(s)
- Heiko Muller
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
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Tinarelli F, Garcia-Garcia C, Nicassio F, Tucci V. Parent-of-origin genetic background affects the transcriptional levels of circadian and neuronal plasticity genes following sleep loss. Philos Trans R Soc Lond B Biol Sci 2014; 369:20120471. [PMID: 24446504 DOI: 10.1098/rstb.2012.0471] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sleep homoeostasis refers to a process in which the propensity to sleep increases as wakefulness progresses and decreases as sleep progresses. Sleep is tightly organized around the circadian clock and is regulated by genetic and epigenetic mechanisms. The homoeostatic response of sleep, which is classically triggered by sleep deprivation, is generally measured as a rebound effect of electrophysiological measures, for example delta sleep. However, more recently, gene expression changes following sleep loss have been investigated as biomarkers of sleep homoeostasis. The genetic background of an individual may affect this sleep-dependent gene expression phenotype. In this study, we investigated whether parental genetic background differentially modulates the expression of genes following sleep loss. We tested the progeny of reciprocal crosses of AKR/J and DBA/2J mouse strains and we show a parent-of-origin effect on the expression of circadian, sleep and neuronal plasticity genes following sleep deprivation. Thus, we further explored, by in silico, specific functions or upstream mechanisms of regulation and we observed that several upstream mechanisms involving signalling pathways (i.e. DICER1, PKA), growth factors (CSF3 and BDNF) and transcriptional regulators (EGR2 and ELK4) may be differentially modulated by parental effects. This is the first report showing that a behavioural manipulation (e.g. sleep deprivation) in adult animals triggers specific gene expression responses according to parent-of-origin genomic mechanisms. Our study suggests that the same mechanism may be extended to other behavioural domains and that the investigation of gene expression following experimental manipulations should take seriously into account parent-of-origin effects.
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Affiliation(s)
- Federico Tinarelli
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, , via Morego, 30, 16163 Genova, Italy
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D'Antonio M, Guerra RF, Cereda M, Marchesi S, Montani F, Nicassio F, Di Fiore PP, Ciccarelli FD. Recessive cancer genes engage in negative genetic interactions with their functional paralogs. Cell Rep 2013; 5:1519-26. [PMID: 24360954 DOI: 10.1016/j.celrep.2013.11.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/25/2013] [Accepted: 11/18/2013] [Indexed: 01/01/2023] Open
Abstract
Cancer genetic heterogeneity offers a wide repertoire of molecular determinants to be screened as therapeutic targets. Here, we identify potential anticancer targets by exploiting negative genetic interactions between genes with driver loss-of-function mutations (recessive cancer genes) and their functionally redundant paralogs. We identify recessive genes with additional copies and experimentally test our predictions on three paralogous pairs. We confirm digenic negative interactions between two cancer genes (SMARCA4 and CDH1) and their corresponding paralogs (SMARCA2 and CDH3). Furthermore, we identify a trigenic negative interaction between the cancer gene DNMT3A, its functional paralog DNMT3B, and a third gene, DNMT1, which encodes the only other human DNA-methylase domain. Although our study does not exclude other causes of synthetic lethality, it suggests that functionally redundant paralogs of cancer genes could be targets in anticancer therapy.
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Affiliation(s)
- Matteo D'Antonio
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Rosalinda F Guerra
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Matteo Cereda
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Stefano Marchesi
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Francesca Montani
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Francesco Nicassio
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Pier Paolo Di Fiore
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy; IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy
| | - Francesca D Ciccarelli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy; Division of Cancer Studies, King's College London, London SE1 1UL, UK.
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Nicassio F. Mouldy Sioud (ed): siRNA and miRNA Gene Silencing: from Bench to Bedside. Mol Biotechnol 2013. [DOI: 10.1007/s12033-012-9525-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Montani F, Carletti RM, Marzi MJ, Bucci G, Nicassio F, Di Fiore PP. Abstract 5280: Identification of serum circulating non-coding RNAs as diagnostic markers by Next Generation Sequencing (NGS) and low-density array. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-5280] [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
Background. High incidence and mortality rate tumours present a more favourable prognosis if diagnosed in early stages (Jemal A. et al, 2011). Screening programs based on effective radiological techniques (e.g. mammography or low dose spiral CT) promise a mortality reduction, but their application on large scale suffers of disadvantages such as the use of ionizing radiation, overdiagnosis risk and high costs. Thus, the identification of molecular markers for cancer early diagnosis, especially if detectable through a simple non-invasive blood test, would provide powerful tools for the improvement of screening programs. Recently, a novel class of small non-coding RNAs, namely microRNAs, has been identified. MiRNA are extremely stable in biological fluids and their levels are different in malignant vs. control sera, making them a promising class of biological markers for early diagnosis. Indeed, studies from our and other labs led to the identification of “miRNA signatures” able to predict the presence of tumours even within a population of asymptomatic high-risk individuals (Bianchi F. et al., 2011; Boeri M. et al., 2011). However, methods used in these studies rely on QPCR approaches, which require previous knowledge on the molecules to be investigated. Indeed, the real complexity of circulating RNAs is still obscure, comprising other classes of molecules not yet investigated that could behave as novel biomarkers. The recent development of high-throughput sequencing technologies (Next Generation Sequencing - NGS) provided instruments to reveal the complexity of nucleic acids, but a complete protocol for the identification of circulating RNAs has not been established nor compared with current available approaches (i.e. QPCR).
Aim: Our aim is to develop a simultaneous and comparative protocol for serum miRNA analysis, which encompasses both high-throughput QPCR and sequencing analysis in order to reveal the complexity of circulating small-RNAs.
Methods: Total RNA has been isolated from the serum of healthy donors and analysed simultaneously by low-density QPCR (TaqMan Low Density Array, Life Technologies) and by NGS (Illumina).
Results: A step-wise protocol to simultaneously analyze non-coding RNAs using NGS technology (Illumina) and high-throughput QPCR has been developed. The protocol has been optimized to allow both analyses using even limited amount of serum (up to 1mL). Both platforms resulted as highly efficient and quantitative, although NGS manages to score many molecules and RNA species that could not be analysed by current QPCR platforms, thus revealing a major complexity of circulating non-coding RNAs.
Conclusion: We proposed that the combined use of NGS and QPCR platforms would allow a wider and more detailed analysis of circulating RNAs, expanding our ability to fish out robust and efficient molecular markers for early detection of cancer.
Citation Format: Francesca Montani, Rose Mary Carletti, Matteo J. Marzi, Gabriele Bucci, Francesco Nicassio, Pier Paolo Di Fiore. Identification of serum circulating non-coding RNAs as diagnostic markers by Next Generation Sequencing (NGS) and low-density array. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5280. doi:10.1158/1538-7445.AM2013-5280
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Marzi MJ, Puggioni EMR, Dall'Olio V, Bucci G, Bernard L, Bianchi F, Crescenzi M, Di Fiore PP, Nicassio F. Differentiation-associated microRNAs antagonize the Rb-E2F pathway to restrict proliferation. ACTA ACUST UNITED AC 2013; 199:77-95. [PMID: 23027903 PMCID: PMC3461518 DOI: 10.1083/jcb.201206033] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [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] [Indexed: 01/15/2023]
Abstract
Transcriptional regulation by Rb–E2F and posttranscriptional regulation by microRNAs control the expression of cell cycle and DNA replication genes and restrict cellular proliferation. The cancer-associated loss of microRNA (miRNA) expression leads to a proliferative advantage and aggressive behavior through largely unknown mechanisms. Here, we exploit a model system that recapitulates physiological terminal differentiation and its reversal upon oncogene expression to analyze coordinated mRNA/miRNA responses. The cell cycle reentry of myotubes, forced by the E1A oncogene, was associated with a pattern of mRNA/miRNA modulation that was largely reciprocal to that induced during the differentiation of myoblasts into myotubes. The E1A-induced mRNA response was preponderantly Retinoblastoma protein (Rb)-dependent. Conversely, the miRNA response was mostly Rb-independent and exerted through tissue-specific factors and Myc. A subset of these miRNAs (miR-1, miR-34, miR-22, miR-365, miR-29, miR-145, and Let-7) was shown to coordinately target Rb-dependent cell cycle and DNA replication mRNAs. Thus, a dual level of regulation—transcriptional regulation via Rb–E2F and posttranscriptional regulation via miRNAs—confers robustness to cell cycle control and provides a molecular basis to understand the role of miRNA subversion in cancer.
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Affiliation(s)
- Matteo J Marzi
- Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
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Bianchi F, Nicassio F, Veronesi G, di Fiore PP. Circulating microRNAs: next-generation biomarkers for early lung cancer detection. Ecancermedicalscience 2012; 6:246. [PMID: 22518197 PMCID: PMC3324328 DOI: 10.3332/ecancer.2012.246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 02/10/2012] [Indexed: 01/21/2023] Open
Abstract
Early diagnosis of lung cancer by low-dose computed tomography is an effective strategy to reduce cancer mortality in high-risk individuals. However, recruitment of at-risk individuals with asymptomatic lung cancer still remains challenging. We developed a minimal invasive serum test, based on the detection of circulating microRNAs, which can identify at-risk individuals with asymptomatic early stage non-small cell lung carcinomas with 80% accuracy.
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Affiliation(s)
- F Bianchi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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42
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Bianchi F, Nicassio F, Marzi M, Belloni E, Dall'Olio V, Bernard L, Pelosi G, Maisonneuve P, Veronesi G, Di Fiore PP. A serum circulating miRNA diagnostic test to identify asymptomatic high-risk individuals with early stage lung cancer. EMBO Mol Med 2011; 3:495-503. [PMID: 21744498 PMCID: PMC3377091 DOI: 10.1002/emmm.201100154] [Citation(s) in RCA: 274] [Impact Index Per Article: 21.1] [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: 03/23/2011] [Revised: 05/14/2011] [Accepted: 05/31/2011] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the first cause of cancer mortality worldwide, and its early detection is currently the main available strategy to improve disease prognosis. While early diagnosis can be successfully achieved through tomography-based population screenings in high-risk individuals, simple methodologies are needed for effective cancer prevention programs. We developed a test, based on the detection of 34 microRNAs (miRNAs) from serum, that could identify patients with early stage non-small cell lung carcinomas (NSCLCs) in a population of asymptomatic high-risk individuals with 80% accuracy. The signature could assign disease probability accurately either in asymptomatic or symptomatic patients, is able to distinguish between benign and malignant lesions, and to capture the onset of the malignant disease in individual patients over time. Thus, our test displays a number of features of clinical relevance that project its utility in programs for the early detection of NSCLC.
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Affiliation(s)
- Fabrizio Bianchi
- IFOM, The FIRC Institute for Molecular Oncology FoundationAt the IFOM-IEO Campus, Milan, Italy
- Dipartimento di Medicina, Chirurgia ed Odontoiatria, Universita' degli Studi di MilanoMilan, Italy
| | - Francesco Nicassio
- IFOM, The FIRC Institute for Molecular Oncology FoundationAt the IFOM-IEO Campus, Milan, Italy
| | - Matteo Marzi
- IFOM, The FIRC Institute for Molecular Oncology FoundationAt the IFOM-IEO Campus, Milan, Italy
| | - Elena Belloni
- Department of Experimental Oncology, European Institute of OncologyAt the IFOM-IEO Campus, Milan, Italy
| | - Valentina Dall'Olio
- Cogentech, Consortium for Genomic Technologies at the IFOM-IEO CampusMilan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, European Institute of OncologyAt the IFOM-IEO Campus, Milan, Italy
| | - Giuseppe Pelosi
- Division of Pathology, European Institute of OncologyMilan, Italy
| | - Patrick Maisonneuve
- Division of Epidemiology and Biostatistics, European Institute of OncologyMilan, Italy
| | - Giulia Veronesi
- Division of Thoracic Surgery, European Institute of OncologyMilan, Italy
| | - Pier Paolo Di Fiore
- IFOM, The FIRC Institute for Molecular Oncology FoundationAt the IFOM-IEO Campus, Milan, Italy
- Dipartimento di Medicina, Chirurgia ed Odontoiatria, Universita' degli Studi di MilanoMilan, Italy
- Department of Experimental Oncology, European Institute of OncologyAt the IFOM-IEO Campus, Milan, Italy
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Monti L, Cinquetti R, Guffanti A, Nicassio F, Cremona M, Lavorgna G, Bianchi F, Vignati F, Cittaro D, Taramelli R, Acquati F. In silico prediction and experimental validation of natural antisense transcripts in two cancer-associated regions of human chromosome 6. Int J Oncol 2009; 34:1099-108. [PMID: 19287968 DOI: 10.3892/ijo_00000237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antisense transcription has long been recognized as a mechanism involved in the regulation of gene expression. Therefore, several human diseases associated with abnormal patterns of gene expression might display antisense RNA-mediated pathogenetic mechanisms. Such issue could be particularly relevant for cancer pathogenesis, since deregulated gene expression has long been established as a hallmark of cancer cells. Herein, we report on a bioinformatic search for antisense transcription in two cancer-associated regions of human chromosome 6 (6q21 and 6q27). Natural antisense transcripts (NATs) for several genes in both genomic regions were predicted in silico and subsequently validated by strand-specific RT-PCR. Detailed experimental validation by quantitative real-time RT-PCR of five putative cancer related sense-antisense transcript pairs revealed a single candidate tumor suppressor gene (RPS6KA2) whose expression levels display marked cancer-related changes that are likely mediated by its antisense RNA in a breast cancer cell line model.
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Affiliation(s)
- Laura Monti
- Department of Biotechnology and Molecular Sciences, University of Insubria, I-21100 Varese, Italy
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Vissers JH, Nicassio F, van Lohuizen M, Di Fiore PP, Citterio E. The many faces of ubiquitinated histone H2A: insights from the DUBs. Cell Div 2008; 3:8. [PMID: 18430235 PMCID: PMC2373781 DOI: 10.1186/1747-1028-3-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [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] [Received: 03/19/2008] [Accepted: 04/22/2008] [Indexed: 11/11/2022] Open
Abstract
Monoubiquitination of H2A is a major histone modification in mammalian cells. Understanding how monoubiquitinated H2A (uH2A) regulates DNA-based processes in the context of chromatin is a challenging question. Work in the past years linked uH2A to transcriptional repression by the Polycomb group proteins of developmental regulators. Recently, a number of mammalian deubiquitinating enzymes (DUBs) that catalyze the removal of ubiquitin from H2A have been discovered. These studies provide convincing evidence that H2A deubiquitination is connected with gene activation. In addition, uH2A regulatory enzymes have crucial roles in the cellular response to DNA damage and in cell cycle progression. In this review we will discuss new insights into uH2A biology, with emphasis on the H2A DUBs.
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Affiliation(s)
- Joseph Ha Vissers
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Francesco Nicassio
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Pier Paolo Di Fiore
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy.,Istituto Europeo di Oncologia, Via Ripamonti 435, 20141, Milan, Italy.,Dipartimento di Medicina, Chirurgia ed Odontoiatria, Universita' di Milano, 20112, Milan, Italy
| | - Elisabetta Citterio
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Bianchi F, Nuciforo P, Vecchi M, Bernard L, Tizzoni L, Marchetti A, Buttitta F, Felicioni L, Nicassio F, Di Fiore PP. Survival prediction of stage I lung adenocarcinomas by expression of 10 genes. J Clin Invest 2008; 117:3436-44. [PMID: 17948124 DOI: 10.1172/jci32007] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 08/01/2007] [Indexed: 01/03/2023] Open
Abstract
Adenocarcinoma is the predominant histological subtype of lung cancer, the leading cause of cancer deaths in the world. At stage I, the tumor is cured by surgery alone in about 60% of cases. Markers are needed to stratify patients by prognostic outcomes and may help in devising more effective therapies for poor prognosis patients. To achieve this goal, we used an integrated strategy combining meta-analysis of published lung cancer microarray data with expression profiling from an experimental model. The resulting 80-gene model was tested on an independent cohort of patients using RT-PCR, resulting in a 10-gene predictive model that exhibited a prognostic accuracy of approximately 75% in stage I lung adenocarcinoma when tested on 2 additional independent cohorts. Thus, we have identified a predictive signature of limited size that can be analyzed by RT-PCR, a technology that is easy to implement in clinical laboratories.
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Affiliation(s)
- Fabrizio Bianchi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
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46
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Bianchi F, Nicassio F, Di Fiore PP. Unbiased vs. biased approaches to the identification of cancer signatures: the case of lung cancer. Cell Cycle 2008; 7:729-34. [PMID: 18239450 DOI: 10.4161/cc.7.6.5591] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Expression profiling analysis of human cancers is a promising approach to obtain precise molecular classification of cancers, to develop stratification tools for therapeutic regimens, and to predict the biological behavior of neoplasia. Direct profiling of human cancers (herein defined as "the unbiased approach") presents, however, intrinsic problems connected with the high genetic noise embedded in the system. This, in turn, leads to fitting of the noise in the data (the so-called "overtraining") with consequent instability of the identified signatures, when applied on different cohorts of patients. To circumvent these problems, "biased approaches" - which exploit the molecular knowledge of cancer obtained in model systems - are being developed. Biased approaches, however, are not problem-free, in that they provide information limited to single oncogenic events, thereby failing, at least in principle, to capture the complex repertoire of alterations of human cancers. In this review, we compare the two approaches and provide a test case, from our studies, of how "integrated" strategies, which combine biased and unbiased approaches, might lead to the identification of stable and reliable predictive signatures in cancer.
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Affiliation(s)
- Fabrizio Bianchi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
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47
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Nicassio F, Corrado N, Vissers JHA, Areces LB, Bergink S, Marteijn JA, Geverts B, Houtsmuller AB, Vermeulen W, Di Fiore PP, Citterio E. Human USP3 is a chromatin modifier required for S phase progression and genome stability. Curr Biol 2007; 17:1972-7. [PMID: 17980597 DOI: 10.1016/j.cub.2007.10.034] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Revised: 10/03/2007] [Accepted: 10/04/2007] [Indexed: 11/16/2022]
Abstract
Protein ubiquitination is critical for numerous cellular functions, including DNA damage response pathways. Histones are the most abundant monoubiquitin conjugates in mammalian cells; however, the regulation and the function of monoubiquitinated H2A (uH2A) and H2B (uH2B) remain poorly understood. In particular, little is known about mammalian deubiquitinating enzymes (DUBs) that catalyze the removal of ubiquitin from uH2A/uH2B. Here we identify the ubiquitin-specific protease 3 USP3 as a deubiquitinating enzyme for uH2A and uH2B. USP3 dynamically associates with chromatin and deubiquitinates H2A/H2B in vivo. The ZnF-UBP domain of USP3 mediates uH2A-USP3 interaction. Functional ablation of USP3 by RNAi leads to delay of S phase progression and to accumulation of DNA breaks, with ensuing activation of DNA damage checkpoint pathways. In addition, we show that in response to ionizing radiation, (1) uH2A redistributes and colocalizes in gamma-H2AX DNA repair foci and (2) USP3 is required for full deubiquitination of ubiquitin-conjugates/uH2A and gamma-H2AX dephosphorylation. Our studies identify USP3 as a novel regulator of H2A and H2B ubiquitination, highlight its role in preventing replication stress, and suggest its involvement in the response to DNA double-strand breaks. Together, our results implicate USP3 as a novel chromatin modifier in the maintenance of genome integrity.
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Affiliation(s)
- Francesco Nicassio
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
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48
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Nicassio F, Bianchi F, Capra M, Vecchi M, Confalonieri S, Bianchi M, Pajalunga D, Crescenzi M, Bonapace IM, Di Fiore PP. A cancer-specific transcriptional signature in human neoplasia. J Clin Invest 2005; 115:3015-25. [PMID: 16224537 PMCID: PMC1253624 DOI: 10.1172/jci24862] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [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: 02/25/2005] [Accepted: 07/26/2005] [Indexed: 02/06/2023] Open
Abstract
The molecular anatomy of cancer cells is being explored through unbiased approaches aimed at the identification of cancer-specific transcriptional signatures. An alternative biased approach is exploitation of molecular tools capable of inducing cellular transformation. Transcriptional signatures thus identified can be readily validated in real cancers and more easily reverse-engineered into signaling pathways, given preexisting molecular knowledge. We exploited the ability of the adenovirus early region 1 A protein (E1A) oncogene to force the reentry into the cell cycle of terminally differentiated cells in order to identify and characterize genes whose expression is upregulated in this process. A subset of these genes was activated through a retinoblastoma protein/E2 viral promoter required factor-independent (pRb/E2F-independent) mechanism and was overexpressed in a fraction of human cancers. Furthermore, this overexpression correlated with tumor progression in colon cancer, and 2 of these genes predicted unfavorable prognosis in breast cancer. A proof of principle biological validation was performed on one of the genes of the signature, skeletal muscle cell reentry-induced (SKIN) gene, a previously undescribed gene. SKIN was found overexpressed in some primary tumors and tumor cell lines and was amplified in a fraction of colon adenocarcinomas. Furthermore, knockdown of SKIN caused selective growth suppression in overexpressing tumor cell lines but not in tumor lines expressing physiological levels of the transcript. Thus, SKIN is a candidate oncogene in human cancer.
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Affiliation(s)
- Francesco Nicassio
- IFOM, Istituto Fondazione Italiana per la Ricerca sul Cancro di Oncologia Molecolare, Milan, Italy
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49
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Citterio E, Papait R, Nicassio F, Vecchi M, Gomiero P, Mantovani R, Di Fiore PP, Bonapace IM. Np95 is a histone-binding protein endowed with ubiquitin ligase activity. Mol Cell Biol 2004; 24:2526-35. [PMID: 14993289 PMCID: PMC355858 DOI: 10.1128/mcb.24.6.2526-2535.2004] [Citation(s) in RCA: 152] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Np95 is an important determinant in cell cycle progression. Its expression is tightly regulated and becomes detectable shortly before the entry of cells into S phase. Accordingly, Np95 is absolutely required for the G1/S transition. Its continued expression throughout the S/G2/M phases further suggests additional roles. Indeed, Np95 has been implicated in DNA damage response. Here, we show that Np95 is tightly bound to chromatin in vivo and that it binds to histones in vivo and in vitro. The binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. A novel protein domain, the SRA-YDG domain, contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo. Np95 contains a RING finger. We show that this domain confers E3 ubiquitin ligase activity on Np95, which is specific for core histones, in vitro. Finally, Np95 shows specific E3 activity for histone H3 when the endogenous core octamer, coimmunoprecipitating with Np95, is used as a substrate. Histone ubiquitination is an important determinant in the regulation of chromatin structure and gene transcription. Thus, the demonstration that Np95 is a chromatin-associated ubiquitin ligase suggests possible molecular mechanisms for its action as a cell cycle regulator.
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Bonapace IM, Latella L, Papait R, Nicassio F, Sacco A, Muto M, Crescenzi M, Di Fiore PP. Np95 is regulated by E1A during mitotic reactivation of terminally differentiated cells and is essential for S phase entry. J Cell Biol 2002; 157:909-14. [PMID: 12058012 PMCID: PMC2174046 DOI: 10.1083/jcb.200201025] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [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] [Indexed: 12/18/2022] Open
Abstract
Terminal differentiation exerts a remarkably tight control on cell proliferation. However, the oncogenic products of DNA tumor viruses, such as adenovirus E1A, can force postmitotic cells to proliferate, thus representing a powerful tool to study progression into S phase. In this study, we identified the gene encoding Np95, a murine nuclear phosphoprotein, as an early target of E1A-induced transcriptional events. In terminally differentiated (TD) cells, the activation of Np95 was specifically induced by E1A, but not by overexpression of E2F-1 or of the cyclin E (cycE)-cyclin-dependent kinase 2 (cdk2) complex. In addition, the concomitant expression of Np95 and of cycE-cdk2 was alone sufficient to induce S phase in TD cells. In NIH-3T3 cells, the expression of Np95 was tightly regulated during the cell cycle, and its functional ablation resulted in abrogation of DNA synthesis. Thus, expression of Np95 is essential for S phase entry. Previous evidence suggested that E1A, in addition to its well characterized effects on the pRb/E2F-1 pathway, activates a parallel and complementary pathway that is also required for the reentry in S phase of TD cells (Tiainen, M., D. Spitkousky, P. Jansen-Dürr, A. Sacchi, and M. Crescenzi. 1996. Mol. Cell. Biol. 16:5302-5312). From our results, Np95 appears to possess all the characteristics to represent the first molecular determinant identified in this pathway.
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