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Pedrazzoli E, Bianchi A, Umbach A, Amistadi S, Brusson M, Frati G, Ciciani M, Badowska KA, Arosio D, Miccio A, Cereseto A, Casini A. An optimized SpCas9 high-fidelity variant for direct protein delivery. Mol Ther 2023; 31:2257-2265. [PMID: 36905119 PMCID: PMC10362380 DOI: 10.1016/j.ymthe.2023.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/08/2022] [Revised: 02/08/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Electroporation of the Cas9 ribonucleoprotein (RNP) complex offers the advantage of preventing off-target cleavages and potential immune responses produced by long-term expression of the nuclease. Nevertheless, the majority of engineered high-fidelity Streptococcus pyogenes Cas9 (SpCas9) variants are less active than the wild-type enzyme and are not compatible with RNP delivery. Building on our previous studies on evoCas9, we developed a high-fidelity SpCas9 variant suitable for RNP delivery. The editing efficacy and precision of the recombinant high-fidelity Cas9 (rCas9HF), characterized by the K526D substitution, was compared with the R691A mutant (HiFi Cas9), which is currently the only available high-fidelity Cas9 that can be used as an RNP. The comparative analysis was extended to gene substitution experiments where the two high fidelities were used in combination with a DNA donor template, generating different ratios of non-homologous end joining (NHEJ) versus homology-directed repair (HDR) for precise editing. The analyses revealed a heterogeneous efficacy and precision indicating different targeting capabilities between the two variants throughout the genome. The development of rCas9HF, characterized by an editing profile diverse from the currently used HiFi Cas9 in RNP electroporation, increases the genome editing solutions for the highest precision and efficient applications.
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Affiliation(s)
- Eleonora Pedrazzoli
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Andrea Bianchi
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Alessandro Umbach
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Simone Amistadi
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Mégane Brusson
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, INSERM UMR 1163, Paris, France
| | - Giacomo Frati
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, INSERM UMR 1163, Paris, France
| | - Matteo Ciciani
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | | | - Daniele Arosio
- Biophysics Institute, National Research Council of Italy, 38123 Trento, Italy
| | - Annarita Miccio
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, INSERM UMR 1163, Paris, France
| | - Anna Cereseto
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy.
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Umbach A, Maule G, Kheir E, Cutarelli A, Foglia M, Guarrera L, Fava LL, Conti L, Garattini E, Terao M, Cereseto A. Generation of corrected hiPSC clones from a Cornelia de Lange Syndrome (CdLS) patient through CRISPR-Cas-based technology. Stem Cell Res Ther 2022; 13:440. [PMID: 36056433 PMCID: PMC9438151 DOI: 10.1186/s13287-022-03135-0] [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] [Received: 04/07/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare multisystem genetic disorder which is caused by genetic defects involving the Nipped-B-like protein (NIPBL) gene in the majority of clinical cases (60–70%). Currently, there are no specific cures available for CdLS and clinical management is needed for life. Disease models are highly needed to find a cure. Among therapeutic possibilities are genome editing strategies based on CRISPR-Cas technology. Methods A comparative analysis was performed to test the most recent CRISPR-Cas technologies comprising base- and prime-editors which introduce modifications without DNA cleavages and compared with sequence substitution approaches through homology directed repair (HDR) induced by Cas9 nuclease activity. The HDR method that was found more efficient was applied to repair a CdLS-causing mutation in the NIPBL gene. Human-induced pluripotent stem cells (hiPSCs) derived from a CdLS patient carrying the c.5483G > A mutation in the NIPBL were modified through HDR to generate isogenic corrected clones. Results This study reports an efficient method to repair the NIPBL gene through HDR mediated by CRISPR-Cas and induced with a compound (NU7441) inhibiting non-homologous end joining (NHEJ) repair. This sequence repair method allowed the generation of isogenic wild-type hiPSCs clones with regular karyotype and preserved pluripotency. Conclusions CdLS cellular models were generated which will facilitate the investigation of the disease molecular determinants and the identification of therapeutic targets. In particular, the hiPSC-based cellular models offer the paramount advantage to study the tissue differentiation stages which are altered in the CdLS clinical development. Importantly, the hiPSCs that were generated are isogenic thus providing the most controlled experimental set up between wild-type and mutated conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03135-0.
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Affiliation(s)
- Alessandro Umbach
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Giulia Maule
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Eyemen Kheir
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | | | - Marika Foglia
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca Guarrera
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca L Fava
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Luciano Conti
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Anna Cereseto
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy.
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Pröbstl C, Umbach A, Beineke A, Körber H, Goericke-Pesch S. Immune cell characterization in spontaneous autoimmune orchitis in dogs. Theriogenology 2022; 187:219-226. [DOI: 10.1016/j.theriogenology.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/07/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
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Villa C, Legato M, Umbach A, Riganti C, Jones R, Martini B, Boido M, Medana C, Facchinetti I, Barni D, Pinto M, Arguello T, Belicchi M, Fagiolari G, Liaci C, Moggio M, Ruffo R, Moraes CT, Monguzzi A, Merlo GR, Torrente Y. Treatment with ROS detoxifying gold quantum clusters alleviates the functional decline in a mouse model of Friedreich ataxia. Sci Transl Med 2021; 13:13/607/eabe1633. [PMID: 34408077 DOI: 10.1126/scitranslmed.abe1633] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 06/15/2021] [Indexed: 12/15/2022]
Abstract
Friedreich ataxia (FRDA) is caused by the reduced expression of the mitochondrial protein frataxin (FXN) due to an intronic GAA trinucleotide repeat expansion in the FXN gene. Although FRDA has no cure and few treatment options, there is research dedicated to finding an agent that can curb disease progression and address symptoms as neurobehavioral deficits, muscle endurance, and heart contractile dysfunctions. Because oxidative stress and mitochondrial dysfunctions are implicated in FRDA, we demonstrated the systemic delivery of catalysts activity of gold cluster superstructures (Au8-pXs) to improve cell response to mitochondrial reactive oxygen species and thereby alleviate FRDA-related pathology in mesenchymal stem cells from patients with FRDA. We also found that systemic injection of Au8-pXs ameliorated motor function and cardiac contractility of YG8sR mouse model that recapitulates the FRDA phenotype. These effects were associated to long-term improvement of mitochondrial functions and antioxidant cell responses. We related these events to an increased expression of frataxin, which was sustained by reduced autophagy. Overall, these results encourage further optimization of Au8-pXs in experimental clinical strategies for the treatment of FRDA.
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Affiliation(s)
- Chiara Villa
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Via F. Sforza 35, 20122 Milano, Italy
| | - Mariella Legato
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Via F. Sforza 35, 20122 Milano, Italy
| | - Alessandro Umbach
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza, 52 10126 Torino, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Via Santena 5/bis, 10126 Torino, Italy
| | - Rebecca Jones
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza, 52 10126 Torino, Italy
| | - Beatrice Martini
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Via F. Sforza 35, 20122 Milano, Italy
| | - Marina Boido
- Department of Neuroscience "Rita Levi Montalcini", Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Regione Gonzole 10, Orbassano,10043 Torino, Italy
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza, 52 10126 Torino, Italy
| | - Irene Facchinetti
- Department of Material Science, University of Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Dario Barni
- Department of Material Science, University of Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Milena Pinto
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Tania Arguello
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Marzia Belicchi
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Via F. Sforza 35, 20122 Milano, Italy
| | - Gigliola Fagiolari
- Neuromuscular and Rare Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Carla Liaci
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza, 52 10126 Torino, Italy
| | - Maurizio Moggio
- Neuromuscular and Rare Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Riccardo Ruffo
- Department of Material Science, University of Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Angelo Monguzzi
- Department of Material Science, University of Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Giorgio R Merlo
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza, 52 10126 Torino, Italy
| | - Yvan Torrente
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Via F. Sforza 35, 20122 Milano, Italy.
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Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Ala U, Provero P, DiCunto F, Merlo GR. Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors. Front Cell Neurosci 2019; 12:518. [PMID: 30687010 PMCID: PMC6338052 DOI: 10.3389/fncel.2018.00518] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 01/09/2023] Open
Abstract
Alternative polyadenylation (APA) is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3′ untranslated region (3′UTR). Variations in length and sequence of the 3′UTR may underlie changes of post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During embryonic development a large array of mRNAs exhibit APA, with a prevalence of the longer 3′UTR versions in differentiating cells. Little is known about polyA+ site usage during differentiation of mammalian neural progenitors. Here we exploit a model of adherent neural stem (ANS) cells, which homogeneously and efficiently differentiate into GABAergic neurons. RNAseq data shows a global trend towards lengthening of the 3′UTRs during differentiation. Enriched expression of the longer 3′UTR variants of Pes1 and Gng2 was detected in the mouse brain in areas of cortical and subcortical neuronal differentiation, respectively, by two-probes fluorescent in situ hybridization (FISH). Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. In the insect, Elav regulates polyA+ site choice while interacting with paused Pol-II promoters. We tested the role of Elavl3 in ANS cells, by silencing Elavl3 and observed consistent changes in 3′UTR length and delayed neuronal differentiation. These results indicate that choice of the polyA+ site and lengthening of 3′UTRs is a possible additional mechanism of posttranscriptional RNA modification involved in neuronal differentiation.
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Affiliation(s)
- Elena Grassi
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Roberto Santoro
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Alessandro Umbach
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Anna Grosso
- Department of Neurosciences, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Life Science and System Biology, University of Turin, Turin, Italy
| | - Francesco Neri
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Life Science and System Biology, University of Turin, Turin, Italy
| | - Luciano Conti
- Centre for Integrative Biology-CIBIO, University of Trento, Povo, Italy
| | - Ugo Ala
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Ferdinando DiCunto
- Department of Molecular Biotechnology, University of Turin, Turin, Italy.,Department of Neurosciences, University of Turin, Turin, Italy
| | - Giorgio R Merlo
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
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Zamboni V, Armentano M, Sarò G, Ciraolo E, Ghigo A, Germena G, Umbach A, Valnegri P, Passafaro M, Carabelli V, Gavello D, Bianchi V, D'Adamo P, de Curtis I, El-Assawi N, Mauro A, Priano L, Ferri N, Hirsch E, Merlo GR. Disruption of ArhGAP15 results in hyperactive Rac1, affects the architecture and function of hippocampal inhibitory neurons and causes cognitive deficits. Sci Rep 2016; 6:34877. [PMID: 27713499 PMCID: PMC5054378 DOI: 10.1038/srep34877] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 11/12/2022] Open
Abstract
During brain development, the small GTPases Rac1/Rac3 play key roles in neuronal migration, neuritogenesis, synaptic formation and plasticity, via control of actin cytoskeleton dynamic. Their activity is positively and negatively regulated by GEFs and GAPs molecules, respectively. However their in vivo roles are poorly known. The ArhGAP15 gene, coding for a Rac-specific GAP protein, is expressed in both excitatory and inhibitory neurons of the adult hippocampus, and its loss results in the hyperactivation of Rac1/Rac3. In the CA3 and dentate gyrus (DG) regions of the ArhGAP15 mutant hippocampus the CR+, PV+ and SST+ inhibitory neurons are reduced in number, due to reduced efficiency and directionality of their migration, while pyramidal neurons are unaffected. Loss of ArhGAP15 alters neuritogenesis and the balance between excitatory and inhibitory synapses, with a net functional result consisting in increased spike frequency and bursts, accompanied by poor synchronization. Thus, the loss of ArhGAP15 mainly impacts on interneuron-dependent inhibition. Adult ArhGAP15−/− mice showed defective hippocampus-dependent functions such as working and associative memories. These findings indicate that a normal architecture and function of hippocampal inhibitory neurons is essential for higher hippocampal functions, and is exquisitely sensitive to ArhGAP15-dependent modulation of Rac1/Rac3.
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Affiliation(s)
- Valentina Zamboni
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Maria Armentano
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Gabriella Sarò
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Elisa Ciraolo
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Alessandra Ghigo
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Giulia Germena
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Alessandro Umbach
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | | | | | | | | | - Veronica Bianchi
- IRCSS San Raffaele Scientific Institute and San Raffaele University, Division of Neuroscience, Milano, Italy
| | - Patrizia D'Adamo
- IRCSS San Raffaele Scientific Institute and San Raffaele University, Division of Neuroscience, Milano, Italy
| | - Ivan de Curtis
- IRCSS San Raffaele Scientific Institute and San Raffaele University, Division of Neuroscience, Milano, Italy
| | - Nadia El-Assawi
- Department of Neurosciences, University of Turin &Div. of Neurology and Neurorehabilitation, S.Giuseppe Hospital, Istituto Auxologico Italiano IRCCS, Piancavallo (VB), Italy
| | - Alessandro Mauro
- Department of Neurosciences, University of Turin &Div. of Neurology and Neurorehabilitation, S.Giuseppe Hospital, Istituto Auxologico Italiano IRCCS, Piancavallo (VB), Italy
| | - Lorenzo Priano
- Department of Neurosciences, University of Turin &Div. of Neurology and Neurorehabilitation, S.Giuseppe Hospital, Istituto Auxologico Italiano IRCCS, Piancavallo (VB), Italy
| | - Nicola Ferri
- Department of Pharmaceutical and Pharmacological Science, University of Padova, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Giorgio R Merlo
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
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Umbach A, Hoyer A, Brünger WH. Spatial resolution tests of scanning Auger microscopy under different topographical conditions. SURF INTERFACE ANAL 1989. [DOI: 10.1002/sia.740140618] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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