1
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Bonfiglio F, Lasorsa VA, Cantalupo S, D'Alterio G, Aievola V, Boccia A, Ardito M, Furini S, Renieri A, Morini M, Stainczyk S, Westermann F, Paolella G, Eva A, Iolascon A, Capasso M. Inherited rare variants in homologous recombination and neurodevelopmental genes are associated with increased risk of neuroblastoma. EBioMedicine 2022; 87:104395. [PMID: 36493725 PMCID: PMC9732128 DOI: 10.1016/j.ebiom.2022.104395] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 08/08/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common solid extracranial paediatric tumour. Genome-wide association studies have driven the discovery of common risk variants, but no large study has investigated the contribution of rare variants to NB susceptibility. Here, we conducted a whole-exome sequencing (WES) of 664 NB cases and 822 controls and used independent validation datasets to identify genes with rare risk variants and involved pathways. METHODS WES was performed at 50× depth and variants were jointly called in cases and controls. We developed two models to identify mutations with high clinical impact (P/LP model) and to discover less penetrant risk mutations affecting non-canonical cancer pathways (RPV model). We performed a gene-level collapsing test using Firth's logistic regression in 242 selected cancer predisposition genes (CPGs) and a gene-sets burden analysis of biologically-informed pathways. FINDINGS Twelve percent of patients carried P/LP variants in CPGs and showed a significant enrichment (P = 2.3 × 10-4) compared to controls (6%). We identified P/LP variants in 45 CPGs enriched in homologous recombination (HR) pathway. The most P/LP enriched genes in NB were BRCA1, ALK and RAD51C. Additionally, we found higher RPV burden in gene-sets of neuron differentiation, neural tube development and synapse assembly, and in gene-sets associated with neurodevelopmental disorders (NDD). INTERPRETATION The high fraction of NB patients with P/LP variants indicates the need of genetic counselling. Furthermore, inherited rare variants predispose to NB development by affecting mechanisms related to HR and neurodevelopmental processes, and demonstrate that NDD genes are altered in NB at the germline level. FUNDING Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Lotta al Neuroblastoma, Associazione Oncologia Pediatrica e Neuroblastoma, Regione Campania, Associazione Giulio Adelfio onlus, and Italian Health Ministry.
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Affiliation(s)
- Ferdinando Bonfiglio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
| | - Vito Alessandro Lasorsa
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Sueva Cantalupo
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe D'Alterio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,European School of Medical Medicine, University of Milan, Milan, Italy
| | - Vincenzo Aievola
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Martina Ardito
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabine Stainczyk
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy,Corresponding author. Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Via Gaetano Salvatore 486, 80145 Napoli, Italy.
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2
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Catapano R, Sepe L, Toscano E, Paolella G, Chiurazzi F, Barbato SP, Bruzzese D, Arianna R, Grosso M, Romano S, Romano MF, Costanzo P, Cesaro E. Biological relevance of ZNF224 expression in chronic lymphocytic leukemia and its implication IN NF-kB pathway regulation. Front Mol Biosci 2022; 9:1010984. [PMID: 36425656 PMCID: PMC9681601 DOI: 10.3389/fmolb.2022.1010984] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/20/2022] [Indexed: 12/21/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, whose presentation and clinical course are highly variable. Identification of novel prognostic factors may contribute to improving the CLL classification and providing indications for treatment options. The zinc finger protein ZNF224 plays a key role in cell transformation, through the control of apoptotic and survival pathways. In this study, we evaluated the potential application of ZNF224 as a novel marker of CLL progression and therapy responsiveness. To this aim, we analyzed ZNF224 expression levels in B lymphocytes from CLL patients at different stages of the disease and in patients showing different treatment outcomes. The expression of ZNF224 was significantly increased in disease progression and dramatically decreased in patients in complete remission after chemotherapy. Gene expression correlation analysis performed on datasets of CLL patients revealed that ZNF224 expression was well correlated with that of some prognostic and predictive markers. Moreover, bioinformatic analysis coupled ZNF224 to NF-κB pathway, and experimental data demonstrated that RNA interference of ZNF224 reduced the activity of the NF-κB survival pathway in CLL cells. Consistently with a pro-survival role, ZNF224 knockdown raised spontaneous and drug-induced apoptosis and inhibited the proliferation of peripheral blood mononuclear cells from CLL patients. Our findings provide evidence for the involvement of ZNF224 in the survival of CLL cells via NF-κB pathway modulation, and also suggest ZNF224 as a prognostic and predictive molecular marker of CLL disease.
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Affiliation(s)
- Rosa Catapano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Elvira Toscano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Federico Chiurazzi
- Division of Hematology, Department of Clinical and Experimental Medicine, University of Naples Federico II, Naples, Italy
| | - Serafina Patrizia Barbato
- Division of Hematology, Department of Clinical and Experimental Medicine, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rosa Arianna
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Maria Fiammetta Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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3
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Toscano E, Sepe L, del Giudice G, Tufano R, Paolella G. A three component model for superdiffusive motion effectively describes migration of eukaryotic cells moving freely or under a directional stimulus. PLoS One 2022; 17:e0272259. [PMID: 35917375 PMCID: PMC9345344 DOI: 10.1371/journal.pone.0272259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Although the simple diffusion model can effectively describe the movement of eukaryotic cells on a culture surface observed at relatively low sampling frequency, at higher sampling rates more complex models are often necessary to better fit the experimental data. Currently available models can describe motion paths by involving additional parameters, such as linearity or directional persistence in time. However sometimes difficulties arise as it is not easy to effectively evaluate persistence in presence of a directional bias. Here we present a procedure which helps solve this problem, based on a model which describes displacement as the vectorial sum of three components: diffusion, persistence and directional bias. The described model has been tested by analysing the migratory behaviour of simulated cell populations and used to analyse a collection of experimental datasets, obtained by observing cell cultures in time lapse microscopy. Overall, the method produces a good description of migration behaviour as it appears to capture the expected increase in the directional bias in presence of wound without a large concomitant increase in the persistence module, allowing it to remain as a physically meaningful quantity in the presence of a directional stimulus.
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Affiliation(s)
- Elvira Toscano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
| | - Leandra Sepe
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
| | - Giusy del Giudice
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
| | | | - Giovanni Paolella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
- * E-mail:
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4
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D’Alterio G, Lasorsa VA, Bonfiglio F, Cantalupo S, Rosato BE, Andolfo I, Russo R, Esposito U, Frisso G, Abete P, Cassese GM, Servillo G, Gentile I, Piscopo C, Della Monica M, Fiorentino G, Boccia A, Paolella G, Ferrucci V, de Antonellis P, Siciliano R, Asadzadeh F, Cerino P, Buonerba C, Pierri B, Zollo M, Iolascon A, Capasso M. Germline rare variants of lectin pathway genes predispose to asymptomatic SARS-CoV-2 infection in elderly individuals. Genet Med 2022; 24:1653-1663. [PMID: 35511137 PMCID: PMC9068606 DOI: 10.1016/j.gim.2022.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 01/31/2023] Open
Abstract
PURPOSE Emerging evidence suggest that infection-dependent hyperactivation of complement system (CS) may worsen COVID-19 outcome. We investigated the role of predicted high impact rare variants - referred as qualifying variants (QVs) - of CS genes in predisposing asymptomatic COVID-19 in elderly individuals, known to be more susceptible to severe disease. METHODS Exploiting exome sequencing data and 56 CS genes, we performed a gene-based collapsing test between 164 asymptomatic subjects (aged ≥60 years) and 56,885 European individuals from the Genome Aggregation Database. We replicated this test comparing the same asymptomatic individuals with 147 hospitalized patients with COVID-19. RESULTS We found an enrichment of QVs in 3 genes (MASP1, COLEC11, and COLEC10), which belong to the lectin pathway, in the asymptomatic cohort. Analyses of complement activity in serum showed decreased activity of lectin pathway in asymptomatic individuals with QVs. Finally, we found allelic variants associated with asymptomatic COVID-19 phenotype and with a decreased expression of MASP1, COLEC11, and COLEC10 in lung tissue. CONCLUSION This study suggests that genetic rare variants can protect from severe COVID-19 by mitigating the activity of lectin pathway and prothrombin. The genetic data obtained through ES of 786 asymptomatic and 147 hospitalized individuals are publicly available at http://espocovid.ceinge.unina.it/.
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Affiliation(s)
- Giuseppe D’Alterio
- European School of Molecular Medicine, Università degli Studi di Milano, Milan, Italy,CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Ferdinando Bonfiglio
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
| | - Sueva Cantalupo
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Barbara Eleni Rosato
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Immacolata Andolfo
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Roberta Russo
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Giulia Frisso
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Pasquale Abete
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Naples, Italy
| | - Gian Marco Cassese
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Naples, Italy
| | - Giuseppe Servillo
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Ivan Gentile
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. Antonio Cardarelli, Naples, Italy
| | - Matteo Della Monica
- Medical and Laboratory Genetics Unit, A.O.R.N. Antonio Cardarelli, Naples, Italy
| | - Giuseppe Fiorentino
- Cotugno Hospital, Azienda Ospedaliera di Rilievo Nazionale Ospedali dei Colli, Naples, Italy
| | | | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Veronica Ferrucci
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Pasqualino de Antonellis
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Roberto Siciliano
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Fathem Asadzadeh
- European School of Molecular Medicine, Università degli Studi di Milano, Milan, Italy,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Carlo Buonerba
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana,” University of Salerno, Baronissi, Italy
| | - Biancamaria Pierri
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy,Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana,” University of Salerno, Baronissi, Italy
| | - Massimo Zollo
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate, Naples, Italy,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
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5
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Ferrucci V, Kong DY, Asadzadeh F, Marrone L, Boccia A, Siciliano R, Criscuolo G, Anastasio C, Quarantelli F, Comegna M, Pisano I, Passariello M, Iacobucci I, Monica RD, Izzo B, Cerino P, Fusco G, Viscardi M, Brandi S, Pierri BM, Borriello G, Tiberio C, Atripaldi L, Bianchi M, Paolella G, Capoluongo E, Castaldo G, Chiariotti L, Monti M, De Lorenzo C, Yun KS, Pascarella S, Cheong JH, Kim HY, Zollo M. Long-chain polyphosphates impair SARS-CoV-2 infection and replication. Sci Signal 2021; 14:14/690/eabe5040. [PMID: 34230209 PMCID: PMC8432949 DOI: 10.1126/scisignal.abe5040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Long-chain, inorganic polyphosphates (polyPs), which are found in many cells in the blood, have cytoprotective and antiviral activities, particularly against HIV-1 infection. Ferrucci et al. tested the effects of polyPs of various lengths on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro. Molecular docking and binding analyses showed that polyPs bound to the host receptor ACE2, which facilitates viral entry, and a viral RNA polymerase required for replication. Both proteins underwent proteasomal degradation in cells incubated with polyP120, the optimal species tested, resulting in inhibition of SARS-CoV-2 replication and a reduced inflammatory response. Given that polyPs have low toxicity, these results suggest that their potential therapeutic use should be further explored. Inorganic polyphosphates (polyPs) are linear polymers composed of repeated phosphate (PO43−) units linked together by multiple high-energy phosphoanhydride bonds. In addition to being a source of energy, polyPs have cytoprotective and antiviral activities. Here, we investigated the antiviral activities of long-chain polyPs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In molecular docking analyses, polyPs interacted with several conserved amino acid residues in angiotensin-converting enzyme 2 (ACE2), the host receptor that facilitates virus entry, and in viral RNA-dependent RNA polymerase (RdRp). ELISA and limited proteolysis assays using nano– LC-MS/MS mapped polyP120 binding to ACE2, and site-directed mutagenesis confirmed interactions between ACE2 and SARS-CoV-2 RdRp and identified the specific amino acid residues involved. PolyP120 enhanced the proteasomal degradation of both ACE2 and RdRp, thus impairing replication of the British B.1.1.7 SARS-CoV-2 variant. We thus tested polyPs for functional interactions with the virus in SARS-CoV-2–infected Vero E6 and Caco2 cells and in primary human nasal epithelial cells. Delivery of a nebulized form of polyP120 reduced the amounts of viral positive-sense genomic and subgenomic RNAs, of RNA transcripts encoding proinflammatory cytokines, and of viral structural proteins, thereby presenting SARS-CoV-2 infection in cells in vitro.
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Affiliation(s)
- Veronica Ferrucci
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Dae-Young Kong
- Ginxen Co., Ltd., 2F, Daewoong Building, Seocho-gu, Seoul, South Korea
| | | | - Laura Marrone
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Angelo Boccia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | | | - Giuseppina Criscuolo
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | | | | | - Marika Comegna
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Ida Pisano
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy
| | - Margherita Passariello
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Ilaria Iacobucci
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Department of Chemical Sciences, University "Federico II", Via Cinthia 4, Naples 80125, Italy
| | | | - Barbara Izzo
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples 80055, Italy
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples 80055, Italy
| | - Maurizio Viscardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples 80055, Italy
| | - Sergio Brandi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples 80055, Italy
| | | | - Giorgia Borriello
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples 80055, Italy
| | - Claudia Tiberio
- U.O.C. di Patologia Clinica Ospedale D. Cotugno, Azienda Sanitaria Ospedali dei Colli, Naples 80131, Italy
| | - Luigi Atripaldi
- U.O.C. di Patologia Clinica Ospedale D. Cotugno, Azienda Sanitaria Ospedali dei Colli, Naples 80131, Italy
| | - Martina Bianchi
- Sapienza Università di Roma, Department of Biochemical Sciences "A. Rossi Fanelli", Rome 00185, Italy
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Ettore Capoluongo
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,DAI Medicina di Laboratorio e Trasfusionale, AOU Azienda Ospedaliera "Federico II", Naples 80131, Italy
| | - Giuseppe Castaldo
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Lorenzo Chiariotti
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Maria Monti
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Department of Chemical Sciences, University "Federico II", Via Cinthia 4, Naples 80125, Italy
| | - Claudia De Lorenzo
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy
| | - Kyong-Seop Yun
- HaimBio Co. Ltd, Industrial Park, Korea University, Seongbuk-gu, Seoul, South Korea
| | - Stefano Pascarella
- Sapienza Università di Roma, Department of Biochemical Sciences "A. Rossi Fanelli", Rome 00185, Italy
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea.
| | - Hong-Yeoul Kim
- Ginxen Co., Ltd., 2F, Daewoong Building, Seocho-gu, Seoul, South Korea. .,HaimBio Co. Ltd, Industrial Park, Korea University, Seongbuk-gu, Seoul, South Korea
| | - Massimo Zollo
- CEINGE Biotecnologie Avanzate, Naples 80145, Italy. .,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), "Federico II" University of Naples, Naples 80131, Italy.,DAI Medicina di Laboratorio e Trasfusionale, AOU Azienda Ospedaliera "Federico II", Naples 80131, Italy
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6
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Discepolo V, Lania G, Ten Eikelder MLG, Nanayakkara M, Sepe L, Tufano R, Troncone R, Auricchio S, Auricchio R, Paolella G, Barone MV. Pediatric Celiac Disease Patients Show Alterations of Dendritic Cell Shape and Actin Rearrangement. Int J Mol Sci 2021; 22:ijms22052708. [PMID: 33800150 PMCID: PMC7962447 DOI: 10.3390/ijms22052708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Celiac disease (CD) is a frequent intestinal inflammatory disease occurring in genetically susceptible individuals upon gluten ingestion. Recent studies point to a role in CD for genes involved in cell shape, adhesion and actin rearrangements, including a Rho family regulator, Rho GTPase-activating protein 31 (ARHGAP31). In this study, we investigated the morphology and actin cytoskeletons of peripheral monocyte-derived dendritic cells (DCs) from children with CD and controls when in contact with a physiological substrate, fibronectin. DCs were generated from peripheral blood monocytes of pediatric CD patients and controls. After adhesion on fibronectin, DCs showed a higher number of protrusions and a more elongated shape in CD patients compared with controls, as assessed by immunofluorescence actin staining, transmitted light staining and video time-lapse microscopy. These alterations did not depend on active intestinal inflammation associated with gluten consumption and were specific to CD, since they were not found in subjects affected by other intestinal inflammatory conditions. The elongated morphology was not a result of differences in DC activation or maturation status, and did not depend on the human leukocyte antigen (HLA)-DQ2 haplotype. Notably, we found that ARH-GAP31 mRNA levels were decreased while RhoA-GTP activity was increased in CD DCs, pointing to an impairment of the Rho pathway in CD cells. Accordingly, Rho inhibition was able to prevent the cytoskeleton rearrangements leading to the elongated morphology of celiac DCs upon adhesion on fibronectin, confirming the role of this pathway in the observed phenotype. In conclusion, adhesion on fibronectin discriminated CD from the controls' DCs, revealing a gluten-independent CD-specific cellular phenotype related to DC shape and regulated by RhoA activity.
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Affiliation(s)
- Valentina Discepolo
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | - Giuliana Lania
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | | | - Merlin Nanayakkara
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (L.S.); (R.T.)
| | - Rossella Tufano
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (L.S.); (R.T.)
| | - Riccardo Troncone
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | - Renata Auricchio
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | - Giovanni Paolella
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
| | - Maria Vittoria Barone
- European Laboratory for the Investigation of Food Induced Diseases, Department of Translational Medical Science, Section of Pediatrics, and ELFID, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (V.D.); (G.L.); (M.N.); (R.T.); (S.A.); (R.A.); (G.P.)
- Correspondence:
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7
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Ferrucci V, Asadzadeh F, Collina F, Siciliano R, Boccia A, Marrone L, Spano D, Carotenuto M, Chiarolla CM, De Martino D, De Vita G, Macrì A, Dassi L, Vandenbussche J, Marino N, Cantile M, Paolella G, D'Andrea F, di Bonito M, Gevaert K, Zollo M. Prune-1 drives polarization of tumor-associated macrophages (TAMs) within the lung metastatic niche in triple-negative breast cancer. iScience 2020; 24:101938. [PMID: 33426510 PMCID: PMC7779777 DOI: 10.1016/j.isci.2020.101938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 06/26/2020] [Revised: 10/22/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
M2-tumor-associated macrophages (M2-TAMs) in the tumor microenvironment represent a prognostic indicator for poor outcome in triple-negative breast cancer (TNBC). Here we show that Prune-1 overexpression in human TNBC patients has positive correlation to lung metastasis and infiltrating M2-TAMs. Thus, we demonstrate that Prune-1 promotes lung metastasis in a genetically engineered mouse model of metastatic TNBC augmenting M2-polarization of TAMs within the tumor microenvironment. Thus, this occurs through TGF-β enhancement, IL-17F secretion, and extracellular vesicle protein content modulation. We also find murine inactivating gene variants in human TNBC patient cohorts that are involved in activation of the innate immune response, cell adhesion, apoptotic pathways, and DNA repair. Altogether, we indicate that the overexpression of Prune-1, IL-10, COL4A1, ILR1, and PDGFB, together with inactivating mutations of PDE9A, CD244, Sirpb1b, SV140, Iqca1, and PIP5K1B genes, might represent a route of metastatic lung dissemination that need future prognostic validations. Prune-1 correlates to M2-TAMs confirming lung metastatic dissemination in GEMM Cytokines and EV proteins are responsible of M2-TAMs polarization processes A small molecule with immunomodulatory properties ameliorates metastatic dissemination Identification of gene variants within immune response and cell adhesion in TNBC
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Affiliation(s)
- Veronica Ferrucci
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy.,European School of Molecular Medicine (SEMM), University of Milan, Milan, Italy
| | - Fatemeh Asadzadeh
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | - Francesca Collina
- Pathology Unit, Istituto Nazionale Tumori-IRCS- Fondazione G.Pascale, Naples 80131, Italy
| | | | | | - Laura Marrone
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | | | - Marianeve Carotenuto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | | | - Daniela De Martino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | - Gennaro De Vita
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | | | - Luisa Dassi
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy
| | - Jonathan Vandenbussche
- VIB-UGent Centre for Medical Biotechnology, Ghent 9052, Belgium.,Department of Biomolecular Medicine, Ghent University, B9052 Ghent, Belgium
| | - Natascia Marino
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Department of Medicine, Indiana University-Purdue University Indianapolis, Indianapolis 46202, USA
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale Tumori-IRCS- Fondazione G.Pascale, Naples 80131, Italy
| | | | - Francesco D'Andrea
- Dipartimento di Sanità pubblica - AOU, Università; degli Studi di Napoli Federico II, Naples 80131, Italy
| | - Maurizio di Bonito
- Pathology Unit, Istituto Nazionale Tumori-IRCS- Fondazione G.Pascale, Naples 80131, Italy
| | - Kris Gevaert
- VIB-UGent Centre for Medical Biotechnology, Ghent 9052, Belgium.,Department of Biomolecular Medicine, Ghent University, B9052 Ghent, Belgium
| | - Massimo Zollo
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy.,European School of Molecular Medicine (SEMM), University of Milan, Milan, Italy.,DAI Medicina di Laboratorio e Trasfusionale, AOU Federico II, Naples 80131, Italy
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8
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Rosi A, Paolella G, Biasini B, Scazzina F. Dietary habits of adolescents living in North America, Europe or Oceania: A review on fruit, vegetable and legume consumption, sodium intake, and adherence to the Mediterranean Diet. Nutr Metab Cardiovasc Dis 2019; 29:544-560. [PMID: 31078365 DOI: 10.1016/j.numecd.2019.03.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 12/13/2022]
Abstract
AIMS This review aimed at investigating fruit, vegetable and legume consumption, salt/sodium intake, and the adherence to the Mediterranean dietary pattern in adolescents, three key aspects towards the adoption of a healthy diet. DATA SYNTHESIS Three separate searches were carried out on PubMed and Scopus, using the same procedure, searching for studies published in the previous decade with data on fruit and/or vegetable or legume consumption, salt or sodium intake, and adherence to the Mediterranean Diet assessed using the KIDMED questionnaire. The review included a total of 58 papers, which describe original investigations on healthy adolescents (10-19 years old) living in North America, Europe or Oceania, with a sample size >150 participants. The average fruit and vegetable consumption has been found strongly below the recommended values of 400 grams or 5 portions per day in almost all the examined populations. Very little is known about adolescents' legume consumption. Few available data have been found also for sodium intake and, for the majority of the screened populations, levels were far above the recommended 5 grams per day. Lastly, a medium-low adherence to the Mediterranean Diet has been found for adolescents living in Mediterranean Countries. CONCLUSIONS Adolescents living in North America, Europe or Oceania are far from being compliant with the nutritional recommendations for fruit, vegetables, legumes, and sodium, and they do not follow the principles of the Mediterranean Diet. Educational and behavioural interventions are required to improve adolescents' dietary patterns.
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Affiliation(s)
- A Rosi
- Department of Food and Drugs, University of Parma, Parma, Italy.
| | - G Paolella
- Department of Chemistry and Biology, University of Salerno, Salerno, Italy.
| | - B Biasini
- Department of Food and Drugs, University of Parma, Parma, Italy.
| | - F Scazzina
- Department of Food and Drugs, University of Parma, Parma, Italy.
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9
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D'Argenio V, Petrillo M, Pasanisi D, Pagliarulo C, Colicchio R, Talà A, de Biase MS, Zanfardino M, Scolamiero E, Pagliuca C, Gaballo A, Cicatiello AG, Cantiello P, Postiglione I, Naso B, Boccia A, Durante M, Cozzuto L, Salvatore P, Paolella G, Salvatore F, Alifano P. The complete 12 Mb genome and transcriptome of Nonomuraea gerenzanensis with new insights into its duplicated "magic" RNA polymerase. Sci Rep 2016; 6:18. [PMID: 28442708 PMCID: PMC5431353 DOI: 10.1038/s41598-016-0025-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 09/04/2016] [Accepted: 11/02/2016] [Indexed: 11/09/2022] Open
Abstract
In contrast to the widely accepted consensus of the existence of a single RNA polymerase in bacteria, several actinomycetes have been recently shown to possess two forms of RNA polymerases due the to co-existence of two rpoB paralogs in their genome. However, the biological significance of the rpoB duplication is obscure. In this study we have determined the genome sequence of the lipoglycopeptide antibiotic A40926 producer Nonomuraea gerenzanensis ATCC 39727, an actinomycete with a large genome and two rpoB genes, i.e. rpoB(S) (the wild-type gene) and rpoB(R) (the mutant-type gene). We next analyzed the transcriptional and metabolite profiles in the wild-type gene and in two derivative strains over-expressing either rpoB(R) or a mutated form of this gene to explore the physiological role and biotechnological potential of the "mutant-type" RNA polymerase. We show that rpoB(R) controls antibiotic production and a wide range of metabolic adaptive behaviors in response to environmental pH. This may give interesting perspectives also with regard to biotechnological applications.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | - Mauro Petrillo
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Daniela Pasanisi
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.,Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Caterina Pagliarulo
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Roberta Colicchio
- Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Maria Stella de Biase
- Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | - Mario Zanfardino
- Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | | | - Chiara Pagliuca
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | - Antonio Gaballo
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.,CNR NANOTEC - Institute of Nanotechnology, Center of Nanotechnology c/o Campus Ecotekne, Lecce, Italy
| | | | | | | | | | | | - Miriana Durante
- CNR - Institute of Sciences of Food Production (ISPA), Operative Unit of Lecce, Lecce, Italy
| | | | - Paola Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | - Giovanni Paolella
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy. .,Department of Molecular Medicine and Medical Biotechnology, Federico II University Medical School, Naples, Italy.
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.
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10
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Lepretti M, Paolella G, Giordano D, Marabotti A, Gay F, Capaldo A, Esposito C, Caputo I. 4-Nonylphenol reduces cell viability and induces apoptosis and ER-stress in a human epithelial intestinal cell line. Toxicol In Vitro 2015; 29:1436-44. [DOI: 10.1016/j.tiv.2015.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 11/25/2022]
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11
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Agliarulo I, Matassa DS, Amoroso MR, Maddalena F, Sisinni L, Sepe L, Ferrari MC, Arzeni D, Avolio R, Paolella G, Landriscina M, Esposito F. TRAP1 controls cell migration of cancer cells in metabolic stress conditions: Correlations with AKT/p70S6K pathways. Biochim Biophys Acta 2015; 1853:2570-9. [PMID: 26071104 DOI: 10.1016/j.bbamcr.2015.05.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/14/2015] [Accepted: 05/28/2015] [Indexed: 12/17/2022]
Abstract
Cell motility is a highly dynamic phenomenon that is essential to physiological processes such as morphogenesis, wound healing and immune response, but also involved in pathological conditions such as metastatic dissemination of cancers. The involvement of the molecular chaperone TRAP1 in the regulation of cell motility, although still controversial, has been recently investigated along with some well-characterized roles in cancer cell survival and drug resistance in several tumour types. Among different functions, TRAP1-dependent regulation of protein synthesis seems to be involved in the migratory behaviour of cancer cells and, interestingly, the expression of p70S6K, a kinase responsible for translation initiation, playing a role in cell motility, is regulated by TRAP1. In this study, we demonstrate that TRAP1 silencing enhances cell motility in vitro but compromises the ability of cells to overcome stress conditions, and that this effect is mediated by the AKT/p70S6K pathway. In fact: i) inhibition of p70S6K activity specifically reduces migration in TRAP1 knock-down cells; ii) nutrient deprivation affects p70S6K activity thereby impairing cell migration only in TRAP1-deficient cells; iii) TRAP1 regulates the expression of both AKT and p70S6K at post-transcriptional level; and iii) TRAP1 silencing modulates the expression of genes involved in cell motility and epithelial-mesenchymal transition. Notably, a correlation between TRAP1 and AKT expression is found in vivo in human colorectal tumours. These results provide new insights into TRAP1 role in the regulation of cell migration in cancer cells, tumour progression and metastatic mechanisms.
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Affiliation(s)
- Ilenia Agliarulo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Francesca Maddalena
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy
| | - Lorenza Sisinni
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Maria Carla Ferrari
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Diana Arzeni
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Matteo Landriscina
- Clinical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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12
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Matassa DS, Agliarulo I, Amoroso MR, Maddalena F, Sepe L, Ferrari MC, Sagar V, D'Amico S, Loreni F, Paolella G, Landriscina M, Esposito F. TRAP1-dependent regulation of p70S6K is involved in the attenuation of protein synthesis and cell migration: relevance in human colorectal tumors. Mol Oncol 2014; 8:1482-94. [PMID: 24962791 DOI: 10.1016/j.molonc.2014.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 02/12/2014] [Revised: 05/20/2014] [Accepted: 06/04/2014] [Indexed: 12/24/2022] Open
Abstract
TNF receptor-associated protein 1 (TRAP1) is an HSP90 chaperone involved in stress protection and apoptosis in mitochondrial and extramitochondrial compartments. Remarkably, aberrant deregulation of TRAP1 function has been observed in several cancer types with potential new opportunities for therapeutic intervention in humans. Although previous studies by our group identified novel roles of TRAP1 in quality control of mitochondria-destined proteins through the attenuation of protein synthesis, molecular mechanisms are still largely unknown. To shed further light on the signaling pathways regulated by TRAP1 in the attenuation of protein synthesis, this study demonstrates that the entire pathway of cap-mediated translation is activated in cells following TRAP1 interference: consistently, expression and consequent phosphorylation of p70S6K and RSK1, two translation activating kinases, are increased upon TRAP1 silencing. Furthermore, we show that these regulatory functions affect the response to translational stress and cell migration in wound healing assays, processes involving both kinases. Notably, the regulatory mechanisms controlled by TRAP1 are conserved in colorectal cancer tissues, since an inverse correlation between TRAP1 and p70S6K expression is found in tumor tissues, thereby supporting the relevant role of TRAP1 translational regulation in vivo. Taken as a whole, these new findings candidate TRAP1 network for new anti-cancer strategies aimed at targeting the translational/quality control machinery of tumor cells.
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Affiliation(s)
- Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Ilenia Agliarulo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Maria Rosaria Amoroso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Francesca Maddalena
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Maria Carla Ferrari
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vinay Sagar
- Department of Biology, University of Rome 'Tor Vergata', Via Ricerca Scientifica, Rome 00133, Italy
| | - Silvia D'Amico
- Department of Biology, University of Rome 'Tor Vergata', Via Ricerca Scientifica, Rome 00133, Italy
| | - Fabrizio Loreni
- Department of Biology, University of Rome 'Tor Vergata', Via Ricerca Scientifica, Rome 00133, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Matteo Landriscina
- Clinical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
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13
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D'Argenio V, Notomista E, Petrillo M, Cantiello P, Cafaro V, Izzo V, Naso B, Cozzuto L, Durante L, Troncone L, Paolella G, Salvatore F, Di Donato A. Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern. BMC Genomics 2014; 15:384. [PMID: 24884518 PMCID: PMC4059872 DOI: 10.1186/1471-2164-15-384] [Citation(s) in RCA: 38] [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: 11/05/2013] [Accepted: 05/08/2014] [Indexed: 11/24/2022] Open
Abstract
Background Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome. Results PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism. Conclusions In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-384) contains supplementary material, which is available to authorized users.
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14
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D'Argenio V, Frisso G, Precone V, Boccia A, Fienga A, Pacileo G, Limongelli G, Paolella G, Calabrò R, Salvatore F. DNA sequence capture and next-generation sequencing for the molecular diagnosis of genetic cardiomyopathies. J Mol Diagn 2013; 16:32-44. [PMID: 24183960 DOI: 10.1016/j.jmoldx.2013.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [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: 01/18/2012] [Revised: 07/03/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022] Open
Abstract
Hypertrophic cardiomyopathy is a relatively frequent disease with a prevalence of 0.2% worldwide and a remarkable genetic heterogeneity, with more than 30 causative genes reported to date. Current PCR-based strategies are inadequate for genomic investigations involving many candidate genes. Here, we report a next-generation sequencing procedure associated with DNA sequence capture that is able to sequence 202 cardiomyopathy-related genes simultaneously. We developed a complementary data analysis pipeline to select and prioritize genetic variants. The overall procedure can screen a large number of target genes simultaneously, thereby potentially revealing new disease-causing and modifier genes. By using this procedure, we analyzed hypertrophic cardiomyopathy patients in a shorter time and at a lower cost than with current procedures. The specificity of the next-generation sequencing-based procedure is at least as good as other techniques routinely used for mutation searching, and the sensitivity is much better. Analysis of the results showed some novel variants potentially involved in the pathogenesis of hypertrophic cardiomyopathy: a missense mutation in MYH7 and a nonsense variant in INS-IGF2 (patient 1), a splicing variant in MYBPC3 and an indel/frameshift variant in KCNQ1 (patient 2), and two concomitant variations in CACNA1C (patient 3). Sequencing of DNA from the three patients within a pool allowed detection of most variants identified in each individual patient, indicating that this approach is a feasible and cost-effective procedure.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giulia Frisso
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Vincenza Precone
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | | | - Antonella Fienga
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe Pacileo
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Giuseppe Limongelli
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Giovanni Paolella
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Raffaele Calabrò
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy; IRCCS-Fondazione SDN, Naples, Italy.
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Sepe L, Ferrari MC, Cantarella C, Fioretti F, Paolella G. Ras Activated ERK and PI3K Pathways Differentially Affect Directional Movement of Cultured Fibroblasts. Cell Physiol Biochem 2013; 31:123-42. [DOI: 10.1159/000343355] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2012] [Indexed: 11/19/2022] Open
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Castoria G, D'Amato L, Ciociola A, Giovannelli P, Giraldi T, Sepe L, Paolella G, Barone MV, Migliaccio A, Auricchio F. Androgen-induced cell migration: role of androgen receptor/filamin A association. PLoS One 2011; 6:e17218. [PMID: 21359179 PMCID: PMC3040221 DOI: 10.1371/journal.pone.0017218] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [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: 09/03/2010] [Accepted: 01/25/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Androgen receptor (AR) controls male morphogenesis, gametogenesis and prostate growth as well as development of prostate cancer. These findings support a role for AR in cell migration and invasiveness. However, the molecular mechanism involved in AR-mediated cell migration still remains elusive. METHODOLOGY/PRINCIPAL FINDINGS Mouse embryo NIH3T3 fibroblasts and highly metastatic human fibrosarcoma HT1080 cells harbor low levels of transcriptionally incompetent AR. We now report that, through extra nuclear action, AR triggers migration of both cell types upon stimulation with physiological concentrations of the androgen R1881. We analyzed the initial events leading to androgen-induced cell migration and observed that challenging NIH3T3 cells with 10 nM R1881 rapidly induces interaction of AR with filamin A (FlnA) at cytoskeleton. AR/FlnA complex recruits integrin beta 1, thus activating its dependent cascade. Silencing of AR, FlnA and integrin beta 1 shows that this ternary complex controls focal adhesion kinase (FAK), paxillin and Rac, thereby driving cell migration. FAK-null fibroblasts migrate poorly and Rac inhibition by EHT impairs motility of androgen-treated NIH3T3 cells. Interestingly, FAK and Rac activation by androgens are independent of each other. Findings in human fibrosarcoma HT1080 cells strengthen the role of Rac in androgen signaling. The Rac inhibitor significantly impairs androgen-induced migration in these cells. A mutant AR, deleted of the sequence interacting with FlnA, fails to mediate FAK activation and paxillin tyrosine phosphorylation in androgen-stimulated cells, further reinforcing the role of AR/FlnA interaction in androgen-mediated motility. CONCLUSIONS/SIGNIFICANCE The present report, for the first time, indicates that the extra nuclear AR/FlnA/integrin beta 1 complex is the key by which androgen activates signaling leading to cell migration. Assembly of this ternary complex may control organ development and prostate cancer metastasis.
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Affiliation(s)
- Gabriella Castoria
- Dipartimento di Patologia Generale, II Università di Napoli, Napoli, Italy
| | - Loredana D'Amato
- Dipartimento di Patologia Generale, II Università di Napoli, Napoli, Italy
| | | | - Pia Giovannelli
- Dipartimento di Patologia Generale, II Università di Napoli, Napoli, Italy
| | - Tiziana Giraldi
- Dipartimento di Patologia Generale, II Università di Napoli, Napoli, Italy
| | - Leandra Sepe
- Dipartimento di Biochimica e Biotecnologie Mediche, Università ‘Federico II’, Napoli, Italy
| | - Giovanni Paolella
- Dipartimento di Biochimica e Biotecnologie Mediche, Università ‘Federico II’, Napoli, Italy
| | - Maria Vittoria Barone
- European Laboratory for the Investigation of Food Induced Disease, Dipartimento di Pediatria, Università ‘Federico II’, Napoli, Italy
| | - Antimo Migliaccio
- Dipartimento di Patologia Generale, II Università di Napoli, Napoli, Italy
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D'Argenio G, Petillo O, Margarucci S, Torpedine A, Calarco A, Koverech A, Boccia A, Paolella G, Peluso G. Colon OCTN2 gene expression is up-regulated by peroxisome proliferator-activated receptor gamma in humans and mice and contributes to local and systemic carnitine homeostasis. J Biol Chem 2010; 285:27078-27087. [PMID: 20558736 PMCID: PMC2930707 DOI: 10.1074/jbc.m110.109678] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [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: 02/02/2010] [Revised: 05/07/2010] [Indexed: 12/25/2022] Open
Abstract
In the large intestine organic cation transporter type-2 (OCTN2) is recognized as a transporter of compounds such as carnitine and colony sporulation factor, promoting health of the colon intestinal epithelium. Recent reports suggest that OCTN2 expression in small intestine is under control of peroxisome proliferator-activated receptor-alpha (PPARalpha). However, PPARalpha contribution to colonic OCTN2 expression remains controversial. Here we examined the transcriptional regulation of colon OCTN2 gene by PPARgamma. To exclude any additional modulation of other PPAR to OCTN2 expression, we used both in vivo and in vitro PPAR-null models and specific PPAR inhibitors. The PPARgamma agonists thiazolidinediones increased both OCTN2 mRNA and protein expression in colonic epithelial cell lines independently by PPARalpha expression. The induction was blocked only by PPARgamma antagonists or by gammaORF4, a PPARgamma isoform with dominant negative activity, suggesting a PPARgamma-dependent mechanism. A conserved noncanonical PPAR-responsive element was found by computational analysis in the first intron of human OCTN2 gene and validated by EMSA assay. Promoter-reporter assays further confirmed transcriptional functionality of the putative PPAR response element, whereas selective mutation caused complete loss of responsiveness to PPARgamma activation. Finally, adenovirus-mediated overexpression of constitutively active PPARgamma mutant increased colon OCTN2 expression in PPARalpha(-/-) mice. Interestingly, animals overexpressing colon PPARgamma showed a significant increase in plasma carnitine, thus demonstrating the functional contribution of large intestine to systemic carnitine homeostasis. This study reveals a PPARgamma-dependent absorption machinery in colon that is likely involved in the health of colon epithelium, in the microbiota-host interactions and in the absorption of nutraceuticals and drugs.
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Affiliation(s)
- Giuseppe D'Argenio
- Gastroenterologia, Dipartimento di Medicina Clinica e Sperimentale, Federico II University, 80131 Naples, Italy
| | - Orsolina Petillo
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy
| | - Sabrina Margarucci
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy
| | - Angela Torpedine
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy
| | - Anna Calarco
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy
| | | | - Angelo Boccia
- Dipartimento di Biochimica e Biotecnologie Mediche, Federico II University, CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
| | - Giovanni Paolella
- Dipartimento di Biochimica e Biotecnologie Mediche, Federico II University, CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
| | - Gianfranco Peluso
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy.
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Barone MV, Nanayakkara M, Paolella G, Maglio M, Vitale V, Troiano R, Ribecco MTS, Lania G, Zanzi D, Santagata S, Auricchio R, Troncone R, Auricchio S. Gliadin peptide P31-43 localises to endocytic vesicles and interferes with their maturation. PLoS One 2010; 5:e12246. [PMID: 20805894 PMCID: PMC2923621 DOI: 10.1371/journal.pone.0012246] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [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: 03/24/2010] [Accepted: 07/22/2010] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Celiac Disease (CD) is both a frequent disease (1:100) and an interesting model of a disease induced by food. It consists in an immunogenic reaction to wheat gluten and glutenins that has been found to arise in a specific genetic background; however, this reaction is still only partially understood. Activation of innate immunity by gliadin peptides is an important component of the early events of the disease. In particular the so-called "toxic" A-gliadin peptide P31-43 induces several pleiotropic effects including Epidermal Growth Factor Receptor (EGFR)-dependent actin remodelling and proliferation in cultured cell lines and in enterocytes from CD patients. These effects are mediated by delayed EGFR degradation and prolonged EGFR activation in endocytic vesicles. In the present study we investigated the effects of gliadin peptides on the trafficking and maturation of endocytic vesicles. METHODS/PRINCIPAL FINDINGS Both P31-43 and the control P57-68 peptide labelled with fluorochromes were found to enter CaCo-2 cells and interact with the endocytic compartment in pulse and chase, time-lapse, experiments. P31-43 was localised to vesicles carrying early endocytic markers at time points when P57-68-carrying vesicles mature into late endosomes. In time-lapse experiments the trafficking of P31-43-labelled vesicles was delayed, regardless of the cargo they were carrying. Furthermore in celiac enterocytes, from cultured duodenal biopsies, P31-43 trafficking is delayed in early endocytic vesicles. A sequence similarity search revealed that P31-43 is strikingly similar to Hrs, a key molecule regulating endocytic maturation. A-gliadin peptide P31-43 interfered with Hrs correct localisation to early endosomes as revealed by western blot and immunofluorescence microscopy. CONCLUSIONS P31-43 and P57-68 enter cells by endocytosis. Only P31-43 localises at the endocytic membranes and delays vesicle trafficking by interfering with Hrs-mediated maturation to late endosomes in cells and intestinal biopsies. Consequently, in P31-43-treated cells, Receptor Tyrosine Kinase (RTK) activation is extended. This finding may explain the role played by gliadin peptides in inducing proliferation and other effects in enterocytes from CD biopsies.
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Affiliation(s)
- Maria Vittoria Barone
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Merlin Nanayakkara
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Giovanni Paolella
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Biochemistry Department, University of Naples, Federico II, Naples, Italy
| | - Mariantonia Maglio
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Virginia Vitale
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Raffaele Troiano
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Maria Teresa Silvia Ribecco
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
- CEINGE–Biotecnologie Avanzate, Naples, Italy
| | - Giuliana Lania
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Delia Zanzi
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Sara Santagata
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Renata Auricchio
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Riccardo Troncone
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
| | - Salvatore Auricchio
- Pediatric Department and European Laboratory for the Investigation of Food-Induced Disease (ELFID), University of Naples Federico II, Naples, Italy
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Abstract
Background Cell motility plays a central role in development, wound-healing and tumour invasion. Cultures of eucariotic cells are a complex system where most cells move according to 'random' patterns, but may also be induced to a more coordinate migration by means of specific stimuli, such as the presence of chemical attractants or the introduction of a mechanical stimulus. Various tools have been developed that work by keeping track of the paths followed by specific objects and by performing statistical analysis on the recorded path data. The available tools include desktop applications or macros running within a commercial package, which address specific aspects of the process. Results An online application, MotoCell, was developed to evaluate the motility of cell populations maintained in various experimental conditions. Statistical analysis of cell behaviour consists of the evaluation of descriptive parameters such as average speed and angle, directional persistence, path vector length, calculated for the whole population as well as for each cell and for each step of the migration; in this way the behaviour of a whole cell population may be assessed as a whole or as a sum of individual entities. The directional movement of objects may be studied by eliminating the modulo effect in circular statistics analysis, able to evaluate linear dispersion coefficient (R) and angular dispersion (S) values together with average angles. A case study is provided where the system is used to characterize motility of RasV12 transformed NIH3T3 fibroblasts. Conclusion Here we describe a comprehensive tool which takes care of all steps in cell motility analysis, including interactive cell tracking, path editing and statistical analysis of cell movement, all within a freely available online service. Although based on a standard web interface, the program is very fast and interactive and is immediately available to a large number of users, while exploiting the web approach in a very effective way. The ability to evaluate the behaviour of single cells allows to draw the attention on specific correlations, such as linearity of movement and deviation from the expected direction. In addition to population statistics, the analysis of single cells allows to group the cells into subpopulations, or even to evaluate the behaviour of each cell with respect to a variable reference, such as the direction of a wound or the position of the closest cell.
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Affiliation(s)
- Concita Cantarella
- DBBM Dipartimento di Biochimica e Biotecnologie Mediche, Universita' di Napoli FEDERICO II, Via S. Pansini 5, Naples, Italy.
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Elce A, Boccia A, Cardillo G, Giordano S, Tomaiuolo R, Paolella G, Castaldo G. Three novel CFTR polymorphic repeats improve segregation analysis for cystic fibrosis. Clin Chem 2009; 55:1372-9. [PMID: 19443567 DOI: 10.1373/clinchem.2008.119545] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Molecular diagnosis for cystic fibrosis (CF) is based on the direct identification of mutations in the CFTR gene [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] (detection rate about 90% with scanning procedures) and on segregation analysis of intragenic polymorphisms for carrier and prenatal diagnosis in about 20% of CF families in which 1 or both causal mutations are unknown. METHODS We identified 3 novel intragenic polymorphic repeats (IVS3polyA, IVS4polyA, and IVS10CA repeats) in the CFTR gene and developed and validated a procedure based on the PCR followed by capillary electrophoresis for large-scale analysis of these polymorphisms and the 4 previously identified microsatellites (IVS1CA, IVS8CA, IVS17bTA, and IVS17bCA repeats) in a single run. We validated the procedure for both single- and 2-cell samples (for a possible use in preimplantation diagnosis), and on a large number of CF patients bearing different genotypes and non-CF controls. RESULTS The allelic distribution and heterozygosity results suggest that the 3 novel polymorphisms strongly contribute to carrier and prenatal diagnosis of CF in families in which 1 or both causal mutations have not been identified. At least 1 of the 4 previously identified microsatellites was informative in 78 of 100 unrelated CF families; at least 1 of all 7 polymorphisms was informative in 98 of the families. Finally, the analysis of haplotypes for the 7 polymorphisms revealed that most CF mutations are associated with different haplotypes, suggesting multiple slippage events but a single origin for most CFTR mutations. CONCLUSIONS The analysis of the 7 polymorphisms is a rapid and efficient tool for routine carrier, prenatal, and preimplantation diagnosis of CF.
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Affiliation(s)
- Ausilia Elce
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
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Elce A, Tomaiuolo R, Boccia A, Paolella G, Castaldo G. DIRECT SEQUENCING OF CSTs IN CYSTIC FIBROSIS PATIENTS BEARING UNDEFINITE GENOTYPE. J Cyst Fibros 2008. [DOI: 10.1016/s1569-1993(08)60515-9] [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: 10/21/2022]
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Cozzuto L, Petrillo M, Silvestro G, Di Nocera PP, Paolella G. Systematic identification of stem-loop containing sequence families in bacterial genomes. BMC Genomics 2008; 9:20. [PMID: 18201379 PMCID: PMC2267715 DOI: 10.1186/1471-2164-9-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 06/14/2007] [Accepted: 01/17/2008] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. These sequences have often been claimed to be transcribed and fulfill a functional role. A previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (SLS). Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing a common secondary structure. RESULTS The initial clustering procedure identified clusters of similar sequences in 29 genomes, corresponding to about 1% of the whole population. Sequences selected in this way have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM analysis. 25 of them include all well-known SLS containing repeats and others reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions. CONCLUSION Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that, even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at the RNA level.
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Affiliation(s)
- Luca Cozzuto
- CEINGE Biotecnologie Avanzate scarl, Via Comunale Margherita 482, 80145 Napoli, Italy.
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Abstract
Bioinformatic tools are often used by researchers through interactive Web interfaces, resulting in a strong demand for computational resources. The tools are of different kind and range from simple, quick tasks, to complex analyses requiring minutes to hours of processing time and often longer than that. Batteries of computational nodes, such as those found in parallel clusters, provide a platform of choice for this application, especially when a relatively large number of concurrent requests is expected. Here, we describe a scheduling architecture operating at the application level, able to distribute jobs over a large number of hierarchically organized nodes. While not contrasting and peacefully living together with low-level scheduling software, the system takes advantage of tools, such as SQL servers, commonly used in Web applications, to produce low latency and performance which compares well and often surpasses that of more traditional, dedicated schedulers. The system provides the basic functionality necessary to node selection, task execution and service management and monitoring, and may combine loosely linked computational resources, such as those located in geographically distinct sites.
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Affiliation(s)
- Angelo Boccia
- CEBSMA, Università degli Studi di Napoli Federico II, Napoli, Italy.
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Barone MV, Gimigliano A, Castoria G, Paolella G, Maurano F, Paparo F, Maglio M, Mineo A, Miele E, Nanayakkara M, Troncone R, Auricchio S. Growth factor-like activity of gliadin, an alimentary protein: implications for coeliac disease. Gut 2007; 56:480-8. [PMID: 16891357 PMCID: PMC1856836 DOI: 10.1136/gut.2005.086637] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
BACKGROUND Gliadins, a family of wheat proteins, are central to the pathogenesis of celiac disease (CD). In addition to 'immunogenic' effects, gliadin directly affects cultured cells and intestine preparations, and produces damage in vivo, via a separate 'toxic' peptide, such as A-gliadin p31-43 (P31-43). AIMS Understanding the molecular mechanisms underlying direct non T-cell mediated effects of gliadin peptides, and assessing their potential role in promoting CD. METHOD Gliadin effects were tested on a number of cell lines and on cultured mucosa samples by evaluating cytoskeleton rearrangements, endocytosis, proliferation and apoptosis. Standard biochemical methods were used to assess prolonged epidermal growth factor receptor (EGFR) activation. RESULTS Crude gliadin peptic-tryptic peptides (PTG], or P31-43 alone, fully reproduce the effects of epidermal growth factor (EGF] on actin cytosketon, cell cycle and cell proliferation of various cell lines. Inhibitor studies demonstrate the role of EGFR in the early response to gliadin exposure, pointing to activation of the EGFR pathway. Peptide P31-43 is not similar to any EGFR ligand, but can delay inactivation of the EGFR interfering with its endocytosis. Gliadin-induced delay of EGFR endocytosis in cultured intestinal biopsies, together with S-phase entry of epithelial intestinal cells, confirm a role for EGFR activation in CD. CONCLUSION The ability of gliadin peptides to delay EGFR inactivation through interference with the endocytic pathway suggests a model where gliadin fragments amplify the effects of trace amounts of EGF, and possibly of other growth factors, by prolonging receptor activation. The results, using cultures of coeliac intestinal biopsies, highlight the role of the EGF pathway in establishing and maintaining the typical atrophic and proliferative alterations of the small intestine in CD.
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Affiliation(s)
- Maria Vittoria Barone
- Dipartimento di Pediatria European Laboratory For the Investigation of Food Induced Disease, Università degli Studi di Napoli Federico II, CAP 80131, Napoli, Italy
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Abstract
BACKGROUND Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions, where base pairing is less affected by interactions with the translation machinery. Relatively large stem-loops significantly contribute to the formation of more complex secondary structures, often important for the activity of sequence elements controlling gene expression. RESULTS Systematic analysis of the distribution of stem-loop structures (SLSs) in 40 wholly-sequenced bacterial genomes is presented. SLSs were searched as stems measuring at least 12 bp, bordering loops 5 to 100 nt in length. G-U pairing in the stems was allowed. SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and composition. The large majority of SLSs fall within protein-coding regions but enrichment of specific, non random, SLS sub-populations of higher stability was observed within the intergenic regions of the chromosomes of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs. Some intergenic SLS regions are members of novel repeated sequence families. CONCLUSION In depth analysis of SLS features and distribution in 40 different bacterial genomes showed the presence of non random populations of such structures in all species. Many of these structures are plausibly transcribed, and might be involved in the control of transcription termination, or might serve as RNA elements which can enhance either the stability or the turnover of cotranscribed mRNAs. Three previously undescribed families of repeated sequences were found in Yersiniae, Bordetellae and Enterococci.
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Affiliation(s)
- Mauro Petrillo
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
| | - Giustina Silvestro
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| | - Pier Paolo Di Nocera
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
- Dipartimento SAVA Università del Molise Via De Sanctis, 86100 Campobasso, Italy
- Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
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Milanesi L, Petrillo M, Sepe L, Boccia A, D'Agostino N, Passamano M, Di Nardo S, Tasco G, Casadio R, Paolella G. Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinformatics 2005; 6 Suppl 4:S20. [PMID: 16351747 PMCID: PMC1866387 DOI: 10.1186/1471-2105-6-s4-s20] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular processes, such as proliferation, maintenance of cell shape, apoptosys. In many members of the family, additional non-kinase domains contribute further specialization, resulting in subcellular localization, protein binding and regulation of activity, among others. About 500 genes encode members of the kinase family in the human genome, and although many of them represent well known genes, a larger number of genes code for proteins of more recent identification, or for unknown proteins identified as kinase only after computational studies. Results A systematic in silico study performed on the human genome, led to the identification of 5 genes, on chromosome 1, 11, 13, 15 and 16 respectively, and 1 pseudogene on chromosome X; some of these genes are reported as kinases from NCBI but are absent in other databases, such as KinBase. Comparative analysis of 483 gene regions and subsequent computational analysis, aimed at identifying unannotated exons, indicates that a large number of kinase may code for alternately spliced forms or be incorrectly annotated. An InterProScan automated analysis was perfomed to study domain distribution and combination in the various families. At the same time, other structural features were also added to the annotation process, including the putative presence of transmembrane alpha helices, and the cystein propensity to participate into a disulfide bridge. Conclusion The predicted human kinome was extended by identifiying both additional genes and potential splice variants, resulting in a varied panorama where functionality may be searched at the gene and protein level. Structural analysis of kinase proteins domains as defined in multiple sources together with transmembrane alpha helices and signal peptide prediction provides hints to function assignment. The results of the human kinome analysis are collected in the KinWeb database, available for browsing and searching over the internet, where all results from the comparative analysis and the gene structure annotation are made available, alongside the domain information. Kinases may be searched by domain combinations and the relative genes may be viewed in a graphic browser at various level of magnification up to gene organization on the full chromosome set.
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Affiliation(s)
- Luciano Milanesi
- Biomedical Technologies Institute (ITB), National Research Council, Milano, Italy
- CILEA, Segrate, Italy
| | | | - Leandra Sepe
- Biomedical Technologies Institute (ITB), National Research Council, Milano, Italy
- Dipartimento di Biochimica e Biotecnologie Mediche, Universita' di Napoli Federico II, Italy
| | | | - Nunzio D'Agostino
- Biomedical Technologies Institute (ITB), National Research Council, Milano, Italy
| | - Myriam Passamano
- Biomedical Technologies Institute (ITB), National Research Council, Milano, Italy
| | - Salvatore Di Nardo
- Biomedical Technologies Institute (ITB), National Research Council, Milano, Italy
| | - Gianluca Tasco
- Biomedical Technologies Institute (ITB), National Research Council, Milano, Italy
- Department of Biology, University of Bologna, Italy
| | - Rita Casadio
- Department of Biology, University of Bologna, Italy
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate, Napoli, Italy
- Dipartimento di Biochimica e Biotecnologie Mediche, Universita' di Napoli Federico II, Italy
- Dipartimento SAVA, Universita' del Molise, Italy
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Boccia A, Petrillo M, di Bernardo D, Guffanti A, Mignone F, Confalonieri S, Luzi L, Pesole G, Paolella G, Ballabio A, Banfi S. DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. Nucleic Acids Res 2005; 33:D505-10. [PMID: 15608249 PMCID: PMC539965 DOI: 10.1093/nar/gki011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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] [Indexed: 11/14/2022] Open
Abstract
The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human–mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.
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Ferreira J, Paolella G, Ramos C, Lamond AI. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J Cell Biol 1997; 139:1597-610. [PMID: 9412456 PMCID: PMC2132633 DOI: 10.1083/jcb.139.7.1597] [Citation(s) in RCA: 172] [Impact Index Per Article: 6.4] [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] [Indexed: 02/05/2023] Open
Abstract
We have analyzed the spatial organization of large scale chromatin domains in chinese hamster fibroblast, human lymphoid (IM-9), and marsupial kidney epithelial (PtK) cells by labeling DNA at defined stages of S phase via pulsed incorporation of halogenated deoxynucleosides. Most, if not all, chromosomes contribute multiple chromatin domains to both peripheral and internal nucleoplasmic compartments. The peripheral compartment contains predominantly late replicating G/Q bands, whereas early replicating R bands preferentially localize to the internal nucleoplasmic compartment. During mitosis, the labeled chromatin domains that were separated in interphase form a pattern of intercalated bands along the length of each metaphase chromosome. The transition from a banded (mitotic) to a compartmentalized (interphasic) organization of chromatin domains occurs during the late telophase/early G1 stage and is independent of transcriptional activation of the genome. Interestingly, generation of micronuclei with a few chromosomes showed that the spatial separation of early and late replicating chromatin compartments is recapitulated independently of chromosome number, even in micronuclei containing only a single chromosome. Our data strongly support the notion that the compartmentalization of large-scale (band size) chromatin domains seen in the intact nucleus is a magnified image of a similar compartmentalization occurring in individual chromosome territories.
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Affiliation(s)
- J Ferreira
- Institute of Histology, Faculty of Medicine, 1699 Lisboa codex, Portugal
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30
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Abstract
Hammerhead ribozymes are efficient RNA enzymes characterized by a typical hammerhead secondary structure and a number of conserved bases. Little is known about the role of the ribose-phosphate backbone, although it is obviously important since a DNA molecule with the same base sequence is not a catalyst. Here we describe the synthesis of artificial ribozymes where modified (2'-O-allyl- and 2'-O-methyl-) ribonucleotides substitute for the corresponding ribonucleotides. A systematic analysis of partially substituted polymers identified a minimum set of six non-contiguous positions where insertion of modified ribonucleotides strongly affects catalytic activity. Surprisingly, ribozymes completely substituted except for these six ribonucleotides are still very active. These molecules efficiently cleave in trans target RNAs in a sequence-specific way, but, unlike RNA ribozymes, are very resistant to nuclease degradation and are very stable in serum. These properties make such synthetic polymers potentially useful for in vivo gene expression studies and therapeutic applications.
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Rocchi M, Vitale E, Covone A, Romeo G, Santamaria R, Buono P, Paolella G, Salvatore F. Assignment of human aldolase C gene to chromosome 17, region cen----q21.1. Hum Genet 1989; 82:279-82. [PMID: 2731939 DOI: 10.1007/bf00291170] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The mapping of the gene coding for human aldolase C has been studied using a specific cDNA probe and genomic blots from a panel of human-hamster somatic cell hybrids. The results show that the aldolase C gene is on chromosome 17. In situ experiments have restricted the mapping to the region 17cen----q21.1. Using the same panel of human-hamster somatic cell hybrids, we have confirmed the localization of aldolase A and B on chromosomes 16 and 9, respectively.
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Affiliation(s)
- M Rocchi
- Laboratorio di Genetica Molecolare, Istituto G. Gaslini, Genoa, Italy
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32
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Abstract
ED-A and ED-B are facultative type III homologies of fibronectin, encoded by alternatively spliced exons, described in man and in rat. A hybrid alpha-globin-fibronectin minigene containing the ED-B region from the human gene has been transfected in human cell lines derived from various tissues, in order to study the processing of the generated precursor RNA in the different cell environments. In most tested lines the pre-RNA is alternatively spliced and produces two mature RNAs, with and without the ED-B exon, in different ratios that closely resemble the corresponding endogenous fibronectin RNAs. In a hepatoma cell line, Hep 3B, only one RNA is produced, in which the ED-B exon is absent; the same pattern of splicing is observed in liver. The data show that all the information required to produce accurate and regulated alternative splicing of the ED-B exon is contained in the fragment used and cell specific factors are necessary for the pre-RNA to be differentially spliced in the various cell lines. In contrast, expression in Hep 3B of a similar gene containing the ED-A area failed to reproduce the liver specific splicing pattern. Therefore regulation of ED-A processing is likely to involve different mechanisms to those responsible for control of ED-B splicing.
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Affiliation(s)
- M V Barone
- Sir William Dunn School of Pathology, University of Oxford, UK
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33
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Izzo P, Costanzo P, Lupo A, Rippa E, Paolella G, Salvatore F. Human aldolase A gene. Structural organization and tissue-specific expression by multiple promoters and alternate mRNA processing. Eur J Biochem 1988; 174:569-78. [PMID: 3391172 DOI: 10.1111/j.1432-1033.1988.tb14136.x] [Citation(s) in RCA: 55] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The complete nucleotide sequence of the human aldolase A isoenzyme gene is reported. The cloned gene sequence, spanning 7530 bp, includes twelve exons and occurs as a single copy per haploid human genome. The structural organization of the gene is quite complex: eight exons containing the coding sequence are common to all mRNAs extracted from human and other mammalian sources; four additional exons are present in the 5' untranslated region, of these one is contained in the ubiquitous type of mRNA, the second is in the muscle-specific type of mRNA and the third and fourth are in a minor species of mRNA found in human liver tissue. Furthermore, the determined sequence includes 1000 nucleotides upstream from the first exon (exon I) in the 5' flanking region, and 400 nucleotides, which include the polyadenylation signal, downstream from the termination codon. S1-nuclease-protection analysis of the 5' end of mRNA extracted from human cultured fibroblasts, muscle and hepatoma cell lines indicates the existence of four different transcription-initiation sites. The latter are also supported by the presence of conventional sequences for eukaryotic promoters. Therefore, the four promoters on the same gene generate different tissue-specific transcripts, which share the translated sequence, but each has a unique 5' untranslated region as a result of differential mRNA processing. The nucleotide homology at the coding region and the intron-exon organization of the three human and mammalian aldolase A, B and C genes confirm that they arose from a common ancestral gene, and that aldolase B diverged first.
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Affiliation(s)
- P Izzo
- Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di Napoli
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34
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Affiliation(s)
- P Buono
- Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di Napoli, Italy
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35
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Paolella G, Henchcliffe C, Sebastio G, Baralle FE. Sequence analysis and in vivo expression show that alternative splicing of ED-B and ED-A regions of the human fibronectin gene are independent events. Nucleic Acids Res 1988; 16:3545-57. [PMID: 3375063 PMCID: PMC336511 DOI: 10.1093/nar/16.8.3545] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The structure of two alternatively spliced regions. ED-A and ED-B, of human fibronectin gene, was determined, in order to show whether any similarity was present between the two. Although some interesting features are present in each, no obvious common structure or sequence homology was found. Functional analysis of the alternative splicing events was carried out by transient expression in Hela cells. A hybrid gene was constructed by inserting the ED-B region into the third exon of the human alpha 1-globin gene. The transfected hybrid gene is expressed and produces, in Hela cells, two alternatively spliced RNAs, showing a pattern very similar to that observed for the endogenous fibronectin gene in fibroblasts. Cotransfection of this gene with a similar gene containing the ED-A region, shows that no interference is present between the two alternative splicing processes.
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Affiliation(s)
- G Paolella
- Sir William Dunn School of Pathology, University of Oxford, UK
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36
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Costanzo P, Izzo P, Lupo A, Rippa E, Paolella G, Salvatore F. Human aldolase A gene: structural organization and expression in tumor cell lines. Ital J Biochem 1988; 37:8-13. [PMID: 2838431] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The structural intron/exon organization of the cloned human aldolase A gene is reported. The gene is composed of twelve exons, including the coding and the 5' and 3' non-coding regions. Four mRNAs, different at the 5' non-coding region, are transcribed from this gene in a tissue-specific manner. The study of the expression of aldolase A gene in normal liver and neoplastic cell lines demonstrated the resurgence of foetal pattern of expression in all tumor liver cell lines and HeLa cells, thus supporting the foetalism theory for this gene system.
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Affiliation(s)
- P Costanzo
- Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Napoli
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37
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Abstract
Peripheral blood DNA was hybridized to the full-length cDNA and the cloned structural gene of human aldolase B. With PvuII endonuclease a restriction fragment length polymorphism was detected that was present in the heterozygous state in about 21% of the individuals tested. A map of the human aldolase gene was constructed for the two groups of individuals found to produce different fragments after PvuII digestion. This allowed the localization of the polymorphic site within the gene, which was found to be due to the loss of a PvuII site in the last intron upstream from the 3' end. This polymorphism may be used as a genetic marker to study individuals affected by hereditary fructose intolerance.
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Affiliation(s)
- G Paolella
- Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di Napoli, Italy
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38
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Zardi L, Carnemolla B, Siri A, Petersen TE, Paolella G, Sebastio G, Baralle FE. Transformed human cells produce a new fibronectin isoform by preferential alternative splicing of a previously unobserved exon. EMBO J 1987; 6:2337-42. [PMID: 2822387 PMCID: PMC553637 DOI: 10.1002/j.1460-2075.1987.tb02509.x] [Citation(s) in RCA: 229] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Purification and amino acid sequence analysis of a proteolytic fragment of fibronectin (FN) from transformed human cells demonstrated that a high percentage of these FN molecules contains an extra amino acid sequence which is present only in a very low percentage of FN molecules from normal fibroblasts and is undetectable in plasma FN. This new amino acid sequence introduces into the FN molecule a site very sensitive to a number of proteolytic enzymes. By analyzing the cellular mRNA and genomic clones, we have demonstrated that this sequence derives from a differential splicing pattern of the FN mRNA precursors, which leads in transformed cells to a high-level expression of an extra type III homology repeat (ED-B) coded for by a previously unobserved exon. Here we also report the complete sequence of this new exon. These results demonstrate that in malignant cells the mechanisms regulating the splicing of FN mRNA precursors are altered.
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Affiliation(s)
- L Zardi
- Cell Biology Laboratory, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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39
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Izzo P, Costanzo P, Lupo A, Rippa E, Borghese AM, Paolella G, Salvatore F. A new human species of aldolase A mRNA from fibroblasts. Eur J Biochem 1987; 164:9-13. [PMID: 3030757 DOI: 10.1111/j.1432-1033.1987.tb10984.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A full-length cDNA aldolase A clone was isolated from a human fibroblast cDNA library and completely sequenced. Excluding the poly(A) tail, the clone covers 1095 base pairs (bp) of the coding region, plus 199 bp downstream for the termination codon and 146 bp upstream for the initiation codon, within a total of 1440 bp. Primer extension experiments performed with human cultured fibroblast mRNA indicate an elongated product of a further 40 bp. These results evaluated together with those obtained in a concurrent study concerning aldolase A mRNA isolated from human liver are direct evidence of aldolase A mRNA multiplicity in man. The data also suggest the existence in mammals of three different classes of aldolase A mRNA, which would account for tissue specificity and resurgence of foetal expression in tumors.
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41
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Bruni CB, Carlomagno MS, Formisano S, Paolella G. Primary and secondary structural homologies between the HIS4 gene product of Saccharomyces cerevisiae and the hisIE and hisD gene products of Escherichia coli and Salmonella typhimurium. Mol Gen Genet 1986; 203:389-96. [PMID: 3528746 DOI: 10.1007/bf00422062] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A detailed comparative analysis of the Escherichia coli and Salmonella typhimurium hisIE and hisD gene products and the functionally equivalent, single, HIS4 gene product of Saccharomyces cerevisiae permitted several insights concerning the relationship between these genes. Our analysis supports the idea that HIS4 results from the fusion of his IE and hisD. The comparison permitted a more precise definition of the functional domains of hisI/HIS4A and hisE/HIS4B as well as the two functional domains of hisD/HIS4C. The homologies between the bacterial and yeast sequences suggest a region of the hisD/HIS4C protein that may constitute one of the active centres. A large fragment at the amino terminal region of the yeast protein is missing from the bacterial hisIE gene product and is probably not needed for catalytic activity. Another region of non-homology in the yeast protein is probably a peptide bridge connecting the HIS4AB domain to HIS4C. Although the overall homology at the level of amino acid sequence is modest (about 38%) there is a striking similarity when the hydropathic patterns and predicted secondary structural configurations of these proteins are compared.
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42
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Paolella G, Buono P, Mancini FP, Izzo P, Salvatore F. Structure and expression of mouse aldolase genes. Brain-specific aldolase C amino acid sequence is closely related to aldolase A. Eur J Biochem 1986; 156:229-35. [PMID: 3009179 DOI: 10.1111/j.1432-1033.1986.tb09572.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Brain-specific aldolase C amino acid sequence (greater than 75% of the coding region) was determined for the first time. Two cDNA clones, pAM1 and pAM2, were identified, from a mouse brain library, by using human aldolase B cDNA as a probe. The larger one, pAM2, identified as a cDNA for aldolase C, has been completely sequenced and covers the 5'-untranslated region of the mRNA and the codons for amino acids 1-227 of the protein. The sequence indicates that aldolase C is more akin to aldolase A than to aldolase B. A cDNA library from mouse muscle was also screened, allowing the identification of clones pAM3 and pAM4, which contain cDNAs for aldolase A. The sequence obtained from pAM3 covers 70% of the coding sequence (amino acids 99-355) from the -COOH part of the protein. The cDNAs for the three aldolases, A, B and C, have been hybridized to RNA from various rat tissues. The results confirm the tissue specificity of the expression of the mRNA for the different isoenzymes and support the hypothesis that aldolase C expression, as aldolase A and B, is regulated at the transcriptional level or, in any case, via mRNA concentration.
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Abstract
A microcomputer program which locates tRNA genes within long DNA sequences is described. The search is performed either by identifying tRNA-like secondary structures or by locating eukaryotic RNA polymerase III promoter consensus sequences. The program is also useful in finding inverted repeats allowing the formation of stem-loop secondary structures in tRNA. The program has been developed in BASIC and 6502 Assembler and runs on the Apple II plus and IIe microcomputers. The execution is quite fast; all the operations are carried out in 1-90 s, depending on the required task and on the sequence length.
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Affiliation(s)
- G Paolella
- Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di Napoli, Italy
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44
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Abstract
A fast general purpose DNA handling program has been developed in BASIC and machine language. The program runs on the Apple II plus or on the Apple IIe microcomputer, without additional hardware except for disk drives and printer. The program allows file insertion and editing, translation into protein sequence, reverse translation, search for small strings and restriction enzyme sites. The homology may be shown either as a comparison of two sequences or through a matrix on screen. Two additional features are: (i) drawing restriction site maps on the printer; and (ii) simulating a gel electrophoresis of restriction fragments both on screen and on paper. All the operations are very fast. The more common tasks are carried out almost instantly; only more complex routines, like finding homology between large sequences or searching and sorting all the restriction sites in a long sequence require longer, but still quite acceptable, times (generally under 30 s).
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Affiliation(s)
- G Paolella
- Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università di Napoli, Italy
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Paolella G, Santamaria R, Izzo P, Costanzo P, Salvatore F. Isolation and nucleotide sequence of a full-length cDNA coding for aldolase B from human liver. Nucleic Acids Res 1984; 12:7401-10. [PMID: 6548561 PMCID: PMC320170 DOI: 10.1093/nar/12.19.7401] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two recombinant clones, pA2 and pA3, containing cDNA sequences for human aldolase B have been isolated from a full length human liver cDNA library. The larger one, pA3, has been subcloned in M13 phage and completely sequenced with the chain terminator method. The sequence covers 1,600 nucleotides including the whole coding region (1,050 nucleotides), 67 nucleotides from the 5' non-coding region and the whole 3' non-coding region, 440 nucleotides long, down to the poly-A tail. Comparison with rabbit aldolase A and with a partial sequence of rat aldolase B, shows a homology of about 76% for aldolase A and of about 94% for aldolase B, which indicates that the sequenced cDNA codes for the liver isoenzyme. This is the first complete sequence reported for human aldolase B. The pA3 clone strongly hybridizes to 18S mRNA from human adult liver as expected from the size of the isolated cDNA.
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46
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Valentino V, Mariottini A, Delfini R, Ciappetta P, Paolella G. Digitalized venous angiography in the investigation of the neck vessels. Acta Neurochir (Wien) 1984; 72:271-81. [PMID: 6382946 DOI: 10.1007/bf01406876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An X-ray imaging system, using digital subtraction techniques, has been developed. The authors relate the results of a comparative study in 20 patients, affected by cervical occlusive vascular disease, whose arterial cervical system has been investigated both by conventional angiography and intravenous digital subtraction angiography. Indications, advantages and limitations of this new computerized apparatus are discussed.
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Abstract
The authors present a case of injury to the 4th lumbar root secondary to a gunshot wound. The lesion was not directly related to the traumatic action of the projectile, but was caused by the compressive action of disc material forced into the vertebral canal as a result of the destructive effects of a 7.65 caliber bullet.
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Abstract
The essential sequences needed for Alu repeat transcription by RNA polymerase III were mapped. Experimental evidence is presented showing that the Alu repeat promoters are organised in a bipartite structure similar to the split tRNA promoters as suggested by DNA sequence homology. Furthermore, by combining fragments from efficiently and inefficiently transcribed natural Alu repeats in several recombinant clones, it was possible to investigate the regions responsible for their differences. It is clear that, apart from the short stretches of homology with the tRNA consensus sequence, there is very little constraint in the promoter sequences. However, our studies indicate that some influence on the efficiency of transcription may be exerted by regions outside the accepted promoter components.
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Affiliation(s)
- G Paolella
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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49
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Paolella G, Ciliberto G, Traboni C, Cimino F, Salvatore F. Effect of adenosylhomocysteine and other analog thioethers on a prokaryotic tRNA (guanine-7)-methyltransferase. Arch Biochem Biophys 1982; 219:149-54. [PMID: 6758702 DOI: 10.1016/0003-9861(82)90143-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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