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Cazzoli R, Romeo F, Pallavicini I, Peri S, Romanenghi M, Pérez-Valencia JA, Hagag E, Ferrucci F, Elgendy M, Vittorio O, Pece S, Foiani M, Westermarck J, Minucci S. Endogenous PP2A inhibitor CIP2A degradation by chaperone-mediated autophagy contributes to the antitumor effect of mitochondrial complex I inhibition. Cell Rep 2023; 42:112616. [PMID: 37289585 DOI: 10.1016/j.celrep.2023.112616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 04/15/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Combined inhibition of oxidative phosphorylation (OXPHOS) and glycolysis has been shown to activate a PP2A-dependent signaling pathway, leading to tumor cell death. Here, we analyze highly selective mitochondrial complex I or III inhibitors in vitro and in vivo to elucidate the molecular mechanisms leading to cell death following OXPHOS inhibition. We show that IACS-010759 treatment (complex I inhibitor) induces a reactive oxygen species (ROS)-dependent dissociation of CIP2A from PP2A, leading to its destabilization and degradation through chaperone-mediated autophagy. Mitochondrial complex III inhibition has analogous effects. We establish that activation of the PP2A holoenzyme containing B56δ regulatory subunit selectively mediates tumor cell death, while the arrest in proliferation that is observed upon IACS-010759 treatment does not depend on the PP2A-B56δ complex. These studies provide a molecular characterization of the events subsequent to the alteration of critical bioenergetic pathways and help to refine clinical studies aimed to exploit metabolic vulnerabilities of tumor cells.
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Affiliation(s)
- Riccardo Cazzoli
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy
| | - Francesco Romeo
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Isabella Pallavicini
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy
| | - Sebastiano Peri
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy
| | - Mauro Romanenghi
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy
| | - Juan Alberto Pérez-Valencia
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Mildred-Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC) University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Eman Hagag
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Filippo Ferrucci
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Mildred-Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC) University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Mohamed Elgendy
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Mildred-Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC) University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Orazio Vittorio
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Randwick, NSW, Australia; School of Biomedical Sciences, UNSW Sydney, Randwick, NSW, Australia
| | - Salvatore Pece
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Marco Foiani
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Institute of Biomedicine, University of Turku, Turku, Finland
| | - Saverio Minucci
- Department of Experimental Oncology, IEO IRCCS, Istituto Europeo di Oncologia, Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy.
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Attili S, Sharma R, Peri S, Singaraju M, Dadireddy P, Kistampally P. 411P Cost-effective analysis of the various cancer screening methods in the community: Pooled analysis of camps of 5 years from 2017-to 2022. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.442] [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: 12/05/2022] Open
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3
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Allegri P, Rosa R, Masala A, Rissotto R, Rissotto F, Crivelli MG, Peri S. Clinical effectiveness of a new oral curcumin formulation in acute non-infectious uveitic macular edema: a 12-month observational study. Eur Rev Med Pharmacol Sci 2022; 26:46-53. [PMID: 35049018 DOI: 10.26355/eurrev_202201_27746] [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: 06/14/2023]
Abstract
OBJECTIVE Oral supplementation with curcumin demonstrated a beneficial effect on some ocular diseases, including uveitis and macular edema. This study aimed to evaluate the effectiveness and safety of a curcumin formulation with the hydrophilic carrier (CHC; Diabec®, Alfa Intes, Italy) as an adjuvant to standard steroid treatment in adults suffering from acute non-infectious uveitic macular edema (NIUME). PATIENTS AND METHODS This was a monocenter prospective observational study carried out between January 2019 and May 2020 on consecutive patients with a new diagnosis of NIUME. Patients were treated with standard therapy or with a CHC add-on to standard treatment. The observation period for each patient was 12 months. The Best Corrected Visual Acuity (BCVA) and the Central Macular Thickness (CMT) were the primary outcomes; Foveal Avascular Zone (FAZ) and intraocular pressure (IOP) were also assessed, along with safety data. RESULTS A total of 43 eyes of 26 patients were analyzed. CHC-treated eyes showed an improvement in mean BCVA from baseline (0.34 logMar) to T6 (0.20 logMar) and T12 (0.19 logMar; p≤0.05 and p≤0.01, respectively); CMT decreased from a mean of 320 μm (T0) to 278 μm (T6; p≤0.05) and 272 μm (T12; p≤0.01). A significant improvement of mean BCVA in the CHC group at T6 and T12 was reported compared to the control group (p≤0.01). FAZ and IOP showed no statistically significant variations in both groups. No adverse events were recorded. CONCLUSIONS CHC as an adjuvant treatment improved the anatomical and functional outcomes, without significant side effects in eyes affected by the recent onset of NIUME, compared to the sole standard therapy.
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Affiliation(s)
- P Allegri
- Inflammatory Eye Diseases Referral Center, Rapallo Hospital, Genoa, Italy.
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4
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Vaddeboina N, Attili S, Peri S, Sunkavalli C, Dilip P. Feasibility and comparison study of augmented breast self examination vs. conventional breast self examination rural Indian women for early detection- results of POC study. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)30795-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Bagnolini G, Milano D, Manerba M, Schipani F, Ortega JA, Gioia D, Falchi F, Balboni A, Farabegoli F, De Franco F, Robertson J, Pellicciari R, Pallavicini I, Peri S, Minucci S, Girotto S, Di Stefano G, Roberti M, Cavalli A. Synthetic Lethality in Pancreatic Cancer: Discovery of a New RAD51-BRCA2 Small Molecule Disruptor That Inhibits Homologous Recombination and Synergizes with Olaparib. J Med Chem 2020; 63:2588-2619. [PMID: 32037829 PMCID: PMC7997579 DOI: 10.1021/acs.jmedchem.9b01526] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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Synthetic lethality
is an innovative framework for discovering
novel anticancer drug candidates. One example is the use of PARP inhibitors
(PARPi) in oncology patients with BRCA mutations.
Here, we exploit a new paradigm based on the possibility of triggering
synthetic lethality using only small organic molecules (dubbed “fully
small-molecule-induced synthetic lethality”). We exploited
this paradigm to target pancreatic cancer, one of the major unmet
needs in oncology. We discovered a dihydroquinolone pyrazoline-based
molecule (35d) that disrupts the RAD51-BRCA2 protein–protein
interaction, thus mimicking the effect of BRCA2 mutation. 35d inhibits the homologous recombination in a human pancreatic
adenocarcinoma cell line. In addition, it synergizes with olaparib
(a PARPi) to trigger synthetic lethality. This strategy aims to widen
the use of PARPi in BRCA-competent and olaparib-resistant
cancers, making fully small-molecule-induced synthetic lethality an
innovative approach toward unmet oncological needs.
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Affiliation(s)
- Greta Bagnolini
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Domenico Milano
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marcella Manerba
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jose Antonio Ortega
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Dario Gioia
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Federico Falchi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Fulvia Farabegoli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Francesca De Franco
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Corciano, Perugia, Italy
| | - Janet Robertson
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Corciano, Perugia, Italy
| | - Roberto Pellicciari
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Corciano, Perugia, Italy
| | - Isabella Pallavicini
- Department of Experimental Oncology at the IEO, European Institute of Oncology IRCCS, IFOM-IEO Campus, Via Adamello 16, 20100 Milan, Italy
| | - Sebastiano Peri
- Department of Experimental Oncology at the IEO, European Institute of Oncology IRCCS, IFOM-IEO Campus, Via Adamello 16, 20100 Milan, Italy
| | - Saverio Minucci
- Department of Biosciences, University of Milan, Via Celoria 26, 20100 Milan, Italy.,Department of Experimental Oncology at the IEO, European Institute of Oncology IRCCS, IFOM-IEO Campus, Via Adamello 16, 20100 Milan, Italy
| | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Giuseppina Di Stefano
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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6
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Peri S, Biagioni A, Cianchi F, Skalamera I, Staderini F, Schiavone N, Papucci L, Magnelli L. Chemotherapy resistance-associated epithelial to endothelial transition in gastric cancer. J BIOL REG HOMEOS AG 2018; 32:30. [PMID: 30761866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- S Peri
- Department Of Biotechnology, Chemistry And Pharmacy, University of Siena - Department of Experimental and Clinical Biomedical Sciences "Mario Serio", university of Florence
| | - A Biagioni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence
| | - F Cianchi
- Department of Surgery and Translational Medicine (DCMT), University of Florence
| | - I Skalamera
- Department of Surgery and Translational Medicine (DCMT), University of Florence
| | - F Staderini
- Department of Surgery and Translational Medicine (DCMT), University of Florence
| | - N Schiavone
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence
| | - L Papucci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence
| | - L Magnelli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence
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Boyd J, Luo B, Peri S, Wirchansky B, Hughes L, Forsythe C, Wu H, Morgan M. Novel genetic alterations in serous borderline tumors of the ovary revealed by whole exome sequencing. Gynecol Oncol 2013. [DOI: 10.1016/j.ygyno.2013.04.363] [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: 10/26/2022]
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8
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Nurchis C, Chiarello T, Bianchi C, Ferelli E, Morotti F, Gamba S, Riceputi L, Brega A, Trovato F, Zuccarelli S, Borgna S, Peri S. DGI-012 Antibiotics Monitoring: The Experience of Liguria Region, Italy. Eur J Hosp Pharm 2013. [DOI: 10.1136/ejhpharm-2013-000276.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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9
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Bolier AR, Peri S, Oude Elferink RPJ, Beuers U. The challenge of cholestatic pruritus. Acta Gastroenterol Belg 2012; 75:399-404. [PMID: 23402082] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Pruritus can be the dominant symptom of cholestatic liver disease but is difficult to treat since unraveling its pathophysiology is a great challenge. Serum autotaxin activity correlates with pruritus intensity, but its causal relationship, expression pattern and exact mode of action during cholestasis remain to be established. The anion exchange resin cholestyramine, the PXR agonist rifampicin, the opioid antagonist naltrexone and the serotonine reuptake inhibitor sertraline are recommended by evidence-based guidelines as stepwise therapeutic approaches to treat itch in cholestasis. Rifampicin, the most effective antipruritic agent in cholestatic itch, has been shown to reduce autotaxin transcription in vitro. Experimental approaches include UVB phototherapy, extracorporeal albumin dialysis, nasobiliary drainage and in desperate cases even liver transplantation. Relevant clinical observations along with the different metabolic, neurologic and endocrine targets of available therapies in cholestatic pruritus are reviewed here.
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Affiliation(s)
- A R Bolier
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, The Netherlands
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Ureña R, Peri S, del Ramo J, Torreblanca A. Metal and metallothionein content in tissues from wild and farmed Anguilla anguilla at commercial size. Environ Int 2007; 33:532-9. [PMID: 17157913 DOI: 10.1016/j.envint.2006.10.007] [Citation(s) in RCA: 11] [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] [Subscribe] [Scholar Register] [Received: 02/26/2006] [Revised: 07/03/2006] [Accepted: 10/23/2006] [Indexed: 05/12/2023]
Abstract
Metallothionein and metal content (Cd, Zn, Hg, Cu, Fe, Pb and Mn) were determined in various organs of commercially available eel (Anguilla anguilla) of similar size obtained from a local farm and from The Albufera Lake in Valencia (Spain). Farmed fish showed statistically significant higher Cd concentrations in liver and kidney whereas wild individuals had higher levels of Pb in blood and Zn in kidney. Significant positive correlations were found between metallothionein and Cd in kidney of farmed eel and between metallothionein and Cu in liver of wild ones. No statistically significant differences were found between the two populations in the concentration of any of the metals analyzed in muscle and in all instances these levels were lower than the limits established by the Spanish legislation for fish destined for human consumption.
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Affiliation(s)
- R Ureña
- Department of Functional Biology, University of Valencia, C/ Dr. Moliner, 50, 46100 Burjassot (Valencia), Spain
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11
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Freddi O, Pendino A, Leone M, Peri S, Fernandez J, Raggi E. Epidemilogy study of 349 burn patients in the emergency public hospital of Rosario city. Burns 2007. [DOI: 10.1016/j.burns.2006.10.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Willeke F, Assad A, Findeisen P, Schromm E, Grobholz R, von Gerstenbergk B, Mantovani A, Peri S, Friess HH, Post S, von Knebel Doeberitz M, Schwarzbach MHM. Overexpression of a member of the pentraxin family (PTX3) in human soft tissue liposarcoma. Eur J Cancer 2006; 42:2639-46. [PMID: 16959485 DOI: 10.1016/j.ejca.2006.05.035] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 05/05/2006] [Accepted: 05/10/2006] [Indexed: 11/21/2022]
Abstract
A unique feature of human soft tissue liposarcoma is a stable (12;16)(q13;p11) translocation observed mainly in myxoid and roundcell liposarcomas. This translocation results in FUS/CHOP fusion transcripts with a corresponding oncogenic protein. We hypothesised that genes downstream of FUS/CHOP might serve as attractive candidates for novel tumour associated antigens. Among a panel of analysed genes, only pentraxin related gene (PTX3) demonstrated high expression in liposarcomas as compared to normal tissues. The analysis of RNA and protein expression demonstrated concordant results. However, the level of RNA and protein overexpression did not correlate in all cases. Finally, PTX3 expression was not related to presence of a FUS/CHOP fusion transcript within the liposarcoma tissues. PTX3 has been associated with adipocyte differentiation and now, additionally, is characterised by a markedly increased expression in human soft tissue liposarcoma. This finding mandates further research efforts to clarify the exact role of PTX3 in liposarcoma oncogenesis.
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Affiliation(s)
- F Willeke
- Department of Surgery, Mannheim University Clinic, University of Heidelberg, Theodor Kutzer Ufer 1-3, 68135 Mannheim, Germany.
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Ranganadha Rao PV, Peri S, Porichha D, Nehemaiah E. A review of trends in new case-detection in Subarnapur district of Orissa. Indian J Lepr 2006; 78:153-65. [PMID: 16927850] [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: 05/11/2023]
Abstract
Trends in new case-detection are analysed by reviewing the demographic and leprosy epidemiological data and current indicators in Subarnapur district, Orissa State and India. Population-specific new case-detection rates were calculated for analysis. The trend of skin-smear positive cases over a period of 10 years was reviewed in respect of smear positive cases of 1991. During the years 2002 to 2004, a sudden fall was noticed in the new cases detected in both India and Orissa state, whereas the decline in Subarnapur district was more gradual. The fall in the female-specific new case-detection rates is found to be rapid from 11 to 2.5 over the last three years. This also indirectly indicated the health-seeking behaviour of women in accessing health services and hence required a changed strategy. A similar rapid decline was observed in child-specific new case-detection rates. On analysiS, the decline of highly bacilliferous cases from 1991 to 2001 was found to be statistically significant. The analysis also brought out the fact that cases with bacterial index of 1+, 2+ and 3+, though small in numbers, were detected during the last three years indicating continued presence of cases with low bacterial density in the community. The review indicates a definite decline in the occurrence of new cases in all groups. Caution needs to be exercised about continued presence of cases with low bacterial index though in small numbers. The rapid decrease of cases in all groups during the years 2004 and 2005 warrants meticulous surveillance. The surveillance activities could include monitoring of population-specific new case-detection rates and skin-smear positive cases at district and state levels in order to advise on leprosy eradication programme strategies.
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Affiliation(s)
- P V Ranganadha Rao
- LEPRA Society, PB No 1518, Krishnapuri Colony, West Maredpally, Secunderabad.
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14
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Peri S, Ibarrola N, Blagoev B, Mann M, Pandey A. Corrigendum: Author correction. Trends Genet 2002. [DOI: 10.1016/s0168-9525(02)02662-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
More than two decades ago Marilyn Kozak proposed the scanning model of translation initiation, whereby translation is initiated at the first AUG codon that is in a particular context. In this article, we re-examine the context of initiator codons using a large dataset of curated human transcripts. We find that more than 40% of transcripts contain AUG codons upstream of the actual start codon and that most authentic AUGs contain three or more mismatches from the consensus sequence, CCACCaugG. Also, in a large fraction of transcripts, the sequences surrounding the initiator codon deviate more from the consensus than those surrounding upstream AUGs, indicating that translation initiation from downstream AUGs is more common than generally believed.
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Affiliation(s)
- S Peri
- Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, Denmark
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16
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Abstract
General Protein/Mass Analysis for Windows (GPMAW) is a valuable piece of software for any molecular biologist, biochemist or mass spectrometrist wishing to analyze protein or peptide sequences. All steps from the acquisition of protein sequence from a built-in web interface, to proteolytic digests, theoretical peptide fragmentation, detailed annotation of sequences and secondary structure prediction, can be performed rapidly and intuitively without first having to spend days reading manuals.
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Affiliation(s)
- S Peri
- Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, M, Odense, Denmark
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17
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Affiliation(s)
- S Peri
- Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, Denmark
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18
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Gnanasekaran TV, Peri S, Arockiasamy A, Krishnaswamy S. Profiles from structure based sequence alignment of porins can identify beta stranded integral membrane proteins. Bioinformatics 2000; 16:839-42. [PMID: 11108707 DOI: 10.1093/bioinformatics/16.9.839] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Supplementary information: http://gene.tn.nic.in/sk/profiles/
Contact: krishna@mrna.tn.nic.in
To whom correspondence should be addressed.
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Affiliation(s)
- T V Gnanasekaran
- Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai, India
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Affiliation(s)
- A W Eberhardt
- Department of Mechanical Engineering, University of Alabama at Birmingham 35294-4461, USA
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20
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Dhar KM, Sastry VV, Peri S, Goud ML. Artificial feeding practices in rural community--a cross sectional study in Warangal area (Andhra Pradesh). Indian J Public Health 1994; 38:27. [PMID: 7883310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- K M Dhar
- Community Medicine Dept., Kakatiya Medical College, Warangal, Andhra Pradesh
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21
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Sroka H, Dressler R, Peri S, Loven D. Neurologic and neuropsychological support for patients with brain tumors. Eur J Cancer 1993. [DOI: 10.1016/0959-8049(93)91695-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Chandra KS, Peri S, Moorthy L, Rao B. Diminished translucency, a common roentgenographic feature of tropical pulmonary eosinophilia. Chest 1989; 95:940. [PMID: 2924640 DOI: 10.1378/chest.95.4.940a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Rao MN, Kumar CS, Peri S. Goitre in tribal areas of Andhra Pradesh. Indian Pediatr 1987; 24:651-3. [PMID: 3443507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Singh HD, Peri S. Peak expiratory flow rate in South Indian adults. Indian J Physiol Pharmacol 1979; 23:315-20. [PMID: 528035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peak Expiratory Flow Rate (PEFR) was measured with a Wright Peak Flow Meter in 851 healthy men and women of two categories; Group I--students and staff of the Medical College constituting the middle income group, and Group II--healthy individuals from the poorer class with an income of less than Rs.200/-per month, forming the lower income group. In both categories women had much lower values than men, and in both sexes the values in the subjects of the poor income group was significantly lower. The PEFR was found to correlate best with height in subjects below 30 years, and with age in older subjects. The mean values, standard deviations and regression equations are given for the different groups. Present values are also compared with some western and Indian data.
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Singh HD, Peri S. Peak expiratory flow rates in South Indian children and adolescents. Indian Pediatr 1978; 15:473-8. [PMID: 721263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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