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Jimenez-Guardeño JM, Ortega-Prieto AM, Menendez Moreno B, Maguire TJA, Richardson A, Diaz-Hernandez JI, Diez Perez J, Zuckerman M, Mercadal Playa A, Cordero Deline C, Malim MH, Martinez-Nunez RT. Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2. PLoS Comput Biol 2022; 18:e1010330. [PMID: 35849631 PMCID: PMC9333455 DOI: 10.1371/journal.pcbi.1010330] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 07/28/2022] [Accepted: 06/27/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic has accelerated the need to identify new antiviral therapeutics at pace, including through drug repurposing. We employed a Quadratic Unbounded Binary Optimization (QUBO) model, to search for compounds similar to Remdesivir, the first antiviral against SARS-CoV-2 approved for human use, using a quantum-inspired device. We modelled Remdesivir and compounds present in the DrugBank database as graphs, established the optimal parameters in our algorithm and resolved the Maximum Weighted Independent Set problem within the conflict graph generated. We also employed a traditional Tanimoto fingerprint model. The two methods yielded different lists of lead compounds, with some overlap. While GS-6620 was the top compound predicted by both models, the QUBO model predicted BMS-986094 as second best. The Tanimoto model predicted different forms of cobalamin, also known as vitamin B12. We then determined the half maximal inhibitory concentration (IC50) values in cell culture models of SARS-CoV-2 infection and assessed cytotoxicity. We also demonstrated efficacy against several variants including SARS-CoV-2 Strain England 2 (England 02/2020/407073), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). Lastly, we employed an in vitro polymerization assay to demonstrate that these compounds directly inhibit the RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2. Together, our data reveal that our QUBO model performs accurate comparisons (BMS-986094) that differed from those predicted by Tanimoto (different forms of vitamin B12); all compounds inhibited replication of SARS-CoV-2 via direct action on RdRP, with both models being useful. While Tanimoto may be employed when performing relatively small comparisons, QUBO is also accurate and may be well suited for very complex problems where computational resources may limit the number and/or complexity of possible combinations to evaluate. Our quantum-inspired screening method can therefore be employed in future searches for novel pharmacologic inhibitors, thus providing an approach for accelerating drug deployment.
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Affiliation(s)
- Jose M. Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - Thomas J. A. Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Adam Richardson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - Javier Diez Perez
- Fujitsu Technology Solutions S.A., Pozuelo de Alarcón, Madrid, Spain
| | - Mark Zuckerman
- South London Virology Centre, King’s College Hospital, London, United Kingdom
| | | | | | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rocio Teresa Martinez-Nunez
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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2
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Akpobolokemi T, Martinez-Nunez RT, Raimi-Abraham BT. Tackling the global impact of substandard and falsified and unregistered/unlicensed anti-tuberculosis medicines. Medicine Access @ Point of Care 2022; 6:23992026211070406. [PMID: 36204519 PMCID: PMC9413333 DOI: 10.1177/23992026211070406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Substandard and falsified (SF) medicines are a global health challenge with the
World Health Organization (WHO) estimating that 1 in 10 of medicines in low- and
middle-income countries (LMICs) are SF. Antimicrobials (i.e. antimalarials,
antibiotics) are the most commonly reported SF medicines. SF medicines
contribute significantly to the global burden of infectious diseases and
antimicrobial resistance (AMR). This article discusses the challenges associated
with the global impact of SF and unregistered/unlicensed antimicrobials with a
focus on anti-TB medicines. Tuberculosis (TB) is the 13th leading cause of death
worldwide, and is currently the second leading cause of death from a single
infectious agent, ranking after COVID-19 and above HIV/AIDS. Specifically in the
case of TB, poor quality of anti-TB medicines is among the drivers of the
emergence of drug-resistant TB pathogens. In this article, we highlight and
discuss challenges including the emergence of SF associated AMR, patient
mistrust and lack of relevant data. We also present study reports to inform
meaningful change. Recommended solutions involve the adaptation of interventions
from high-income countries (HICs) to LMICS, the need for improvement in the
uptake of medication authentication tools in LMICs, increased stewardship, and
the need for global and regional multidisciplinary legal and policy cooperation,
resulting in improved legal sanctions.
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Affiliation(s)
- Tamara Akpobolokemi
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, UK
| | - Rocio Teresa Martinez-Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, Faculty of Life Sciences & Medicine, King’s College London, Guy’s Hospital, London, UK
| | - Bahijja Tolulope Raimi-Abraham
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, UK
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3
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Lista MJ, Matos PM, Maguire TJA, Poulton K, Ortiz-Zapater E, Page R, Sertkaya H, Ortega-Prieto AM, Scourfield E, O’Byrne AM, Bouton C, Dickenson RE, Ficarelli M, Jimenez-Guardeño JM, Howard M, Betancor G, Galao RP, Pickering S, Signell AW, Wilson H, Cliff P, Kia Ik MT, Patel A, MacMahon E, Cunningham E, Doores K, Agromayor M, Martin-Serrano J, Perucha E, Mischo HE, Shankar-Hari M, Batra R, Edgeworth J, Zuckerman M, Malim MH, Neil S, Martinez-Nunez RT. Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation. PLoS One 2021; 16:e0256813. [PMID: 34525109 PMCID: PMC8443028 DOI: 10.1371/journal.pone.0256813] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), RNAdvance Blood/Viral (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared One-step RT-qPCR reagents: TaqMan Fast Virus 1-Step Master Mix (FastVirus, ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna® Universal Probe One-Step RT-qPCR Kit (Luna, NEB). We used primer-probes that detect viral N (EUA CDC) and RdRP. RNA extraction methods provided similar results, with Beckman performing better with our primer-probe combinations. Luna proved most sensitive although overall the three reagents did not show significant differences. N detection was more reliable than that of RdRP, particularly in samples with low viral titres. Importantly, we demonstrated that heat treatment of nasopharyngeal swabs at 70°C for 10 or 30 min, or 90°C for 10 or 30 min (both original variant and B 1.1.7) inactivated SARS-CoV-2 employing plaque assays, and had minimal impact on the sensitivity of the qPCR in clinical samples. These findings make SARS-CoV-2 testing portable in settings that do not have CL-3 facilities. In summary, we provide several testing pipelines that can be easily implemented in other laboratories and have made all our protocols and SOPs freely available at https://osf.io/uebvj/.
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Affiliation(s)
- Maria Jose Lista
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Pedro M. Matos
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Thomas J. A. Maguire
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Inflammation Biology, School of Immunology and Microbial Sciences, Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College London, London, United Kingdom
| | - Kate Poulton
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
- Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
| | - Robert Page
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- King’s Health Partners Integrated Cancer Centre, School of Cancer and Pharmaceutical Sciences, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Helin Sertkaya
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ana M. Ortega-Prieto
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Edward Scourfield
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Aoife M. O’Byrne
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Centre for Inflammation Biology and Cancer Immunology (CIBCI), Centre for Rheumatic Diseases (CRD–EULAR Centre of Excellence), King’s College London, London, United Kingdom
| | - Clement Bouton
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ruth E. Dickenson
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Mattia Ficarelli
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jose M. Jimenez-Guardeño
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Mark Howard
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
| | - Gilberto Betancor
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rui Pedro Galao
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Suzanne Pickering
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Adrian W. Signell
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Harry Wilson
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Penelope Cliff
- Viapath pathology laboratories at St Thomas’ Hospital, London, United Kingdom
| | - Mark Tan Kia Ik
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Amita Patel
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Eithne MacMahon
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Emma Cunningham
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Katie Doores
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Monica Agromayor
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Juan Martin-Serrano
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Esperanza Perucha
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Centre for Inflammation Biology and Cancer Immunology (CIBCI), Centre for Rheumatic Diseases (CRD–EULAR Centre of Excellence), King’s College London, London, United Kingdom
| | - Hannah E. Mischo
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Manu Shankar-Hari
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rahul Batra
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Jonathan Edgeworth
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Mark Zuckerman
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- South London Specialist Virology Centre, King’s College Hospital, London, United Kingdom
| | - Michael H. Malim
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Stuart Neil
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rocio Teresa Martinez-Nunez
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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4
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Lista MJ, Matos PM, Maguire TJA, Poulton K, Ortiz-Zapater E, Page R, Sertkaya H, Ortega-Prieto AM, O’Byrne AM, Bouton C, Dickenson RE, Ficarelli M, Jimenez-Guardeño JM, Howard M, Betancor G, Galao RP, Pickering S, Signell AW, Wilson H, Cliff P, Ik MTK, Patel A, MacMahon E, Cunningham E, Doores K, Agromayor M, Martin-Serrano J, Perucha E, Mischo HE, Shankar-Hari M, Batra R, Edgeworth J, Zuckerman M, Malim MH, Neil S, Martinez-Nunez RT. Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation. medRxiv 2021:2020.04.22.20074351. [PMID: 33851184 PMCID: PMC8043481 DOI: 10.1101/2020.04.22.20074351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), RNAdvance Blood/Viral (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared One-step RT-qPCR reagents: TaqMan Fast Virus 1-Step Master Mix (FastVirus, ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna ® Universal Probe One-Step RT-qPCR Kit (Luna, NEB). We used primer-probes that detect viral N (EUA CDC) and RdRP (PHE guidelines). All RNA extraction methods provided similar results. FastVirus and Luna proved most sensitive. N detection was more reliable than that of RdRP, particularly in samples with low viral titres. Importantly, we demonstrate that treatment of nasopharyngeal swabs with 70 degrees for 10 or 30 min, or 90 degrees for 10 or 30 min (both original variant and B 1.1.7) inactivates SARS-CoV-2 employing plaque assays, and that it has minimal impact on the sensitivity of the qPCR in clinical samples. These findings make SARS-CoV-2 testing portable to settings that do not have CL-3 facilities. In summary, we provide several testing pipelines that can be easily implemented in other laboratories and have made all our protocols and SOPs freely available at https://osf.io/uebvj/ .
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Affiliation(s)
- Maria Jose Lista
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Pedro M. Matos
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Thomas J. A. Maguire
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Inflammation Biology, School of Immunology and Microbial Sciences. Asthma UK Centre in Allergic Mechanisms of Asthma. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Kate Poulton
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Elena Ortiz-Zapater
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Randall Centre for Cell & Molecular Biophysics. Guy’s Campus, King’s College London, SE1 1UL, UK
- Peter Gorer Department of Immunobiology. Guy’s Campus, King’s College London, SE1 9RT, UK
| | - Robert Page
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Inflammation Biology, School of Immunology and Microbial Sciences. Asthma UK Centre in Allergic Mechanisms of Asthma. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Helin Sertkaya
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Ana M. Ortega-Prieto
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Aoife M. O’Byrne
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Centre for Inflammation Biology and Cancer Immunology (CIBCI). Centre for Rheumatic Diseases (CRD – EULAR Centre of Excellence). Guy’s Campus, King’s College London SE1 1UL, UK
| | - Clement Bouton
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Ruth E Dickenson
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Mattia Ficarelli
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Jose M. Jimenez-Guardeño
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Mark Howard
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Peter Gorer Department of Immunobiology. Guy’s Campus, King’s College London, SE1 9RT, UK
| | - Gilberto Betancor
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Rui Pedro Galao
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Suzanne Pickering
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Adrian W Signell
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Harry Wilson
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | | | - Mark Tan Kia Ik
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Amita Patel
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Eithne MacMahon
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Emma Cunningham
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Katie Doores
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Monica Agromayor
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Juan Martin-Serrano
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Esperanza Perucha
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Centre for Inflammation Biology and Cancer Immunology (CIBCI). Centre for Rheumatic Diseases (CRD – EULAR Centre of Excellence). Guy’s Campus, King’s College London SE1 1UL, UK
| | - Hannah E. Mischo
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Manu Shankar-Hari
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Rahul Batra
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Jonathan Edgeworth
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Mark Zuckerman
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Virology. King’s College Hospital (London, UK)
| | - Michael H. Malim
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Stuart Neil
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Rocio Teresa Martinez-Nunez
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
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Sterne-Weiler T, Martinez-Nunez RT, Howard JM, Cvitovik I, Katzman S, Tariq MA, Pourmand N, Sanford JR. Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res 2013; 23:1615-23. [PMID: 23783272 PMCID: PMC3787259 DOI: 10.1101/gr.148585.112] [Citation(s) in RCA: 77] [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: 11/24/2022]
Abstract
Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here, we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of alternative mRNA isoforms. By comparing isoform ratios in cytoplasmic and polyribosomal extracts, we determined that the alternative products of ∼30% (597/1954) of mRNA processing events are differentially partitioned between these subcellular fractions. Many of the events exhibiting isoform-specific polyribosome association are highly conserved across mammalian genomes, underscoring their possible biological importance. We find that differences in polyribosome association may be explained, at least in part by the observation that alternative splicing alters the cis-regulatory landscape of mRNAs isoforms. For example, inclusion or exclusion of upstream open reading frames (uORFs) in the 5′UTR as well as Alu-elements and microRNA target sites in the 3′UTR have a strong influence on polyribosome association of alternative mRNA isoforms. Taken together, our data demonstrate for the first time the potential link between alternative splicing and translational control of the resultant mRNA isoforms.
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Affiliation(s)
- Timothy Sterne-Weiler
- Biomolecular Engineering Department, Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
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