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Amaral AJ, Andrade J, Foxall RB, Matoso P, Matos AM, Soares RS, Rocha C, Ramos CG, Tendeiro R, Serra-Caetano A, Guerra-Assunção JA, Santa-Marta M, Gonçalves J, Gama-Carvalho M, Sousa AE. miRNA profiling of human naive CD4 T cells links miR-34c-5p to cell activation and HIV replication. EMBO J 2017; 36:346-360. [PMID: 27993935 PMCID: PMC5286376 DOI: 10.15252/embj.201694335] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 03/21/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 01/16/2023] Open
Abstract
Cell activation is a vital step for T-cell memory/effector differentiation as well as for productive HIV infection. To identify novel regulators of this process, we used next-generation sequencing to profile changes in microRNA expression occurring in purified human naive CD4 T cells in response to TCR stimulation and/or HIV infection. Our results demonstrate, for the first time, the transcriptional up-regulation of miR-34c-5p in response to TCR stimulation in naive CD4 T cells. The induction of this miR was further consistently found to be reduced by both HIV-1 and HIV-2 infections. Overexpression of miR-34c-5p led to changes in the expression of several genes involved in TCR signaling and cell activation, confirming its role as a novel regulator of naive CD4 T-cell activation. We additionally show that miR-34c-5p promotes HIV-1 replication, suggesting that its down-regulation during HIV infection may be part of an anti-viral host response.
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Affiliation(s)
- Andreia J Amaral
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Jorge Andrade
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Russell B Foxall
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Paula Matoso
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana M Matos
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Rui S Soares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Cheila Rocha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Christian G Ramos
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Rita Tendeiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Serra-Caetano
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - José A Guerra-Assunção
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, UK
| | - Mariana Santa-Marta
- Research Institute for Medicines (iMed ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - João Gonçalves
- Research Institute for Medicines (iMed ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Gama-Carvalho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Ana E Sousa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Fine PEM, Parkhill J, Clark TG, Glynn JR. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 2015; 4. [PMID: 25732036 PMCID: PMC4384740 DOI: 10.7554/elife.05166] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/22/2015] [Indexed: 11/13/2022] Open
Abstract
To improve understanding of the factors influencing tuberculosis transmission and the
role of pathogen variation, we sequenced all available specimens from patients
diagnosed over 15 years in a whole district in Malawi. Mycobacterium
tuberculosis lineages were assigned and transmission networks
constructed, allowing ≤10 single nucleotide polymorphisms (SNPs) difference.
We defined disease as due to recent infection if the network-determined source was
within 5 years, and assessed transmissibility from forward transmissions resulting in
disease. High-quality sequences were available for 1687 disease episodes (72% of all
culture-positive episodes): 66% of patients linked to at least one other patient. The
between-patient mutation rate was 0.26 SNPs/year (95% CI 0.21–0.31). We showed
striking differences by lineage in the proportion of disease due to recent
transmission and in transmissibility (highest for lineage-2 and lowest for lineage-1)
that were not confounded by immigration, HIV status or drug resistance. Transmissions
resulting in disease decreased markedly over time. DOI:http://dx.doi.org/10.7554/eLife.05166.001 Tuberculosis is an important public health threat around the globe and is
particularly common in developing countries. It is difficult to control the spread of
the disease because the bacteria that cause it can spread when an infected individual
coughs or sneezes. It may take years for an infected individual to develop symptoms
of tuberculosis so it can be hard to trace the source of an outbreak, and people
infected with HIV are particularly susceptible to the disease. The bacterium that causes the majority of cases of tuberculosis is called
Mycobacterium tuberculosis. There are several different varieties
or ‘lineages’ of M. tuberculosis, and it is thought
that they may vary in their ability to spread and cause disease. However, the results
of previous studies have been inconsistent and there also seems to be a lot of
variation between strains within the same lineage. In this study, Guerra-Assunção et al. used an approach called whole
genome sequencing alongside more traditional methods to study the spread of
tuberculosis in Malawi. They sequenced the genomes of every available sample of
M. tuberculosis collected from patients in the Karonga district
of Malawi over a 15-year period. This produced high-quality DNA sequence data about
the bacteria responsible for almost 1700 cases of disease. Using this massive amount of data, Guerra-Assunção et al. constructed
networks that showed how the bacteria had spread in the community. This revealed that
there were differences between the ability of the various M.
tuberculosis lineages to cause disease and to spread in communities. For
example, lineage 1 was less likely than the other lineages to cause disease soon
after infecting an individual and was less able to spread. The data also show that the proportion of cases of disease due to recent infection
declined substantially during the 15-year period. This indicates that the
tuberculosis and HIV control programmes in the area have been successful. Guerra-Assunção et al.'s findings show that it is possible to
understand how tuberculosis is transmitted on a large scale. The next challenge is to
understand why the lineages differ in their ability to cause disease and spread
between individuals. DOI:http://dx.doi.org/10.7554/eLife.05166.002
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Affiliation(s)
- J A Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - T Mzembe
- Karonga Prevention Study, Malawi, Malawi
| | - K Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - F Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - L Banda
- Karonga Prevention Study, Malawi, Malawi
| | - A Chiwaya
- Karonga Prevention Study, Malawi, Malawi
| | - R P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P E M Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J Parkhill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - T G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird G, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper JD, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley C, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SMJ, Enright A, Geisler R, Plasterk RHA, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Volhard CN, Hubbard TJP, Crollius HR, Rogers J, Stemple DL. Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013. [DOI: 10.1038/nature12813] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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