Publications
2023
Lista María José, Jousset Anne-Caroline, Cheng Mingpan, Saint-André Violaine, Perrot Elouan, Rodrigues Melissa, Primo Carmelo Di, Gadelle Danielle, Toccafondi Elenia, Segeral Emmanuel, Berlioz-Torrent Clarisse, Emiliani Stéphane, Mergny Jean-Louis, Lavigne Marc
DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence Article de journal
Dans: Retrovirology, vol. 20, no. 1, p. 10, 2023, ISSN: 1742-4690.
Résumé | Liens | BibTeX | Étiquettes: MARQUET, NEGRONI, PAILLART, Unité ARN
@article{pmid37254203,
title = {DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence},
author = {María José Lista and Anne-Caroline Jousset and Mingpan Cheng and Violaine Saint-André and Elouan Perrot and Melissa Rodrigues and Carmelo Di Primo and Danielle Gadelle and Elenia Toccafondi and Emmanuel Segeral and Clarisse Berlioz-Torrent and Stéphane Emiliani and Jean-Louis Mergny and Marc Lavigne},
doi = {10.1186/s12977-023-00627-6},
issn = {1742-4690},
year = {2023},
date = {2023-05-01},
urldate = {2023-05-01},
journal = {Retrovirology},
volume = {20},
number = {1},
pages = {10},
abstract = {BACKGROUND: Once integrated in the genome of infected cells, HIV-1 provirus is transcribed by the cellular transcription machinery. This process is regulated by both viral and cellular factors, which are necessary for an efficient viral replication as well as for the setting up of viral latency, leading to a repressed transcription of the integrated provirus.nnRESULTS: In this study, we examined the role of two parameters in HIV-1 LTR promoter activity. We identified DNA topoisomerase1 (TOP1) to be a potent repressor of this promoter and linked this repression to its catalytic domain. Additionally, we confirmed the folding of a Guanine quadruplex (G4) structure in the HIV-1 promoter and its repressive effect. We demonstrated a direct interaction between TOP1 and this G4 structure, providing evidence of a functional relationship between the two repressive elements. Mutations abolishing G4 folding affected TOP1/G4 interaction and hindered G4-dependent inhibition of TOP1 catalytic activity in vitro. As a result, HIV-1 promoter activity was reactivated in a native chromatin environment. Lastly, we noticed an enrichment of predicted G4 sequences in the promoter of TOP1-repressed cellular genes.nnCONCLUSIONS: Our results demonstrate the formation of a TOP1/G4 complex on the HIV-1 LTR promoter and its repressive effect on the promoter activity. They reveal the existence of a new mechanism of TOP1/G4-dependent transcriptional repression conserved between viral and human genes. This mechanism contrasts with the known property of TOP1 as global transcriptional activator and offers new perspectives for anti-cancer and anti-viral strategies.},
keywords = {MARQUET, NEGRONI, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Toccafondi Elenia, Kanja Marine, Winter Flore, Lener Daniela, Negroni Matteo
A snapshot on HIV-1 evolution through the identification of phylogenetic-specific properties of HIV-1 integrases M/O Article de journal
Dans: PLoS Pathog, vol. 19, no. 3, p. e1011207, 2023, ISSN: 1553-7374.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{pmid36996029,
title = {A snapshot on HIV-1 evolution through the identification of phylogenetic-specific properties of HIV-1 integrases M/O},
author = {Elenia Toccafondi and Marine Kanja and Flore Winter and Daniela Lener and Matteo Negroni},
doi = {10.1371/journal.ppat.1011207},
issn = {1553-7374},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {PLoS Pathog},
volume = {19},
number = {3},
pages = {e1011207},
abstract = {Transmissions of simian viruses to humans has originated the different groups of HIV-1. We recently identified a functional motif (CLA), in the C-terminal domain of the integrase, essential for integration in HIV-1 group M. Here, we found that the motif is instead dispensable in group O isolates, because of the presence, in the N-terminal domain of HIV-1 O of a specific sequence, Q7G27P41H44, that we define as the NOG motif. Alterations of reverse transcription and of 3' processing observed by mutating the CLA motif of IN M are fully rescued to wt levels by inserting the sequence of the NOG motif in the N-ter of the protein. These results indicate that the two motifs (CLA and NOG) functionally complement each other and a working model accounting for these observations is proposed. The establishment of these two alternative motifs seems to be due to the different phylogenetic origin and history of these two groups. Indeed, the NOG motif is already present in the ancestor of group O (SIVgor) while it is absent from SIVcpzPtt, the ancestor of group M. The CLA motif, instead, seems to have emerged after SIVcpzPtt has been transferred to humans, since no conservation is found at the same positions in these simian viruses. These results show the existence of two-group specific motifs in HIV-1 M and O integrases. In each group, only one of the motifs is functional, potentially leading the other motif to diverge from its original function and, in an evolutionary perspective, assist other functions of the protein, further increasing HIV genetic diversity.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2021
Omar R El, Julien E, Biasch K, Guffroy B, Lioure B, Vallat L, Gross I, Domon-Dell C, Lanza F, Gachet C, Negroni M, Freund J N, Tavian M
CDX2 regulates ACE expression in blood development and leukemia cells Article de journal
Dans: Blood Adv, vol. 5, no. 7, p. 2012-2016, 2021, ISBN: 33843985, (2473-9537 (Electronic) 2473-9529 (Linking) Journal Article).
Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {CDX2 regulates ACE expression in blood development and leukemia cells},
author = {R El Omar and E Julien and K Biasch and B Guffroy and B Lioure and L Vallat and I Gross and C Domon-Dell and F Lanza and C Gachet and M Negroni and J N Freund and M Tavian},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33843985},
doi = {10.1182/bloodadvances.2020003563},
isbn = {33843985},
year = {2021},
date = {2021-01-01},
journal = {Blood Adv},
volume = {5},
number = {7},
pages = {2012-2016},
note = {2473-9537 (Electronic)
2473-9529 (Linking)
Journal Article},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Toccafondi E, Lener D, Negroni M
HIV-1 Capsid Core: A Bullet to the Heart of the Target Cell Article de journal
Dans: Front Microbiol, vol. 12, p. 652486, 2021, ISBN: 33868211, (1664-302X (Print) 1664-302X (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {HIV-1 Capsid Core: A Bullet to the Heart of the Target Cell},
author = {E Toccafondi and D Lener and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33868211},
doi = {10.3389/fmicb.2021.652486},
isbn = {33868211},
year = {2021},
date = {2021-01-01},
journal = {Front Microbiol},
volume = {12},
pages = {652486},
abstract = {The first step of the intracellular phase of retroviral infection is the release of the viral capsid core in the cytoplasm. This structure contains the viral genetic material that will be reverse transcribed and integrated into the genome of infected cells. Up to recent times, the role of the capsid core was considered essentially to protect this genetic material during the earlier phases of this process. However, increasing evidence demonstrates that the permanence inside the cell of the capsid as an intact, or almost intact, structure is longer than thought. This suggests its involvement in more aspects of the infectious cycle than previously foreseen, particularly in the steps of viral genomic material translocation into the nucleus and in the phases preceding integration. During the trip across the infected cell, many host factors are brought to interact with the capsid, some possessing antiviral properties, others, serving as viral cofactors. All these interactions rely on the properties of the unique component of the capsid core, the capsid protein CA. Likely, the drawback of ensuring these multiple functions is the extreme genetic fragility that has been shown to characterize this protein. Here, we recapitulate the busy agenda of an HIV-1 capsid in the infectious process, in particular in the light of the most recent findings.},
note = {1664-302X (Print)
1664-302X (Linking)
Journal Article
Review},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rocchi C., Louvat C., Miele A., Batisse J., Guillon C., Ballut L., Lener D., Negroni M., Ruff M., Gouet P., Fiorini F.
The HIV-1 Integrase C-Terminal domain induces TAR RNA structural changes promoting Tat binding Article de journal
Dans: 2021.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{nokey,
title = {The HIV-1 Integrase C-Terminal domain induces TAR RNA structural changes promoting Tat binding},
author = {C. Rocchi and C. Louvat and A. Miele and J. Batisse and C. Guillon and L. Ballut and D. Lener and M. Negroni and M. Ruff and P. Gouet and F. Fiorini},
url = {https://www.biorxiv.org/content/10.1101/2021.10.21.465253v1.full.pdf+html},
doi = {10.1101/2021.10.21.465253},
year = {2021},
date = {2021-01-01},
abstract = {Recent evidence indicated that HIV-1 Integrase (IN) binds genomic viral RNA (gRNA) playing a critical role in viral particle morphogenesis and gRNA stability in host cells. Combining biophysical and biochemical approaches we show that the C-terminal flexible 18-residues tail of IN acts as a sensor of the peculiar apical structure of trans-activation
response element RNA (TAR), directly interacting with its hexaloop. We highlighted how the whole IN C-terminal domain, once bound to TAR, can change its structure assisting the binding of Tat, the HIV trans-activator protein, which finally displaces IN from TAR. Our results are consistent with the emerging role of IN in early stage of proviral transcription and suggest new steps of HIV-1 life cycle that can be considered as therapeutic targets.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
response element RNA (TAR), directly interacting with its hexaloop. We highlighted how the whole IN C-terminal domain, once bound to TAR, can change its structure assisting the binding of Tat, the HIV trans-activator protein, which finally displaces IN from TAR. Our results are consistent with the emerging role of IN in early stage of proviral transcription and suggest new steps of HIV-1 life cycle that can be considered as therapeutic targets.
2020
Duvergé A, Negroni M
Pseudotyping Lentiviral Vectors: When the Clothes Make the Virus Article de journal
Dans: Viruses, vol. 12, no. 11, p. 1311, 2020.
Résumé | Liens | BibTeX | Étiquettes: envelope proteins, gene therapy, lentiviral vectors, NEGRONI, pseudotyping, Unité ARN
@article{Duvergé2020,
title = {Pseudotyping Lentiviral Vectors: When the Clothes Make the Virus },
author = {A Duvergé and M Negroni},
url = {https://doi.org/10.3390/v12111311},
doi = {10.3390/v12111311},
year = {2020},
date = {2020-11-11},
journal = {Viruses},
volume = {12},
number = {11},
pages = {1311},
abstract = {Delivering transgenes to human cells through transduction with viral vectors constitutes one of the most encouraging approaches in gene therapy. Lentivirus-derived vectors are among the most promising vectors for these approaches. When the genetic modification of the cell must be performed in vivo, efficient specific transduction of the cell targetsof the therapy in the absence of off-targeting constitutes the Holy Grail of gene therapy. For viral therapy, this is largely determined by the characteristics of the surface proteins carried by the vector. In this regard, an important property of lentiviral vectors is the possibility of being pseudotyped by envelopes of other viruses, widening the panel of proteins with which they can bearmed. Here, we discuss how this is achieved at the molecular level and what the properties and the potentialities of the different envelope proteins that can be used for pseudotyping these vectorsare.},
keywords = {envelope proteins, gene therapy, lentiviral vectors, NEGRONI, pseudotyping, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Kanja M, Cappy P, Levy N, Oladosu O, Schmidt S, Rossolillo P, Winter F, Gasser R, Moog C, Ruff M, Negroni M, Lener D
NKNK: a New Essential Motif in the C-Terminal Domain of HIV-1 Group M Integrases Article de journal
Dans: J Virol, vol. 94, no. 20, p. e01035-01020, 2020, ISBN: 32727879.
Résumé | Liens | BibTeX | Étiquettes: evolution human immunodeficiency virus integrase phylogenetic groups, NEGRONI, Unité ARN
@article{,
title = {NKNK: a New Essential Motif in the C-Terminal Domain of HIV-1 Group M Integrases},
author = {M Kanja and P Cappy and N Levy and O Oladosu and S Schmidt and P Rossolillo and F Winter and R Gasser and C Moog and M Ruff and M Negroni and D Lener},
url = {https://pubmed.ncbi.nlm.nih.gov/32727879/},
doi = {10.1128/JVI.01035-20},
isbn = {32727879},
year = {2020},
date = {2020-01-01},
journal = {J Virol},
volume = {94},
number = {20},
pages = {e01035-01020},
abstract = {Using coevolution network interference based on comparison of two phylogenetically distantly related isolates, one from the main group M and the other from the minor group O of HIV-1, we identify, in the C-terminal domain (CTD) of integrase, a new functional motif constituted by four noncontiguous amino acids (N222K240N254K273). Mutating the lysines abolishes integration through decreased 3' processing and inefficient nuclear import of reverse-transcribed genomes. Solution of the crystal structures of wild-type (wt) and mutated CTDs shows that the motif generates a positive surface potential that is important for integration. The number of charges in the motif appears more crucial than their position within the motif. Indeed, the positions of the K's could be permutated or additional K's could be inserted in the motif, generally without affecting integration per se Despite this potential genetic flexibility, the NKNK arrangement is strictly conserved in natural sequences, indicative of an effective purifying selection exerted at steps other than integration. Accordingly, reverse transcription was reduced even in the mutants that retained wt integration levels, indicating that specifically the wt sequence is optimal for carrying out the multiple functions that integrase exerts. We propose that the existence of several amino acid arrangements within the motif, with comparable efficiencies of integration per se, might have constituted an asset for the acquisition of additional functions during viral evolution.IMPORTANCE Intensive studies of HIV-1 have revealed its extraordinary ability to adapt to environmental and immunological challenges, an ability that is also at the basis of antiviral treatment escape. Here, by deconvoluting the different roles of the viral integrase in the various steps of the infectious cycle, we report how the existence of alternative equally efficient structural arrangements for carrying out one function opens up the possibility of adapting to the optimization of further functionalities exerted by the same protein. Such a property provides an asset to increase the efficiency of the infectious process. On the other hand, though, the identification of this new motif provides a potential target for interfering simultaneously with multiple functions of the protein.},
keywords = {evolution human immunodeficiency virus integrase phylogenetic groups, NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2018
Smyth R P, Negroni M, Lever A M, Mak J, Kenyon J C
RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity Article de journal
Dans: Front Immunol, vol. 9, p. 2097, 2018, ISBN: 30283444.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, RNA structure immune evasion secondary structure viral RNA viral evolution, Unité ARN
@article{,
title = {RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity},
author = {R P Smyth and M Negroni and A M Lever and J Mak and J C Kenyon},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30283444?dopt=Abstract},
doi = {10.3389/fimmu.2018.02097},
isbn = {30283444},
year = {2018},
date = {2018-01-01},
journal = {Front Immunol},
volume = {9},
pages = {2097},
abstract = {The central dogma of molecular biology describes the flow of genetic information from DNA to protein via an RNA intermediate. For many years, RNA has been considered simply as a messenger relaying information between DNA and proteins. Recent advances in next generation sequencing technology, bioinformatics, and non-coding RNA biology have highlighted the many important roles of RNA in virtually every biological process. Our understanding of RNA biology has been further enriched by a number of significant advances in probing RNA structures. It is now appreciated that many cellular and viral biological processes are highly dependent on specific RNA structures and/or sequences, and such reliance will undoubtedly impact on the evolution of both hosts and viruses. As a contribution to this special issue on host immunity and virus evolution, it is timely to consider how RNA sequences and structures could directly influence the co-evolution between hosts and viruses. In this manuscript, we begin by stating some of the basic principles of RNA structures, followed by describing some of the critical RNA structures in both viruses and hosts. More importantly, we highlight a number of available new tools to predict and to evaluate novel RNA structures, pointing out some of the limitations readers should be aware of in their own analyses.},
keywords = {NEGRONI, RNA structure immune evasion secondary structure viral RNA viral evolution, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2017
Cappy P, Moisan A, Oliveira F De, Plantier J C, Negroni M
HIV-1 sequences in the epidemic suggest an alternative pathway for the generation of the Long Terminal Repeats Article de journal
Dans: Sci Rep, vol. 7, no. 1, p. 13715, 2017, ISBN: 29057964.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {HIV-1 sequences in the epidemic suggest an alternative pathway for the generation of the Long Terminal Repeats},
author = {P Cappy and A Moisan and F De Oliveira and J C Plantier and M Negroni},
url = {https://www.nature.com/articles/s41598-017-14135-z},
doi = {10.1038/s41598-017-14135-z},
isbn = {29057964},
year = {2017},
date = {2017-01-01},
journal = {Sci Rep},
volume = {7},
number = {1},
pages = {13715},
abstract = {To generate the long-terminal repeats (LTR) that border the integrated viral genome, two-strand transfer steps must occur during reverse transcription. Analysis of the genetic polymorphisms that are present in the LTR of HIV-1 heterozygous virions in single infection cycle studies has revealed which of the two copies of genomic RNAs is used for each transfer event. Thus, the first event of strand transfer has been described to be either intra- or intermolecular, while the second event is generally intramolecular. Here, we repeated these analyses using sequences from HIV databases and extended the study to the regions surrounding the LTR. We observed a striking correlation between the pattern of recombination in the LTR and the phylogenetic origin of the surrounding sequences. This correlation suggests that the second-strand transfer can be either intra- or intermolecular and, interestingly, could reflect an effect of proximity between nucleic acids that would guide this transfer. This factor could be particularly relevant for heterozygous viruses containing highly divergent genomic RNAs, such as those considered in the present study.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2016
Smyth R P, Negroni M
A step forward understanding HIV-1 diversity Article de journal
Dans: Retrovirology, vol. 13, no. 1, p. 27, 2016, ISBN: 27093884.
Résumé | Liens | BibTeX | Étiquettes: alternative splicing aminoacyl-tRNA synthetase enzyme kinetics mitochondria mitochondrial disease threonyl-tRNA synthetase, MARQUET, NEGRONI, PAILLART, Unité ARN
@article{,
title = {A step forward understanding HIV-1 diversity},
author = {R P Smyth and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27093884?dopt=Abstract},
doi = {10.1186/s12977-016-0259-8},
isbn = {27093884},
year = {2016},
date = {2016-01-01},
journal = {Retrovirology},
volume = {13},
number = {1},
pages = {27},
abstract = {Human immunodeficiency virus (HIV) populations are characterized by extensive genetic diversity. Antigenic diversification is essential for escape from immune selection and therapy, and remains one of the major obstacles for the development of an efficient vaccine strategy. Even if intensive efforts have been made for understanding the molecular mechanisms responsible for genetic diversity in HIV, conclusive data in vivo is still lacking. Recent works have addressed this issue, focusing on the identification of the sources of genetic diversity during in vivo infections and on the estimate of the pervasiveness of genetic recombination during replication in vivo. Surprisingly, it appears that despite the error-prone nature of the viral polymerase, the bulk of mutations found in patients are indeed due to the effect of a cellular restriction factor. This factor tends to hypermutate the viral genome abolishing viral infectivity. When hypermutation is incomplete, the virus retains infectivity and converts the effect of the cellular factor to its advantage by exploiting it to generate genetic diversity that is beneficial for viral propagation. This view contrasts the long-standing dogma that viral diversity is due to the intrinsic error-prone nature of the viral replication cycle. Besides hypermutations and mutations, recombination is also a pervasive source of genetic diversity. The estimate of the frequency at which this process takes place in vivo has remained elusive, despite extensive efforts in this sense. Now, using single genome amplification, and starting from publically available datasets, it has been obtained a confirmation of the estimates previously made using tissue culture studies. These recent findings are presented here and their implications for the development of future researches are discussed.},
keywords = {alternative splicing aminoacyl-tRNA synthetase enzyme kinetics mitochondria mitochondrial disease threonyl-tRNA synthetase, MARQUET, NEGRONI, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gasser R, Hamoudi M, Pellicciotta M, Zhou Z, Visdeloup C, Colin P, Braibant M, Lagane B, Negroni M
Buffering deleterious polymorphisms in highly constrained parts of HIV-1 envelope by flexible regions. Article de journal
Dans: Retrovirology, vol. 13, no. 1, p. 50, 2016.
Résumé | Liens | BibTeX | Étiquettes: Antigenic variation Coevolution Envelope HIV Viral entry, NEGRONI, Unité ARN
@article{,
title = {Buffering deleterious polymorphisms in highly constrained parts of HIV-1 envelope by flexible regions.},
author = {R Gasser and M Hamoudi and M Pellicciotta and Z Zhou and C Visdeloup and P Colin and M Braibant and B Lagane and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27473399?dopt=Abstract},
doi = {10.1186/s12977-016-0285-6},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {Retrovirology},
volume = {13},
number = {1},
pages = {50},
abstract = {BACKGROUND:
Covariation is an essential process that leads to coevolution of parts of proteins and genomes. In organisms subject to strong selective pressure, coevolution is central to keep the balance between the opposite requirements of antigenic variation and retention of functionality. Being the viral component most exposed to the external environment, the HIV-1 glycoprotein gp120 constitutes the main target of the immune response. Accordingly its more external portions are characterised by extensive sequence heterogeneity fostering constant antigenic variation.
RESULTS:
We report that a single polymorphism, present at the level of the viral population in the conserved internal region C2, was sufficient to totally abolish Env functionality when introduced in an exogenous genetic context. The prominent defect of the non-functional protein is a block occurring after recognition of the co-receptor CCR5, likely due to an interference with the subsequent conformational changes that lead to membrane fusion. We also report that the presence of compensatory polymorphisms at the level of the external and hypervariable region V3 fully restored the functionality of the protein. The functional revertant presents different antigenic profiles and sensitivity to the entry inhibitor TAK 779.
CONCLUSIONS:
Our data suggest that variable regions, besides harbouring intrinsic extensive antigenic diversity, can also contribute to sequence diversification in more structurally constrained parts of the gp120 by buffering the deleterious effect of polymorphisms, further increasing the genetic flexibility of the protein and the antigenic repertoire of the viral population.},
keywords = {Antigenic variation Coevolution Envelope HIV Viral entry, NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Covariation is an essential process that leads to coevolution of parts of proteins and genomes. In organisms subject to strong selective pressure, coevolution is central to keep the balance between the opposite requirements of antigenic variation and retention of functionality. Being the viral component most exposed to the external environment, the HIV-1 glycoprotein gp120 constitutes the main target of the immune response. Accordingly its more external portions are characterised by extensive sequence heterogeneity fostering constant antigenic variation.
RESULTS:
We report that a single polymorphism, present at the level of the viral population in the conserved internal region C2, was sufficient to totally abolish Env functionality when introduced in an exogenous genetic context. The prominent defect of the non-functional protein is a block occurring after recognition of the co-receptor CCR5, likely due to an interference with the subsequent conformational changes that lead to membrane fusion. We also report that the presence of compensatory polymorphisms at the level of the external and hypervariable region V3 fully restored the functionality of the protein. The functional revertant presents different antigenic profiles and sensitivity to the entry inhibitor TAK 779.
CONCLUSIONS:
Our data suggest that variable regions, besides harbouring intrinsic extensive antigenic diversity, can also contribute to sequence diversification in more structurally constrained parts of the gp120 by buffering the deleterious effect of polymorphisms, further increasing the genetic flexibility of the protein and the antigenic repertoire of the viral population.
2015
Geller R, Domingo-Calap P, Cuevas J M, Rossolillo P, Negroni M, Sanjuán R
The external domains of the HIV-1 envelope are a mutational cold spot. Article de journal
Dans: Nat Commun, vol. 6, p. 8571, 2015, ISBN: 26450412.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {The external domains of the HIV-1 envelope are a mutational cold spot.},
author = {R Geller and P Domingo-Calap and J M Cuevas and P Rossolillo and M Negroni and R Sanjuán},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26450412?dopt=Abstract},
doi = {10.1038/ncomms9571},
isbn = {26450412},
year = {2015},
date = {2015-01-01},
journal = {Nat Commun},
volume = {6},
pages = {8571},
abstract = {In RNA viruses, mutations occur fast and have large fitness effects. While this affords remarkable adaptability, it can also endanger viral survival due to the accumulation of deleterious mutations. How RNA viruses reconcile these two opposed facets of mutation is still unknown. Here we show that, in human immunodeficiency virus (HIV-1), spontaneous mutations are not randomly located along the viral genome. We find that the viral mutation rate experiences a threefold reduction in the region encoding the most external domains of the viral envelope, which are strongly targeted by neutralizing antibodies. This contrasts with the hypermutation mechanisms deployed by other, more slowly mutating pathogens such as DNA viruses and bacteria, in response to immune pressure. We show that downregulation of the mutation rate in HIV-1 is exerted by the template RNA through changes in sequence context and secondary structure, which control the activity of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (A3)-mediated cytidine deamination and the fidelity of the viral reverse transcriptase.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Coulibaly S T, Rossolillo P, Winter F, Kretzschmar F K, Brayé M, Martin D P, Lener D, Negroni M
Potent Sensitisation of Cancer Cells to Anticancer Drugs by a Quadruple Mutant of the Human Deoxycytidine Kinase. Article de journal
Dans: PLoS One, vol. 10, no. 10, p. e0140741, 2015, ISBN: 26485161.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {Potent Sensitisation of Cancer Cells to Anticancer Drugs by a Quadruple Mutant of the Human Deoxycytidine Kinase.},
author = {S T Coulibaly and P Rossolillo and F Winter and F K Kretzschmar and M Brayé and D P Martin and D Lener and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26485161?dopt=Abstract},
doi = {10.1371/journal.pone.0140741},
isbn = {26485161},
year = {2015},
date = {2015-01-01},
journal = {PLoS One},
volume = {10},
number = {10},
pages = {e0140741},
abstract = {Identifying enzymes that, once introduced in cancer cells, lead to an increased efficiency of treatment constitutes an important goal for biomedical applications. Using an original procedure whereby mutant genes are generated based on the use of conditional lentivector genome mobilisation, we recently described, for the first time, the identification of a human deoxycytidine kinase (dCK) mutant (G12) that sensitises a panel of cancer cell lines to treatment with the dCK analogue gemcitabine. Here, starting from the G12 variant itself, we generated a new library and identified a mutant (M36) that triggers even greater sensitisation to gemcitabine than G12. With respect to G12, M36 presents an additional mutation located in the region that constitutes the interface of the dCK dimer. The simple presence of this mutation halves both the IC50 and the proportion of residual cells resistant to the treatment. Furthermore, the use of vectors with self-inactivating LTRs leads to an increased sensitivity to treatment, a result compatible with a relief of the transcriptional interference exerted by the U3 promoter on the internal promoter that drives the expression of M36. Importantly, a remarkable effect is also observed in treatments with the anticancer compound cytarabine (AraC), for which a 10,000 fold decrease in IC50 occurred. By triggering the sensitisation of various cancer cell types with poor prognosis to two commonly used anticancer compounds M36 is a promising candidate for suicide gene approaches.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Coulibaly S, Rossolillo P, Negroni M
Mutant human deoxycytidine kinase. Divers
2015, ISBN: EP 15305545.4.
BibTeX | Étiquettes: NEGRONI, Unité ARN
@misc{,
title = {Mutant human deoxycytidine kinase.},
author = {S Coulibaly and P Rossolillo and M Negroni},
isbn = {EP 15305545.4},
year = {2015},
date = {2015-01-01},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
2012
Rossolillo P, Winter F, Simon-Loriere E, Gallois-Montbrun S, Negroni M
Retrovolution: HIV-Driven Evolution of Cellular Genes and Improvement of Anticancer Drug Activation Article de journal
Dans: PLoS Genet, vol. 8, no. 8, p. e1002904, 2012, ISBN: 22927829.
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {Retrovolution: HIV-Driven Evolution of Cellular Genes and Improvement of Anticancer Drug Activation},
author = {P Rossolillo and F Winter and E Simon-Loriere and S Gallois-Montbrun and M Negroni},
url = {http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002904},
doi = {10.1371/journal.pgen.1002904},
isbn = {22927829},
year = {2012},
date = {2012-01-01},
journal = {PLoS Genet},
volume = {8},
number = {8},
pages = {e1002904},
abstract = {In evolution strategies aimed at isolating molecules with new functions, screening for the desired phenotype is generally performed in vitro or in bacteria. When the final goal of the strategy is the modification of the human cell, the mutants selected with these preliminary screenings may fail to confer the desired phenotype, due to the complex networks that regulate gene expression in higher eukaryotes. We developed a system where, by mimicking successive infection cycles with HIV-1 derived vectors containing the gene target of the evolution in their genome, libraries of gene mutants are generated in the human cell, where they can be directly screened. As a proof of concept we created a library of mutants of the human deoxycytidine kinase (dCK) gene, involved in the activation of nucleoside analogues used in cancer treatment, with the aim of isolating a variant sensitizing cancer cells to the chemotherapy compound Gemcitabine, to be used in gene therapy for anti-cancer approaches or as a poorly immunogenic negative selection marker for cell transplantation approaches. We describe the isolation of a dCK mutant, G12, inducing a 300-fold sensitization to Gemcitabine in cells originally resistant to the prodrug (Messa 10K), an effect 60 times stronger than the one induced by the wt enzyme. The phenotype is observed in different tumour cell lines irrespective of the insertion site of the transgene and is due to a change in specificity of the mutated kinase in favour of the nucleoside analogue. The mutations characterizing G12 are distant from the active site of the enzyme and are unpredictable on a rational basis, fully validating the pragmatic approach followed. Besides the potential interest of the G12 dCK variant for therapeutic purposes, the methodology developed is of interest for a large panel of applications in biotechnology and basic research.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Crignis E De, Guglietta S, Foley B T, Negroni M, Narzo A F Di, Costa V Waelti Da, Cavassini M, Bart P A, Pantaleo G, Graziosi C
Nonrandom distribution of cryptic repeating triplets of purines and pyrimidines (RNY)n in gp120 of HIV-1. Article de journal
Dans: AIDS Res Hum Retroviruses, vol. 28, no. 5, p. :493-504, 2012, ISBN: 21902591, (NEGRONI).
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {Nonrandom distribution of cryptic repeating triplets of purines and pyrimidines (RNY)n in gp120 of HIV-1.},
author = {E De Crignis and S Guglietta and B T Foley and M Negroni and A F Di Narzo and V Waelti Da Costa and M Cavassini and P A Bart and G Pantaleo and C Graziosi},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21902591},
doi = {10.1089/AID.2011.0208},
isbn = {21902591},
year = {2012},
date = {2012-01-01},
journal = {AIDS Res Hum Retroviruses},
volume = {28},
number = {5},
pages = {:493-504},
abstract = {We have analyzed purine (R) and pyrimidine (Y) codon patterns in variable and constant regions of HIV-1 gp120 in seven patients infected with different HIV-1 subtypes and naïve to antiretroviral therapy. We have calculated the relative frequency of each in-frame codon RNY, YNR, RNR, and YNY (N=any nucleotide) in variable and constant regions of gp120, in the sequence comprised within indels and at indels' flanking sites. Our data show that hypervariable regions V1, V2, V4, and V5 are characterized by the presence of long stretches of RNY codons constituting the majority of the sequence portion comprised within insertions/deletions. In full length gp120 and within inserted/deleted fragments the number of AVT (V=A, C, G) codons did not exceed 50% of the total RNY codons. RNY strings in variable regions spanned up to 21 codons and were always in-frame. In contrast, RNY strings in constant regions were mostly out-of-frame and their length was limited to 5 codons. The frequency of the codon RNY was found to be significantly higher in variable regions (p<0.0001; t-test), within indels, and at indels' flanking sites (p<0.0001; χ² test). Analysis of the distribution of RNY strings equal to or longer than 5 codons in the full genome of HXB2 also shows that these sequences are mostly out-of-frame, unless they contain a potential N-glycosylation site or an Asparagine. These data suggest that cryptic repeats of RNY may play a role in the genesis of multiple base insertions and deletions in hypervariable regions of gp120.},
note = {NEGRONI},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2011
Simon-Loriere E, Rossolillo P, Negroni M
RNA structures, genomic organization and selection of recombinant HIV Article de journal
Dans: RNA Biol, vol. 8, no. 2, p. 280-286, 2011, ISSN: 1555-8584 (Electronic) 1547-6286 (Linking), (Journal article RNA biology RNA Biol. 2011 Mar 1;8(2).).
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {RNA structures, genomic organization and selection of recombinant HIV},
author = {E Simon-Loriere and P Rossolillo and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21422815},
doi = {10.4161/rna.8.2.15193},
issn = {1555-8584 (Electronic)
1547-6286 (Linking)},
year = {2011},
date = {2011-01-01},
journal = {RNA Biol},
volume = {8},
number = {2},
pages = {280-286},
abstract = {Recombination is an evolutionary mechanism intrinsic to the evolution of many RNA viruses. In retroviruses and notably in the case of HIV, recombination is so frequent that it can be considered as part of its mode of replication. This process not only plays a central role in shaping HIV genetic diversity worldwide, but has also been involved in immune escape and development of resistance to antiviral treatments. Recombination does not create new mutations in the existing genetic repertoire of the virus, but creates new combinations of pre-existing polymorphisms. The simultaneous insertion of multiple substitutions in a single replication cycle leaves little room for the progressive coevolution of regions of proteins, RNA or, more in general, genomes, to accommodate these drastic sequence changes. Therefore, recombination, while allowing the virus to rapidly explore larger sequence space than the slow accumulation of point mutations, also runs the risk of generating non functional viruses. Recombination is the consequence of a switch in the template used during reverse transcription and is promoted by the presence of structured regions in the genomic RNA template. In this review, we discuss new observations suggesting that the distribution of RNA structures along the HIV genome may enhance recombination rates in regions where the resultant progeny is less likely to be impaired, and could therefore maximize the evolutionary value of this source of genetic diversity.},
note = {Journal article
RNA biology
RNA Biol. 2011 Mar 1;8(2).},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2009
Simon-Loriere E, Galetto R, Hamoudi M, Archer J, Lefeuvre P, Martin D P, Robertson D L, Negroni M
Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus Article de journal
Dans: PLoS Pathog, vol. 5, no. 5, p. e1000418, 2009, ISBN: 19424420, (1553-7374 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus},
author = {E Simon-Loriere and R Galetto and M Hamoudi and J Archer and P Lefeuvre and D P Martin and D L Robertson and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19424420},
isbn = {19424420},
year = {2009},
date = {2009-01-01},
journal = {PLoS Pathog},
volume = {5},
number = {5},
pages = {e1000418},
abstract = {The ability of pathogens to escape the host's immune response is crucial for the establishment of persistent infections and can influence virulence. Recombination has been observed to contribute to this process by generating novel genetic variants. Although distinctive recombination patterns have been described in many viral pathogens, little is known about the influence of biases in the recombination process itself relative to selective forces acting on newly formed recombinants. Understanding these influences is important for determining how recombination contributes to pathogen genome and proteome evolution. Most previous research on recombination-driven protein evolution has focused on relatively simple proteins, usually in the context of directed evolution experiments. Here, we study recombination in the envelope gene of HIV-1 between primary isolates belonging to subtypes that recombine naturally in the HIV/AIDS pandemic. By characterizing the early steps in the generation of recombinants, we provide novel insights into the evolutionary forces that shape recombination patterns within viral populations. Specifically, we show that the combined effects of mechanistic processes that determine the locations of recombination breakpoints across the HIV-1 envelope gene, and purifying selection acting against dysfunctional recombinants, can explain almost the entire distribution of breakpoints found within this gene in nature. These constraints account for the surprising paucity of recombination breakpoints found in infected individuals within this highly variable gene. Thus, the apparent randomness of HIV evolution via recombination may in fact be relatively more predictable than anticipated. In addition, the dominance of purifying selection in localized areas of the HIV genome defines regions where functional constraints on recombinants appear particularly strong, pointing to vulnerable aspects of HIV biology.},
note = {1553-7374 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Negroni M, Gallois-Montbrun S, Rossolillo P, Bartolo V Di, Uze G, Simon-Loriere E, Marquet R, Vivet-Boudou V
Lentiviral-based vector and its use in directed evolution of genomic regions, genes and polynucleotides. Divers
2009, ISBN: EP 09290856.5.
Résumé | BibTeX | Étiquettes: MARQUET, NEGRONI, PAILLART, Unité ARN
@misc{,
title = {Lentiviral-based vector and its use in directed evolution of genomic regions, genes and polynucleotides.},
author = {M Negroni and S Gallois-Montbrun and P Rossolillo and V Di Bartolo and G Uze and E Simon-Loriere and R Marquet and V Vivet-Boudou},
isbn = {EP 09290856.5},
year = {2009},
date = {2009-01-01},
abstract = {The present invention concerns a method of directing evolution of a target polynucleotide of interest for obtaining variants of this target polynucleotide, as well as a method to generate genetic variability by preparing a cell library. This invention also relates to a method to isolate or to screen variants of a polynucleotide or variants of a protein able to impact the phenotype of a cell or to confer a desired phenotype to target cells, and to identify these polynucleotide variants or protein variants responsible for this phenotype.},
keywords = {MARQUET, NEGRONI, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
Galetto R, Negroni M
Retroviruses Chapitre d'ouvrage
Dans: Cameron, C; Gotte, M; Raney, K (Ed.): Viral Genome Replication, p. 109-128, Springer-Verlag, 2009, (DOI: 10.1007/b135974_6).
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@inbook{,
title = {Retroviruses},
author = {R Galetto and M Negroni},
editor = {C Cameron and M Gotte and K Raney},
url = {http://www.springerlink.com/content/w873085p48771805},
year = {2009},
date = {2009-01-01},
booktitle = {Viral Genome Replication},
pages = {109-128},
publisher = {Springer-Verlag},
abstract = {Retroviruses are a large group of enveloped RNA viruses infecting vertebrates. The viral particles are spherical and acquire their envelope during budding from the infected cell. The lipid bilayer therefore contains cellular proteins as well as the viral envelope glycoproteins. These glycoproteins are constituted by a transmembrane subunit (TM) associated to the surface protein (SU), present on the virion. Underneath the membrane is a spherical shell constituted by the matrix (MA) protein. Internally is the viral capsid, whose shape varies in different viruses, constituted by the CA protein. This core contains the retroviral enzymes (the reverse transcriptase, RT, the integrase, IN, and the protease, PR), together with the genomic RNA, coated by the nucleocapsid protein (NC).},
note = {DOI: 10.1007/b135974_6},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
2008
Ramirez B C, Simon-Loriere E, Galetto R, Negroni M
Implications of recombination for HIV diversity Article de journal
Dans: Virus Res, vol. 134, no. 1-2, p. 64-73, 2008, ISBN: 18308413, (0168-1702 (Print) 0168-1702 (Linking) Journal Article Research Support, Non-U.S. Gov't Review).
Résumé | Liens | BibTeX | Étiquettes: *Genetic Variation Genome, Genetic, NEGRONI, Unité ARN, Viral HIV/classification/*genetics/immunology/isolation & purification HIV Infections/drug therapy/immunology/transmission/virology Humans *Recombination
@article{,
title = {Implications of recombination for HIV diversity},
author = {B C Ramirez and E Simon-Loriere and R Galetto and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18308413},
isbn = {18308413},
year = {2008},
date = {2008-01-01},
journal = {Virus Res},
volume = {134},
number = {1-2},
pages = {64-73},
abstract = {The human immunodeficiency virus (HIV) population is characterised by extensive genetic variability that results from high error and recombination rates of the reverse transcription process, and from the fast turnover of virions in HIV-infected individuals. Among the viral variants encountered at the global scale, recombinant forms are extremely abundant. Some of these recombinants (known as circulating recombinant forms) become fixed and undergo rapid expansion in the population. The reasons underlying their epidemiological success remain at present poorly understood and constitute a fascinating area for future research to improve our understanding of immune escape, pathogenicity and transmission. Recombinant viruses are generated during reverse transcription as a consequence of template switching between the two genetically different genomic RNAs present in a heterozygous virus. Recombination can thereby generate shortcuts in evolution by producing mosaic reverse transcription products of parental genomes. Therefore, in a single infectious cycle multiple mutations that are positively selected can be combined or, conversely, negatively selected mutations can be removed. Recombination is therefore involved in different aspects of HIV evolution, adaptation to its host, and escape from antiviral treatments.},
note = {0168-1702 (Print)
0168-1702 (Linking)
Journal Article
Research Support, Non-U.S. Gov't
Review},
keywords = {*Genetic Variation Genome, Genetic, NEGRONI, Unité ARN, Viral HIV/classification/*genetics/immunology/isolation & purification HIV Infections/drug therapy/immunology/transmission/virology Humans *Recombination},
pubstate = {published},
tppubtype = {article}
}
Archer J, Pinney J W, Fan J, Simon-Loriere E, Arts E J, Negroni M, Robertson D L
Identifying the important HIV-1 recombination breakpoints Article de journal
Dans: PLoS Comput Biol, vol. 4, no. 9, p. e1000178, 2008, ISBN: 18787691, (1553-7358 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: Computational Biology Evolution, env Genetic Variation Genome, Genetic, Genetic Models, Molecular Genes, NEGRONI, Statistical RNA, Unité ARN, Viral HIV Infections/virology HIV-1/*genetics Humans *Models, Viral/genetics *Recombination
@article{,
title = {Identifying the important HIV-1 recombination breakpoints},
author = {J Archer and J W Pinney and J Fan and E Simon-Loriere and E J Arts and M Negroni and D L Robertson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18787691},
isbn = {18787691},
year = {2008},
date = {2008-01-01},
journal = {PLoS Comput Biol},
volume = {4},
number = {9},
pages = {e1000178},
abstract = {Recombinant HIV-1 genomes contribute significantly to the diversity of variants within the HIV/AIDS pandemic. It is assumed that some of these mosaic genomes may have novel properties that have led to their prevalence, particularly in the case of the circulating recombinant forms (CRFs). In regions of the HIV-1 genome where recombination has a tendency to convey a selective advantage to the virus, we predict that the distribution of breakpoints--the identifiable boundaries that delimit the mosaic structure--will deviate from the underlying null distribution. To test this hypothesis, we generate a probabilistic model of HIV-1 copy-choice recombination and compare the predicted breakpoint distribution to the distribution from the HIV/AIDS pandemic. Across much of the HIV-1 genome, we find that the observed frequencies of inter-subtype recombination are predicted accurately by our model. This observation strongly indicates that in these regions a probabilistic model, dependent on local sequence identity, is sufficient to explain breakpoint locations. In regions where there is a significant over- (either side of the env gene) or under- (short regions within gag, pol, and most of env) representation of breakpoints, we infer natural selection to be influencing the recombination pattern. The paucity of recombination breakpoints within most of the envelope gene indicates that recombinants generated in this region are less likely to be successful. The breakpoints at a higher frequency than predicted by our model are approximately at either side of env, indicating increased selection for these recombinants as a consequence of this region, or at least part of it, having a tendency to be recombined as an entire unit. Our findings thus provide the first clear indication of the existence of a specific portion of the genome that deviates from a probabilistic null model for recombination. This suggests that, despite the wide diversity of recombinant forms seen in the viral population, only a minority of recombination events appear to be of significance to the evolution of HIV-1.},
note = {1553-7358 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Computational Biology Evolution, env Genetic Variation Genome, Genetic, Genetic Models, Molecular Genes, NEGRONI, Statistical RNA, Unité ARN, Viral HIV Infections/virology HIV-1/*genetics Humans *Models, Viral/genetics *Recombination},
pubstate = {published},
tppubtype = {article}
}