RAIN: machine learning-based identification for HIV-1 bNAbs.

Détails

Ressource 1Télécharger: Rain.pdf (5576.37 [Ko])
Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_7E0011402784
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
RAIN: machine learning-based identification for HIV-1 bNAbs.
Périodique
Nature communications
Auteur⸱e⸱s
Foglierini M., Nortier P., Schelling R., Winiger R.R., Jacquet P., O'Dell S., Demurtas D., Mpina M., Lweno O., Muller Y.D., Petrovas C., Daubenberger C., Perreau M., Doria-Rose N.A., Gottardo R., Perez L.
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Statut éditorial
Publié
Date de publication
24/06/2024
Peer-reviewed
Oui
Volume
15
Numéro
1
Pages
5339
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
FNS: 310030_20467
Résumé
Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infections. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoires is still lacking. Here, we develop a straightforward computational method for the Rapid Automatic Identification of bNAbs (RAIN) based on machine learning methods. In contrast to other approaches, which use one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for the accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained and sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of distinct HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using an in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
Mots-clé
HIV-1/immunology, Humans, Machine Learning, HIV Antibodies/immunology, Cryoelectron Microscopy, Antibodies, Neutralizing/immunology, HIV Infections/virology, HIV Infections/immunology, CD4 Antigens/metabolism, CD4 Antigens/immunology, Amino Acid Sequence, HIV Envelope Protein gp120/immunology, HIV Envelope Protein gp120/chemistry
Pubmed
Web of science
Open Access
Oui
Financement(s)
Fonds national suisse
Création de la notice
25/06/2024 8:20
Dernière modification de la notice
26/07/2024 6:02
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