Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Common HIV-1 escape patterns drive the maturation of V2-Apex broadly neutralizing antibodies

PROVIDER: PRJNA396773 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5888730_1.fastq.gz	Fastqsanger.gz
	SRR5888730_2.fastq.gz	Fastqsanger.gz
	SRR5888731_1.fastq.gz	Fastqsanger.gz
	SRR5888731_2.fastq.gz	Fastqsanger.gz
	SRR5888732_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

Human Immunoglobulin Repertoire-Guided Immunogen Design Targeting HIV V2-Apex Broadly Neutralizing Antibody Precursors

Project description:Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy chain complementarity-determining region 3 (HCDR3), suggesting that rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bind inferred germlines for PCT64 and PG9 and have higher affinities for bnAbs; determined cryo-EM structures of ApexGT trimers bound to inferred germline and bnAb forms of PCT64 and PG9; and developed an mRNA-encoded cell-surface trimer for our lead ApexGT candidate. The methods and immunogens developed here have promise to assist the development of an HIV vaccine.

2023-03-11 | PXD033766 | Pride

Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens

Project description:HIV-1 vaccine immunofocusing strategies have the potential to induce broadly reactive nAbs. Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets of neutralizing antibodies (NAbs), the V2 apex and fusion peptide (FP). This dataset contains the raw files used to obtain site-spefific glycan analysis of the membrane-resident HIV-1 trimers

| MSV000088108 | MassIVE

Overcoming steric restrictions of VRC01 HIV-1 neutralizing antibodies through immunization

Project description:Broadly HIV-1 neutralizing VRC01-class antibodies target the CD4-binding site of Env. They are derived from VH1-2*02 antibody heavy chains paired with rare light chains expressing five amino acid long CDRL3s. They have been isolated from infected subjects but have not yet been elicited by immunization. Env-derived immunogens capable of binding the germline forms of VRC01 B cell receptors on naïve B cells have been designed and evaluated in knock-in mice. However, the elicited antibodies cannot bypass glycans present on the conserved position N276 of Env, which restricts access to the CD4-binding site. Efforts to guide the appropriate maturation of these antibodies by sequential immunization have not yet been successful. Here, we report on a two-step immunization scheme that led to the maturation of VRC01-like antibodies capable of accommodating the N276 glycan and displaying autologous tier 2 neutralizing activities. Our results are relevant to clinical trials aiming to elicit VRC01 antibodies.

2020-05-26 | PXD015168 | Pride

Prediction of broadly neutralizing antibodies

Project description:Prediction of broadly neutralizing antibodies

| PRJNA952996 | ENA

Human immunodeficiency virus 1

Project description:Broad neutralizing HIV antibodies

| PRJNA294363 | ENA

Prediction of broadly neutralizing antibodies [Singleron]

Project description:Prediction of broadly neutralizing antibodies [Singleron]

| PRJNA952999 | ENA

Prediction of broadly neutralizing antibodies [10X]

Project description:Prediction of broadly neutralizing antibodies [10X]

| PRJNA952157 | ENA

Prediction of broadly neutralizing antibodies [BD Rhapsody]

Project description:Prediction of broadly neutralizing antibodies [BD Rhapsody]

| PRJNA952998 | ENA

Smart-seq2 data from memory B cells from an individual living with HIV with broadly neutralizing plasma and an individual living with HIV who is aviremic without treatment

Project description:Tissue-like memory, activated memory and resting memory B cells were sorted by FACS from the individual living with HIV (EC17) who was aviremic and transcriptomes generated using the SmartSeq2 protocol. This was to provide a reference set for each memory B cell subset in the context of HIV. Next, HIV-specific memory B cells from the individual with broadly neutralizing plasma were then also sorted by FACS and single cell transcriptomes generated using the SmartSeq2 protocol. The phenotypes of memory B cells from the individual with broadly neutralizing plasma (T125) were then inferred from the reference set using Glmnet and Celltypist packages.

2023-12-24 | E-MTAB-13592 | biostudies-arrayexpress

Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies

Project description:Many human monoclonal antibodies that neutralize multiple clades of HIV-1 are polyreactive and bind avidly to mammalian autoantigens. Indeed, the generation of neutralizing antibodies to the 2F5 and 4E10 epitopes of HIV-1 gp41 in man may be proscribed by immune tolerance since mice expressing the VH and VL regions of 2F5 have a block in B-cell development characteristic of central tolerance. This developmental blockade implies the presence of tolerizing autoantigens that are mimicked by the membrane-proximal external region of HIV-1 gp41. Here we identify human kynureninase (KYNU) and splicing factor 3b subunit 3 (SF3B3) as the primary conserved, vertebrate self-antigens recognized by the 2F5 and 4E10 antibodies, respectively. 2F5 binds the H4 domain of KYNU which contains the complete 2F5 linear epitope (ELDKWA). 4E10 recognizes a conformational epitope of SF3B3 that is strongly dependent on hydrophobic interactions. Opossums carry a rare KYNU H4 domain that abolishes 2F5 binding, but retain all SF3B3 4E10 epitopes. Immunization of opossums with HIV-1 gp140 induced extraordinary titers of serum antibody to the 2F5 ELDKWA epitope but little or nothing to the 4E10 determinant. Identification of structural motif shared by vertebrates and HIV-1 provides direct evidence that immunological tolerance can impair humoral responses to HIV-1. The invitrogen protoarray that contains >9,400 recombinant human proteins was used to identify self-ligands that are recognized by broadly neutralizing HIV-1 antibodies 2F5 and 4E10. An isotype-matched human myeloma protein (151K, Southern Biotech) was used as control.

2012-12-03 | E-GEOD-42673 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data