PXD062784

PXD062784 is an original dataset announced via ProteomeXchange.

Title	Identification of HIV Tat and NF-kB binding proteins associated with semen derived extracellular vesicles In this study, we used orthogonal pull-downs, mobility shift, and electrophoretic protein binding assays coupled with proteomic and secretomic analyses to highlights the previously unappreciated SEV-associated transcriptional repressors that may target HIV Tat to suppress viral transcription.
Description	Semen-derived extracellular vesicles (SEVs) have been shown to inhibit the human immunodeficiency virus type 1 (HIV-1) LTR transactivation through the blockade of the interaction of transactivator of transcription (Tat) and host transcription factors NF-kB and Sp1 (Tat•NF-ᴋB p65 and Tat•Sp1). The ability of SEVs to regulate the activities of transcription factors suggests that SEVs may contain transcription activators and repressors. In this present study, we used orthogonal SEVs-based screens, including pull-downs, mobility shift assays, and electrophoretic protein binding assays coupled with mass spectrometry (MS) to identify host proteins in SEVs that interact with the different transcription factors (SEVs•Tat and SEVs•NF-ᴋB p65 binding proteins). Protein network analysis performed on SEVs•Tat and SEVs•NF-ᴋB p65 complexes revealed interactome networks that associate with 7SK snRNA binding, mRNA Processing, P-TEFb complex, NELF complex. Additionally, Pathway enrichment analyses of SEVs•Tat and SEVs•NF-ᴋB p65 complexes identifies biological functions involved in initiation of transcription and translation elongation at the HIV LTR, formation of HIV and RNA Pol II elongation complexes, protein, nucleic acid, and chromatin binding, as well as chromatin assembly and disassembly. Finally, integrative analysis of SEVs•Tat and SEVs•NF-ᴋB p65 binding proteins identifies four proteins (AKAP9, ARHGEF28, INTS1, BRD2) to be common to both complexes. Immunoprecipitation assays suggest that SEVs-associated BRD2 and NELFB bind HIV Tat. The identification of extracellular interactome of Tat and NF-κB p65 in HIV transcription paves the way for the rational design of novel inhibitors of HIV transcription, with potential for therapeutic targeting.
HostingRepository	PRIDE
AnnounceDate	2026-06-15
AnnouncementXML	Submission_2026-06-14_16:10:07.954.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD062784
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Wasifa Naushad
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-09 10:08:14	ID requested
⏵ 1	2026-06-14 16:10:08	announced

10.6019/PXD062784;

10.1126/scisignal.ado9243;

Okeoma BC, Kaddour H, Naushad W, Paromov V, Chaudhary A, Noghero A, Stapleton JT, Okeoma CM, B and that may impair HIV replication. Sci Signal, 18(903):eado9243(2025) [pubmed]

submitter keyword: HIV, Extracellular Vesicles,TAT,NFKB

Chioma M
contact affiliation	Department of Pathology, Microbiology & Immunology, New York Medical College, Valhalla, NY, USA Lovelace Biomedical Institute, Albuquerque, NM 87108-5127, USA.
contact email	COKEOMA@NYMC.EDU
lab head
Wasifa Naushad
contact affiliation	New York Medical College
contact email	wnaushad@nymc.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD062784

PRIDE project URI

• PRIDE
  1. PXD062784
     1. Label: PRIDE project
     2. Name: Identification of HIV Tat and NF-kB binding proteins associated with semen derived extracellular vesicles In this study, we used orthogonal pull-downs, mobility shift, and electrophoretic protein binding assays coupled with proteomic and secretomic analyses to highlights the previously unappreciated SEV-associated transcriptional repressors that may target HIV Tat to suppress viral transcription.