PXD046363

PXD046363 is an original dataset announced via ProteomeXchange.

Title	Simultaneous selection of nanobodies for immune epitopes in the complex tumor microenvironment
Description	In the rapidly advancing field of synthetic biology, there is a critical need for technology to discover targeting moieties for therapeutic biologics. We developed INSPIRE-seq, an approach that utilizes a nanobody library and next-generation sequencing to identify nanobodies selected for complex environments. INSPIRE-seq enables the parallel enrichment of immune cell-binding nanobodies that penetrate the tumor microenvironment. Clone enrichment and specificity varies across immune cell subtypes in the tumor, lymph node, and spleen. INSPIRE-seq identified a dendritic cell binding clone that binds PHB2. Single-cell RNA sequencing revealed a connection with cDC1s, and immunofluorescence confirmed nanobody-PHB2 colocalization along cell membranes. Structural modeling and docking studies assisted binding predictions and will guide nanobody selection. In this work, we demonstrate that INSPIRE-seq offers an unbiased approach to examine complex microenvironments and assist in the development of nanobodies, which could serve as active drugs, modified to become drugs, or used as targeting moieties.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:28:07.083.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Lemoff
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-24 17:11:56	ID requested
1	2024-01-30 03:02:10	announced
⏵ 2	2024-10-22 06:28:07	announced	2024-10-22: Updated project metadata.

Sekar TV, Elghonaimy EA, Swancutt KL, Diegeler S, Gonzalez I, Hamilton C, Leung PQ, Meiler J, Martina CE, Whitney M, Aguilera TA, Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment. Nat Commun, 14(1):7473(2023) [pubmed]

10.1038/s41467-023-43038-z;

submitter keyword: phage,nanobodies, immune cells

Todd A. Aguilera
contact affiliation	Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
contact email	todd.aguilera@utsouthwestern.edu
lab head
Andrew Lemoff
contact affiliation	UT Southwestern Medical Center
contact email	andrew.lemoff@utsouthwestern.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/2024/01/PXD046363

PRIDE project URI

• PRIDE
  1. PXD046363
     1. Label: PRIDE project
     2. Name: Simultaneous selection of nanobodies for immune epitopes in the complex tumor microenvironment