Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photocatalytic proximity labeling technology for nanoparticle protein corona

ABSTRACT: We designed a photocatalytic proximity labeling technology for in situ labeling of corona proteins. When nanoparticles were exposed in plasma, they were immediately irradiated to induce the photocatalytic reaction, in which the inner Ce6 activated BP in the outer layer. BP was then released from nanoparticles and rapidly coupled to the proteins that adsorbed on particle surface, making these corona proteins tagged with biotin.

ORGANISM(S): Mus Musculus

SUBMITTER: Qiang Zhang

PROVIDER: PXD034930 | iProX | Thu Jun 23 00:00:00 BST 2022

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Fast and Dynamic Mapping of the Protein Corona on Nanoparticle Surfaces by Photocatalytic Proximity Labeling.

Zhang Zibin Z Ren Junji J Dai Wenbing W Zhang Hua H Wang Xueqing X He Bing B Zhang Qiang Q

Advanced materials (Deerfield Beach, Fla.) 20230112 9

Protein corona broadly affects the delivery of nanomedicines in vivo. Although it has been widely studied by multiple strategies like centrifugal sedimentation, the rapidly forming mechanism and the dynamic structure of the protein corona at the seconds level remains challenging. Here, a photocatalytic proximity labeling technology in nanoparticles (nano-PPL) is developed. By fabricating a "core-shell" nanoparticle co-loaded with chlorin e6 catalyst and biotin-phenol probe, nano-PPL technology i ...[more]

PMID: 36477943

Similar Datasets

Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

Project description:Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

| PRJNA925537 | ENA

Unravelling Intracellular Protein Corona Components of Nanoplas-tics via Photocatalytic Protein Proximity Labeling

Project description:Bioaccumulation of nanoplastic particles draws increasing attention regarding environmental sustainability and biosafety. How nanoplastic particles interact with cellular milieu still remains elusive. Herein, we exemplify a general approach to profile the composition of “protein corona” interacting with nanoparticles via the photocatalytic protein proximity labeling method. To enable photocatalytic proximity labeling of proteome interacting with particles, iodine substituted BODIPY (I-BODIPY) is selected as the photosensitizer and covalently conjugated onto amino-polystyrene nanoparticle as a model system. Next, selec-tive proximity labeling of interacting proteins is demonstrated using I-BODIPY labeled nanoplastic particles in both E. coli lysate and live AML 12 cells. Mechanistic studies reveal the covalent modifications of proteins by amino-alkyne substrate is conducted via reactive oxygen species (ROS) photosensitization pathway. Further proteomic analysis uncovers that mitochon-dria-related proteins are intensively involved in protein corona, indicating substantial interactions between nanoplastic particles and mitochondria. In addition, proteostasis network components are also identified accompanied with consequent cellular pro-teome aggregation confirmed by fluorescence imaging. Together, this work exemplifies a general strategy to interrogate the composition of protein corona of nanomaterials by grafting them photo-oxidation property to enable photocatalytic protein proximity labeling function.

2024-01-24 | PXD048855 |

Nanoparticle protein corona LC-MS/MS

Project description:Engineered nanoparticles for biomedical applications require increased effectiveness in targeting specific cells while preserving non-target cells’ safety. Native nanoparticles entering a protein-rich liquid media quickly form a macromolecular structure called protein corona. This protein structure defines the physical interaction between nanoparticles and target cells. We describe SUSTU (surface proteomics for nanoparticle safety, targeting and uptake) a proteomics-based method to analyze the surface of a nanoparticle protein corona. This method provides qualitative and quantitative analysis from the protein corona surface. Those exposed proteins compose the first line of interaction between this macromolecular structure and the cell surface of a target cell. With SUSTU, the spatial and temporal dynamics of the protein corona surface can be studied. Data from SUSTU would ascertain the nanoparticle functionalized groups exposed at destiny; circumventing preliminary in vitro experiments. Therefore this method evaluates nanoparticle targeting and uptake capability and could be integrated into a rapid prototyping strategy which is a major challenge in nanomaterial science.

2017-02-28 | PXD004636 | Pride

Deep-Red and Ultrafast Photocatalytic Proximity Labeling Empowered in situ Dissection of Tumor-Immune Interactions in Primary Tissues

Project description:Immunotherapy efficacy in solid tumors varies greatly, influenced by the tumor microenvironment (TME) and the dynamic tumor-immune interactions within it. Decoding these interactions in situ with minimal interference to native tissue architecture and delicate immune responses is critical for understanding tumor progression and optimizing therapeutic strategies. Here, we introduce CAT-Tissue, a novel deep-red photocatalytic proximity labeling method that enables ultrafast, high-resolution profiling of tumor-immune interactions in primary tissues. By leveraging nanobody-Chlorin e6 as the photocatalyst and biotin-aniline as the probe, CAT-Tissue enabled the rapid and comprehensive detection of various tumor-immune interactions in both coculture systems and primary tumor sections. Coupled with bulk RNA-sequencing, CAT-Tissue revealed distinct gene expression patterns between tumor-neighboring and tumor-distal lymphocytes, highlighting the recognition and immune responses of tumor-neighboring CD8+ T cells, which exhibited activated, effector, and exhausted phenotypes. By leveraging a deep-red photocatalytic proximity cell labeling strategy with excellent tissue penetration and biocompatibility, CAT-Tissue offers a non-genetically encoded platform with high sensitivity and spatiotemporal controllability for rapid profiling tumor-immune interactions within complex tissue environments in situ, which may advance our understanding of tumor immunology and guide the development of more effective immunotherapies.

2025-03-06 | GSE288148 | GEO

Detection of Cell-Cell Interactions via Photocatalytic Cell Tagging

Project description:The growing appreciation of immune cell-cell interactions within disease environments has led to significant efforts to develop highly effective protein-, and cell-based immunotherapies.  However, characterizing these complex cell-cell interactions in high resolution remains challenging.  Thus, technologies that leverage therapeutic-based modalities for profiling intercellular environments can provide unique advantages towards understanding these cellular interactions at molecular-level detail.  To address this, we introduce photocatalytic cell tagging (PhoTag), a platform for profiling cell-cell interactions that utilizes a single domain antibody (VHH) conjugated to a photoactivatable flavin-based cofactor.  Upon irradiation with visible light, the tethered flavin photocatalyst generates phenoxy radical tags for targeted labeling within cell-cell contact environments.  Using anti-PD-1 or anti-PD-L1 VHH flavin conjugates, we demonstrate that PhoTag achieves highly selective synaptic labeling in antigen presenting cell-T cell co-culture systems. By combining the high resolution transcellular biotinylation capability of PhoTag with multi-omics single cell sequencing, we interrogated transient interactions between Peripheral blood mononuclear cell (PBMC) populations and Raji PD-L1 B cells and discovered that specific T cell subtypes can transiently interact more efficiently than others.   We envision that the spatio-temporal and modular nature of PhoTag will enable its broad utilization for detailed profiling of intercellular interactions across different biological systems. 

2022-06-18 | GSE206140 | GEO

Bioorthogonal Photocatalytic Proximity Labeling in Primary Living Samples

Project description:In situ profiling of subcellular proteomic networks in primary and living systems, such as primary cells from native tissues or clinic samples, is crucial for the understanding of life processes and diseases, yet challenging for the current proximity labeling methods (e.g., BioID, APEX) due to their necessity of genetic engineering. Here we report CAT-S, a state-of-the-art bioorthogonal photocatalytic chemistry-enabled proximity labeling method, that expands proximity labeling to a wide range of primary living samples for in situ profiling of subcellular proteomes. Powered by the newly introduced thioQM labeling warhead and targeted bioorthogonal photocatalytic decaging chemistry, CAT-S enables labeling of mitochondrial proteins in living cells with high efficiency and specificity (up to 87%). We applied CAT-S to diverse cell cultures, mouse tissues as well as primary T cells from human blood, portraying the native-state mitochondrial proteomic characteristics, and unveiled a set of hidden mitochondrial proteins in human proteome. Furthermore, CAT-S allows quantitative analysis of the in situ proteomic perturbations on dysfunctional tissue samples, exampled by diabetic mouse kidneys, and revealed the alterations of lipid metabolism machinery that drive the disease progression. Given the advantages of non-genetic operation, generality, efficiency as well as spatiotemporal resolution, CAT-S may open new avenues as a proximity labeling strategy for in situ investigation of subcellular proteomic landscape of primary living samples that are otherwise inaccessible.

2024-05-24 | PXD045791 | Pride

In situ Analysis of Nanoparticle Soft Corona and Dynamic Evolution

Project description:How soft corona i.e., the protein corona’s outer layer contributes to “biological” identity of nanomaterials (NMs) is largely unknown due to a longstanding challenge in capturing protein composition of the soft corona in situ. We herein develop an in situ “Fishing” method that can monitor the dynamic formation of protein corona on ultra-small chiral Cu2S nanoparticles (NPs) allowing us to directly separate and identify their protein composition. This method can detect spatiotemporal processes in the evolution of hard and soft coronas on chiral NPs, revealing subtle differences in their composition even within several minutes. This study highlights the importance of in situ and dynamic analysis of soft/hard corona composition, provides detailed insights into the roles of protein corona composition in mediating the biological responses of NPs, and offers a universal strategy to characterize the soft corona that will serve as a powerful tool for rational design of biomedical NMs.

2022-10-13 | PXD033976 | Pride

Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_EMC2_knockdown]

Project description:Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_EMC2_knockdown]

| PRJNA1269464 | ENA

Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_thapsigargin_treatment]

Project description:Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_thapsigargin_treatment]

| PRJNA1269465 | ENA

Proteotyping rare amyloidosis disease by photocatalytic proteomics profiling

Project description:we present a photocatalytic proteomic method, named Amyloid-ID, as a quantitative approach to identify the composition of amyloid deposits for clinical proteotyping of amyloidosis diseases. Amyloid-ID is enabled by a photosensitized probe analogous to the pan-amyloid sensor Thioflavin T. We show this probe photocatalyzes gradient protein labeling originated from amyloid deposits and enriches them from tissue in a spatially-resolved manner. Next, we exemplify its application in proteotyping the pathogenic protein of the rare Laryngeal Amyloidosis (LA).

2025-01-25 | PXD059313 | Pride

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