Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_EMC2_knockdown]
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PROVIDER: PRJNA1269464 | ENA |
REPOSITORIES: ENA
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Project description:Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_thapsigargin_treatment]
| PRJNA1269465 | ENA
Project description:Apoptosis is a critical outcome of stress-induced processes, with the endoplasmic reticulum (ER) playing a central role in apoptotic protein processing and stress signal transduction. Profiling the ER proteome during stress to cell death offers valuable insights into these processes, but existing methods often suffer from a loss of in situ information or requirement of genetic manipulation. In this study, we introduce CAT-ER, a novel non-genetic ER proteomics system that provides in situ labeling, spatiotemporal resolution, and compatibility across diverse cell types. By combining an ER-targeted iridium photocatalyst with a thio-quinone methide (thioQM) probe, CAT-ER achieves high specificity in enriching ER proteins, comparable to traditional enzymatic methods. Importantly, CAT-ER is free of genetic manipulation, allowing its use in hard-to-transfect cell types like HeLa and immune cells (e.g., Raji, Jurkat, and RAW264.7). Given the high spatiotemporal resolution of CAT-ER, we revealed dynamic ER proteome changes during thapsigargin (Tg)-induced unfolded protein response (UPR) to apoptosis. Notably, NFIP2 mitigated ER stress by halting translation when UPR initiated, while compromised EMC2 delayed apoptosis during prolonged stress. These findings provide novel insights into the molecular dynamics linking the UPR and apoptosis. Collectively, CAT-ER serves as a versatile tool for spatiotemporal proteomic analysis without the need for genetic manipulation, offering a powerful approach to study ER dynamics in various biological contexts.
2025-07-23 | GSE298442 | GEO
Project description:Apoptosis is a critical outcome of stress-induced processes, with the endoplasmic reticulum (ER) playing a central role in apoptotic protein processing and stress signal transduction. Profiling the ER proteome during stress to cell death offers valuable insights into these processes, but existing methods often suffer from a loss of in situ information or requirement of genetic manipulation. In this study, we introduce CAT-ER, a novel non-genetic ER proteomics system that provides in situ labeling, spatiotemporal resolution, and compatibility across diverse cell types. By combining an ER-targeted iridium photocatalyst with a thio-quinone methide (thioQM) probe, CAT-ER achieves high specificity in enriching ER proteins, comparable to traditional enzymatic methods. Importantly, CAT-ER is free of genetic manipulation, allowing its use in hard-to-transfect cell types like HeLa and immune cells (e.g., Raji, Jurkat, and RAW264.7). Given the high spatiotemporal resolution of CAT-ER, we revealed dynamic ER proteome changes during thapsigargin (Tg)-induced unfolded protein response (UPR) to apoptosis. Notably, NFIP2 mitigated ER stress by halting translation when UPR initiated, while compromised EMC2 delayed apoptosis during prolonged stress. These findings provide novel insights into the molecular dynamics linking the UPR and apoptosis. Collectively, CAT-ER serves as a versatile tool for spatiotemporal proteomic analysis without the need for genetic manipulation, offering a powerful approach to study ER dynamics in various biological contexts.
2025-07-23 | GSE298441 | GEO
Project description:Photocatalytic Proximity Labeling Maps RNA and Protein Subcellular Landscapes
| PRJNA1299343 | ENA
Project description:Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
| PRJNA925537 | ENA
Project description:Cellular function relies on the precise spatiotemporal organization of biomolecules within organelles. Mapping the local proteome and transcriptome of specific compartments is crucial for understanding cellular processes but remains challenging. Existing proximity labeling (PL) methods based on enzymes often require genetic manipulation, can suffer from background activity, or are limited to a single molecule type. Here, we introduce a versatile photocatalytic proximity labeling (PhotoPL) platform using targeted photocatalysts and activatable probes to map both RNA and protein landscapes within defined subcellular regions in living cells. The platform's modular design allows for simple redirection to new targets by chemically conjugating the catalyst to different targeting moieties. Visible light activation of organelle-targeted ruthenium complexes generates localized singlet oxygen or initiates electron transfer, which selectively activates inert phenylselenomethyl phenol probes to generate reactive quinone methide intermediates. These intermediates rapidly crosslink proximal proteins and nucleic acids within nanometers of the catalyst. We demonstrate precise targeting of PhotoPL to mitochondria and the endoplasmic reticulum (ER), enabling high-resolution mapping of their respective proteomes and transcriptomes. Comparative analysis reveals distinct molecular signatures and co-enrichment patterns, providing insights into organelle-specific functions, RNA localization mechanisms, and protein-RNA interplay under basal and stress conditions. This chemically controlled, light-triggered PhotoPL strategy offers a powerful and highly adaptable toolbox for dissecting the molecular organization of living cells with high spatiotemporal resolution.
2026-09-26 | GSE304177 | GEO
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
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
Project description:Off-the-shelf proximity labeling
| PRJNA716256 | ENA
Project description:In eukaryotic cells, the precise spatial localization of RNAs and proteins is essential for proper cellular function. Genetically encoded photocatalytic proximity labeling techniques have expanded our ability to map subcellular proteomes and transcriptomes, but their temporal resolution remains limited. Here, we introduce Lantern, an engineered flavoprotein optimized via directed evolution, which enables sub‑minute, spatially resolved labeling of cellular biomolecules. Lantern is targetable to diverse subcellular compartments, including the endoplasmic reticulum, mitochondria, and stress granules (SGs), to map local transcriptomes (CAP-seq) and proteomes (CAP-MS). Using Lantern, we observed that m6A‑enriched RNAs are recruited to SGs within five minutes of stress induction, while ER‑proximal RNAs associate with the SG scaffold protein G3BP1 during early SG assembly. Additionally, Lantern was adapted for cell-surface tagging (CAP-CELL), enabling spatially resolved cell typing and the analysis of cell-cell interactions. Collectively, this study establishes Lantern as a powerful tool that offers unprecedented temporal resolution for investigating the dynamic organization of subcellular molecular networks.
2026-03-27 | GSE292673 | GEO