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ProteomicsDeep Visual Proteomics reveals DNA replication stress as a hallmark of Signet Ring Cell Carcinoma
Background and Aims: Signet-Ring (SR) cell carcinoma (SRCC) is an increasingly prevalent form of gastric cancer, known for its late presentation and poor treatment outcomes. Using our spatial proteomics pipeline, Deep Visual Proteomics (DVP), we aimed to comprehensively explore the SRCC proteome lan...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD053079 | Pride
Deep visual proteomics Signet ring cell carcinoma Precision oncology Spatial proteomics Mass spectrometry Pathology Cancer Case study 
ProteomicsSpatial characterization and stratification of colorectal adenomas by Deep Visual Proteomics
Background and Aims: Colorectal adenomas (CRAs) are precursor lesions that can progress to adenocarcinomas. Current clinical guidelines categorize patients into risk groups based on adenoma characteristics observed during index colonoscopy, but this may lead to overtreatment. Our aim was to establis...
ORGANISM(S): Homo sapiens (Human) 
2024-08-04 | PXD046999 | Pride
Spatial Mass spectrometry Pathology Cancer Colorectal adenoma Proteomics Dvp 
ProteomicsAI-powered Deep Visual Proteomics unmasks critical molecular transitions in pancreatic cancer precursors
Pancreatic ductal adenocarcinoma (PDAC) evolves through precursors, yet the protein programs that govern early progression remain poorly defined. We applied Deep Visual Proteomics - computational pathology, laser microdissection, and mass spectrometry (MS) - to profile normal ducts, acinar-to-ductal...
ORGANISM(S): Homo sapiens (Human) 
2026-03-31 | PXD072559 | Pride
Deep visual proteomics Laser microdissection Pathology foundation models Mass spectrometry Artificial intelligence Precursor Spatial Tumor Pancreatic ductal adenocarcinoma 
ProteomicsMultiplexed Deep Visual Proteomics Resolves Spatial Heterogeneity and Rare Endocrine States in Human Pancreatic Islets
Understanding tissue function requires connecting spatial cellular context with molecular depth, yet such integration remains challenging in complex organs like the pancreas. We developed multiplexed Deep Visual Proteomics (mxDVP), an end-to-end workflow combining high-plex imaging, automated comput...
ORGANISM(S): Homo sapiens (Human) 
2026-09-24 | PXD062166 | Pride
Pancreas Multiplexed imaging Single-cell proteomics Deep visual proteomics Spatial omics 
ProteomicsDeep Visual Proteomics and spatial transcriptomics reveal the landscape of tumor malignancy in borderline ovarian cancer
Women of reproductive age can develop serous borderline tumors (SBT) characterized by the uncontrolled growth of epithelial cells that do not invade the stroma. Despite a good prognosis after surgery, SBT may recur as low-grade serous cancer (LGSC), which is invasive and responds poorly to current s...
ORGANISM(S): Homo sapiens (Human) 
2025-06-20 | PXD046354 | Pride
Spatial Mass spectrometry Ovarian cancer Pathology Serous borderline Multi-omics Low-grade serous cancer Proteomics Malignancy Dvp Geomx 
ProteomicsDeep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation
Intestinal epithelial damage predisposes to chronic disorders like inflammatory bowel disease. The organoid model allows the cultivation, expansion and analysis of primary intestinal epithelial cells and has been instrumental in studying epithelial behavior in homeostasis and disease. Recent advance...
ORGANISM(S): Homo sapiens (Human) 
2025-09-11 | PXD052341 | Pride
Colon Spatial proteomics Deep visual proteomics Organoids Proteomics 
ProteomicsDeciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics
Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we introduced mipDVP, an advanced approach integrating highly multiplexed imaging, single-cell laser microdissection, and sensitive mass spectrometry to spatially prof...
ORGANISM(S): Homo sapiens (Human) 
2024-12-19 | PXD057118 | Pride
Cancer Multiplex staining Mass spectrometry Deep visual proteomics Tumor microenvironment 
ProteomicsDeep Visual Proteomics defines single-cell identity and heterogeneity
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven ima...
ORGANISM(S): Homo sapiens (Human) 
2022-04-27 | PXD023904 | Pride
Microscopy Digital pathology Proteomics Laser microdissection 
ProteomicsBypassing Androgens: CNS-Targeted Estrogen Delivery Rescues the Gonadectomized Male Rat Visual Cortex Neuroproteome
Mass spectrometry-based proteomics has become instrumental for elucidating the molec-ular mechanisms of neurodegeneration, enabling the identification of disease-associated proteomic alterations and protein-level responses to therapeutic interventions. Building on our previous proteomic characteriza...
ORGANISM(S): Rattus norvegicus (Rat) 
2026-09-14 | PXD080450 | Pride
Androgen deprivation  bioinformatics  dhed  gonadectomy  neuroprotection  neuropro-teomics  mass spectrometry  oxidative stress  visual cortex. 
UnknownDeep Visual Proteomics defines single-cell identity and heterogeneity.
Not available
S-EPMC9371970 | biostudies-literature
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