Histopathology-based protein multiplex generation using deep learning

Consortia: CBDS

Andani S, Chen B, Ficek-Pascual J, Heinke S, Casanova R, Hild BF, Sobottka B, Bodenmiller B; Tumor Profiler Consortium; Koelzer VH, Rätsch G.
Nat Mach Intell. 2025;7(8):1292-1307. doi: 10.1038/s42256-025-01074-y. Epub 2025 Aug 4. PMID:40842484

All Beta cell dysfunction occurs independently of insulitis in type 1 diabetes pathogenesis Protein carbamylation and proteomics: from artifacts to elucidation of biological functions Histopathology-based protein multiplex generation using deep learning The integrated stress response promotes macrophage inflammation and migration in autoimmune diabetes Increased longevity of circulating human IgG in an NSG Fc gamma receptor-1 deficient humanized mouse model Receptor-tethered orthogonal IL-2 enhances regulatory T cell therapy Divergent Cell-Type Specific Hypoxia Responses in Human Stem Cell-Derived and Primary Islets Spatially Bound Functional Heterogeneity Drives Modular Organization in Beta Cell Networks Differential immune- and apoptosis-related gene signatures in pancreatic alpha and beta cells contribute to their fate in type 1 diabetes The pathophysiology, presentation and classification of Type 1 diabetes The Heterogeneity of Type 1 Diabetes: Implications for Pathogenesis, Prevention, and Treatment-2024 Diabetes, Diabetes Care, and Diabetologia Expert Forum Loss of Insulin-Positive Cell Clusters Precedes the Decrease in Islet Frequency and β-Cell Area in Type 1 Diabetes LONP1 loss causes mitochondrial mayhem in β-cells The antigen presentation landscape of cytokine-stressed human pancreatic islets A structure-guided approach to predict MHC-I restriction of T cell receptors for public antigens Exendin-4 enhances insulin-positive phenotype of human pluripotent stem cell-derived β cells during transplantation Improved conditioning for hematopoietic chimerism induces islet tolerance to cure diabetes OLIVE Provides Rapid Visualization and Analysis of Chromatin Tracing Experiments Inference of multi-enhancer interactions in T lymphocytes using Hi-Cociety Scalable 3D Bioprinting of Human Islets in a Pancreatic Decellularized Extracellular Matrix-Enriched Bioink for Beta-Cell Replacement Therapy Microvascular homeostasis is compromised in pancreatic islets in a mouse model of beta cell loss and low-grade inflammation Ultrasmall chemogenetic tags with group-transfer ligands Streamlining Multiplexed Tissue Image Analysis with PIPΣX: An Integrated Automated Pipeline for Image Processing and EXploration for Diverse Tissue Types Challenges and Opportunities for Understanding the Pathogenesis of Type 1 Diabetes: An Endocrine Society Scientific Statement Epigenetic adaptation of beta cells across lifespan and disease: age-related demethylation is advanced in type 2 diabetes Pancreatic β-cell regeneration in situ by the ALK3 agonist THR-123 Spatial patterns of hepatocyte glucose flux revealed by stable isotope tracing and multi-scale microscopy Isolation of live human δ cells for genetic and functional analysis Comprehensive molecular impact mapping of common and rare variants at GWAS loci 3D imaging of human pancreas suggests islet sizeand endocrine composition influence their loss intype 1 diabetes Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells RNA editing deficiency models differential immunogenicity of pancreatic α- and β-cells T cell and autoantibody recognition of nucleus-associated islet autoantigens in individuals with type 1 diabetes Solution mapping of MHC-I:TCR interactions using a minimalistic protein system Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets Searching for protein partners of short-chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD) reveals keratin 8 as a novel candidate for interaction in pancreatic β-cells Insulin post-transcriptional regulation via PARP12-mediated ADP- ribosylation 3D imaging of human pancreas suggests islet size and endocrine composition influence their loss in type 1 diabetes Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge Diabetes mellitus polygenic risk scores: heterogeneity and clinical translation Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors Molecular and Inflammatory Etiologies of ß Cell Dysfunction in Type 1 Diabetes Engineered vasculature induces functional maturation of pluripotent stem cell-derived islet organoids Closing the Gap Between Vision and Victory in Type 1 Diabetes: The NIDDK Human Islet Research Network (HIRN) Initiative Advances in Cell Replacement Therapies for Diabetes Functional and Mechanistic Explanation for the Unique Clinical Success of the Glucokinase Activator Dorzagliatin in the Treatment of Type 2 Diabetes Bend It Like Occam: Ductal Origin of New Islet Cells in Human Pancreas After Injury DEC1 Regulates Human β Cell Functional Maturation and Circadian Rhythm Chimeric anti-HLA antibody receptor engineered human regulatory T cells suppress alloantigen-specific B cells from pre-sensitized transplant recipients
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