Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge

Consortia: HPAC, PanKbase

Zhang Z, Bao X, Jiang L, Luo X, Wang Y, Comai A, Waldhaus J, Hansen AS, Li W, Liu J.
bioRxiv [Preprint]. 2025 May 14:2025.05.08.652986. doi: 10.1101/2025.05.08.652986. PMID:40462903

All T cell and autoantibody recognition of nucleus-associated islet autoantigens in individuals with type 1 diabetes 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 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 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 Closing the Gap Between Vision and Victory in Type 1 Diabetes: The NIDDK Human Islet Research Network (HIRN) Initiative Bend It Like Occam: Ductal Origin of New Islet Cells in Human Pancreas After Injury Type 1 diabetes presenting in adults: Trends, diagnostic challenges and unique features Exercise-induced meteorin-like protein protects human pancreatic beta cells from cytokine-induced apoptosis Oxygen dynamics and delivery strategies to enhance beta cell replacement therapy Efficient transduction of pancreas tissue slices with genetically encoded calcium integrators The type 1 diabetes candidate genes PTPN2 and BACH2 regulate novel IFN-α-induced crosstalk between the JAK/STAT and MAPKs pathways in human beta cells Genetic protection from type 1 diabetes resulting from accelerated insulin mRNA decay Target Discovery to Diabetes Therapy-TXNIP From Bench to Bedside With NIDDK IFN-α Induces Heterogenous ROS Production in Human β-Cells Single-cell multiome and spatial profiling reveals pancreas cell type-specific gene regulatory programs driving type 1 diabetes progression The XCL1/XCR1 axis is upregulated in type 1 diabetes and aggravates its pathogenesis Expanding the engineered Treg multiverse TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and -independent mitophagy A Recombinase-Mediated Cassette Exchange Platform for a Triple Independent Inducible Expression System for Human Pluripotent Stem Cells Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues Identification of a vimentin-expressing α-cell phenotype in CF and normal pancreas Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes Generation of Human Chimeric Antigen Receptor Regulatory T Cells NKX2.2 and KLF4 cooperate to regulate α-cell identity Divergent roles of m(6)A in orchestrating brown and white adipocyte transcriptomes and systemic metabolism CryoEM structure of an MHC-I/TAPBPR peptide-bound intermediate reveals the mechanism of antigen proofreading BETA CELL DYSFUNCTION OCCURS INDEPENDENTLY OF INSULITIS IN TYPE 1 DIABETES PATHOGENESIS TMEM55A-mediated PI5P signaling regulates α-cell actin depolymerization and glucagon secretion Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition The N6-methyladenosine RNA epigenetic modification modulates the amplification of coxsackievirus B1 in human pancreatic beta cells G6PC2 controls glucagon secretion by defining the set point for glucose in pancreatic α cells Changes in immunofluorescence staining during islet regeneration in a cystic fibrosis-related diabetes (CFRD) ferret model SARS-CoV-2 Spike S1 subunit triggers pericyte and microvascular dysfunction in human pancreatic islets T Cell Development and Responses in Human Immune System Mice LRH-1/NR5A2 targets mitochondrial dynamics to reprogram type 1 diabetes macrophages and dendritic cells into an immune tolerance phenotype HistoPlexer: Histopathology-based Protein Multiplex Generation using Deep Learning Targeting peptide antigens using a multiallelic MHC I-binding system Engineering synthetic suppressor T cells that execute locally targeted immunoprotective programs Genetic Discovery and Risk Prediction for Type 1 Diabetes in Individuals Without High-Risk HLA-DR3/DR4 Haplotypes The IsletTester mouse: an immunodeficient model with stable hyperglycemia for the study of human islets Sex-specific regulatory architecture of pancreatic islets from subjects with and without type 2 diabetes Trajectory of beta cell function and insulin clearance in stage 2 type 1 diabetes: natural history and response to teplizumab Combinatorial genetic engineering strategy for immune protection of stem cell-derived beta cells by chimeric antigen receptor regulatory T cells β-Cell gene expression stress signatures in types 1 and 2 diabetes 12-Lipoxygenase inhibition delays onset of autoimmune diabetes in human gene replacement mice Beta cell extracellular vesicle PD-L1 as a novel regulator of CD8+ T cell activity and biomarker during the evolution of type 1 diabetes Maturation and persistence of CAR T cells derived from human pluripotent stem cells via chemical inhibition of G9a/GLP
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