Challenges and future directions of AIRR-seq-based diagnostics

Consortia: HPAC

Stervbo U, Filippidis P, Breden F, Cowell LG, Davi F, Greiff V, Langerak AW, Luning Prak ET, Sharland AF, Miho E, Meysman P.
Immunoinformatics (Amst). 2025 Sep;19:100056. doi: 10.1016/j.immuno.2025.100056. Epub 2025 Jul 30. PMID:42180390

Published Works Type 1 diabetes SIRPG risk variants increase SIRPγ expression and CD47 loss enhances CD8(+) T cell cytotoxicity Discovery of Post-Translationally Modified Epitopes in Autoimmunity: Someone Has to Fish so Everyone Can Eat Deletion of a distal IRF4 element prevents inflammation-induced reprogramming of human regulatory T cell fate m(6)A mRNA methylation regulates pancreatic α-cell plasticity Deletion of the T1D risk gene Ormdl3 in β-cells does not impact disease progression Receptor-tethered orthogonal IL-2 enhances regulatory T cell therapy The SenKiller Mouse: Enabling Cell Type-Specific Ablation of Senescent Cells Developmental Control of DNA Damage Responses in α- and β-Cells Shapes the Selective β-Cell Susceptibility in Diabetes Applications of Stem Cell-Derived Islets and Emerging Experimental Platforms to Understand Diabetes Dissecting human organ development using spatial technologies AutoPCR: automated phenotype concept recognition by prompting Imaging mass cytometry reveals functional and immunological changes during type 1 diabetes progression in human pancreata Mapping histologic and functional maturation of human endocrine pancreas across early postnatal periods Challenges and future directions of AIRR-seq-based diagnostics Assessing Extracellular Vesicle Proteins as Predictive Biomarkers for Developing Type 1 Diabetes Optimizing post-transplantation detection of subcutaneously transplanted islets using dithizone staining Real-time in vivo analysis of murine β cells reveals autophagic flux defects before onset of autoimmune diabetes A mitochondrial ROS-dependent antiviral response promotes β cell resilience and is diminished in donors with type 1 diabetes Supervised machine learning identifies impaired mitochondrial quality control in β-cells with development of type 2 diabetes New and emerging therapies in type 1 diabetes mellitus Accounting for Age-Related Increases in HbA1c More Accurately Quantifies Risk of Type 1 Diabetes Progression in Islet Autoantibody-Positive Adults Differential Contributions of IgM and IgG Autoantibodies to Serologic IA2 Reactivity in Type 1 Diabetes Epigenetic adaptation of beta cells across lifespan and disease Beta cell microRNAs function as molecular hubs of type 1 diabetes pathogenesis and as biomarkers of diabetes risk Whole-genome CRISPR screening identifies genetic modifiers of stem cell-derived islet transplantation Beyond bystanders: How β cell stress shapes the autoimmune response in T1D Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes Enhanced hypoxia resistance distinguishes human pluripotent stem cell-derived islets from primary islets Paracrine inhibition via G protein inwardly rectifying potassium channels regulates glucagon secretion from human pancreatic alpha cells Islet-derived T cells from both mice and humans recognize conserved insulin A-chain peptides presented by HLA-C*03:04 Messenger RNA delivery to islet β cells using conjugated lipid nanoparticles Lysine Targeting Group-Transfer Chimeras for Proximity Induction Differential immune- and apoptosis-related gene signatures in pancreatic alpha and beta cells contribute to their fate in type 1 diabetes BRD4 Phosphorylation Regulates the Structure of Chromatin Nanodomains Longitudinal monitoring of type 1 diabetes progression to disease onset Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets Baseline Insulin Secretion Determines Response to Abatacept in Stage 1 Type 1 Diabetes Persistent urinary metabolic signatures in children with type 1 diabetes Activating Muscarinic Receptor Signaling in Intrapancreatic Neurons Is Required for Parasympathetic Cholinergic Control of Pancreatic Cell Function The perfect storm: unraveling the interplay of genetic predisposition and viral triggers in type 1 diabetes pathogenesis DEC1 regulates human β cell functional maturation and circadian rhythm Limitations in PPARα-dependent mitochondrial programming restrain the differentiation of human stem cell-derived β cells ADAR1 editing is necessary for only a small subset of cytosolic dsRNAs to evade MDA5-mediated autoimmunity CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations Compressed sensing expands the multiplexity of imaging mass cytometry Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge Inhibition of cell-mediated immunity in type 1 diabetes by beta cell-targeted PD-1 agonists in pancreas tissue slices Long-term culture of human pancreatic islets reveals reduced metal ion pathways in their gene signature T Cell Antigen Discovery Using Cell-Based Epitope Libraries Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes
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