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Biology subjects

Jin, J.

Publications and source records attributed to Jin, J..

At least 37 records · Page 2Linked to original sources

Multispecific nanobody degraders co-deplete membrane receptors and enable targeted delivery of diverse payloads

Targeting membrane receptors underlies the success of antibody-drug conjugates (ADCs), yet single-receptor formats can be limited by heterogeneous expression, compensatory signaling, and variable internalization. Here we developed Multivalent Interchangeable Nanobody Degradation System (MINDS), a modular nanobody-Fc chassis that co-engages multiple membrane receptors, promotes their lysosomal co-depletion, and enables delivery of diverse intracellular payloads. As a proof of concept, we generated Tritazumab, a trispecific nanobody-Fc targeting three oncogenic receptors EGFR, cMET, and TfR1. Tritazumab incorporates a high-affinity, non-transferrin-competing anti-TfR1 nanobody that drives efficient uptake and lysosomal trafficking, enabling coordinated depletion of all three receptors. Across non-small cell lung cancer models, Tritazumab achieved rapid and sustained multi-receptor surface loss with picomolar degradation potency, reaching near-maximal depletion within approximately 1.5 hours. Conjugation of Tritazumab to MMAE preserved receptor binding and produced substantially greater antiproliferative activity and improved tumor selectivity relative to clinical ADCs in matched cell models, along with potent in vivo tumor growth inhibition and acceptable tolerability in a xenograft model. Extending the platform beyond cytotoxic payloads, a BRD4 molecular glue conjugate improved the selectivity window by > 100-fold and showed marked in vivo efficacy, while an EZH2-targeting PROTAC conjugate achieved an approximately 1,000-fold increase in intracellular degradation potency relative to the free PROTAC. These findings establish MINDS as a modular multispecific degrader-payload platform that integrates receptor co-depletion to enhance anticancer selectivity and efficacy.

cancer biology↗

PRMT7 restricts CD8+ T cells expansion via the NF-κB pathway.

New therapeutics are needed to enhance cytotoxic T lymphocyte (CTL) expansion and effector function for effective tumor control. Here, we show that T cell specific deletion of Prmt7 using CD4-Cre mice increases CD8+ effector differentiation, cytokine secretion, cytolytic activity, and anti-tumor responses. Prmt7 deficiency transcriptionally reprogrammed CD8+ T cells by activating the NF-{kappa}B pathway, boosting proliferation, and elevating effector molecules such as CD25, CD69, and IFN{gamma}. Mechanistically, PRMT7 associated with RelA and restricted its nuclear translocation. To enable therapeutic translation, we developed a PRMT7-targeting PROTAC degrader (MS54). MS54-treated CTLs exhibited NF-{kappa}B pathway activation similar to Prmt7-deficient CTLs. Adoptive transfer of MS54-treated OT-I CTLs significantly improved tumor control in a syngeneic melanoma model. In human CTLs, MS54 enhanced proliferation, activation markers (CD69, CD137), IFN{gamma} production, and cytotoxicity toward melanoma. Together, these findings identify PRMT7 as a negative regulator of CD8+ T cell immunity and highlight MS54 as a promising strategy to improve adoptive T cell therapy.

molecular biology↗

Origin and evolution of grapevine genomes

Grapevines (Vitis) belonging to grape family (Vitaceae) are symbolic fruit crops pivotal to human civilization. The evolutionary history of grapevines divergent from other Vitaceae plants remains mysterious, requiring a family-wide whole-genome phylogenomic analysis. Here, we conduct chromosome-level phylogenomics to investigate the origin and evolution of grapevines using 29 genome assemblies of five genera Vitis, Parthenocissus, Ampelopsis, Tetrastigma, and Cissus, 27 of which are newly released in this study. Phylogenomic and macrosynteny analysis unanimously support Ampelopsis as a sister lineage to Parthenocissus, placing both closer to Vitis, with introgression and incomplete lineage sorting contributing to these relationships. Ancestral genome reconstruction delineates the major chromosome rearrangement events in Vitaceae karyotype evolution, highlighting the conserved karyotype in Vitis and the extensive karyotypic reorganization in Tetrastigma and Cissus. Pan-3D genome analysis highlights the contributions of structural variants (SVs) to the variation of A/B compartments and topologically associated domains (TADs), revealing a strong purifying selection of SVs at TAD boundaries. We further demonstrate that Helitron transposons drive the expansion and expression regulation of NLR immune-receptor genes in Vitis. Importantly, we discovered an NLR gene VbRpv35 from wild grapevine V. bellula resistant to downy mildew (DM), whose heterologous expression in V. vinifera confers enhanced DM resistance. Taken together, we provide phylogenomic insight into the origin and evolution of grapevines and valuable resources for grapevine improvement and understanding angiosperm evolution.

genomics↗

Spatial-neighbour encoding enables fast RNA 3D structure search

Experimental and predicted RNA three-dimensional structures are expanding rapidly, but RNA structure search still lacks a compact residue-level representation that supports database-scale comparison. Using family-held-out ablations across the currently available experimental RNA structure collection, we found that spatial-neighbour features are markedly more informative for family-level discrimination than conventional backbone and base descriptors. Building on this result, we developed RiboSeek, a search framework based on a 20-letter geometric alphabet (RS-20), an 80-letter structure-and-base composite alphabet (RS-80). Across family-level classification and retrieval benchmarks, RS-80 delivered the strongest overall performance, whereas RS-20 most closely tracked US-align TM-score, indicating better preservation of geometric similarity. RiboSeek searches the full experimental RNA structure database in 204 ms per query and can be applied to predicted RNA structure libraries to prioritize candidate structural relationships for downstream analysis.

bioinformatics↗

TIM3+ Tumor Associated M2 Macrophages Impair Antitumor T Cell Immunity and Promote Gastric Cancer Progression and Peritoneal Metastasis

Peritoneal metastases (PM) are the leading cause of cancer-related death in gastric cancer (GC) patients with survival typically < 9 months. Here, we demonstrate that TIM3 and its ligands are increased along the GC continuum and associated with poor survival. Integrated omics analyses and functional studies revealed highly enriched TIM3 in CD163+ tumor associated M2 immunosuppressive macrophages significantly promote tumor cell invasion and tumor growth in vivo, while TIM3 depletion in macrophages reduced tumor cell malignant attributes and increased T cell immunity from PBMCs or CD45+ immune cells of malignant ascites in co-culture system. By cytokine and kinase arrays, we discovered that depletion of TIM3 in macrophages reduced the production of notable secretome of cytokines/chemokines from M2 macrophages; and the protumor function of TIM3+ macrophages rely on the p90RSK1/2/CCL20 axis. Finally, we reveal that TIM3 blockage or genetic KO had superior antitumor activity in combination with anti-PD1 immunotherapy and mitomycin C (MMC) chemotherapy. Together, this study uncovers an important role for TIM3 in tumor associated M2 macrophages and underscores the potential of TIM3 blockage in GC patients with PM. Statement of significanceIn this study, we show TIM3 increases along GC continuum, and highly enriched on tumor associated M2 macrophages that fuel tumor growth; and suppress T cell function via p90RSK1/2/CCL20 axis. TIM3 depletion restores T-cell immunity and curbs tumor growth. TIM3 blockade combined with anti-PD1 and mitomycin C provide a novel therapeutic strategy for GC patients with PM.

immunology↗

The ENL-USP7 Complex Regulates HIV Latency Through BRD4 Stabilization

HIV-1 persists in CD4 T cells and brain microglia through host factors that enforce viral latency, yet the mechanisms that stabilize key transcriptional regulators remain incompletely understood. Here, we identify the YEATS domain-containing protein ENL and its associated deubiquitinase USP7 as a host complex that maintains HIV-1 latency. USP7 stabilizes BRD4 by deubiquitination, suppressing HIV transcription and sustaining viral quiescence. Disruption of the ENL-USP7 complex using selective PROTACs reactivates latent HIV in cell line models, as well as in resting CD4 T cells and microglia isolated from people with HIV on antiretroviral therapy. These findings uncover a critical ENL-USP7-BRD4 axis that enforces HIV-1 latency and highlight USP7 as a potential target for latency-reversing strategies. HighlightsO_LIENL, a YEATS domain-containing crotonylation reader, acts as a suppressor rather than an activator of HIV-1 transcription. C_LIO_LIENL recruits USP7 to stabilize BRD4 and enforce viral latency. C_LIO_LIDisruption of the ENL-USP7-BRD4 axis reactivates latent HIV in T cells and microglia. C_LIO_LITargeting USP7 or ENL reveals a therapeutic vulnerability in HIV reservoirs. C_LI

microbiology↗

Structural and biochemical characterization of a novel inhibitor of NMNAT1, the gatekeeper of nuclear NAD+ biosynthesis

Nicotinamide adenine dinucleotide (NAD+) is crucial for cellular functions including DNA repair and metabolism. Nicotinamide mononucleotide adenylyltransferase (NMNAT) enzymes catalyze the final step of NAD+ synthesis from NMN and ATP. There are three NMNAT isoforms: NMNAT1, NMNAT2, and NMNAT3, located in the nucleus, cytoplasm, and mitochondria, respectively. Nuclear NAD+ promotes disease progression in NAD+-dependent cancers, and it is hypothesized that targeting NMNAT1 with small-molecule inhibitors could be an effective therapeutic strategy. Here, we identify an NMNAT1 inhibitor from a bioactive compound screen and report its effects on NAD+ levels and the viability of NMNAT1-dependent cancer cell lines. The compound AMI-1 is a known inhibitor of Protein Arginine N-Methyltransferase 1, and we find that it also inhibits NMNAT1 with similar potency. Additionally, we determined a cryo-EM structure of NMNAT1 bound to AMI-1 and revealed its mechanism of inhibition. This provides proof of principle for inhibiting NMNAT1 to target NAD+ metabolism in dependent cancers, while also highlighting that caution is warranted when interpreting studies using AMI-1 as a PRMT1 inhibitor, given its effect on NAD+ through NMNAT1. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/716846v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@139e792org.highwire.dtl.DTLVardef@923869org.highwire.dtl.DTLVardef@1b5aa1borg.highwire.dtl.DTLVardef@1b2d797_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia

RationaleBronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility. ObjectivesTo comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development. MethodsTracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age. Measurements and Main ResultsMicrobial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition. ConclusionsOur findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.

microbiology↗

Hierarchical Assembly of Native Cytoplasmic Lattices Revealed by Cryo-EM

Oocytes depend on maternal factors for maturation and early embryogenesis. Cytoplasmic lattices (CPLs) are distinctive fibrillar structures in mammalian oocyte cytoplasm implicated in maternal factor storage and developmental competence, yet their molecular composition and architecture remain elusive. Here, we use cryo-electron microscopy to resolve the high-resolution structure of native mouse oocyte CPLs. We identify 14 intrinsic components of multiple copies that assemble into filaments in which PADI6-mediated self-assembly and two subtypes of subcortical maternal complexes (SCMCs) form the core scaffold. Unexpectedly, we discover that /{beta}-tubulin dimers and two autoinhibited ubiquitination modules (UHRF1-UBE2D3, SKP1-FBXW18) are internal components of CPLs. We also uncover multivalent interactions that organize adjacent CPL filaments into higher-order helical bundles. By integrating CPL structure with biochemical and proteomic data, we propose a hierarchical assembly mechanism of CPLs, from subcomplexes to filaments to supramolecular lattices. Our study offers mechanistic insights into how maternal proteins are spatially organized to ensure successful early embryonic development and provides a structural foundation for understanding female infertility related to CPL-associated gene mutations.

developmental biology↗

Benchmarking and Experimental Validation of Machine Learning Strategies for Enzyme Engineering

Enzyme-directed evolution increasingly relies on computational tools to prioritize mutations, yet their practical value is difficult to assess because kinetic data are often aggregated across heterogeneous assay conditions, inflating apparent generalization. Here we introduce EnzyArena, a curated benchmark in which kinetic parameters (kcat, Km and kcat/Km) are grouped by experimental campaign and measured under matched conditions, thereby minimizing confounders such as pH, temperature, reaction, and batch. Using EnzyArena, we systematically evaluate 20 models spanning four widely used strategies for guiding enzyme evolution: protein-ligand binding affinity prediction, protein stability prediction, zero-shot fitness prediction and enzyme kinetic parameter prediction. Across subsets derived from public databases and 25 independent mutagenesis datasets, most models exhibit weak, fragile or inconsistent correlation with catalytic activity. Kinetic-parameter predictors perform strongly on database-derived subsets but lose their advantage on independent datasets, whereas zero-shot predictors show more consistent generalization. A simple consensus of multiple zero-shot models further improves the precision of identifying beneficial mutants. We prospectively validated these findings in a wet-lab campaign (150 mutants) comparing random mutants, UniKP-prioritized mutants and ESM-1v-prioritized mutants (representing supervised kinetic-parameter prediction and zero-shot fitness prediction, respectively), where ESM-1v achieved the highest utility and UniKP underperformed the random baseline. Together, this study establishes realistic baselines for computational mutant prioritization and highlights consensus zero-shot strategies as a practical starting point for enzyme engineering. Zero-shot fitness predictors are the most competitive and generalizable class, but still achieve only modest correlations on independent datasets. Notably, a simple consensus of multiple zero-shot models substantially improves the precision of identifying superior mutants and currently offers the most practical computational benefit for enzyme engineering. Our work establishes EnzyArena as a fair benchmark for enzyme activity prediction, defines realistic performance baselines for existing tools, and highlights consensus zero-shot strategies as the most useful computational tool in practice for enzyme-directed evolution.

bioengineering↗

A feed-forward loop between niche adenosine and Gzmk⁺ CD8 T cells propagates systemic inflammaging

The causal link between the aging microenvironment and T cell aging remains elusive. Here, we demonstrate that adenosine within aging tissues actively reprograms CD8+ T cells into a pro-aging Granzyme K+ (Gzmk+) population. Mechanistically, senescent cells create an adenosine-rich niche via p16-dependent CD39 upregulation, triggering A2aR signaling to induce Gzmk+ T cell differentiation. Once released, Gzmk promotes systemic inflammaging through PAR1 and complement activation. Crucially, targeting this axis--either via genetic Gzmk ablation or pharmacological A2aR blockade--reverses multi-organ aging phenotypes and significantly extends healthy lifespan in mice. Human analysis reveals age-dependent Gzmk+ T cell accumulation in multi organs, while coffee intake (an A2aR antagonist) inversely correlates with plasma Gzmk levels. Our findings uncover how metabolic niche changes drive T cell aging and establish the adenosine-Gzmk axis as a pivotal therapeutic target for combating age-related diseases.

immunology↗

Reconstructing multi-scale tissue spatial architecture from single-cell RNA-seq with REMAP

Understanding spatial organization of cells is critical for deciphering tissue function and disease. Single-cell RNA-sequencing (scRNA-seq) profiles transcriptomes at scale but loses spatial context, while spatial transcriptomics (ST) preserves spatial information but is constrained by cost and gene coverage. Here, we present REMAP, a deep learning framework that integrates gene expression with neighborhood-level gene-gene covariance to reconstruct multi-scale spatial organization of scRNA-seq data using one or multiple ST references. Across 2D and 3D mouse brain, human fetal cortex, and seven human cancer types, REMAP consistently outperformed existing approaches. Applied to a human multiple sclerosis atlas, REMAP resolved microglial neighborhood heterogeneity, and identified a rare pro-inflammatory microglia-astrocyte subpopulation. Across diverse cancers, REMAP recovered conserved spatially-defined cancer-associated fibroblast subtypes with known prognostic significance. By transforming cost-efficient single-cell datasets into spatially interpretable tissue maps, REMAP enables spatial hypothesis generation, microenvironment discovery, and population-scale inference of conserved and perturbed architectural principles in human disease.

genomics↗

A dimer peptide ligand of vascular endothelial growth factor slows the progression of human gastric tumors in mouse xenografts

Gastric cancer is among the most common cancers and represents a major public health problem worldwide. New therapeutic strategies and drugs are needed. Anti-angiogenic agents targeting the Vascular Endothelial Growth Factor (VEGF) are used in combination therapy in the clinic, although their efficacy remains modest. We believe that these large anti-VEGF antibodies could be advantageously replaced by smaller peptides with better tissue penetration. In this study, we evaluate the efficacy of a previously described dimer peptide ligand of VEGF, D6, in inhibiting the proliferation of gastric cancer cells and the growth of the corresponding murine xenograft. The activity of the D6 peptide in these assays was comparable to that of bevacizumab, the positive control antibody, although the peptide required repeated injections at higher molar concentrations. These promising results justify the continued optimization of the peptide dimer, currently under investigation in our laboratory.

pharmacology and toxicology↗

Vascular signals coordinate cerebellar circuitry development

Neural circuit assembly requires precise coordinated interactions between developing neurons and the vasculature, yet the instructive signals provided by endothelial cells remain largely unknown. Here, we identify a vascular-to-neural signaling axis that orchestrates postnatal cerebellar development. Endothelial-specific deletion of the adaptor protein Dab1 in mice disrupted vascular patterning and uncoupled the growth of major cerebellar neuronal populations. We show that endothelial Dab1 in the cerebellum drives secretion of the morphogen Wnt5a, which acts through Frizzled-2 to restrain granule-cell progenitor proliferation and promote Purkinje-cell dendritic maturation. Endothelial Wnt5a deletion phenocopied Dab1 endothelial mutant (Dab1i{Delta}EC) defects, whereas exogenous Wnt5a restored normal progenitor dynamics in Dab1i{Delta}EC cerebellar slices, demonstrating pathway sufficiency. Functionally, loss of this vascular signal impaired Purkinje-cell firing, diminished parallel-fiber input, reduced synapse formation from both parallel and climbing fibers, and disrupted long-term plasticity. These findings reveal a key instructive role for blood vessels in shaping cerebellar architecture and establishing functional circuit connectivity.

neuroscience↗

Regulation of BCL11A DNA binding and expression in human erythrocyte precursor HUDEP-2 cells

BCL11A is a transcription factor crucial for neurodevelopment and hematopoiesis. It regulates the developmental switch from fetal hemoglobin (HbF) to adult hemoglobin and is a major therapeutic target for sickle cell disease and {beta}-thalassemia. BCL11A exists in multiple isoforms, including the L isoform (containing a single two-finger ZF2-3 DNA-binding domain) and the XL isoform (containing two arrays: the two-finger ZF2-3 and the three-finger ZF4-6). We used three approaches to investigate BCL11A functions. First, we examined DNA recognition by BCL11A, which preferentially binds the short 6-bp DNA motif TGNCCA. ZF4-6 recognizes all four variants of this motif with distinct strand-specific interactions: TGTCCA on the top strand, TG(A/C)CCA on the complementary strand, and the palindromic TGGCCA on either strand. ZF2-3 also binds TGTCCA from the top strand, featuring a unique thymine interaction by ZF2 Phe388. Motif multiplicity within BCL11A binding sites may promote BCL11A oligomerization by enabling multiple ZF arrays to engage DNA simultaneously. Second, we treated HUDEP-2 cells (which express adult hemoglobin) with inhibitors targeting three epigenetic silencing marks - DNA methylation, histone H3 lysine 9 methylation or H3 lysine 27 methylation. All treatments, individually or in combination, increased HbF expression to varying degrees. Notably, FTX6058 markedly reduced BCL11A transcription and translation (likely via effects on LIN28B), while EML741 caused a partial reduction. Third, we screened 213 pomalidomide- and lenalidomide-derived compounds and quantified proportions of HbF+ cells by flow cytometry. Effects of four compounds were analyzed by protein mass spectrometry. Although BCL11A levels themselves were unchanged, all four compounds selectively decreased levels of known pomalidomide targets, with consistently decreased levels of the zinc-finger proteins IKZF1 and ZFP91. Together, our studies clarify how BCL11A recognizes DNA, how its expression can be modulated epigenetically, and how small-molecule degraders influence its regulatory network, providing new avenues for HbF reactivation therapies.

biochemistry↗

BlueNuclei: automated identification and classification of live and dead transfected neurons using interpretable features

In vitro modeling of neuronal disorders using transfected primary neurons is one of the fundamental approaches for studying disease mechanisms and therapeutic screening. Assessing neuronal viability is an everyday yet critical task in such experiments and requires accurate identification and classification of live and dead transfected neurons from dual-channel fluorescence images; however, this step is typically performed manually, resulting in inconsistent, labor-intensive, and poorly scalable analysis due to limitations of existing image analysis tools. Here, we present BlueNuclei, a user-friendly software with two modules: Hyades, which identifies nuclei of transfected neurons using dual-channel fluorescence image processing techniques, and Pleiades, an SVM-based classifier that distinguishes live from dead neurons using human-vision-inspired, biologically interpretable subnuclear features. Benchmarking on real images showed that BlueNuclei achieves near-human accuracy with substantially faster processing and minimal computational resources compared to deep learning alternatives when applied to the classification step. BlueNuclei provides a simple local user interface for data input and interactive visualizations that display classification results, including feature metrics and a confidence score for each nucleus. BlueNuclei offers the first scalable, fully automated, solution to viability assessment of transfected neurons, facilitating in vitro mechanistic studies of genetic neuronal disorders and therapeutic screening.

neuroscience↗

Multifaceted Functional Complexity of SARS-CoV-2 Helicase Nsp13 Underlies Its Integrated Motor and Remodeling Activities

SARS-CoV-2 nonstructural protein 13 (Nsp13) is a superfamily 1 helicase essential for viral replication. Although its canonical ATP-dependent unwinding activity is well established, the broader functional repertoire of Nsp13 remains unclear. Here, we show that Nsp13 encodes a high degree of complexity by acting as a tunable nucleic acid remodeler that integrates motor and non-motor activities within a single protein. Nsp13 operates in multiple mechanistically distinct regimes, including a canonical ATP-dependent helicase mode and a Mg{superscript 2}-primed, ATP-independent remodeling state capable of destabilizing short duplexes, hairpins, and G-quadruplexes. Mg{superscript 2} binding allosterically stabilizes a compact RecA1-RecA2 configuration, priming the enzyme for ATP-independent remodeling. Unwinding polarity is substrate-dependent, with duplexes supporting bidirectional remodeling, whereas G-quadruplexes are preferentially resolved in the 5'[->]3' direction. Beyond strand separation, Nsp13 also exhibits robust strand annealing and nucleic acid chaperone activities. Cofactors, substrate topology, and enzyme concentration dynamically regulate these activities. Together, our findings establish Nsp13 as a highly integrated nucleic acid remodeling system and reveal how a single viral helicase switches between motor-driven and remodeling-dominated states to meet the structural demands of replication and transcription.

biochemistry↗

Immunological Differences in Atopic Dermatitis Across Age Groups: Insights from Single-Cell Multi-Omics

BackgroundAtopic dermatitis (AD) occurs across all ages but presents distinct clinical and immunologic features between children, adults, and older adults. The molecular programs underlying these age-specific immune differences remain poorly understood. MethodsWe performed single-cell multi-omics profiling of peripheral blood mononuclear cells (PBMCs) from 29 AD patients and 29 matched healthy controls (HC), spanning pediatric (0-17 years), adult (18-59 years), and geriatric ([&ge;]60 years) groups. Using Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), we simultaneously quantified transcriptomic (RNA) and surface proteomic (ADT) profiles across [~]280,000 immune cells. Integrated analyses identified 30 immune subsets for cell-type proportion and differential expression analyses. Machine-learning classifiers were trained on significant gene and protein features to distinguish AD subgroups by age. ResultsCompared with HC, AD blood showed enrichment of CD14+ monocytes, plasmacytoid dendritic cells, and CD4+ proliferating T cells. Within AD, pediatric patients had increased {gamma}{delta} T cells, naive CD4+, and naive CD8+ T cells, while geriatric patients exhibited more CD4+ cytotoxic and CD8+ central memory T cells, indicating a shift from naive to effector predominance with aging. Transcriptomic and proteomic analyses revealed distinct programs: pediatric AD was enriched for IL-10 and cytokine-cytokine receptor signaling; adult AD demonstrated activation of metabolic and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-{kappa}B)/Th1/Th17 pathways; and geriatric AD exhibited reduced adaptive immune activity but increased innate signaling. Machine-learning models based on differentially expressed genes and proteins accurately classified AD age groups (transcript-based F1 = 0.70, AUC = 0.79), identifying stable markers such as IRF2, PDK4, ZFP90, CD21, CD94, and CD122. ConclusionsSingle-cell multi-omics profiling revealed immune differences across the AD lifespan, transitioning from developmental tolerance in children to inflammatory and metabolic activation in adults to enhanced innate signaling in geriatric individuals. These findings highlight molecular signatures that could support age-specific diagnostics and therapeutic strategies for AD across the lifespan.

immunology↗