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Results for “cell biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2026

Type 2 conventional dendritic cells and regulatory T cells form a barrier tissue circuit to control allergic inflammation

Chronic allergic diseases are driven by T helper type 2 (Th2) cells in barrier tissues. Despite their profound effects on tissue physiology, Th2 cells represent a rare cell population within tissues, suggesting mechanisms restraining Th2 cell expansion at barrier sites that remain ill defined. Using a murine model of allergic asthma, we demonstrate that effector Th2 cells promote cDC2 activation within the lungs, including expression of the CCR4 ligands that attract Foxp3+ regulatory T cells (Tregs). Selective deletion of Ccr4 in Tregs during the effector Th2 cell response led to increased lung Th2 cells, activated cDC2s, and allergic inflammation. Mechanistically, CCR4 promoted Treg trafficking efficiency and was required to specifically control tissue cDC2 co-stimulatory molecule expression. Lastly, in the airways of humans with allergy, the expression of the CCR4 ligands in activated cDCs correlated with Treg enrichment. In sum, we define a cDC2-Treg feedback circuit within a barrier tissue that restrains effector Th2 cell expansion, revealing a novel role for tissue cDC2s in controlling Th2 cell biology.

immunology↗

bioRxiv2026

Automated LN2 refill device for uninterrupted cryoFIB-SEM operations.

Due to recent technological advances, in situ structural cell biology is becoming a high throughput microscopy technique as all the steps of the workflow, from sample preparation to data analysis, are executed faster, more reliable and more reproducible. Sample thinning by cryoFIB-SEM is an essential tool in preparing electron transparent lamellae of biological specimens suitable for further characterization by cryoET. Modern cryoFIB-SEM instruments can be operated remotely and are capable of automated and unsupervised lamellae preparation. To take full advantage of these developments they need a constant supply of LN2 to maintain cryogenic conditions inside the microscope chamber. Here, we introduce a custom automated LN2 refill system that is compatible with gas cooled cryostages, supports long-term cryoFIB-SEM operations and liberates the user from highly repetitive and manual work. We believe this solution can be utilized with other cryoSEM or cryoFIB-SEM devices requiring N2 gas-flow cooling.

biophysics↗

bioRxiv2026

Culsma: A Formal Language for Laboratory Protocols

Laboratory protocols are commonly communicated in natural language, leaving room for variation in how experimental commitments are understood and carried out. We present Culsma, an executable specification language in which protocols are written as programs. The same program is legible to bench scientists and directly machine-readable by software that checks and runs it. It serves as the protocol's operational specification, making experimental commitments explicit for checking before execution and retaining them in results. Culsma addresses how experimental procedures are modeled: it defines operations by the experimental changes and relationships they establish, giving a fine-grained, compositional basis whose technique- and device-specific realizations remain extensible. We examine this boundary in workflows spanning molecular and cell biology, protein biochemistry, and immunoassays, which combine material handling, separation, and measurement differently, asking which distinctions the operation interface preserves. A maintained, source-linked benchmark broadens this evaluation with versioned checks of source-step correspondence and software execution.

bioinformatics↗

bioRxiv2026

Automated assembly of protein complexes from cryo-EM maps with structure-informed Monte Carlo Tree Search

Structural cell biology aims to visualize functional molecules as they carry out their biological roles in their native cellular context. However, macromolecular complexes in situ have thus far been resolved predominantly at intermediate resolutions, complicating protein identification and structural modeling due to the vast combinatorial space of possible components within a proteome. Here, we developed Cryosearch, a GPU-accelerated framework for automated assembly of macromolecular complexes from proteome-scale monomer libraries. Cryosearch implements Monte Carlo tree search with correlation-based rewards to identify combinations of protein domains that collectively best explain density maps. This approach enables autonomous de novo assembly of molecular complexes from intermediate-resolution maps.

bioinformatics↗

bioRxiv2026

A Spectrum of Possibilities: A Systematic Evaluation of Fluorescent Proteins in Cyanobacteria

Fluorescent reporters cover a wide range of applications in both basic and applied research. Whether a study involves microscopic imaging to study (co)-localization of proteins, FRET, biosensing, or quantifying gene expression, fluorophores are attractive reporter candidates due to their relatively straightforward in vivo readout. For microbiological applications, a wide variety of fluorescent proteins with varying excitation and emission wavelengths, brightness levels, and maturation times are available. Careful consideration is required when selecting from this large suite of proteins, especially when choosing multiple fluorophores. This is further complicated in phototrophic organisms, which exhibit strong autofluorescence, especially towards the red part of the spectrum, effectively eliminating common candidates such as mCherry. In this study, the specific properties and performance of a selection of fluorescent proteins are systematically evaluated against the background of photosynthetic pigment-derived autofluorescence in the cyanobacterium Synechocystis sp. PCC 6803. Specific readouts of different combinations of fluorescent proteins are also analyzed using high-throughput methods, namely plate reader fluorescent scans and single-cell flow cytometry to quantify fluorescence. The ultimate goal is to assess each fluorescent protein with regard to: 1.) Its ability to be discerned from cyanobacterial autofluorescence. 2.) Its compatibility with other fluorophores in this context. 3.) Its overall suitability in cyanobacterial research. Several highly suitable fluorescent proteins for use in cyanobacteria are identified, including mTagBFP2, mNeonGreen and mScarlet-I and suitable combinations, covering nearly the whole spectrum of visible light. This study expands the knowledge and toolset for current and future researchers and uncovers a whole spectrum of possibilities for fluorescent protein selection in cyanobacterial cell biology.

synthetic biology↗

bioRxiv2026

Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity

Most autoimmune disease-associated variants lie in non-coding regions, but the molecular mechanisms linking these variants to gene regulation remain poorly understood. A major unresolved challenge is to determine how disease alleles alter transcription factor (TF) binding, cofactor (COF) recruitment, and enhancer activity at scale. Here, we used the CASCADE method to profile differential binding of five TFs and ten COFs to 2,901 autoimmune disease-associated variants in Jurkat T cells, identifying 516 binding-modulating variants. Variants impacting binding were enriched among MPRA-defined expression-modulating variants and were strongly concordant with allele-specific reporter expression, linking altered TF/COF recruitment to enhancer activity. A majority of variants perturb binding of five major TF families -- ETS, RUNX, SP/KLF, OVOL/MYBL, and bHLH -- all of which have established roles in T cell biology. Notably, we find that ETS and RUNX factor binding is enriched at different variant functional classes, suggesting that they act through distinct regulatory mechanisms at disease loci. We describe allele-dependent regulator "switching" at several loci, where distinct complexes are found at reference and variants alleles, and we identify a recurrent regulatory module involving FOXM1 and the cofactors TIP60, BRD4, NCOA3, and NCOA1 assembling on ETS sites that tracks with gene expression. Together, this integrated biochemical and functional framework prioritizes autoimmune disease-associated variants by linking allele-specific TF/COF binding mechanisms to enhancer activity.

genomics↗

bioRxiv2026

Roles for Phosphatase PP4 in Rhythmicity and Compensation in the Neurospora Circadian System

The circadian clock is a highly conserved timer which allows organisms to anticipate future conditions driven by the 24-hour day on planet Earth. Circadian clocks from fungi to mammals are based on a transcription-translation feedback loop (TTFL) molecular architecture. Progressive phosphorylation of core clock proteins can alter both their activity and stability and is required for all known circadian TTFLs. The mechanism for kinase control of circadian period has been extensively studied; however, the mechanism(s) whereby phosphatases alter period remain less studied. Based on the observation that strains of Neurospora crassa lacking phosphatase pp4 display a short circadian period, we investigated regulation of pp4 and its role in the clockworks. In addition to period shortening, loss of pp4 results in a significant loss of both temperature and nutritional compensation, consistent with substrates within the core clock. We identify the clock-relevant PP4 phosphatase holoenzyme as a heterotrimer, and identify two activators of PP4 which regulate circadian period. Biochemical and cell biological analyses suggest that PP4 acts in the nucleus, and a mass spectrometry-based screen identified NCU07414, a member of the HSP40 chaperone system, as a novel PP4 binding partner whose loss results in a dramatically shortened period of the clock when ablated. A model consistent with the data suggests that PP4 may act in opposition to kinases to influence the rate of accumulation of the clock-relevant phosphorylations that determine circadian period.

genetics↗

bioRxiv2026

Shifts in the population-genetic landscape of the ciliate genus Paramecium

Ciliates are one of the most ecologically diverse and morphologically intricate unicellular organisms. Despite their evolutionary significance and their prominence in cell-biological research, the population-genetic processes governing their diversification have received remarkably little attention. A fundamental unresolved problem is the existence of geographic isolation among free-living protists and its consequences for species richness. We addressed this issue in the model ciliate Paramecium by sequencing genomes of hundreds of isolates collected worldwide, capturing multiple morphological and cryptic species, with multiple populations each. Contrary to previous reports, we found evidence of geographic differentiation in the majority of species. In a few cases, geographic structure became evident when deeply diverging clades in a species were treated separately. This suggests that the biogeographical patterns of Paramecium have been shaped by periods of genetic isolation leading to speciation, with rare events of global dispersal realized over its long evolutionary history. Despite being largely isolated, populations were remarkably similar in their effective population size, recombination rate, and efficacy of natural selection. Across species, selection appears to be least effective in Paramecium aurelia lineages, and most effective in P. bursaria, presumably due to differences in their breeding characteristics. Despite differences among species in the population-genetic environment, patterns of variation across the genome remained consistent. Selective constraints on a core set of genes seemed to have gradually diverged across the species phylogeny. Genes with multiple copies retained from whole-genome duplication events in P. aurelia were found to be under relatively relaxed purifying selection. Moving forward, this dataset will serve to test hypotheses on the ecological and cellular complexity of Paramecium and beyond.

evolutionary biology↗

bioRxiv2026

Establishing the fluorescence-activating and absorption-shifting tag as a fluorescent reporter protein in Methanothermobacter thermautotrophicus ΔH

The thermophilic methanogen Methanothermobacter thermautotrophicus {Delta}H is a model microbe for hydrogenotrophic methanogenesis and an emerging platform host for metabolic engineering. Despite recent advances in its genetic accessibility, the available molecular toolbox lacks fluorescent reporter proteins that are suitable for anaerobic and thermophilic conditions. Here, we established the fluorescence-activating and absorption-shifting tag (FAST) as a reporter protein in M. thermautotrophicus. We expressed codon-optimized variants of FAST by applying established genetic tools, and evaluated the performance for two temperatures and three fluorogens. We demonstrated that FAST is functional in M. thermautotrophicus but exhibits temperature-dependent instability, which is more pronounced at 60{degrees}C compared to 50{degrees}C. Among the tested fluorogens, TFLime and TFAmber yielded comparable fluorescence intensities, while TFCoral resulted in significantly lower fluorescence intensity. Exploiting the partial thermolability of FAST, we characterized the dynamic expression profiles of several promoters, which revealed growth phase-dependent regulation patterns. Our findings challenge previous assumptions of constitutive expression for several promoters. Notably, we identified distinct expression patterns for promoters that are associated with methanogenesis and energy-converting hydrogenases. Our results establish FAST as a versatile fluorescent reporter for thermophilic methanogens and provide new insights into promoter regulation in M. thermautotrophicus. This work expands the genetic toolbox for this microbe and lays the foundation for advanced studies in archaeal cell biology and biotechnology.

microbiology↗

bioRxiv2026

Cost-Effective Purification of Endotoxin-Free LIF, IL-2, and IL-33

We describe a cost-effective Escherichia coli (E. coli)-based platform for producing endotoxin-free cytokines. As a proof of concept, we applied this protocol to purify four representative human and mouse cytokines - mouse leukemia inhibitory factor (mLIF), human interleukin-2 (hIL-2), and human and mouse interleukin-33 (hIL-33 and mIL-33) - and demonstrated their bioactivity to be equivalent to commercial counterparts for direct use in stem cell culture and immune cell activation, both in vitro and in vivo. Reagent costs for producing these proteins are approximately 5%-10% of commercial list prices. This platform is readily adaptable to other costly cytokines and growth factors, providing a scalable and affordable approach to accelerate research in cell biology, tissue engineering, and biomanufacturing.

bioengineering↗

bioRxiv2026

A bifunctional coiled-coil protein generates the membrane-within-condensate architecture of the CO2-fixing pyrenoid

How membranes are integrated into biomolecular condensates is a fundamental question in cell biology. In the algal pyrenoid, an organelle responsible for one-third of global carbon fixation, CO2-delivering thylakoid membranes must penetrate a phase-separated condensate of the CO2-fixing enzyme Rubisco, but the mechanism governing membrane recruitment into the condensate remains unknown. Here, we demonstrate that the Chlamydomonas reinhardtii protein MITH1 acts as a molecular anchor that brings membrane into the pyrenoid condensate. MITH1 dimerizes into an extended coiled coil with an N-terminal amphipathic helix that binds thylakoid membrane. The coiled coil contains multiple novel binding sites for the Rubisco large subunit, allowing the condensate to wet onto the membrane. The coiled coil extends away from the membrane and promotes membrane organization within the condensate. These findings solve a longstanding mechanistic question in pyrenoid biogenesis and reveal general principles for how membranes are integrated into biological condensates.

molecular biology↗

bioRxiv2026

Azacytidine restores T cell function in AML by modulating DNA methylation

AML is an aggressive blood cancer associated with poor clinical outcomes. Chemotherapy remains the standard of treatment, but unfortunately relapse is very common, highlighting the need for alternative therapies. T cell dysfunction and exhaustion are prominent in AML and may represent a barrier to effective immunotherapy yet remains poorly studied in AML. DNA methylation is a major driver of T cell exhaustion and inhibition of de novo methylation can block exhaustion and restore T cell function in chronic viral infections and other cancers but is understudied in AML. Here, we investigated the impact of azacytidine (Aza), an FDA-approved hypomethylating agent, on T cell exhaustion in AML. Using a spontaneous AML mouse model and samples from patients with AML, we found that Aza treatment modulates T cell function. In vivo Aza-treatment of AML-bearing mice decreased tumor burden and reshaped CD8+ T cell states, with increases in frequencies of memory subsets and decreases in regulatory T cells (Tregs). Functionally, Aza treatment overcame the impaired proliferation displayed by both CD4 and CD8+ T cells in our model. DNA methylation sequencing of T cells after Aza treatment revealed hypomethylation and increased expression of stem-like precursor gene TCF7 and E2F2, a regulator of cell cycle progression and proliferation. Similar changes in phenotypes were observed in cultures of AML patient samples treated with Aza. Collectively, we show that Aza remodels epigenetic and functional states in AML and has the potential to reverse T cell exhaustion, with enhanced memory and proliferation capacity. Our work generates a mechanistic framework that provides rationale of combining hypomethylating agents with T cell-based immunotherapies in this lethal disease. Data Sharing StatementRRBS data is available in GEO under the accession number GSE328721. For original data please contact Dr. Evan F. Lind. Key PointsAzacytidine mediated epigenetic modulation can alleviate T cell exhaustion in AML Translational RelevanceImmune therapy has shown limited efficacy in AML, despite increasing evidence of T cell dysfunction in this malignancy. Azacytidine (Aza) is an FDA approved drug for AML, but patients develop therapy resistance and relapse. Studies have mainly focused on Azas tumor intrinsic effects. In this study, we investigated the impact of Aza on immune function, especially T cell exhaustion in AML, since exhaustion is a major mechanism of disease resistance. We demonstrated that Aza can modulate T cell phenotype and restore T cell proliferation. Mechanistically, Aza induces epigenetic reprogramming in T cells and increases the expression of a stem-like precursor marker, TCF7. By shifting the focus on T cell biology, our study provides a rationale for combining Aza with other immunotherapies that can enhance durable immune responses in this malignancy.

immunology↗

bioRxiv2026

Cytopenias and Functional Defects in a Novel Murine Model of VPS45 Severe Congenital Neutropenia

Mutations in the VPS45 gene are associated with a rare form of severe congenital neutropenia (SCN5), a life-threatening inherited error of immunity. We developed and characterized a novel mouse model of SCN5 by CRISPR/Cas9-mediated knock-in of pathogenic VPS45 E238K and T224N mutations. Both Vps45 mutations led to decreased protein expression in bone marrow cells. In vivo phenotyping demonstrated a non-Mendelian genetic distribution with reduced numbers of knock-in homozygotes Vps45E238K. Vps45E238K knock-in homozygous mice showed reduced body weight, reduced body condition with age, and increased mortality. As in human SCN5, Vps45E238K knock-in homozygotes demonstrated neutropenia and lymphopenia. Functionally, Vps45E238K knock-in homozygote neutrophils exhibited increased lipopolysaccharide-induced apoptosis and decreased peroxide production, phagocytic capacity and in vivo cell migration, phenocopying the functional defects reported in patients. Vps45T224N knock-in homozygous mice showed a milder phenotype or no abnormalities. In conclusion, this mouse model phenocopies, in part, human SCN5. It provides a novel platform for future studies of the pathophysiology of defects in neutrophil number and function in human SCN5, potential therapies for the disease, and the biochemistry and cell biology of VPS45. Summary statementWe report a mouse model of severe congenital neutropenia due to VPS45 missense mutations. It represents the first animal model of human neutropenia due to a defect in intracellular trafficking.

immunology↗

bioRxiv2026

Development of a tryptophan-based dual selection system reveals the spatial organization of S-layer assembly during cytokinesis in Sulfolobus acidocaldarius

Sulfolobus acidocaldarius is a thermoacidophilic archaeon used as a model system for studying fundamental cellular processes and for emerging biotechnological applications. However, the limited availability of selectable markers restricts advanced genetic manipulation in this organism. Here, we report the development of a tryptophan auxotrophy-based selection system in S. acidocaldarius. A {Delta}trpBA mutant was constructed in the {Delta}pyrE background strain using a classical pop-in/pop-out recombination strategy. The resulting mutant exhibited little growth defects in rich medium, likely due to exogenous tryptophan supplied by complex nutrients, but failed to grow in a newly developed defined Brock-based amino acid dropout medium lacking tryptophan. Exploiting both uracil and tryptophan auxotrophies, we achieved dual-plasmid co-transformation and co-expression of the surface layer proteins and a dominant-negative mutant of the AAA-ATPase Vps4, revealing that the accumulation of surface layer lattice forming protein SlaA at the midzone of division-arrested cells together with its membrane anchor SlaB. Together, these results provide evidence for spatial regulation of S-layer assembly during archaeal cytokinesis while expanding the genetic toolkit available for S. acidocaldarius. ImportanceSulfolobus acidocaldarius is a key archaeal model organism for studying cellular processes shared with more complex life and is increasingly used for biotechnological applications. Here, we establish tryptophan auxotrophy as a new selectable marker in S. acidocaldarius, expanding the range of genetic selection systems available in this organism. By developing a defined Brock-based dropout medium, we enable stringent amino acid auxotrophy selection and precise control over nutrient composition. This system can be combined with existing uracil-based selection to support dual auxotrophy workflows, enabling co-transformation, simultaneous expression of multiple proteins, and more sophisticated genetic manipulation strategies. Using both markers, we show that S-layer proteins are localised to the division bridge in cytokinesis-arrested cells. This exemplifies ways in which the expanding molecular genetic tool kit available for Sulfolobus acidocaldarius is furthering our understanding of archaeal cell biology.

Molecular Biology↗

bioRxiv2026

msaGUI: Multispectral Analysis Graphical User Interface for Ratiometric Analysis and Background Correction

Chemical imaging is a powerful branch of modern microscopy encumbered by a lack of flexible, high-throughput analysis tools. Bespoke analytical pipelines typically perform ratiometric analysis on two layers in a multispectral image to describe the relative composition of molecules in a sample. This strategy has been implemented across fields, spanning histopathology, cell biology, environmental science, and materials science. The commercialization of chemical imaging microscopes has facilitated the collection of large multispectral datasets, necessitating accessible ways to process them. This paper describes Multispectral Analysis Graphical User Interface (msaGUI), a desktop graphical user interface to analyze individual and batch datasets of multispectral images. Data is loaded as CSV, TSV, or TIFFs and processed through a user-defined sequence of modular image operations that can be flexibly combined, e.g. to reduce spectral crosstalk or background noise. After analysis, data is visualized as exportable images, histograms, and statistics. To yield publication-quality figures, outputted images are fully customizable. Written in Python with open-source libraries, the msaGUI program is packaged into an executable for Windows and Mac for a fully no-code application. Other operating systems are supported via the Python source code. In summary, msaGUI provides a rapid and user-friendly solution for analyzing and visualizing multispectral data.

biophysics↗

bioRxiv2026

Glutaredoxins rapidly reduce glutathione hydroper- and polysulfides

Hydropersulfides have gained attention in cell biology as excellent nucleophiles and membrane-protective radical scavengers. They form perthiyl radicals, which terminate radical chain reactions through self-recombination, leading to the formation of polysulfides. It is currently unknown how polysulfides are subsequently reduced again in non-enzymatic or enzymatic metabolic pathways. Here we used stopped-flow kinetic measurements in combination with mass spectrometry to show that the model class I glutaredoxin from the malaria parasite Plasmodium falciparum (PfGrx) rapidly reduces the polysulfides glutathione trisulfide (GS3G) and glutathione tetrasulfide (GS4G), yielding the glutathionylated enzyme and the corresponding glutathione hydropersulfide GSSH and hydrotrisulfide GS3H. The second-order rate constants of these enzymatic reductions [≥]107 M-1s-1 are even slightly higher than for glutathione disulfide (GSSG). In contrast, PfGrx was inactive or only moderately active using cystine or cysteine trisulfide as oxi-dants. GSSH and GS3H are further reduced by PfGrx with second-order rate constants on the order of 106-107 M-1s-1, yielding the glutathionylated enzyme as well as hydrogen sulfide (H2S) and hydrogen disulfide (H2S2), respectively. Thus, glutaredoxins specifically recognize the glutathione moiety of glutathione (hydro)polysulfides and glutathione hydropersulfide. Due to the rapid reduction of glutathionylated glutaredoxins by reduced glutathione (GSH), glutathione (hydro)per/polysulfides are efficiently converted to GSSG and H2S or the corresponding hydrogen polysulfides. As a consequence, the steady-state concentration of glutathione (hydro)per/polysulfides should be tightly controlled in subcellular compartments containing active glutaredoxins and high GSH concentrations.

biochemistry↗

bioRxiv2026

A Comparative Study of MBTI and Learning Style- Based Grouping for Enhancing Group Effectiveness and Balance in a Pedagogical Setting

Effective group work is central to Problem-Based Learning (PBL) in higher education, yet the optimal strategy for forming student groups remains unclear. This study compared MBTI-based grouping, informed by personality types and Keirsey temperaments, with Learning Style-Based (LSB) grouping, grounded in Kolbs Experiential Learning Theory, to assess their impact on group functioning and role performance. Participants were undergraduate students enrolled in Cell Biology (Fall 2022 and Fall 2023) and Introduction to Biology Laboratory (Fall 2023) courses. Students completed MBTI and Kolb Learning Style assessments, and groups and roles (Leader, Communicator, Organizer) were assigned accordingly. Results indicated that LSB-based groups consistently outperformed MBTI-based groups across multiple performance metrics, including productivity, listening, sense of safety, belonging, and overall satisfaction. All metrics showed statistically significant decreases in MBTI-based groups except contribution, which did not differ significantly between grouping strategies. Role performance ratings were significantly higher for Leaders and Communicators in LSB groups, while no significant differences were observed for the Organizer role. Correlation analyses revealed that satisfaction was strongly associated with perceived productivity in MBTI-based groups, whereas in LSB-based groups, satisfaction was more strongly correlated with psychological safety. These findings suggest that learning style alignment may better support effective collaboration and group climate in PBL settings than personality-based grouping.

scientific communication and education↗

bioRxiv2026

DPCGS: a computational framework for linking GWAS to single-cell transcriptomics in complex traits and diseases

Complex traits and diseases arise from the interplay between genetic variation and cellular heterogeneity, making it essential to understand how genetic risk manifests at the cellular level. However, connecting genome-wide association studies (GWAS) to specific cell populations remains challenging due to cellular complexity and the prevalence of noncoding variants. Here, we present DPCGS, a computational framework that systematically integrates GWAS summary statistics with single-cell RNA-sequencing (scRNA-seq) data to identify trait-associated cell subpopulations, genes, and regulatory programs. Unlike existing approaches that primarily evaluate pathway enrichment or cell-type-level associations, DPCGS quantifies the enrichment of genetically prioritized genes within individual cells through a statistically calibrated gene-set scoring strategy, enabling high-resolution mapping of genetic risk to cellular states. Benchmarking across simulated and diverse human single-cell datasets demonstrates that DPCGS achieves superior accuracy, sensitivity, and robustness compared with existing methods, including scDRS and scPagwas. Applying DPCGS to Alzheimers disease and asthma reveals disease-associated cellular populations and uncovers potential molecular drivers, including CD74, FOS, and AP-1 family regulatory programs, providing insights into disease-specific immune and cellular mechanisms. By bridging genetic discoveries from GWAS with functional interpretation at single-cell resolution, DPCGS establishes a generalizable framework for dissecting the cellular architecture of complex traits and diseases. This approach enables systematic discovery of disease-relevant cell subpopulations, regulatory networks, and potential therapeutic targets, offering broad applications in human genetics, single-cell biology, and precision medicine.

bioinformatics↗